Coatings of HfO2, Ta2O5, TiO2, and Nb2O5 were evaluated as protection layers for p-InP photocathodes in aqueous acidic electrolytes. Each candidate protection layer was characterized based on several criteria: interfacial conduction of photogenerated electrons, thermodynamic and kinetic stability of the overlayer throughout the relevant potential and pH range for cathodic fuel-forming half-reactions, and inhibition of the primary anodic and/or chemical dissolution processes that limit electrode stability. Both conduction of photogenerated electrons and inhibition of anodic oxidation were evaluated using V3+/2+ in 5.0 M HCl(aq) as a one-electron redox couple with a potential close to that of hydrogen evolution in acidic media. Failure modes due to cathodic plating of metal, as well as anodic dissolution and chemical dissolution processes, were evaluated for photocathodes made from etched p-InP, platinized p-InP, and p-InP photoelectrodes that had been coated with the various oxide films and then platinized for use in photoelectrochemical hydrogen evolution in acidic aqueous electrolytes. Nb2O5 best met all of the previously specified criteria, in contrast, TiO2 was found to be thermodynamically and kinetically unstable in acid over the potential range relevant for the hydrogen evolution and/or CO2 reduction electrochemical half-reactions. The protocols developed in this work are broadly applicable for determining the effectiveness of other materials and semiconductors as protection layers for photocathodes.
\r\n\r\nThe electrochemical charge transfer rate at mechanically exfoliated graphene electrodes have also been investigated to probe the coupling distance into the electrode by which redox species in solution electronically couple. Scanning electrochemical cell microscopy (SECCM) was used to measure the rates of charge transfer and to reduce the effect of graphene defects on the electrochemical measurements. The rates of charge transfer with Co(en)33+/2+, Ru(NH3)63+/2+, and IrCl62-/3- redox couples were determined on graphene with different thicknesses, suggesting a coupling distance of 0.3 nm. However, real coupling distance may differ due to the convoluting effects of surface defects, errors inherent to SECCM, and uncertainty in the thickness of graphene.
", "doi": "10.7907/cx9r-zs82", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:17748", "collection": "thesis", "collection_id": "17748", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11032025-231619710", "primary_object_url": { "basename": "varner-samuel-thesis-final.pdf", "content": "final", "filesize": 38687357, "license": "other", "mime_type": "application/pdf", "url": "/17748/1/varner-samuel-thesis-final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Part I: Kinetic Mechanisms and Thermodynamics in Diblock Copolymer Micelles & Part II: Inhomogeneous Thermodynamics of Polar Fluids and Ionic Liquids", "author": [ { "family_name": "Varner", "given_name": "Samuel L.", "orcid": "0000-0002-1365-1027", "clpid": "Varner-Samuel-L" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Chan", "given_name": "Garnet K.", "orcid": "0000-0001-8009-6038", "clpid": "Chan-G-K" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I: Electrolytes are ubiquitous in our world and play essential roles in biology, consumer products, and energy storage. Fundamentally, an electrolyte consists of charged species and a solvent, both of which significantly influence its behavior in the bulk and near interfaces. While it is relatively straightforward to predict charge interactions in a vacuum, the presence of a liquid solvent mediates these interactions in complex and nontrivial ways. Moreover, the interaction of ions with surfaces is highly nuanced and can be strongly affected by the specific chemistry of the ions, solvent, and interface. This is especially relevant in the context of the electric double layer, a subject of scientific inquiry since 1853. Gaining a deeper understanding of these intricate effects and how they govern electrolyte behavior is critical not only for explaining biologically relevant phenomena such as macromolecular complexation, but also for designing batteries and supercapacitors with optimized energy storage performance.
\r\n\r\nThis work presents an analysis of three distinct systems in which the behavior of charged and polar fluids were poorly understood. One area of focus is the effect of introducing non-polar solvents on the charging behavior and energy storage performance of room-temperature ionic liquid supercapacitors, with particular attention to specific surface effects and complex tricritical surface phase behavior. Another topic explored is the entropic origin of ionic interactions in polar solvents, highlighting how entropy is the dominant force driving ion association. Separately, we also investigate the unique surface polarization that arises in asymmetric polar fluids at liquid\u2013vapor interfaces, revealing subtle interfacial phenomena driven solely by molecular asymmetry.
\r\n\r\nPart II: Block copolymers can undergo microphase separation to form a range of ordered nanostructures, including lamellae, lattice-ordered spheres and cylinders, and even network phases. In selective solvents, they self-assemble into micelles, similar to surfactant molecules. However, unlike surfactants, block copolymers often contain hundreds or thousands of repeat units, which significantly slows their dynamics and equilibration. As a result, solutions of diblock copolymer micelles are frequently kinetically trapped far from equilibrium due to large free energy barriers associated with equilibration mechanisms such as chain exchange, micelle fusion, and micelle fission. For applications ranging from viscosity modification and drug delivery to nanoreactors, understanding these kinetic processes is essential. Moreover, developing strategies to achieve consistent and stable micelle size distributions remains a key challenge, particularly in systems far from equilibrium.
\r\n\r\nThis work analyzes the single-chain exchange mechanism in highly segregated copolymer micelles, with particular attention to its chain length dependence, a topic that has been actively debated since the introduction of the Halperin and Alexander theory in 1989. The kinetics of chain exchange are examined under two representative regimes: one involving polymeric solvents, where the micelle core gradually shrinks, and the other involving small-molecule solvents, where the core fully collapses. A combination of simulation and sampling techniques is employed to compare the thermodynamics of the underlying free energy landscape with the actual kinetic pathways of chain escape.
\r\n\r\nThis work also analyzes the kinetic pathways involved in a widely used copolymer micelle preparation technique known as thin film dissolution, or direct dissolution. Mesoscale molecular dynamics simulations are performed to provide a molecular-level picture of micelle formation, starting from both ordered and disordered initial states. In parallel, a mean-field theory is developed to assess how closely the intermediate structures and the final micelles resemble equilibrium configurations.
", "doi": "10.7907/p5ca-t067", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:16593", "collection": "thesis", "collection_id": "16593", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07262024-075858049", "primary_object_url": { "basename": "ye_benjamin_2025_thesis.pdf", "content": "final", "filesize": 44395146, "license": "other", "mime_type": "application/pdf", "url": "/16593/3/ye_benjamin_2025_thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Image Charge Effects Near Solid Surfaces", "author": [ { "family_name": "Ye", "given_name": "Benjamin Bobin", "orcid": "0000-0003-0253-6311", "clpid": "Ye-Benjamin-Bobin" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Giapis", "given_name": "Konstantinos P.", "orcid": "0000-0002-7393-298X", "clpid": "Giapis-K-P" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Ion\u2013surface interactions underpin fundamental biological and technological processes and hold the key to advancing the performance of modern electrochemical devices, such as electric double-layer capacitors (EDLCs). As such, a comprehensive understanding of the mechanistic details governing these interactions and their effects on the electrical double layer structure and charge transport is crucial. However, accurately modeling ion\u2013surface interactions in theory and simulations remains challenging due to the complexities and computational cost associated with properly treating dielectric discontinuities at ion\u2013surface interfaces. This thesis leverages the efficient method of image charges in coarse-grained molecular dynamics simulations to capture the correct behavior at the ion\u2013surface interface and unravel anomalous phenomena in various charged soft matter systems with conductive metal surfaces. Specifically, we construct a molecular model to demonstrate a spontaneous symmetry breaking transition in room-temperature ionic liquid EDLCs that provides a molecular mechanism for a hysteresis in the capacitance behavior observed experimentally. We also introduce a physically motivated soft-core model, the Gaussian core model with smeared electrostatics (GCMe), which addresses the limitations of traditional hard-core force fields in representing bulky organic ions and their spread charges, while also being orders of magnitude faster. Using GCMe, we then characterize the effects of the polyelectrolyte chain length, electrolyte polarizability, and electrode material on the energy storage of polymerized ionic liquid EDLCs, and the ion adsorption behavior and charging/discharging dynamics in polyelectrolyte EDLCs. Finally, we present MDCraft, an open-source Python assistant designed to streamline computational research workflows by providing tools for simulation setup, data analysis, and visualization. This comprehensive study not only enhances the understanding of ion-surface interactions but also offers practical insights and tools for advancing the design and optimization of systems involving charged species near surfaces, such as next-generation electrochemical energy storage devices.", "doi": "10.7907/fjpq-wn07", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17233", "collection": "thesis", "collection_id": "17233", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05152025-202058082", "primary_object_url": { "basename": "Stradley_Thesis.pdf", "content": "final", "filesize": 41167317, "license": "other", "mime_type": "application/pdf", "url": "/17233/3/Stradley_Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Materials and Interfaces to Enable Reversible Mg Electrochemistry for Energy Storage Applications", "author": [ { "family_name": "Stradley", "given_name": "Steven Hartzel", "orcid": "0009-0009-7154-608X", "clpid": "Stradley-Steven-Hartzel" } ], "thesis_advisor": [ { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Giapis", "given_name": "Konstantinos P.", "orcid": "0000-0002-7393-298X", "clpid": "Giapis-K-P" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Climate change drives the need for a dramatically increased deployment of electric vehicles and intermittent renewable energy sources. Each of these depends intimately on batteries for range and reliability. Although Li-ion batteries are the current industry standard for electrochemical energy storage, they are based on scarce and unevenly distributed resources. It is thus crucial to develop rechargeable battery chemistries based on more energy dense and resource equitable materials. Orders of magnitude more abundant and energy dense than Li, Mg is an attractive alternative to Li for energy storage. Despite its many attractive properties, deployment of Mg-based chemistries is hindered by a lack of cathode, anode, and electrolyte materials which support Mg electrochemistry and are mutually compatible. This thesis endeavors to deploy new materials to sustain reversible Mg electrochemistry and to understand how certain material properties impact electrochemical performance. First, we investigate new cathode materials based on Earth-abundant transition metal chlorides. These cathodes cycle somewhat reversibly but are prone to rapid capacity fade due to active material dissolution and shuttle. We identify electrolyte modification as a means to combat this fade. Next, we characterize halide-free Mg electrolytes based on weakly coordinating Si-centered anions. These electrolytes display impressively high oxidative stabilities but also relatively high reductive overpotentials and a fatal vulnerability to passivation by H\u2082O. We then consider a class of electrolytes based on B-centered anions with aryl ligands. These systems show exceptionally low reductive overpotentials among halide-free Mg electrolytes. We increase the bulk of the anion and correspondingly observe a slight increase in the reductive overpotential and an enhancement in rate performance. Though this class of compounds shows a low oxidative stability, the structure-property relationships gleaned from it may prove useful in future electrolyte studies. Finally, we deploy Al as an Earth-abundant, high capacity alloying anode for Mg-based batteries. Though the native kinetics for Mg-Al alloying prove too sluggish for practical systems, we use Bi to enhance the alloying kinetics of Al by two orders of magnitude. Though alloying capacity is limited by a large particle size, we present a viable method for enhancing Al alloying kinetics to relevant rates, thereby unlocking a highly desirable material for future studies. Taken together, this work expands the scope of cathode, electrolyte, and anode materials which support reversible Mg electrochemistry. Though imperfect, the lessons we learn from them may inform future design decisions to enable reversible Mg-based batteries.", "doi": "10.7907/vs2j-ep54", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17120", "collection": "thesis", "collection_id": "17120", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03312025-221040469", "primary_object_url": { "basename": "PhD Thesis_SLee.pdf", "content": "final", "filesize": 40115968, "license": "other", "mime_type": "application/pdf", "url": "/17120/7/PhD Thesis_SLee.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Multiscale Design, Fabrication, and Mechanical Analysis of Structural Hierarchies in Functional Materials", "author": [ { "family_name": "Lee", "given_name": "Seola", "orcid": "0000-0002-4538-0890", "clpid": "Lee-Seola" } ], "thesis_advisor": [ { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" } ], "thesis_committee": [ { "family_name": "Ravichandran", "given_name": "Guruswami", "orcid": "0000-0002-2912-0001", "clpid": "Ravichandran-G" }, { "family_name": "Daraio", "given_name": "Chiara", "orcid": "0000-0001-5296-4440", "clpid": "Daraio-C" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Hierarchical structuring has emerged as a powerful strategy in functional material design to enhance mechanical performance and impart functional properties across multiple scales. In architected materials, leveraging tessellated multiscale geometrical features enables unconventional properties such as ultra-low density and high energy absorption. Similarly, in functional polymers, rational design of molecular chemistries and polymer microstructures allows for tunable mechanical properties and stimuli-responsive behaviors. However, a substantial knowledge gap persists in understanding how multiscale interactions connect to determine the macroscale performance of these materials. This gap arises from challenges in scalable fabrication, multiscale characterization, and limited mechanistic insight from theory and simulations. To address these challenges, this thesis presents a comprehensive approach that integrates scalable fabrication, multiscale characterization, and theoretical modeling to develop hierarchical materials with tunable functionalities. Specifically, we (1) demonstrate scalable fabrication of hierarchical materials using additive manufacturing, (2) investigate the bulk mechanical responses by tuning the smallest level in hierarchical design, and (3) perform multiscale studies to bridge the gap between unit-level interactions and macroscale performance.
\r\n\r\nIn the first study, we explore the role of structural hierarchies in architected polymeric materials for enhanced energy dissipation. Using metasurface-based holographic lithography, we fabricate nano-architected polymeric sheets and demonstrate how geometrical parameters for unit cell design such as relative density and beam aspect ratio influence stiffness, energy dissipation, and deformation modes. These findings highlight the significance of hierarchical structuring in enhancing mechanical performance and establish design principles for scalable manufacturing. In the second study, we focus on dynamic polymers and examine how dynamic crosslinking at the molecular level influences macroscale material responses. A single-step stereolithography approach is developed to tune molecular-level controls in the material. Through multiscale modeling and experimental characterizations, we reveal how dynamic bonding mechanisms govern stiffness, stretchability, and fracture energy. The results underscore the significance of multiscale interactions in tuning mechanical behavior and suggest a pathway for designing materials with programmable responses. In the final study, we build on these insights by integrating molecular-level controls with nonlinear structural responses such as buckling and shape transformations. The central premise is that molecular interactions dictate local responsiveness, while structural geometries can amplify or suppress these responses through localized deformation or stress redistribution. As a demonstration, we explore how tailored viscoelasticity and controlled instabilities can determine the buckling mode of a structural beam. This synergistic interplay highlights the potential of the materials requiring programmed reconfigurability, shape morphing, and stimuli-responsive properties.
\r\n\r\nThe findings presented in this thesis offer a robust framework for bridging molecular-level design with macro-scale performance through scalable fabrication and characterization strategies. By expanding the design space of material-level behavior, this work lays the groundwork for developing next-generation materials with enhanced functionality, adaptability, and intelligence for applications such as soft robotics, healthcare, and sustainable materials.
", "doi": "10.7907/1ee0-bc98", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:16545", "collection": "thesis", "collection_id": "16545", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07092024-204040190", "type": "thesis", "title": "Part I: Multi-Valent Ion Effects on Polyelectrolyte Structure and Thermodynamics & Part II: Hydrodynamic Self-Propulsion", "author": [ { "family_name": "Glisman", "given_name": "Alec Gregory", "orcid": "0000-0001-9677-1958", "clpid": "Glisman-Alec-Gregory" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I: Polyelectrolytes are a class of charged polymers that have found widespread utility in water treatment, drug delivery, and scale inhibition, among other applications. For many of these applications, it is crucial to control the phase stability of the polyelectrolyte solution. The long-ranged nature of the electrostatic interactions in polyelectrolyte solutions and the polyelectrolyte's connectivity lead to a rich phase behavior that can be challenging to study, especially in the presence of other ions or surfaces. In scale inhibition applications, polyelectrolytes such as poly(acrylic acid) (PAA) are used to prevent the dissolution of sparingly soluble salts, such as calcium carbonate, in water. While the significant influence of small ions on polyelectrolyte solution phase behavior is recognized, the precise molecular mechanisms driving the resulting phase stability remain largely elusive.
\r\n\r\nPolyelectrolyte theory suggests that a polyelectrolyte's behavior and adsorption properties in solution are strongly tied to the polymer chain conformation and charge distribution, which in turn is influenced by solution ionic strength and ionic valency. Consequently, we expect the polyelectrolyte performance to be highly dependent on the solution conditions and the molecular features of the polyelectrolyte. Previous computational studies have studied general polyelectrolytes in solution with coarse-grained and implicit solvent models and provided insights into the chain conformational transitions. However, they disagree on the mechanisms underlying aqueous polyelectrolytes salting out of suspension and are unable to yield chemically specific insights. We seek to better understand the antiscalant mechanisms of polyelectrolytes using all-atom molecular dynamics to capture solvation and polymer chemistry effects on the mechanisms of polyelectrolytes preventing scale nucleation and slowing growth.
\r\n\r\nThe current work investigates the structure and thermodynamics of polyelectrolytes in bulk solution and at crystalline interfaces with added multi-valent ions. The presence of multi-valent ions, such as Ca2+, can significantly influence polyelectrolyte conformation via ion bridging non-neighboring charged monomers as well as screening the electrostatic interactions. We employ all-atom molecular dynamics simulations to investigate the binding modes of Ca2+ onto a PAA chain, Ca2+\u2013PAA complex aqueous stability, and PAA adsorption onto a crystalline CaCO3 surface. In each of these cases, we find that the balance between ion bridging, electrostatic screening, and water-mediated interactions plays a crucial role in determining the polyelectrolyte's behavior in solution and at an interface.
\r\n\r\n\r\nPart II: Active bodies undergo self-propulsive motion in a fluid medium and span a broad range of length and time scales. Many active systems spontaneously self-organize into visually striking structures: fish schooling, birds flocking, and bacterial colonies growing. Current models of this emergent behavior in the inertial regime are mainly phenomenological and lack consideration of the fluid-mediated interactions between bodies.
\r\n\r\nTo address this limitation, we seek to advance physics-based models of swimmers by explicitly incorporating the fluid mechanical interactions between bodies. We aim to discern the fluid medium's role in group dynamics and determine whether it can reproduce the observed emergent phenomenon without resorting to phenomenologically based interaction rules. To that end, we focus specifically on swimming in high Reynolds number flows, where inertial forces dominate, and draw comparisons to the well-studied low Reynolds number (Stokes) regime. We begin by deriving the equations of motion for a collection of unconstrained spherical particles in potential flow and extend the model to include viscous dissipation and rigid body motion constraints for many bodies with arbitrary kinematics.
\r\n\r\nWe then consider the case of a single swimmer consisting of three linked spheres in potential flow. Through this, we find self-propulsion without needing external forces or momentum transfer via vortex shedding. We compare the inertial swimmer to an identical swimmer in the Stokes regime\u2014where fluid inertia is neglected\u2014and find that the structure of the equations of motion is identical in both flow regimes. Notably, the Stokes hydrodynamics are longer-ranged at leading order, leading to a more significant net displacement of the swimmer after one period of articulation. Finally, our study provides analytical insight into the swimming of a deformable body through an expansion of the non-linear spatial dependence of the hydrodynamic interactions.
", "doi": "10.7907/gf6m-gs53", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:16680", "collection": "thesis", "collection_id": "16680", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08282024-022514845", "primary_object_url": { "basename": "Bruch_Dorian_2025.pdf", "content": "final", "filesize": 11174069, "license": "other", "mime_type": "application/pdf", "url": "/16680/1/Bruch_Dorian_2025.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Theoretical Modeling of Interactions Between Electrolytes and Surfaces", "author": [ { "family_name": "Bruch", "given_name": "Dorian Wayne", "orcid": "0000-0002-3983-4841", "clpid": "Bruch-Dorian-Wayne" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Electrolytes are ubiquitous in science and engineering and are of active interest, owing to their applications biology, energy storage, colloidal suspensions, and even climate. Near a surface, electrolyte solutions exhibit a plethora of rich thermodynamic and structural phenomena, owing to the interplay of long-ranged electrostatics and nonelectrostatic interactions between ionic species, solvent, and the surface. In this thesis, we present a pedagogical formulation for the thermodynamics of electrolyte solutions near charged surfaces, followed by an examination of interactions and structure of different types of electrolytes near surfaces. Specifically, we investigate the difference between constant surface charge and constant surface potential boundaries in electrolyte solutions, the capacitance applications, double-layer structure, and screening behavior of a zwitterionic polymers, as well as the effect of image charge on structure, capacitance, and forces in simple electrolytes near metal, dielectric, and dielectrically-saturated metal surfaces. We conclude with a Gaussian-fluctuation model for ions with soft-core excluded volume interactions.", "doi": "10.7907/eey8-et93", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:16432", "collection": "thesis", "collection_id": "16432", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292024-020036252", "primary_object_url": { "basename": "THESIS_FINAL_MKP_v2.pdf", "content": "final", "filesize": 5847418, "license": "other", "mime_type": "application/pdf", "url": "/16432/1/THESIS_FINAL_MKP_v2.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Improvement of Microbial Detection and Analysis Techniques in Complex Biological Environments", "author": [ { "family_name": "Porter", "given_name": "Michael Koizumi", "orcid": "0000-0002-0777-7563", "clpid": "Porter-Michael-Koizumi" } ], "thesis_advisor": [ { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Human bodies are home to a vast assortment of microbes, including bacteria, fungi, and viruses. These microbes live within their human hosts, interacting with each other and influencing states of health and disease. Despite their prevalence and importance, studying host-microbe interactions has been limited by the dearth of appropriate tools and approaches, and an underappreciation for the role of biophysics. \r\nThis thesis describes the development and application of novel tools and approaches for studying bacteria, fungi, and viruses to uncover their potential roles in human health and disease.
\r\n\r\nIn my first project, we investigated bacterial aggregation, a phenomenon related to important host-microbe interactions such as biofilm formation and the clearance of pathogens from the gastrointestinal tract. We found that bacteria aggregate in the presence of polymers (such as dietary fiber) via a mechanism that is qualitatively consistent with depletion-type forces under gut-like conditions. Surprisingly, motile bacteria aggregate more than nonmotile bacteria in viscous, high-polymer concentrations due to the higher effective diffusivity and inter-bacterial collisions enabled by motility. These two results give insight on how the foods (such as fiber) that we consume can physically affect the structure of microbes and other matter in the gut.
\r\n\r\nIn my next projects, we investigated viral-load kinetics to understand the best testing modality for early detection of SARS-CoV-2 via a large community-based household transmission study. By collecting longitudinal, paired saliva and nasal-swab specimens from SARS-CoV-2 patients starting from the incident of infection, we quantified the viral-load trajectories of COVID-19-positive participants in each specimen type over time. Our results revealed that viral loads increased quickly and reached a higher peak in nasal-swab specimens, whereas viral loads were detectable earlier but reached a lower maximum in saliva. Both specimen types exhibited a temporal trend whereby viral loads were higher in specimens collected in the morning compared with the evening. In samples where infectious viral titer was measured, we found that the ratio of N gene viral load and infectious viral titer did not remain consistent throughout the course of infection. These three results help us understand the heterogeneity of SARS-CoV-2 disease progression in different individuals, and how the analytical sensitivity of a diagnostic, the specimen type, and time of sampling can be crucial in conducting community surveillance programs during a pandemic. \r\nFinally, we extended and co-validated for fungi a novel sample-preparation method that enriches fungal cells in host-rich samples to enable the first demonstration of deep metagenomic sequencing of fungal communities directly from clinical samples (without a culture step). Our results show that this method depletes host DNA by over 1000-fold by mass, improving taxonomic classification and gene calling, as well as enabling de novo metagenome assembled genome (MAG) assembly in samples dominated by human biomass.
", "doi": "10.7907/7chb-wk98", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16212", "collection": "thesis", "collection_id": "16212", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10222023-023442759", "primary_object_url": { "basename": "Villafuerte_Fernando_2024.pdf", "content": "final", "filesize": 16747509, "license": "other", "mime_type": "application/pdf", "url": "/16212/1/Villafuerte_Fernando_2024.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Additive Manufacturing of Batteries and IR-Active Microparticles: Polyborane-Based Electrolytes for Solid State Batteries and Additively Manufactured, TiN-Coated Microbridges", "author": [ { "family_name": "Villafuerte", "given_name": "Fernando Joaquin", "orcid": "0000-0003-0958-7111", "clpid": "Villafuerte-Fernando-Joaquin" } ], "thesis_advisor": [ { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Faber", "given_name": "Katherine T.", "orcid": "0000-0001-6585-2536", "clpid": "Faber-K-T" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Advances in additive manufacturing (AM) processes are continuously opening up the material design space, providing scientists with opportunities to explore the relationship between structure, processing, and materials properties in new contexts. The first project presented in this thesis presents the design and refinement of a novel, polyborane-based solid electrolyte, whose design and investigation were motivated by the advent of additively manufactured, 3D electrodes, which could play a pivotal role in enabling next-generation batteries that can store more energy without sacrificing power. The first iteration of this electrolyte was synthesized by hydroborating polybutadiene with 9-borabicyclo(3.3.1)nonane (9-BBN). The resultant poly(9-BBN) was then reacted with precise amounts of n-butyllithium (n-BuLi), an organolithium reagent, to create the final polymer electrolyte. The polymer electrolyte films were assembled into a custom apparatus for impedance measurements, and though found to be ionically conductive, these measurements were not consistent, even within films made from the same batch of polymer in solution.
\r\n\r\nThis necessitated the modification of the electrolyte into a UV-cured version, which was achieved by hydroboration of polybutadiene using 9-BBN. The resulting poly(9BBN)-co-polybutadiene is treated with lithium tert-butoxide (LiOtBu) and crosslinked to produce a precursor resin, which is then drop cast onto PTFE spacers, UV-cured for 5 minutes, dried, and assembled into coin cells for electrochemical impedance spectroscopy (EIS) and into pans for differential scanning calorimetry (DSC). The ionic conductivity of the PBEs as measured by EIS as a function of molar salt ratio, r = molLi/molB, does not track with their measured glass transition temperatures, Tg or the activation energies, Ea, extracted from fitting the Vogel-Tammann-Fulcher (VTF) equation to the conductivity data. Beyond r = 0.33, values for Tg and Ea demonstrate insensitivity to increasing concentration, while conductivity continues to change with concentration and reaches a maximum at r = 0.75. Moreover, measurement of ionic conductivity of control PBE films without boron on the polybutadiene backbone confirms that the presence of Lewis-acidic boron groups is necessary for ionic solvation and conduction. Further analysis that compared the PBEs to a well-studied PEO-based electrolyte in the literature through the calculation of a reduced conductivity to control for polymer viscosity and segmental motion revealed that PBEs obtain optimal conductivity at higher salt concentrations than PEO, and that their ionic conductivities are far below that of PEO. We posit that we are observing a mechanism of ionic conduction in a glassy regime partially decoupled from the relaxation of the polymer host. We attribute these effects to the strong interaction between the Lewis-acidic boron centers and the strongly Lewis-basic tert-butoxide anions, which limits ionic conductivity by suppressing motion of the anions and presenting a large activation barrier for motion of Li+, which is optimized at high concentrations where the distance between the boron-anion centers is sufficiently small to increase the probability of a hopping event from one center to another.
\r\n\r\nNanorods fashioned from noble metals are ideal for maximizing extinction of electromagnetic radiation, which is necessary for plasmonically active materials in numerous applications, from contrast agents for biological imaging to effective obscurants. Key challenges that prevent nanorods from being employed for these technological applications include the prohibitively expensive cost of Au and Ag, their lack of requisite thermal and chemical stability, and the limitations in resolution and attainable feature sizes produced by existing wet chemistry techniques. The second project in this thesis focuses on the development of an AM process to create arrays of TiN-coated microbridges with lengths of 4.749 microns, cross-sections with dimensions of 0.692 by 2.256 microns, and effective aspect ratios of 3.368, that are capable of attenuating light reflected from a TiN-coated sapphire substrate by more than 80% in the mid-infrared (mid-IR), as measured by Fourier Transform Infrared (FTIR) spectroscopy. FTIR spectroscopy measurements further reveal attenuation of light transmitted through the same TiN-coated structures by up to 35% in the near- to mid-IR. These results indicate a promising pathway for AM of plasmonically active microparticles with broad reflectance and transmittance attenuation of light in the near- and mid-IR.
", "doi": "10.7907/jc8h-gs34", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16488", "collection": "thesis", "collection_id": "16488", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06032024-222110855", "type": "thesis", "title": "Low-Energy Plasma\u2013Surface Interactions at Airless Icy Bodies", "author": [ { "family_name": "Grayson", "given_name": "Robert Wall", "orcid": "0000-0002-8044-9654", "clpid": "Grayson-Robert-Wall" } ], "thesis_advisor": [ { "family_name": "Giap", "given_name": "Konstantinos P.", "orcid": "0000-0002-7393-298X", "clpid": "Giapis-K-P" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Giapis", "given_name": "Konstantinos P.", "orcid": "0000-0002-7393-298X", "clpid": "Giapis-K-P" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Nordheim", "given_name": "Thomas A.", "orcid": "0000-0001-5888-4636", "clpid": "Nordheim-Thomas-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Low-energy plasma surface interactions occur in many solar system environments and are especially important in the magnetospheres of gas giants. Within these magnetospheres orbit a catalogue of icy moons, some of which famously host interior liquid-water oceans. They are continuously exposed to a cold, corotating plasma \u201cwind,\u201d resulting in bombardment by heavy reactive ions, with peak number fluxes in the hyperthermal energy regime (10s to 100s of eV). Despite their abundance, these low-energy ions have been mostly overlooked in planetary science because they are poor drivers of radiolysis. In this thesis we take a combined experimental-theoretical approach to understanding the interaction of hyperthermal water group molecules/ions with relevant surfaces, motivated by some specific solar system observations, mostly from the Saturn system.
\r\n \r\nWe begin with experimental case studies of water-group ion scattering on carbonaceous (Chapter 2) and chloride-salt surfaces (Chapter 3), focusing on the emission of secondary negative ions. For carbonaceous surfaces, we detect surprisingly energetic carbon fragments, apparently emitted by near-threshold sputtering processes. The most abundant products (O\u207b, C2\u207b, C2H\u207b) are consistent with mass range for negative PUIs of unknown origin observed near Dione and Rhea. The reported mass ranges, however, have been estimated for pick-up of initially stationary ions, which is a poor assumption for the products we observe. Our experiments with chloride salts (relevant to Jupiter\u2019s moon Europa) are complicated by surface charging but provide kinematic evidence of reactive scattering and single knock-on sputter processes. Specifically, we observe abstraction of Cl from Pt to form chlorine monoxide anions. We then describe a modification of our scattering apparatus to enable exposure of ice targets, developing a one-of-a-kind experimental facility (Chapter 6). Some limited and preliminary results for Ar\u207a and O\u207a bombardment of amorphous water ice follow, which are more revealing of experimental challenges than of surface chemistry and dynamics.
\r\n \r\nOur theoretical efforts include Reactive Molecular Dynamics simulations of collision-induced chemistry in ices using the ReaxFF formalism. These reveal a novel non-radiolytic process (an Eley-Rideal reaction) for formation of molecular oxygen in low-energy (2\u221250 eV) water-group molecule bombardment of crystalline water ice, relevant to the maintenance of O\u2082 exospheres at Saturn\u2019s moons Dione and Rhea (Chapter 4). With the addition of CH\u2084 to the ice (as a clathrate), bombardment results in formation of methanol and formaldehyde at yields as great as 10% and 5%, respectively (Chapter 5). Two mechanisms are observed for methanol synthesis: one a typical radiolysis process and the second a two-step non-radiolytic mechanism. We provide preliminary results for an HCN/CH\u2084/H\u2082O ice target in Chapter 8 to motivate further study of the role that hyperthermal reactive ions play in synthesis of prebiotic organics. Finally, in Chapter 7, we describe a Monte-Carlo model for the production and transport of H\u2082 in the Enceladus due to plasma-surface interactions. Radiolysis by suprathermal electrons is the primary contributor, but the calculated mixing ratio falls several orders of magnitude short of the reported ~1%, which lends credibility to the notion that H\u2082 is being emitted from Enceladus\u2019 internal ocean.
", "doi": "10.7907/fn7c-k591", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:15222", "collection": "thesis", "collection_id": "15222", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292023-054311609", "primary_object_url": { "basename": "QuineThesis_Caltech.pdf", "content": "final", "filesize": 61426395, "license": "other", "mime_type": "application/pdf", "url": "/15222/1/QuineThesis_Caltech.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Tunability of Gas Adsorption Enthalpies in Carbonaceous Materials for Energy-Related Applications", "author": [ { "family_name": "Quine", "given_name": "Cullen Mackenzie", "orcid": "0000-0002-7301-0969", "clpid": "Quine-Cullen-Mackenzie" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Ahn", "given_name": "Channing C.", "clpid": "Ahn-C-C" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Schwab", "given_name": "Keith C.", "orcid": "0000-0001-8216-4815", "clpid": "Schwab-K-C" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Stadie", "given_name": "Nicholas", "orcid": "0000-0002-1139-7846", "clpid": "Stadie-P-Nicholas" }, { "family_name": "Ahn", "given_name": "Channing C.", "clpid": "Ahn-C-C" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_eng" } ], "abstract": "Carbonaceous materials provide a porous, high surface area framework for the adsorption of gases through physisorption. Physisorption operates through van der Waals forces, resulting in highly reversible, densified gas storage. The density of adsorbed gas species approaches the bulk liquid density, providing a method to increase the volumetric energy density of hydrogen and natural gas at conditions where the adsorbate is a non-liquid in the bulk phase. This dissertation explores the tunability of the strength of gas adsorption to surfaces of carbon adsorbents, known as the enthalpy of adsorption. Two methods are studied: modification of the surface atomic composition and microstructural changes to the carbon porosity. Applications are considered for both energy storage and carbon capture applications.
\r\n\r\nThe first chapter presents a brief overview of the energy storage field, with emphasis on non-conventional methods to store gases efficiently. Chapter 2 provides the thermodynamic and statistical mechanical derivations used throughout this work, and the assumptions that go into the models used to analyze adsorption data. Chapter 3 reports work on a copper-modified commercial carbon MSC-30 for hydrogen storage, which exhibits an activated dissociative chemisorption desorption feature around ambient temperature. Chapter 4 presents the densification of a novel architected carbon structure, zeolite-templated carbon, for adsorbed natural gas storage. Through the pelletization process, the pore morphology of the underlying adsorbent framework is compressed, resulting in increased adsorption enthalpies with applied pelletization pressure. Chapter 5 focuses on the tunability of pore structure through potassium hydroxide activation, and the resulting adsorption properties pertinent to carbon dioxide capture from a simulated flue-gas stream. The last chapter provides insight into the work as a whole and identifies areas of future work that would improve the fundamental understanding and broader impact of adsorbent materials.
", "doi": "10.7907/r5ad-1j85", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15181", "collection": "thesis", "collection_id": "15181", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05162023-225200255", "primary_object_url": { "basename": "Thesis_Ziyi_0522.pdf", "content": "final", "filesize": 12313820, "license": "other", "mime_type": "application/pdf", "url": "/15181/1/Thesis_Ziyi_0522.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Temperature Dependence of Gas Physisorption Energy: Experimental and Computational Studies of Krypton on Porous Carbon", "author": [ { "family_name": "Wang", "given_name": "Ziyi", "orcid": "0000-0003-0811-921X", "clpid": "Wang-Ziyi" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Stadie", "given_name": "Nicholas", "orcid": "0000-0002-1139-7846", "clpid": "Stadie-P-Nicholas" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This work comprehensively investigated the temperature dependence of physical adsorption energy, combining theoretical, computational, and experimental approaches. A thermodynamic analysis of the 2D ideal gas and the slit-pore models highlighted the role of van der Waal potentials in the adsorption energy and isotherm fitting methods, especially Henry's law. Experimental data of krypton adsorption on CNS-201 and MSC-30 porous carbon materials revealed a significant weakening in the isosteric adsorption energy with temperatures from 250 K to 330 K. Using the zero-coverage Henry's constants and Clausius\u2013Clapeyron equation, the adsorption energies weaken for 13% and 15% for CNS-201 and MSC-30. The corresponding changing rates are 4.35k_B for CNS-201 and 3.65k_B for MSC-30.
\r\n\r\nThe DFT-based computational study with the slit-pore model showed the van der Waal potentials of different-sized pores. Then it showed how the structures of the pores significantly influence the surface dynamics and the internal energies of the adsorbates at different temperatures. Gas molecules adsorbed in pores of different sizes have different heat capacities larger than the gas phase, leading to a temperature dependence of adsorption energy. Monte Carlo calculation indicated that displacements of adsorbent atoms caused by thermal vibration slightly weaken the van der Waal potentials but have a negligible effect on the temperature dependence of the adsorption energy.
\r\n\r\nThe distribution of pore sizes plays a crucial role in the temperature dependence of the overall adsorption energy. With increasing temperature, the pores with higher energy states become more accessible due to the Boltzmann distribution, weakening the statistically averaged internal energy. Adsorption energy weakening of 5% and 15% for CNS-201 and MSC-30 are given by combining the computational van der Waal potentials and experimentally measured pore sizes. The changing rates are 0.62k_B and 2.03k_B.
", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15007", "collection": "thesis", "collection_id": "15007", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08252022-035254306", "primary_object_url": { "basename": "Hojin Kim Thesis 082822.pdf", "content": "final", "filesize": 14813302, "license": "other", "mime_type": "application/pdf", "url": "/15007/6/Hojin Kim Thesis 082822.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "New Long End-Associative Polymers for Mist Control in I. Aqueous Solutions and II. Hydrocarbon Solvents", "author": [ { "family_name": "Kim", "given_name": "Hojin", "orcid": "0000-0002-0257-7300", "clpid": "Kim-Hojin" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Robb", "given_name": "Maxwell J.", "orcid": "0000-0002-0528-9857", "clpid": "Robb-M-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Ultralong linear polymers are well known to be useful in a variety of applications such as mist control, drag reduction, and agricultural spray drift control. However, the application of ultralong linear polymers is limited by shear degradation of the ultralong polymer chains that occurs under strong flow conditions. To overcome the issue of shear degradation, our group previously designed long end-associative polymers that can self-assemble into megasupramolecules (Mw > 2000 kg/mol) in low polarity solvents like jet fuel. The previously developed long end associative polymers had polycyclooctadiene backbones (1,4 polybutadiene) with carboxylic acid or tertiary amine end groups that associated via hydrogen bonding. They were shear degradation resistant and used as mist-control agents that provided fire-protection to jet fuel at concentrations as low as 0.3wt%.
\r\n\r\nBuilding upon the previous work, this thesis describes efforts toward expanding the applicability of long end-associative polymers. We first describe the design and synthesis of water-soluble long end-associative polymers for agricultural spray mist-control. We synthesized telechelic polyacrylamides using reversible addition fragmentation chain transfer (RAFT) polymerization. We explored two types of associations that can form stable supramolecules in water: host-guest interactions between adamantane and beta-cyclodextrin (Chapter 1), and metal-ligand association between terpyridine and transition metal ions (Chapter 2). Careful optimization of polymerization conditions allowed the synthesis of ultra-high molecular weight telechelic polyacrylamides with narrow polydispersity. We found that the terpyridine functionalized polyacrylamides with Mw 820 kg/mol could assemble into megasupramolecules (Mw > 2000 kg/mol) upon addition of Fe(II) or Ni(II).
\r\n\r\nIn Chapters 3 and 4, we return to long end-associative polymers in hydrocarbon solvents. In Chapter 3, we tackle the issue of poor solubility of the previous generation of associative PCODs in a highly nonpolar solvent, PAO. In Chapter 4, we develop a new generation of end groups for improved solubility and ease of synthesis.
\r\n\r\nFinally in Chapter 5, we discuss polyDODT (poly(3,6-dioxa-1,8-octanedithiol)), a polydisulfide that tends to form a mixture of linear and cyclic species. We present new methods to detect the presence of linear species in the mixture, as well as an alternative synthesis route for synthesis of polyDODT.
", "doi": "10.7907/rsx9-qt39", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15170", "collection": "thesis", "collection_id": "15170", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05142023-192053975", "primary_object_url": { "basename": "Linghui_Wang_Thesis.pdf", "content": "final", "filesize": 43812065, "license": "other", "mime_type": "application/pdf", "url": "/15170/1/Linghui_Wang_Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Ion Transport in Temperature Sensitive Polyelectrolytes", "author": [ { "family_name": "Wang", "given_name": "Linghui", "orcid": "0000-0003-2492-7364", "clpid": "Wang-Linghui" } ], "thesis_advisor": [ { "family_name": "Daraio", "given_name": "Chiara", "orcid": "0000-0001-5296-4440", "clpid": "Daraio-C" } ], "thesis_committee": [ { "family_name": "Minnich", "given_name": "Austin J.", "orcid": "0000-0002-9671-9540", "clpid": "Minnich-A-J" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Bernardi", "given_name": "Marco", "orcid": "0000-0001-7289-9666", "clpid": "Bernardi-Marco" }, { "family_name": "Daraio", "given_name": "Chiara", "orcid": "0000-0001-5296-4440", "clpid": "Daraio-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Temperature sensors are widely employed and play a key role in many industries, such as automotive vehicles, medical devices, environmental monitoring, and process control. The state-of-the-art thermal sensing elements are made of rigid and costly inorganic materials, such as vanadium oxide and platinum. These materials have limitations for emerging applications such as wearable devices and prosthetic devices. Ideal temperature sensing materials for such applications need to be flexible, reliable under mechanical deformation, and suitable for large-area production. Electrical conductive polymers were found to be a promising solution because of their flexibility and solution processability. However, they often lag in temperature resolution compared to their inorganic counterparts.
\r\n \r\nA recent discovery revealed that the ionic conductivity of crosslinked pectin, a biopolymer extracted from plant cell walls, has a record-high temperature response. It is biocompatible, flexible when hydrated, and solution-processable, making it a strong candidate for wearable temperature sensing and conformal temperature mapping. However, open questions remain about the origin of its temperature sensitivity and the principles governing its ion transport. Furthermore, the heterogeneity of the complex molecular structure of pectin presents challenges to its integration in sensing devices.
\r\n \r\nIn this thesis, we study the origin of the high thermal sensitivity in pectin and develop a synthetic polyelectrolyte that mimics its key structure and properties. In Chapter 3, we focus on the ion transport mechanism in crosslinked pectin. We show that the binding between multivalent ions and certain chemical functional groups of pectin plays a critical role in its temperature sensitivity. In Chapter 4, the impact of water content on the ion transport and dielectric processes in crosslinked pectin is also investigated. In the following chapter, we present a novel synthetic polyelectrolyte designed to mimic pectin with a simpler structure. It has superior flexibility, high temperature sensitivity, and is stable under mechanical deformation. To further study this new material, we examine its ion transport dynamics under varying humidity and temperature conditions in Chapter 7. We discover that temperature and humidity have a similar effect on ion transport. Overall, we showed a biomimetic approach to design temperature sensitive polymers where the strong ion-polymer binding is the key to the ultrahigh temperature response.
", "doi": "10.7907/zsat-9s73", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:16057", "collection": "thesis", "collection_id": "16057", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-145117270", "primary_object_url": { "basename": "Thesis_Caltech_Thesis_LaTeX_Template__with_logo____Amylynn_Chen (1).pdf", "content": "final", "filesize": 15428051, "license": "other", "mime_type": "application/pdf", "url": "/16057/1/Thesis_Caltech_Thesis_LaTeX_Template__with_logo____Amylynn_Chen (1).pdf", "version": "v4.0.0" }, "type": "thesis", "title": "3D in situ Chemical Synthesis: Additive Manufacturing of Functional Polymeric Materials via Vat Photo-polymerization", "author": [ { "family_name": "Chen", "given_name": "Amylynn C.", "orcid": "0000-0002-8112-5862", "clpid": "Chen-Amylynn-C" } ], "thesis_advisor": [ { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" } ], "thesis_committee": [ { "family_name": "Gao", "given_name": "Wei", "orcid": "0000-0002-8503-4562", "clpid": "Gao-Wei" }, { "family_name": "Faber", "given_name": "Katherine T.", "orcid": "0000-0001-6585-2536", "clpid": "Faber-K-T" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "As additively manufacturing gains popularity in rapid-prototyping, manufacturing and customized production, there is a continuous demand in seeking for new materials with advanced functionalities to satisfy the wide range of applications in aerospace, construction, optics, actuation, dentistry, biomedical practices and even food industry. Vat photopolymerization (VP), a light-enabled AM technique, is particularly promising due to its ability to achieve good surface quality, high resolution, and large volumetric throughput. The vast majority of materials obtained by VP are covalently-crosslinked thermosets with nondegradable carbon backbones. This highly crosslinked molecular structure gives rise to stiff and brittle materials, limiting the structural functionality in desired applications.
\r\n\r\nThis thesis explores a variety of molecular structures for new VP photopolymers: a) dynamically-crosslinked compliant polymer, b) interpenetrating network (IPN) hydrogel, and c) covalently-crosslinked polymer with labile group (ex. ester) insertion to polymer backbone. With the dynamic crosslinking system, we demonstrate tunable mechanical behaviors of the metal-coordinated supramolecular polymers. These materials display a range of failure strain of 450% - 940% and ultimate tensile strength of 12.4 - 2.2 MPa with varying resin compositions. To incorporate multifunctionality, we design thermoresponsive IPN hydrogels by fabricating a hydrophilic host polymer network via VP and a subsequent formation a thermoresponsive 2nd network (poly(N-Isopropylacrylamide)). The architected IPNs consistently display strong polymer-liquid phase separation behavior and a tunable water release behavior with volumetric shrinkage between 30% and 70% upon heating at 50oC. Finally, to promote the degradability of the acylate-based photoresin, we demonstrated successful incorporation for ester functional groups into the polymer backbone via radical ring opening polymerization of cyclic ketene acetals. The obtained polymer undergoes 84% mass loss within 7 hours under hydrolytic degradation condition. Overall, we demonstrated VP as a powerful technique to achieve one-pot synthesis and fabrication of functional materials. Our explorations on the development of degradable photopolymers, thermoresponsive double-network hydrogels, and metal-coordinated supramolecular polymers provide valuable insights into the impact of resin formulation on mechanical properties. From analyzing the molecular weight of 3DP materials to finetuning of phase separation behavior and degradability, we demonstrate that VP provides a new platform to inspire advanced photoresin design strategies for desirable mechanical performance.
", "doi": "10.7907/ca3e-rc06", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:16062", "collection": "thesis", "collection_id": "16062", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-194724728", "type": "thesis", "title": "Stochastic Foundations for Single-Cell RNA Sequencing", "author": [ { "family_name": "Gorin", "given_name": "Gennady", "orcid": "0000-0001-6097-2029", "clpid": "Gorin-Gennady" } ], "thesis_advisor": [ { "family_name": "Pachter", "given_name": "Lior S.", "orcid": "0000-0002-9164-6231", "clpid": "Pachter-L" } ], "thesis_committee": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Chong", "given_name": "Shasha", "orcid": "0000-0002-5372-311X", "clpid": "Chong-Shasha" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" }, { "family_name": "Pachter", "given_name": "Lior S.", "orcid": "0000-0002-9164-6231", "clpid": "Pachter-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Single-cell RNA sequencing, which quantifies cell transcriptomes, has seen widespread adoption, accompanied by proliferation of analysis methods. However, there has been relatively little systematic investigation of its best practices and their underlying assumptions, leading to challenges and discrepancies in interpretation. I present a set of generic, principled strategies for modeling the biological and technical components of sequencing experiments and use case studies to motivate their application to sequencing data.
", "doi": "10.7907/jn6n-x368", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:16067", "collection": "thesis", "collection_id": "16067", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-223752519", "primary_object_url": { "basename": "AndrewFriedmanThesis.pdf", "content": "final", "filesize": 14702200, "license": "other", "mime_type": "application/pdf", "url": "/16067/1/AndrewFriedmanThesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Scalable Fabrication of Micro-Architected Water Filtering Membranes", "author": [ { "family_name": "Friedman", "given_name": "Andrew Collin", "clpid": "Friedman-Andrew-Collin" } ], "thesis_advisor": [ { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Giapis", "given_name": "Konstantinos P.", "orcid": "0000-0002-7393-298X", "clpid": "Giapis-K-P" }, { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Polymer-based filtration devices are predominantly mass manufactured via mechanical spinning or electrospinning of heated polymer materials or fiberglass to create a randomly oriented fibrous network. This technique, while effective at producing materials necessary for traditional filtering applications, fails to afford control over morphology, both macro- and microscopically. The filtering material produced often relies exclusively on its randomly assembled porosity (and occasionally on its surface charge) to capture materials from filtered fluids but provides little means for targeted analyte capture without bulk surface coating or functionalization. This thesis seeks to demonstrate a unique approach to filtration membrane manufacture via a novel high-throughput holographic lithography and contact lithography process in the visible spectrum that utilizes a customized negative-tone photoresist inherently capable of localized surface modification.
\r\n\r\nThis thesis first describes the development of a large-scale holographic lithography process, from conceptualization to implementation, and demonstrates its efficacy by examining produced materials. A phase metasurface mask is utilized to produce a periodic intensity distribution of incident photons. This mask is irradiated at 0.23-0.25 W via linear raster scanning of a 2.2 mm diameter 532 nm laser at 1.5 mm/s and a scan offset of 0.4 mm to produce a homogeneous exposure profile in visible-light sensitized SU-8 negative-tone photoresist. Subsequent photoresist development results in 30\u201340 \u00b5m-thick nano-architected sheets with 2.1 \u00d7 2.4 cm\u00b2 lateral dimensions and ~500 nm-wide struts organized in layered 3D brick-and-mortar-like patterns to result in ~50\u201370% porosity. Scanning electron micrographs of cross-sectioned materials reveal how pattern morphology varies with cure depth, and furthermore how the lack of complete porosity disqualifies this material for application as a membrane filter.
\r\n\r\nThis thesis subsequently focuses on the development of a novel glycidyl methacrylate (GMA)-based negative-tone photoresist for implementation in the previously described lithography system to produce materials more amenable to functional membrane filter production. GMA is polymerized with a photo-caged aminated monomer, 2-((((2-nitrobenzyl)oxy)carbonyl)amino)ethyl 2-methyloxirane-2-carboxylate (ONBAMA) via free radical polymerization (FRP) and atom-transfer radical polymerization (ATRP) to produce ~30 kDa statistical co-polymers at an 85:15 monomer ratio, respectively. These linear co-polymers are then mixed with a photoacid generator (PAG) to produce a 532 nm sensitized negative-tone photoresist. Pre- and post-exposure bake temperatures are selected via glass-transition temperature identification (~62 \u00b0C) with differential scanning calorimetry (DSC) experiments, and cure depth varying with optical exposure dose is examined via establishment of contrast curves. The photoresist is then utilized in the previously described lithography system to produce square arrays of ~25 um circular holes, and the resulting films are characterized via optical and scanning electron microscopy.
\r\n\r\nThis thesis concludes with an examination of the poly(GMA-rand-ONBAMA) films implemented as water-permeable filtration membranes. Efficacy of surface functionalization and solution capture explored via amine deprotection and subsequent tagging with fluorescein isothiocyanate (FITC) dye. The presence and intensity uniformity of tagged samples are examined via confocal microscopy. Transmission of water is justified analytical examination and phenomenologically demonstrated via droplet loading of supported membranes with methylene blue-dyed water. Results are preliminary but indicate potential application of manufactured films as water filters.
\r\n\r\nIn summary, this thesis provides a foundation for the development of nano- and micro-architected materials at large scale and details its implementation for the design and preliminary testing of a GMA-based photoresist for water filtering membrane manufacture. Future research on optimizing photoresist design for mechanical stability could enable utilization of similar membranes for protein capture from biological fluids for use in diagnostic tools and assay automation.
", "doi": "10.7907/rktj-2v55", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15167", "collection": "thesis", "collection_id": "15167", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05132023-220300179", "primary_object_url": { "basename": "230520_Ifkovits_Zachary_Thesis.pdf", "content": "final", "filesize": 5054710, "license": "other", "mime_type": "application/pdf", "url": "/15167/1/230520_Ifkovits_Zachary_Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Strategies for Enabling Stable and Efficient (Photo)Electrochemical Water Splitting", "author": [ { "family_name": "Ifkovits", "given_name": "Zachary Philip", "orcid": "0000-0003-2538-0794", "clpid": "Ifkovits-Zachary-Philip" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Flagan", "given_name": "Richard C.", "orcid": "0000-0001-5690-770X", "clpid": "Flagan-R-C" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The electrolysis of water splits H\u2082O into its constituent parts, generating H\u2082 fuel and O\u2082 as a by-product. Although electrolysis has been known since late 1700s and has a consistently expanding industrial capacity, several barriers still exist to its widespread utilization as a clean method of generating hydrogen for industrial uses or as a grid-scale energy storage chemical. Among these, the materials and costs constraints surrounding the use of precious metal catalysts and expenses associated with balance-of-system costs are of primary importance. In this thesis, the first point is addressed by utilizing earth-abundant catalysts for chemical, electrochemical, and photoelectrochemical water splitting reactions. Specifically, MnySb1-yOx catalysts were synthesized for use as both cerium-mediated chemical water oxidation catalysts and as electrochemical water oxidation catalysts, furthering steps towards removing Ir from industrial electrolysis devices. Addition of Sb was shown to stabilize reactive Mn centers in these configurations, offering enhanced stability over pure Mn oxide catalysts. Reduction of electrolyzer balance-of-system costs were addressed in this thesis through the integration of multiple components of a solar-powered electrolysis system into a single, integrated photoelectrochemical water splitting device. Specifically, electrodeposition conditions were shown to affect the spontaneous mesostructuring of Ni-P hydrogen evolution catalysts on silicon photocathodes, leading to enhanced transmission of light to the semiconductor substrate. Furthermore, Y\u2082SiO\u2085 protective layers were shown to mitigate the corrosion of Si photocathodes in alkaline environments, an electrochemical environment known to be destructive towards silicon.", "doi": "10.7907/jt8t-w739", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:16071", "collection": "thesis", "collection_id": "16071", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06032023-004803929", "primary_object_url": { "basename": "Steve_Kim_Thesis_compressed.pdf", "content": "final", "filesize": 4723734, "license": "other", "mime_type": "application/pdf", "url": "/16071/4/Steve_Kim_Thesis_compressed.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Design Rules for Multi-Electron Systems in Next-Generation Batteries: From Mg Electrode-Electrolyte Interface to Anion Redox Activation in Li-Rich Sulfides", "author": [ { "family_name": "Kim", "given_name": "Seong Shik (Steve)", "orcid": "0000-0003-2604-6392", "clpid": "Kim-Seong-Shik-Steve" } ], "thesis_advisor": [ { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Agapie", "given_name": "Theodor", "orcid": "0000-0002-9692-7614", "clpid": "Agapie-T" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Li-ion batteries (LIBs) have revolutionized the modern world, powering portable electronic devices and more recently realizing electrification of transportation. With more technological advancements that further improved the performance, LIBs also play an important role as one of the most promising energy storage systems in transforming into renewable energy sources and achieving net zero emissions. However, state-of-the-art intercalation-based LIBs are beginning to mature and reach their theoretical capacity limits. To further improve the electrochemical performance of batteries and meet growing demands of energy storage applications, there have been growing efforts to increase the energy density beyond the limits of conventional LIBs. In this thesis, we examine two examples of multi-electron systems\u2013Mg electrolytes and Li-rich sulfide cathode materials\u2013to gain insights and establish design principles.
\r\n\r\nFirst, we explore the magnesium aluminum chloride complex (MACC) electrolyte to study the role of the electrode-electrolyte interface in Mg charge transfer. We demonstrate that MACC electrolyte which normally requires electrolytic conditioning can be chemically activated by the small addition of Mg(HMDS)\u2082. Solution-phase characterization reveals that Mg(HMDS)\u2082 helps prevent the formation of passivating film on the Mg surface by scavenging trace amounts of H\u2082O. Mg(HMDS)\u2082 also reacts with MACC to form free Cl\u207b which decorates the Mg surface which facilitates Mg electrodeposition and stripping.
\r\n\r\nNext, we investigate three different alkali-rich sulfides-LiNaFeS\u2082, LiNaCoS\u2082, and Li1.33-1.33zTi0.67+0.33zVaczS\u2082 - to probe the role of electronic and physical structure in governing reversible anion redox. We demonstrate that cryomilling LiNaFeS\u2082 mitigates particle fracturing by increasing microstrain and reducing crystallite size. Isostructural LiNaCoS\u2082 exhibits more covalent interactions between the transition metal-d and S-p states compared to LiNaFeS\u2082, but undergoes an irreversible conversion reaction. Lastly, Li\u2082TiS\u2083 exhibits no electrochemical activity, but introducing cationic vacancies in Li1.33-1.33zTi0.67+0.33zVaczS\u2082 activates S oxidation. Li1.33-1.33zTi0.67+0.33zVaczS\u2082 is studied further to study first-cycle activation and voltage hysteresis in Li-rich sulfides.
", "doi": "10.7907/v52j-t589", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:14989", "collection": "thesis", "collection_id": "14989", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07272022-064642720", "type": "thesis", "title": "Applications of Genetically Engineered Bacillus subtilis in Biocatalysis and Functional Materials", "author": [ { "family_name": "Hui", "given_name": "Yue", "orcid": "0000-0002-0354-0382", "clpid": "Hui-Yue" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "thesis_committee": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Bacillus subtilis is a gram-positive model bacterium that forms endospores as a response to nutrient limitation and other environmental stresses. The B. subtilis spore contains a dehydrated core, where the bacterial genome is safely stored, and multilayer proteinaceous coats, protecting the spore from various physical and chemical insults. Because of the outstanding resilience of the B. subtilis spore, it has attracted increasing interest for application in biotechnology. In this thesis, we demonstrate the utilization of genetically engineered B. subtilis cells and spores for heterologous protein display and functional material synthesis and characterization.
\r\n\r\nIn Chapter 1, we review the fundamentals of sporulation and germination in B. subtilis. We highlight notable biotechnological applications of native and engineered B. subtilis spores in recent years. We also discuss limitations associated with prior studies that inspire us to pursue the work in this thesis.
\r\n\r\nIn Chapter 2, we describe the T7 RNA polymerase (RNAP) enabled high density protein display on B. subtilis spores (TIED) method. The TIED constructs employ a coat protein promoter \u2013 PcotG, PcotV, or PcotZ \u2013 to drive the expression of the T7 RNAP. Target proteins are fused to the C-terminus of a spore crust protein \u2013 CotY or CotZ \u2013 and subjected to amplification by the T7 promoter. We prepare the endogenous constructs in which coat protein promoters directly regulate fusion protein expression for comparison with TIED. In addition, we develop a supplementary procedure to harvest spores before mother cell lysis, further improving the loading density of the target proteins. We verify the performance of the TIED architectures with a fluorescent reporter protein, mWasabi. Together with the early harvest protocol, the TIED method substantially enhances the total expression level and loading density of the crust-mWasabi fusion proteins relative to the endogenous expression system, as evidenced by bulk fluorescence measurements and microscopy.
\r\n\r\nIn Chapter 3, we implement the TIED architectures described in Chapter 2 for enzyme display on B. subtilis spores. We demonstrate the spore-based biocatalyst platform with three enzymes \u2013 lipase A and lipase B secreted by vegetative B. subtilis, and an engineered peroxidase, APEX2. We manifest that TIED enables massive accumulation of all three enzymes on the spore surface, with loading densities in the range of 106-107 enzymes per spore. Further, TIED-enzymes show comparable catalytic performance to the respective free-form enzymes, enhanced catalytic activity in methanol, and increased temperature stability. We conduct Michaelis-Menten studies to elucidate the kinetic characteristics of TIED-enzymes and their free form counterparts. Finally, we demonstrate that TIED-enzymes are not only recyclable, but also fully renewable after loss of activity through induction of germination and sporulation, demonstrating the potential for perpetual regeneration of the immobilized biocatalysts.
\r\n\r\nIn Chapter 4, we describe a new class of living composite materials (LCMs), in which genetically engineered B. subtilis cells and spores are effectively crosslinked into the surrounding polymeric scaffold. The resulting LCMs can be dried to yield portable materials. When re-immersed in aqueous media, entrapped cells and spores in previously- dried LCMs exhibit metabolic activity, including synthesis and secretion of recombinant proteins. Notably, we show that the scaffold based on photopolymerization of N-(hydroxymethyl) acrylamide (NHMAA) achieves effective cellular confinement, showing no evidence of cellular leakage over a period of 72 hours. We envision that the design principles elucidated in this work can provide a promising route to functional living materials engineered for biomedical and other applications.
", "doi": "10.7907/cdja-ck19", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15182", "collection": "thesis", "collection_id": "15182", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05162023-233932300", "primary_object_url": { "basename": "balzerThesis.pdf", "content": "final", "filesize": 17705659, "license": "other", "mime_type": "application/pdf", "url": "/15182/1/balzerThesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Polyelectrolytes Near Solid Surfaces", "author": [ { "family_name": "Balzer", "given_name": "Christopher James", "orcid": "0000-0002-9767-8437", "clpid": "Balzer-Christopher-James-J" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" }, { "family_name": "Frischknecht", "given_name": "Amalie L.", "orcid": "0000-0003-2112-2587", "clpid": "Frischknecht-Amalie-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Polyelectrolytes are ubiquitous in nature and in the products we use daily. The combination of their connectivity and charge lead to many useful properties in solution and near surfaces. Electrostatic forces dominate much of the behavior of charged species near solid surfaces; however, nonelectrostatic forces arising ion specific interactions or from varying polymer chemistry play an important role in tuning electrolyte and polyelectrolyte properties. The balance of these forces depends on factors like the salt concentration, solution pH, and properties of the surface. The current work outlines the thermodynamics of charged systems and investigates the structure and phase behavior of polyelectrolytes near solid surfaces. In particular, the work covers the thermodynamic aspects of preferential adsorption of small ions in electric double layers, polyelectrolyte adsorption, polymer-mediated interactions of surfaces using strong and weak electrolytes, surface phase transitions and contact angles of complex coacervates on solid surfaces, complexation-induced conformational phase transitions of polyelectrolyte brushes, and electro-swelling of weak polyelectrolyte brushes. The wide variety of problems addressed here reflects the variety of applications of polyelectrolytes and contexts in which polyelectrolytes appear.
", "doi": "10.7907/kga2-1820", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:14523", "collection": "thesis", "collection_id": "14523", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03222022-221436705", "type": "thesis", "title": "A Bubble Is Born: Nucleation and Early Growth of CO\u2082 Bubbles in Polymer Foams", "author": [ { "family_name": "Ylitalo", "given_name": "Andrew Samuel", "orcid": "0000-0003-4086-3508", "clpid": "Ylitalo-Andrew-Samuel" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" }, { "family_name": "Flagan", "given_name": "Richard C.", "orcid": "0000-0001-5690-770X", "clpid": "Flagan-R-C" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Gas bubble nucleation is a fundamental phenomenon both throughout the natural sciences and in the production of foams for lightweight, functional materials; it is also the basis for many a bubbly beverage. Enhancing bubble nucleation in polyurethane insulating foams used for refrigeration can further reduce their low thermal conductivity without resorting to hazardous blowing agents used in the past. Experimental challenges of measuring the kinetics of the rapid, multiscale process of bubble nucleation pose a roadblock to investigation of suitable processing conditions, as well as the development of theoretical models of bubbles and foams.
\r\n \r\nHere, using a microfluidic flow-focusing technique developed for measurement of protein and chemical kinetics, we built a microfluidic cell to probe gas bubble nucleation of CO\u2082 in polyol, a model system for polyurethane insulating foams, at controlled pressure with millisecond resolution over acquisition times sufficient for optical, IR, and X-ray measurements. This technique allows for repeated measurements of bubble nucleation at any degree of supersaturation without the interference of heterogeneous nucleation from surfaces. By extrapolating a model fit to high-speed optical microscopy measurements of bubble growth backward in time, we estimated the degree of supersaturation at nucleation for thousands of bubbles. Estimates of the nucleation rate based on Poisson statistics were consistent with predictions by a string method model based on density functional theory and G-ADSA measurements. This model predicted that the addition of cyclopentane (a common physical blowing agent in polyurethane foams) can dramatically reduce the nucleation energy barrier due to the formation of a liquid-like layer of cyclopentane and CO\u2082 along the surface of the bubble that reduces the interfacial tension, which previous models have only predicted at significantly higher saturation pressures. This prediction was supported by thermodynamic measurement of a three-phase coexistence under similar conditions, which is a known fingerprint for such nucleation pathways, and measurement of significantly higher bubble nucleation rates upon the addition of cyclopentane. These findings shed light on the possibility of a previously unappreciated role of physical blowing agents like cyclopentane in enhancing bubble nucleation by opening up a qualitatively distinct and more favorable nucleation pathway.
", "doi": "10.7907/cdgw-7c18", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14567", "collection": "thesis", "collection_id": "14567", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04292022-213605156", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 12618424, "license": "other", "mime_type": "application/pdf", "url": "/14567/1/thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Transport and Microrheology of Active Colloids", "author": [ { "family_name": "Peng", "given_name": "Zhiwei", "orcid": "0000-0002-9486-2837", "clpid": "Peng-Zhiwei" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Active colloids are micron-sized particles that self-propel through viscous fluids by converting energy extracted from their environment into mechanical motion. The origin or mechanism of their locomotion can be either biological or synthetic ranging from motile bacteria to artificial phoretic particles. Owing to their ability to self-propel, active colloids are out of thermodynamic equilibrium and exhibit interesting macroscopic or collective dynamics. In particular, active colloids exhibit accumulation at confining boundaries, upstream swimming in Poiseuille flow, and a reduced or negative apparent shear viscosity. My work has been focused on a theoretical and computational understanding of the dynamics of active colloids under the influence of confinement and external fluid flows, which are ubiquitous in biological processes. I consider the transport of active colloids in channel flows, the microrheology of active colloids, and lastly I propose and study a vesicle propulsion system based on the learned principles.
\r\n\r\nA generalized Taylor dispersion theory is developed to study the transport of active colloids in channel flows. I show that the often-observed upstream swimming can be explained by the biased upstream reorientation due to the flow vorticity. The longitudinal dispersion of active colloids includes the classical shear-enhanced dispersion and an active swim diffusivity. Their coupling results in a non-monotonic variation of the dispersivity as a function of the flow speed. To understand the effect of particle shape on the transport of active colloids, a simulation algorithm is developed that is able to faithfully resolve the inelastic collision between an ellipsoidal particle and the channel walls. I show that the collision-induced rotation for active ellipsoids can suppress upstream swimming. I then investigate the particle-tracking microrheology of active colloids. I show that active colloids exhibit a swim-thinning microrheology and a negative microviscosity can be observed when certain hydrodynamic effects are considered. I show that the traditional constant-velocity probe model is not suitable for the quantification of fluctuations in the suspension. To resolve this difficulty, a generalized microrheology model that closely mimics the experimental setup is developed. I conclude by proposing a microscale propulsion system in which active colloids are encapsulated in a vesicle with a semi-permeable membrane that allows water to pass through. By maintaining an asymmetric number density distribution, I show that the vesicle can self-propel through the surrounding viscous fluid.
", "doi": "10.7907/wa00-y892", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14456", "collection": "thesis", "collection_id": "14456", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12212021-202554260", "type": "thesis", "title": "Computational Methods for Simulating and Parameterizing Nucleic Acid Secondary Structure Thermodynamics and Kinetics", "author": [ { "family_name": "Fornace", "given_name": "Mark Evan", "orcid": "0000-0002-5829-5839", "clpid": "Fornace-Mark-Evan" } ], "thesis_advisor": [ { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "thesis_committee": [ { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Chan", "given_name": "Garnet K.", "orcid": "0000-0001-8009-6038", "clpid": "Chan-G-K" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Nucleic acid secondary structure models offer a simplified but powerful lens through which to view, analyze, and design nucleic acid chemistry. Computational approaches based on such models are central to current research directions across molecular programming, synthetic biology, and the life sciences more broadly. Our framework combines three ingredients. First, we develop new recursions to include contributions from coaxial and dangle stacking in an efficient and principled way. Second, we formulate the concept of an evaluation algebra, which defines the mathematical form of each subproblem in the dynamic program. Whereas previous modeling efforts have relied on case-by-case handling of different thermodynamic quantities, we use evaluation algebras to elegantly and efficiently compute a variety of physical quantities using the same recursions. Third, we develop efficient operation orders for a variety of physical quantities of experimental interest. Combining our advances, we are able to achieve speedups of 20-120x and scalable calculations of complexes of up to 30,000 nucleotides. Our achievements promise to dramatically expand the scope and utility of computational analysis and design of nucleic acid thermodynamics.
\r\n\r\nWhile current dynamic programming algorithms achieve efficient computation of thermodynamic quantities for a given nucleic acid sequence, they do not provide kinetic information. Therefore, investigations of secondary structure kinetics rely on stochastic simulations of trajectories in secondary structure space. We improve upon these simulation methodologies to achieve lower computational complexities and large empirical speedups. We extend our algorithms to an ensemble which fully includes coaxial and dangle stacking states, expanding the scope of the kinetic analysis that is currently possible.
\r\n\r\nCurrent secondary structure models are parametrized using thermodynamic information gleaned from decades of melt experiments of RNA and DNA in specific experimental conditions. Only rough kinetic information is currently available from past experiments, and information on solvent and material dependence is lacking. We develop a fully computational approach based on Gaussian processes and molecular dynamics in order to provide a generic method for estimating thermodynamic and kinetic parameters, applicable conceptually to any nucleic acid material and experimental setting of interest. Our methodology offers an atomistic view of nucleic acid base pairing and faithfully reproduces most experimental data. It thus provides a powerful black-box approach for extensibly calculating the kinetic and thermodynamic parameters that secondary structure models require.
", "doi": "10.7907/ayeg-at42", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14617", "collection": "thesis", "collection_id": "14617", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252022-172145394", "type": "thesis", "title": "Mechanical Approach to Active Matter: Reverse Osmotic Effect and Motility-Induced Phase Separation", "author": [ { "family_name": "Row", "given_name": "Hyeongjoo", "orcid": "0000-0003-3623-512X", "clpid": "Row-Hyeongjoo" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Thomson", "given_name": "Matthew", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The defining feature of active matter, self-propulsion requires constant consumption of energy to be maintained. As a result, active matter systems are inherently out of equilibrium and some principles that are accepted as common knowledge, particularly from thermodynamics, do not apply to the active matter systems. Arguably the most popular example is the motility-induced phase separation (MIPS) -- active matter can spontaneously phase separate into liquid-like dense phase and gas-like sparse phase even without any attractive interactions between the self-propelling constituents. In this thesis, I demonstrate the utility of a mechanical perspective in revealing and understanding the underlying physics of seemingly confounding behaviors of active matter systems. In Chapters 2 and 3, I consider the mechanics of a suspension of active colloidal particles when the transport properties (self-propelling speed and diffusivities) vary spatially. The mechanical analysis reveals the reverse-osmotic nature of active matter systems with a spatial variation in activity. I provide an explanation for why physical processes governed by the osmotic pressure of particles can appear in a reversed manner in active matter systems, e.g. a fluid can flow from regions of high concentration to low in a suspension of active colloids. In Chapter 4, I develop a mechanical theory of phase coexistence that applies to both equilibrium and nonequilibrium systems. By applying the mechanical theory to MIPS, I find phase coexistence conditions of the MIPS that allow a construction of a phase diagram, which excellently agrees with the results from computer simulations. The mechanical theory also allows access to the microscopic structure of phase interfaces. By investigating the interfacial structure, I discover interesting nonequilibrium interfacial behavior of the MIPS. I find that the width of the MIPS interface varies nonmonotically with the activity of particles and provide a mechanical explanation for the phenomena.", "doi": "10.7907/qef0-e420", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14630", "collection": "thesis", "collection_id": "14630", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262022-231652129", "primary_object_url": { "basename": "20220526_LhotaR_thesis.pdf", "content": "final", "filesize": 6574294, "license": "other", "mime_type": "application/pdf", "url": "/14630/1/20220526_LhotaR_thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Rheological Characterization of Polymer Additives for Mist Control and Drag Reduction", "author": [ { "family_name": "Lhota", "given_name": "Red C.", "orcid": "0000-0002-8481-3716", "clpid": "Lhota-Red-C" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "McKeon", "given_name": "Beverley J.", "orcid": "0000-0003-4220-1583", "clpid": "McKeon-B-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Long flexible polymers in solution at low concentrations strongly change the extensional properties of fluids due to chain stretching that resists flow, while their compact conformation in shear has weak effects. This dramatic difference between their effects on extension and shear is desirable in a variety of applications--controlling drop size in sprayed mists, reducing drag in turbulent flow, and preventing rebound in drop impact. Traditional long covalent polymers, however, are not practical in many applications because they undergo mechanical degradation, i.e. chain scission, under strong flow conditions. Megasupramolecular polymer systems, consisting of long end-associative telechelic polymers that assemble in solutions into multi-million molecular weight supramolecules, meet this practical need. Through association, they act like traditional covalently-bonded polymers in extension, while reversibly dissociating under the strong flows that cause scission for those long polymers.
\r\nThis thesis examines the interplay of flow and degradation that imposes an upper-bound on useful lengths of invididual end-associative chains (how long is too long) (Chapters 2 and 3); the quiescent coil size that affects the onset of stretching in fluids of interest (water and polyalphaolefin lubricant) (Chapters 2 and 4);\r\nrheological approachs to detect variations in the degree of end-functionalization that affect formation of ultra-long supramolecules (Chapter 5); and the changes to turbulent flow when long polymers are present at low concentration (Chapter 2). Ultimately, the audience who might enjoy this thesis is limited by barriers of rheological jargon. In the pursuit of broader rheological and overall scientific understanding, I describe evidence-based pedagogical techniques and my approach to implementing them in chemical engineering and polymer physics classrooms (Chapter 6).
", "doi": "10.7907/wav1-4t47", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14457", "collection": "thesis", "collection_id": "14457", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12222021-065913893", "primary_object_url": { "basename": "Thesis_Orland_Bateman_final_record-14458.pdf", "content": "final", "filesize": 5958689, "license": "other", "mime_type": "application/pdf", "url": "/14457/10/Thesis_Orland_Bateman_final_record-14458.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Design and Application of Novel Membrane Materials", "author": [ { "family_name": "Bateman", "given_name": "Orland Christopher Lycurgue", "orcid": "0000-0002-6985-494X", "clpid": "Bateman-Orland-Christopher-Lycurgue" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Diallo", "given_name": "Mamadou S.", "clpid": "Diallo-Mamadou-S" } ], "thesis_committee": [ { "family_name": "Faber", "given_name": "Katherine T.", "orcid": "0000-0001-6585-2536", "clpid": "Faber-K-T" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Diallo", "given_name": "Mamadou S.", "clpid": "Diallo-Mamadou-S" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Membrane technology is uniquely suited to meet the growing need for more sustainable processes due to membranes\u2019 tailorable selectivity and energy efficiency. Efforts to further improve membrane performance and modify them for new applications have found success in academic studies with a versatile class of membranes known as mixed-matrix membranes (MMM). Mixed-matrix membranes combine the strength and controlled morphology of semicrystalline polymeric membranes with superior functionality of a separate material dispersed in the polymer matrix. The strength and toughness of the resulting membranes depends on polymer morphology, including degree of crystallinity and pore structure. Control of the membrane morphology is achieved by kinetically trapping a partially phase separated state, for example, using Nonsolvent Induced Phase Separation (NIPS) to drive liquid-liquid and solid-liquid demixing. However, the processes used to control the polymer morphology are influenced by the functional particles and can result in novel morphologies. In Chapter 2, we used a promising strategy for stably incorporating functional polymeric particles in a structural polymer matrix to investigate the role of the particles during NIPS. The interplay of functional polymeric particle loading and nonsolvent induced phase separation are examined using x-ray diffraction (to deduce the crystal morph adopted by polyvinylidene difluoride, PVDF) and scanning electron microscopy (to observe membrane morphology and the size and distribution of functional particles). We found that the interaction between nonsolvent and functional particles enables a shift in crystal phase usually not attainable with our solvent.
\r\n\r\nIn addition to studying the fundamentals underlying MMM formation, we investigated two applications for novel membrane materials: purification of therapeutic antibodies and size-selective particle capture. Purification of proteins for medical use requires several chromatographic steps in order to produce solutions of sufficient purity. For many years, the gold standard in the field was resin-based packed bed chromatography; however, more recently membrane chromatography has gained prevalence due to its faster processing time, lower cost, and low operating pressure. With these advantages come the drawbacks of low binding capacity and a sensitivity to the concentration of salt ions in the solution. To address these two drawbacks, we investigated the chromatographic abilities of a modified MMM, in Chapter 3, and a novel membrane material comprising an MMM-ceramic composite, in Chapter 4. We discovered that the performance of the modified MMM is dependent on crosslinker chemistry and crosslink density. Upon optimization, the modified membrane demonstrated a binding capacity consistent with the upper range of available literature values as well as reduced sensitivity to salt. In addition, the development of the novel MMM-ceramic composite enables the use of a broader range of polymer matrix compositions for membrane chromatography.
\r\n\r\nCapture of pathogens from complex fluids, such as blood, has received substantial attention due to rising rates of sepsis and antibiotic resistance. \tIn Chapter 5, we pursued the capture of pathogens from model fluids using the size-based separation capabilities of dendritic ceramic membranes. We found that interactions between the ceramic surface and the suspended particles played a significant role in membrane performance.
", "doi": "10.7907/9w23-ax66", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14643", "collection": "thesis", "collection_id": "14643", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05272022-201237457", "primary_object_url": { "basename": "jacobson_daniel_2022_thesis.pdf", "content": "final", "filesize": 12284959, "license": "other", "mime_type": "application/pdf", "url": "/14643/2/jacobson_daniel_2022_thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Computational Studies of Dendritic Deposition and Trajectory Phase Coexistence", "author": [ { "family_name": "Jacobson", "given_name": "Daniel Rance", "orcid": "0000-0001-7990-4093", "clpid": "Jacobson-Daniel-Rance" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Flagan", "given_name": "Richard C.", "orcid": "0000-0001-5690-770X", "clpid": "Flagan-R-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Many out-of-equilibrium systems display collective transitions in the behavior of particles akin to phase transitions. The field of nonequilibrium statistical mechanics seeks to develop new theories and methods to characterize these phenomena. In this thesis, we advance this aim by presenting computational studies of two different kinds of nonequilibrium transitions: the compact-to-dendritic (CTD) transition in the deposition of Brownian particles and trajectory phase coexistence (TPC) in stochastic dynamical systems.
\r\n\r\nThe CTD transition occurs when Brownian particles (like ions, colloids, or misfolded proteins) deposit from all sides onto a reactive cluster. While the cluster initially maintains a compact morphology, upon reaching a critical radius, it spontaneously develops dendritic branches. Although the size of the critical radius depends on the deposition conditions, this relationship is not well understood at a mechanistic level. Here, we show that contrary to previous evidence, the critical radius in Brownian dynamics simulations follows the behavior predicted by a continuum analysis. That is, dendrites emerge when the cluster circumference exceeds the length that particles can diffuse in the characteristic reaction timescale. Consequently, our results provide microscopic validation for continuum methods that are widely applied to study dendrite formation in electrodeposition and lithium metal batteries.
\r\n\r\nTrajectory phase coexistence (TPC) arises when qualitatively different trajectory behaviors interconvert in a stochastic dynamical system. This type of coexistence plays a central role in theories of glassy dynamics. In this work, we focus on two different research areas related to TPC. First, we introduce an importance sampling method, Variational Ansatz for Rare Dynamics (VARD), for characterizing a system's rate function. VARD is technically and conceptually straightforward yet can still sample the large deviations of many-body models found in the literature. We then examine the meaning of kinks in the scaled cumulant generating function (SCGF). Although these singularities are often taken to be proof that TPC occurs, a more precise understanding of the connection between kinks and coexistence remains lacking. By characterizing the dynamics of two kinds of random walkers, we show that kinks actually result from diverging timescales in the dynamics and do not always indicate the presence of TPC.
", "doi": "10.7907/dje7-ey77", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14534", "collection": "thesis", "collection_id": "14534", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03292022-234015177", "type": "thesis", "title": "Path Space Markov Chain Monte Carlo Methods for Molecular Simulation", "author": [ { "family_name": "Rosa-Ra\u00edces", "given_name": "Jorge Luis", "orcid": "0000-0003-2311-2948", "clpid": "Rosa-Ra\u00edces-Jorge-Luis" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Stuart", "given_name": "Andrew M.", "orcid": "0000-0001-9091-7266", "clpid": "Stuart-A-M" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Path space Markov-chain Monte Carlo (McMC) provides a versatile framework for simulating the structure and dynamics of condensed-phase systems aptly described by classical and quantum Boltzmann statistics. This thesis comprises our efforts to design, analyze and improve path space McMC algorithms to achieve numerically advantageous, and physically accurate, simulation of molecular processes across a range of scales. To improve molecular dynamics (MD) simulations of atomically resolved systems exhibiting pronounced nuclear quantum effects, we introduce a family of integrators for non-preconditioned path-integral MD exhibiting dimension-free statistical accuracy and efficiency, and enabling a many-fold increase in time-step stability relative to conventional approaches at no additional computational cost or implementation complexity. The integrators come with robust performance guarantees that are borne out in thermostatted ring-polymer MD simulations of realistic condensed-phase models. Concurrently, toward extending the range of accessible timescales in stochastic MD simulations of mesoscale coarse-grained molecular systems, we introduce a parallel-in-time integrator for the overdamped Langevin equation based on McMC evaluation of a path-integral representation of the many time-step stochastic MD transition kernel. The parallel-in-time integrator achieves simultaneous integration of multiple stochastic MD time-steps at no greater wall-time cost and with no lesser accuracy than a standard Euler--Maruyama integrator does in serial, and thus instantiates new opportunities to accelerate stochastic dynamics simulations on massively parallel computer architectures. Our work along these two methodological avenues extends the utility of path space McMC across applications in molecular simulation and has broader implications in other disciplines that require accurate and efficient simulations of Markov diffusion processes in state spaces or path spaces.
", "doi": "10.7907/10jr-hg67", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14312", "collection": "thesis", "collection_id": "14312", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07232021-171251780", "type": "thesis", "title": "Cotranslational Pulling Forces Alter Outcomes of Protein Synthesis", "author": [ { "family_name": "Zimmer", "given_name": "Matthew Holden", "orcid": "0000-0002-1437-2636", "clpid": "Zimmer-Matthew-Holden" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Clemons", "given_name": "William M.", "orcid": "0000-0002-0021-889X", "clpid": "Clemons-W-M" }, { "family_name": "Voorhees", "given_name": "Rebecca M.", "orcid": "0000-0003-1640-2293", "clpid": "Voorhees-R-M" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "As nascent proteins are synthesized by the ribosome, interactions between the nascent protein and its environment can create pulling forces that are transmitted to the ribosome's catalytic center. These forces can affect the rate and outcomes of translation. We use atomistic and coarse-grained simulation to characterize the origins of pulling forces, the propagation of force to catalytic center of the ribosome, and the effects of force on synthetic outcomes. We uncover a novel form of pulling force-mediated regulation in which the forces generated by the integration of a transmembrane helix induce frameshifting in a viral polyprotein. Computational force measurements of hundreds of mutant viral sequences in combination with deep mutational scanning experiments reveal the structural and sequence-level features that enable this powerful regulatory mechanism. Force measurements are also used to provide a molecular picture for complex pulling force experiments on multispanning membrane proteins. In particular, we identify signatures of cotranslational helix packing interactions and the translocation of surface helices. To understand how forces are propagated through the nascent protein in the ribosomal exit tunnel, we ran and analyzed hundreds of microseconds of atomistic molecular dynamics with an applied pulling force on the nascent protein. The simulations reveal how the secondary structure of nascent proteins and their interactions with the ribosome control force propagation. The inhibition of force transduction by nascent protein-ribosome interactions explains how amino acids tens of angstroms away from the catalytic center of the ribosome can still influence the force-induced restart of stalled ribosomes.
", "doi": "10.7907/p7vk-cf03", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14329", "collection": "thesis", "collection_id": "14329", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08202021-200738765", "type": "thesis", "title": "Molecular Simulations of Charge Transport for Energy Storage and Conversion Applications", "author": [ { "family_name": "Kim", "given_name": "Jeongmin", "orcid": "0000-0002-7405-8200", "clpid": "Jeongmin-Kim" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" }, { "family_name": "Jones", "given_name": "Simon C.", "orcid": "0000-0002-1952-3720", "clpid": "Jones-Simon-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Molecular simulation plays a variety of roles in accelerating the development of energy materials, from providing a fundamental understanding of molecular processes to predicting their performance spanning a wide range of chemical space. In this thesis, we present molecular simulation studies of charge transport both in bulk energy materials and at their interfaces to provide molecular principles for advanced rechargeable batteries in part I and electricity generation using a metal nanofilm from water motion in part II.
\r\n\r\nIn part I, we discuss ion transport and interfacial electron transfer in polymeric battery materials, both of which are closely associated with battery operation. As a bulk electrolyte and a solid electrolyte interphase (SEI), polymeric materials often benefit rechargeable batteries, allowing for enhanced safety and increased energy density. Firstly, we propose a unique mechanism of lithium-ion transport in polymer-based electrolytes, including conjugated polymers with an imidazolium sidechain and polyborane-based single-ion conductors, which utilizes the formation of a percolating ion network to facilitate lithium ion transport. Secondly, we discuss interfacial ion solvation structure and dynamics that are closely related to interfacial electron-transfer kinetics. Simulations provide molecular insights into how a functional SEI passivates a metal electrode, thereby accelerating materials discovery such as an artificial SEI of self-assembled monolayers.
\r\n\r\nIn part II, we present molecular principles of energy conversion from a flow of ionic solution to electricity using metal nanolayers. The energy conversion emerges at a water-solid interface and requires a boundary of an electrical double layer at which ion adsorption and desorption occur along with the flow. We discuss charge induction mechanisms related to a heterolayered structure of a metal nanolayer and investigate factors that affect energy conversion efficiency in two different modes of operation, namely a flow cell and a wavetank.
", "doi": "10.7907/5haz-ch54", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14441", "collection": "thesis", "collection_id": "14441", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12052021-002539806", "type": "thesis", "title": "Swimming in Potential Flow", "author": [ { "family_name": "Glisman", "given_name": "Alec Gregory", "orcid": "0000-0001-9677-1958", "clpid": "Glisman-Alec-Gregory" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Hunt", "given_name": "Melany L.", "orcid": "0000-0001-5592-2334", "clpid": "Hunt-M-L" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Active bodies undergo self-propulsive motion in a fluid medium and span a broad range of length and time scales. This report focuses specifically on the motion at high Reynolds number, where inertial forces dominate the fluid dynamics. Many active systems spontaneously self-organize into visually striking structures: fish schooling, birds flocking, and bacterial colonies growing. Current models of emergent behavior in the inertial regime are mainly phenomenological and do not account for the fluid-mediated interactions between bodies. We seek to advance physical models of swimmers in high inertia environments. To this end, we explicitly model the hydrodynamics to discern what role the fluid medium plays in active group dynamics and whether it can reproduce the observed emergent phenomenon without the imposition of phenomenologically based interaction rules.
\r\n\r\nA minimal swimmer model consisting of three linked spheres is constructed, and we find self-propulsion without external forces or momentum transfer via vortex shedding. The inertial swimmer is also compared to an identical swimmer in the Stokes regime---where fluid inertia is neglected. The Stokes hydrodynamics are longer-ranged at leading order, and we demonstrate that the stronger hydrodynamic interactions lead to a greater center of mass translation after a period of articulation.
", "doi": "10.7907/6xkb-rs66", "publication_date": "2022", "thesis_type": "masters", "thesis_year": "2022" }, { "id": "thesis:14445", "collection": "thesis", "collection_id": "14445", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12102021-231944176", "primary_object_url": { "basename": "KjeldbjergCamilla2022Thesis.pdf", "content": "final", "filesize": 57009594, "license": "other", "mime_type": "application/pdf", "url": "/14445/1/KjeldbjergCamilla2022Thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "The Effects of Confinement in Active Matter: the Casimir Effect, Partitioning, and Hindered Diffusion", "author": [ { "family_name": "Kjeldbjerg", "given_name": "Camilla Maria", "orcid": "0000-0003-2224-0534", "clpid": "Kjeldbjerg-Camilla-Maria" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Seinfeld", "given_name": "John H.", "orcid": "0000-0003-1344-4068", "clpid": "Seinfeld-J-H" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Active matter describes a class of materials for which constituent \"particles\" convert chemical energy into mechanical motion leading to self-propulsion (swimming). The origins of this swimming motion for both biological and synthetic constituents is a thriving area of research. However, here we focus on the physical properties and mechanics of the active matter systems. We model active particles using the active Brownian particle (ABP) model that is the simplest model that captures the essential physics, where a particle translates with a swim speed U0 in a direction q for a characteristic reorientation time \tτR; the average length they move between each reorientation is called the run, or persistence, length ℓ = U0τR. Owing to this persistent swimming, the ABPs distribute non-homogenously near surfaces, accumulating at no-flux boundaries leading to a concentration boundary layer near solid surfaces. Active particles often have an effective size—their run length—which can be much larger than their geometric size such that they experience confinement in geometries whose size is on the order of the run length. Active systems are inherently far from equilibrium, and we cannot appeal to properties of equilibrium thermodynamic such as the chemical potential to predict the partitioning. Fortunately, active particles are still subject to the laws of mechanics, and in this work, we present a simple macroscopic balance that allows one to predict behavior without detailed calculations. We predict the attractive force between two parallel plates in a reservoir (also called the Casimir effect) and find that the average concentration between the plates equals that in the bulk reservoir independent of the degree of confinement (ratio of run length to the spacing between the plates). We then examine the confinement effects in a channel geometry, where the behavior is fundamentally different, and the average concentration grows linearly with the degree of confinement. The understanding of these fundamental geometries motivated us to look into more complex geometries such as porous media. Based on dimensional analysis and our predictive model, we explain the transient behavior and steady-state partitioning of active particles between a fluid reservoir and a porous medium. Lastly, we discuss the hindered diffusion in periodic porous media and how the diffusion depends not only on the porosity of the medium but also on the degree of confinement. We believe that utilizing the insights in effects of confinement for these fundamental geometries and the porous media will be valuable in designing optimal structures for enhancing or isolating active particles.
", "doi": "10.7907/avfw-fh81", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14045", "collection": "thesis", "collection_id": "14045", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01042021-220032574", "type": "thesis", "title": "Data-Driven Protein Engineering", "author": [ { "family_name": "Wu", "given_name": "Zachary", "orcid": "0000-0003-2429-9812", "clpid": "Wu-Zachary" } ], "thesis_advisor": [ { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Yue", "given_name": "Yisong", "orcid": "0000-0001-9127-1989", "clpid": "Yue-Yisong" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Directed evolution has enabled the adaptation of natural protein sequences for an endless variety of human applications. Given a starting point - a sequence with measurable activity - directed evolution is able to improve protein sequences by iteratively accumulating beneficial mutations. However, directed evolution requires investing large experimental effort, which continues to be the major bottleneck in efficient protein optimization. To this end, we describe a framework for incorporating machine learning in the directed evolution process to maximize the utility of generated experimental data in Chapter 2. In Chapter 3, we then show that this framework outperforms traditional directed evolution methods on an empirical fitness landscape. However, directed evolution is fundamentally limited by its need for a starting point, or a sequence with measurable activity. To tackle this issue, we test the ability of nascent deep learning techniques for generating short, functional amino acid sequences in Chapter 4. Encouraged by this success, we attempted to generate full length enzymatic sequences for desired substrates without success. However, we were able to apply this deep learning approach to model other aspects of enzymatic protein sequences in Chapter 5. Finally, the field of data-driven protein sequence generation is enjoying a recent surge in interest, and we provide an updated review of protein engineering with machine learning, focusing on recent work in deep generative modeling in Chapter 1.
", "doi": "10.7907/nx3c-qb44", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:13968", "collection": "thesis", "collection_id": "13968", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09272020-215437294", "type": "thesis", "title": "Nanometer-sized Aerosol Particles in the Atmosphere: Measurement, Analysis, and Impact", "author": [ { "family_name": "Kong", "given_name": "Weimeng (Stephanie)", "orcid": "0000-0002-9432-2857", "clpid": "Kong-Weimeng-Stephanie" } ], "thesis_advisor": [ { "family_name": "Seinfeld", "given_name": "John H.", "orcid": "0000-0003-1344-4068", "clpid": "Seinfeld-J-H" }, { "family_name": "Flagan", "given_name": "Richard C.", "orcid": "0000-0001-5690-770X", "clpid": "Flagan-R-C" } ], "thesis_committee": [ { "family_name": "Seinfeld", "given_name": "John H.", "orcid": "0000-0003-1344-4068", "clpid": "Seinfeld-J-H" }, { "family_name": "Flagan", "given_name": "Richard C.", "orcid": "0000-0001-5690-770X", "clpid": "Flagan-R-C" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "New particle formation (NPF) from gaseous precursor vapors is frequently observed in the ambient environment and contributes to a major source of global cloud condensation nuclei (CCN). The survival and CCN activation of newly formed particles are highly dependent on particle growth below 10 nm. Characterizing and understanding nanoparticle early growth will therefore help to quantify the impact of NPF on cloud reflectivity and global energy budget. In this work, I first present a recently developed instrument, the Caltech nano-Scanning Electrical Mobility Spectrometer (nSEMS), which consists of a charge conditioner, a novel differential mobility analyzer (DMA), and a two-stage condensation particle counter (CPC). This new design, coupled with a data inversion method that combines empirical calibration and COMSOL simulation, can help to measure nanoparticle size distributions from 1.5 nm to 25 nm more accurately. This instrument was employed in the experiments conducted in the Cosmics Leaving OUtdoor Droplets (CLOUD) chamber at the European Organization for Nuclear Research (CERN) to better understand NPF, particle growth and survival. Multiple experimental parameters were varied to study the influence of different highly oxygenated molecules (HOMs) and inorganic trace gases, such as ammonia and nitrogen oxides on particle early growth. Experiment results have suggested a novel mechanism that may help to explain nanoparticle formation and growth in highly polluted urban environments or in the cold free troposphere. In as little as a few minutes, freshly nucleated particles as small as 2 nanometers in diameter can grow very rapidly due to simultaneous condensation of nitric acid and ammonia. This can help them to survive through the so-called \"valley of death\" where they would otherwise be lost to larger particles, and instead allow them to grow to sizes where they are less vulnerable to loss and can continue on to sizes where they influence local air quality or climate. Further, the laboratory results of nanoparticle growth were incorporated into the Global Model of Aerosol Processes (GLOMAP) model to study the impact of this extremely rapid growth on the global CCN budget. Having realized the importance of conducting well-controlled chamber experiments and of using chamber experimental data, we established an online data infrastructure, the Index of Chamber Atmospheric Research in the United States (ICARUS), for storing, sharing, and using chamber data. A combined effort of the described works contributes to better measuring the size distribution of nanoparticles and to understanding their impact on global climate.
", "doi": "10.7907/893j-7x60", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14258", "collection": "thesis", "collection_id": "14258", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072021-223407413", "type": "thesis", "title": "Tensor Network Methods for Nonequilibrium Statistical Mechanics", "author": [ { "family_name": "Helms", "given_name": "Phillip Laurence", "orcid": "0000-0002-6064-3193", "clpid": "Helms-Phillip-Laurence" } ], "thesis_advisor": [ { "family_name": "Chan", "given_name": "Garnet K.", "orcid": "0000-0001-8009-6038", "clpid": "Chan-Garnet-K-L" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Chan", "given_name": "Garnet K.", "orcid": "0000-0001-8009-6038", "clpid": "Chan-Garnet-K-L" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Minnich", "given_name": "Austin J.", "orcid": "0000-0002-9671-9540", "clpid": "Minnich-A-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Large deviation theory has emerged as a powerful mathematical scaffolding for studying nonequilibrium statistical mechanics, particularly for characterizing the macroscopic effects of microscopic fluctuations. While the large deviation approach is firmly established, it relates the effects of fluctuations to the likelihood of exponentially rare events, which naively requires exponentially large simulation costs. This, in turn, necessitates the development of appropriate numerical simulation techniques. While the standard Monte Carlo toolkit has expanded to incorporate methods towards making rare events typical, in this thesis I propose and evaluate a powerful unorthodox approach adopted from quantum simulation, namely tensor network algorithms, which can work in concert with standard methods to deepen our understanding of nonequilibrium phenomena.
\r\n\r\nAs a testbed for this novel approach, I consider the dynamical phase behavior of several versions of the simple exclusion process, a paradigmatic model of classical driven diffusion. Using a matrix product state, a one-dimensional tensor network ansatz, and the density matrix renormalization group algorithm, a corresponding optimization routine, I characterize the dynamical phase transition between a jammed and maximal current phase in both the one-dimensional and multi-lane simple exclusion processes. The matrix product state is found to be an efficient representation of the nonequilibrium steady-state biased to arbitrarily rare currents via large deviation theory. Because the one-dimensional ansatz is limited to finite-width systems, I extend this success to study the fully two-dimensional simple exclusion process. There, the projected entangled pair state, a two-dimensional tensor network ansatz, is used with the time evolution via block decimation algorithm to demonstrate that the phase transition observed in one-dimension persists in the fully two-dimensional system.
\r\n\r\nTowards the goal of making tensor network methods adaptable for a broad range of physically important systems, both classical and quantum, I also present progress towards studying systems in the continuum limit with interacting particles in two dimensions. This builds upon previous work proposing tensor network representations of quantum operators with long-range interactions in two dimensions by evaluating three operator representations in practice and finding two competitive and viable approaches.
", "doi": "10.7907/kram-8g47", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14212", "collection": "thesis", "collection_id": "14212", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312021-221223611", "type": "thesis", "title": "Context-Dependent, Combinatorial Logic of BMP Signaling", "author": [ { "family_name": "Klumpe", "given_name": "Heidi Elizabeth", "orcid": "0000-0001-8938-2006", "clpid": "klumpe-Heidi-Elizabeth" } ], "thesis_advisor": [ { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" } ], "thesis_committee": [ { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Goentoro", "given_name": "Lea A.", "orcid": "0000-0002-3904-0195", "clpid": "Goentoro-L-A" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Evolution generated diverse signaling proteins for the control of multicellular patterns and organ- isms. These include the proteins of the Bone Morphogenetic Protein (BMP) pathway. Nearly a dozen BMPs activate the BMP pathway to promote the formation of tissues as diverse as bone, cartilage, blood vessels, and the kidney, making them attractive therapeutics for regenerating those tissues in adults. During development, the response to a given BMP depends heavily on context, such as which other BMPs are present and which BMP receptors are expressed on the cell being ac- tivated. However, despite knowing that context matters, the overall logic of this context-dependent signal processing, including the roles of specific ligands and receptors in shaping context and how this logic arises from biochemical features of specific pathway components, remains unclear. Inspired by maps of gene epistasis and drug interactions that functionally classify members of complex biological systems, we comprehensively measured responses to all pairs of ten BMP homodimers (BMP2, BMP4, BMP5, BMP6, BMP7, BMP9, BMP10, GDF5, GDF6, and GDF7), combining robotic liquid handling with a high-throughput fluorescent reporter of pathway activa- tion. These data functionally classify ligands into \"equivalence groups,\" or ligands that combine in the same way with all other ligands across combinations. Surprisingly, the functional groupings do not correlate with similarity of ligand sequence and can change with cell context. Together, the context-dependent equivalence groups summarize the diverse responses to combinations of BMP ligands and their dependence on specific BMP receptors. The experimentally observed pairwise responses are also consistent with a mathematical model where BMP ligands compete for limited BMP receptors with different affinities and then produce outputs with different ligand-specific activ- ities. Ultimately, these results provide a useful reference for explaining the unique effects of BMP combinations in different tissues or time points in development, as well as highlighting counter- intuitive mechanisms for this complex signal processing. Chapter 1 provides an introduction to how and why we study cell-cell signaling. Chapter 2 provides a summary of the determination of equivalence groups, their dependence on receptor context, and fitting the mathematical model of receptor competition. Chapter 3 provides suggestions for future work, including recommendations for improved model fitting as well as crucial extensions to the definitions of BMP \"combinations\" and \"context\" to deepen our understanding and control of this critical pathway.", "doi": "10.7907/3vv4-bk06", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:13614", "collection": "thesis", "collection_id": "13614", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01102020-003449091", "type": "thesis", "title": "Resistance is Futile: Physical Science, Systems Biology and Single-Cell Analysis to Understanding the Plastic and Heterogeneous Nature of Melanoma and Their Role in Non-Genetic Drug Resistance", "author": [ { "family_name": "Su", "given_name": "Yapeng", "orcid": "0000-0002-6305-8467", "clpid": "Su-Yapeng" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Baltimore", "given_name": "David L.", "clpid": "Baltimore-D-L" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Baltimore", "given_name": "David L.", "clpid": "Baltimore-D-L" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Melanoma is the most deadly form of skin cancer due to its great metastatic potential. Targeted therapy that inhibits the BRAF-V600E driver mutation has shown impressive initial responses in melanoma patients. However, drug resistance, as the universal phenomenon for any cancer therapy, always limits treatment efficacy and compromises outcomes. As the early-step of resistance development, non-genetic mechanisms enable cancer cells to transition into a drug-resistant state in as early as a few days after drug treatment without alteration of the genome. This early mechanism is, to a large extent, due to the heterogeneous and highly plastic nature of tumor cells. Therefore, it imperative to understand the plastic and heterogeneous nature of the melanoma cells in order to identify combination therapies that can overcome resistance.
\r\n\r\nIn this thesis, we investigate these two fundamental natures of non-genetic drug resistance using BRAF inhibition of BRAF-mutant melanomas as the model system. These melanoma cells undergo multi-step, reversible drug-induced cell-state transitions from the original sensitive phenotype to a drug-resistant one.
\r\n\r\nWe first conducted bulk analysis to characterize the detailed kinetics of the entire transition from drug-sensitive state towards drug-resistant state, revealing expression changes of thousands of genes and extensive chromatin remodeling. A 3-step computational biology approach greatly simplified the complexity and revealed that the whole cell-state transition was controlled by a gene module activated within just the first three days of drug treatment, with the RelA transcription factor driving chromatin remodeling to establish an epigenetic program encoding long-term phenotype changes towards resistance. From there, a detailed mechanism connecting tumor epigenetic plasticity with non-genetic drug resistance was resolved through in-depth molecular biology experiments. The mechanism was validated in clinical patient samples.
\r\n\r\nWe further investigated heterogeneity by moving from bulk cellular studies to single-cell analysis. The single-cell view further revealed that two driving forces from both cell-state interconversions and phenotype-specific drug selection control the cell-state transition dynamics. The single-cell studies also pinpointed the signaling network hub, RelA, as the driver molecule of the initiation of the adaptive transition. These two competing driving forces were further quantitatively modeled via a thermodynamic-inspired surprisal analysis and a modified Fokker-Planck-type kinetic model.
\r\n\r\nFinally, using integrated single-cell proteomic and metabolic technology I developed to characterize the early-stage signaling and metabolic changes upon initial drug responses, we further identified two distinct paths connecting drug-sensitive and drug-tolerant states. Melanoma cells exclusively traverse one of the two paths depending on the level of MITF in the drug-na\u00efve cells. The two trajectories are associated with distinct signaling and metabolic susceptibilities and are independently druggable.
\r\n\r\nIn total, this thesis combines and synergizes various physical science and systems biology approaches together with several unique single-cell technologies and analysis to obtain a deep and comprehensive understanding of non-genetic drug resistance in cancer. The findings from this thesis provide several novel insights into the rational design of effective combination therapy for overcoming the development of resistance in response to cancer treatments.
", "doi": "10.7907/78ZP-Y270", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:11808", "collection": "thesis", "collection_id": "11808", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10062019-213347699", "primary_object_url": { "basename": "porubsky_nicholas_2019.pdf", "content": "final", "filesize": 28767176, "license": "other", "mime_type": "application/pdf", "url": "/11808/1/porubsky_nicholas_2019.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Enhanced Algorithms for Analysis and Design of Nucleic Acid Reaction Pathways", "author": [ { "family_name": "Porubsky", "given_name": "Nicholas James", "orcid": "0000-0001-6330-2645", "clpid": "Porubsky-Nicholas-James" } ], "thesis_advisor": [ { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" } ], "thesis_committee": [ { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "clpid": "Ismagilov-R-F" }, { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Nucleic acids provide a powerful platform for programming at the molecular level. This is possible because the free energy of nucleic acid structures is dominated by the local interactions of base pairing and base pair stacking. The nearest neighbor secondary structure model implied by these energetics has enabled development of a set of algorithms for calculating thermodynamic quantities of nucleic acid sequences. Molecular programmers and synthetic biologists continue to extend their reach to larger, more complicated nucleic acid complexes, reaction pathways, and systems. This necessitates a focus on new algorithm development and efficient implementations to enable analysis and design of such systems.
\r\n\r\nConcerning analysis of nucleic acids, we collect seemingly diverse algorithms under a unified three-component dynamic programming framework consisting of: 1) recursions that specify the dependencies between subproblems and incorporate the details of the structural ensemble and the free energy model, 2) evaluation algebras that define the mathematical form of each subproblem, 3) operation orders that specify the computational trajectory through the dependency graph of subproblems. Changes to the set of recursions allows operation over the complex ensemble including coaxial and dangle stacking states, affecting all thermodynamic quantities. An updated operation order for structure sampling allows simultaneous generation of a set of structures sampled from the Boltzmann distribution in time that scales empirically sublinearly in the number of samples and leads to an order of magnitude or more speedup over repeated single-structure sampling.
\r\n\r\nFor the problem of sequence design for reaction pathway engineering, we introduce an optimization algorithm to minimize the multitstate test tube ensemble defect, which simultaneously designs for reactant, intermediate, and product states along the reaction pathway (positive design) and against crosstalk interactions (negative design). Each of these on-pathway or crosstalk states is represented as a target test tube ensemble containing arbitrary numbers of on-target complexes, each with a target secondary structure and target concentration, and arbitrary numbers of off-target complexes, each with vanishing target concentration. Our test tube specification formalism enables conversion of a reaction pathway specification into a set of target test tubes. Sequences are designed subject to a set of hard constraints allowing specification of properties such as sequence composition, sequence complementarity, prevention of unwanted sequence patterns, and inclusion of biological sequences. We then extend this algorithm with soft constraints, enhancing flexibility through new constraint types and reducing design cost by up to two orders of magnitude in the most highly constrained cases. These soft constraints enable multiobjective design of the multitstate test tube ensemble defect simultaneously with heuristics for avoiding kinetic traps and equalizing reaction rates to further aid reaction pathway engineering.
\r\n", "doi": "10.7907/M8CZ-MW98", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:11328", "collection": "thesis", "collection_id": "11328", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12232018-185711169", "type": "thesis", "title": "Computational Heterogeneous Electrochemistry \u2013 From Quantum Mechanics to Machine Learning", "author": [ { "family_name": "Huang", "given_name": "Yufeng", "orcid": "0000-0002-0373-2210", "clpid": "Huang-Yufeng" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Because of coulomb interactions and complex surface morphologies, rigorous methods for heterogeneous electrochemical catalysis were not well-established. Thus, for different types of electrochemical systems, a specific strategy must be adapted. In this thesis, we first used the cluster model to study the chemistry on a 1D chain of MoS2 edges. Then, a rigorous grand canonical potential kinetics (GCP-K) method was developed for general crystalline systems. Starting from quantum mechanical calculations, the method gave rise to a different picture from the traditional description given by the Butler-Volmer kinetics. Next, we studied the chemical selectivity of CO2 reduction on polycrystalline copper nanoparticles. Because of the complexity of the reaction sites, we combined the reactive force field, density functional theory, and machine learning method to predict the reactive sites on 20,000 sites on a roughly 200,000-atom nanoparticle. Such a strategy opens up new way to understand chemistries on a much wider range of complex structures that were impossible to study theoretically. Lastly, we formulated a machine learning force field strategy using atomic energies for amorphous systems. We have shown that such a method can be used to reproduce quantum mechanical accuracies for molecular dynamics. This method will enable the accurate study of the dynamics of heterogeneous systems during electrochemical reactions. In summary, we have developed quantum chemical methods and machine learning strategies to reformulate rigorous ways to study a wide range of heterogeneous electrochemical catalysts.
", "doi": "10.7907/MCGV-Y790", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11131", "collection": "thesis", "collection_id": "11131", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07232018-084606596", "primary_object_url": { "basename": "Burkholder_Eric_2019_Final.pdf", "content": "final", "filesize": 9016177, "license": "other", "mime_type": "application/pdf", "url": "/11131/1/Burkholder_Eric_2019_Final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Single Particle Motion in Active Matter", "author": [ { "family_name": "Burkholder", "given_name": "Eric William", "orcid": "0000-0001-7420-4290", "clpid": "Burkholder-Eric-William" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "\"Active matter\" refers to a broad class of materials in which the constituent particles or organisms are able to self-propel (swim) by some internal physicochemical mechanism. Though the origin of this self-propulsive motion is a rich area of study, we are primarily interested in the collective effects of this motion on the physical properties — and in particular, the rheology — of the active material as a whole. As such we model self-propulsive motion using the minimal active Brownian particle (ABP) model: a particle of size a , swims in a direction q with a speed U0, and the direction of its motion changes randomly over some time scale \u03c4R.
\r\n\r\nOn a macroscopic scale, active motion leads to unique hydrodynamic and mechanical stresses exerted by the particles on their embedding medium. These stresses arise from the microscopic force associated with particle locomotion — the swim force F swim. Though the idea of the swim force is widely recognized in the abstract, little attention has been given to the characterization and mechanical consequences of this force. In this work we are particularly interested the role of the swim force in the effective motion of passive constituents in active environments, and how the swim force affects long-ranged hydrodynamic interactions (HI) in active suspensions. We examine these issues through the lens of microrheology: tracking the motion of a colloidal probe particle through an active medium, and using its motions to infer the effective viscoelastic properties of the suspension.
\r\n\r\nUsing generalized Taylor dispersion theory, we find an activity-driven enhancement to the diffusion of the probe in an active medium. This first-principles theory unites many experimental observations of tracer diffusion, and provides simple physical descriptions of the problem that do not rely on the specific self-propulsion mechanism of the swimmer. This same framework is then used to compute the suspension microviscosity (as measured by the drag on the probe particle), and the fluctuation-dissipation relation in an active system. We find that activity reduces the drag on the probe, but the drag is still larger than it would be in a Newtonian fluid; this stands in contrast to experimental measurements of reduced shear viscosities. We show that the microviscosity of a suspension is reduced — and may even become negative! — due to HI, and that this effect is not due to the fluid velocity disturbance associated with the swimmers' self-propulsion.
", "doi": "10.7907/SGHS-CH87", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11146", "collection": "thesis", "collection_id": "11146", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08142018-105206326", "type": "thesis", "title": "Conformations and Charge Fluctuations in Polyelectrolyte Solutions", "author": [ { "family_name": "Shen", "given_name": "Kevin", "orcid": "0000-0001-9715-7474", "clpid": "Shen-Kevin" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "From DNA and RNA encoding life to flocculation agents used in water remediation, charged polymers (polyelectrolytes) are prevalent in nearly all facets of our lives. The charged nature of polyelectrolytes has rendered them useful in many applications, from the stabilization of colloids to the formation of nanoparticles for drug or gene delivery. There are open questions regarding the factors that dictate polyelectrolyte stability, and electrostatic fluctuations, first elucidated by Debye and H\u00fcckel for simple electrolytes, are key to the thermodynamic description of such charged systems. Electrostatic fluctuations lead to ionic clouds around charges, leading to favorable energy decreases. While charge-fluctuations are well-described for simple electrolytes, the impact of polyelectrolyte (PE) charge connectivity on charge fluctuations is much less well understood: a huge number of degrees of freedom must be considered in order to describe the multicomponent nature of polyelectrolyte solutions and the large number of conformations the polyelectrolytes themselves can assume. Past theories have both under- and over-estimated the connectivity effects on electrostatic fluctuations, and do not give a clear picture of the transition from weak to strong electrostatic fluctuations.
\r\n\r\nMy work has focused on coming up with a theory that self-consistently accounts for the coupling of chain connectivity and electrostatic fluctuations, thus spanning electrostatic fluctuations from weak to intermediate fluctuation strengths. In particular, I present a novel renormalized Gaussian fluctuation (RGF) theory that identifies the renormalization of chain structure as a key physical consequence of intermediate-strength electrostatic fluctuations. The theory self-consistently couples chain structure with the thermodynamics, and mediates the transition from weak, linearized fluctuations to the onset of stronger fluctuation effects like ion pairing. While the onset of these different fluctuation effects has a clear sequence, they are all coupled and must be determined self-consistently. A key concept introduced by the theory is the notion of the polyelectrolyte self energy, which describes the electrostatic work required to charge the molecule in solution, and provides a useful perspective from which to understand and rationalize the effects of chain conformation on thermodynamic behavior. We use the theory to study the phase behavior of polyelectrolyte solutions and connect theory to experimental results.
", "doi": "10.7907/Y6VG-0297", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11276", "collection": "thesis", "collection_id": "11276", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11162018-140640407", "type": "thesis", "title": "Bioresorbable Vascular Scaffolds Gain Ductility, Resistance to Hydrolysis, and Radial Strength via a Unique Poly L-lactide Microstructure", "author": [ { "family_name": "Ramachandran", "given_name": "Karthik", "orcid": "0000-0003-1820-7555", "clpid": "Ramachandran-Karthik" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "orcid": "0000-0002-3680-4399", "clpid": "Ismagilov-R-F" }, { "family_name": "Robb", "given_name": "Maxwell J.", "orcid": "0000-0002-0528-9857", "clpid": "Robb-M-J" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Advances in tissue engineering over the past few decades are poised to revolutionize drug delivery and biomedical implants. Bioresorbable vascular scaffolds (BVS), which are made from the semicrystalline polymer poly (L-lactide), are an example of polymers saving and improving the quality of human life. BVSs are emerging as a promising alternative to metal stents for the treatment of coronary heart disease (CHD), one of the leading causes of death in the world. In contrast to permanent stents, BVSs are designed to have a limited lifespan in the body; they restore blood flow through the occluded artery by lending it support for 3-6 months, but are completely resorbed in 2-3 years, leaving behind a healthy artery. This transient character of BVS restores vasomotion in the treated artery and can eliminate the risk of thrombosis, a dreaded complication regarded as the bane of stenting.
\r\n\r\nThe promising success of the first and currently only clinically-approved BVS (FDA-approval in 2016) provides an impetus to continue its development. The struts of the BVS (~ 150\u03bcm) are nearly two times thicker than in metal stents (~ 80\u03bcm). A thicker device is challenging to implant and is unable to treat smaller and tortuous arteries. Furthermore, clinicians speculate that irregular blow flow over thicker struts may contribute towards thrombosis. An added complication of working with BVSs is that they are difficult to visualize with X-rays owing to the low atomic mass of polymers. The need for a BVS that is thinner, stronger, and radio-opaque is the motivation for this thesis, which aims to extend the benefits of transient implants to a broader patient population. Chapter I provides a brief chronological overview of the evolution of cardiovascular therapeutics to combat CHD. Chapters II and III elucidate micron-scale gradients in the PLLA microstructure of the clinically-approved BVS that overcome PLLA\u2019s inherent brittleness and provide lasting radial support to the artery. Chapter IV discusses the fabrication of novel instrumentation to establish structure-property relationships for scaffolds, and Chapter V explores polylactide nanocomposites that not only increase radial strength in a thinner profile but also provide radio-opacity.
", "doi": "10.7907/9146-5159", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11560", "collection": "thesis", "collection_id": "11560", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292019-133006433", "type": "thesis", "title": "Use of Recombinant Self-Associating Proteins for Altering Cellular Fate and Behavior", "author": [ { "family_name": "Kozlowski", "given_name": "Mark Tybalt", "orcid": "0000-0003-4714-8697", "clpid": "Kozlowski-Mark-Tybalt" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The behavior of mammalian and bacterial cells is governed by their surroundings, and the interactions of cells with their nearest neighbors. In this work, I will demonstrate how self-associating proteins such as leucine zippers or SpyTag and SpyCatcher can be used either in hydrogels for cell culture, or to drive the aggregation of cells into artificial, engineered communities. I further demonstrate how these self-associating protein-based materials can either alter the fate of cultured cells, or directly change cellular behavior through the activation of a quorum sensing circuit.
\r\n\r\nIn the first chapter, I discuss protein-based methods for making different types of organoids. Organoids are groups of cells derived from stem or progenitor cells that form a multicellular structure consisting of different cell types. These organoids are currently of interest as disease model systems, pharmaceutical test platforms, and replacement tissues. However, most studies of organoids to date have derived them from Matrigel-based cultures. While versatile and inexpensive, Matrigel is undefined, suffers from batch-to-batch variability, and its xenogeneic nature means that organoids derived from Matrigel are unlikely to be approved for clinical use. In Chapter 1, I review current state-of-the-art materials developed as alternatives to Matrigel, such as naturally-derived extracellular matrices, synthetic hydrogels, and recombinant proteins serving as artificial extracellular matrices. I consider the advantages and disadvantages of each method, as well as speculate on possible future directions for the field.
\r\n\r\nOf these alternatives to Matrigel, recombinant protein-based artificial extracellular matrices have the advantage of being easy to engineer, as genetic encoding of the material allows precise control over molecular weight and functionality. Development of these types of materials has long been a focus of work in our laboratory, and in Chapter 2, I discuss the development of two protein-based hydrogels expressed in Escherichia coli, which are based on a previously-reported PEP hydrogel. These new \u201cPEXEP-type\u201d hydrogels are physically cross-linked by leucine zippers derived from rat cartilage oligomeric matrix protein (COMPcc), incorporate chemical cues from fibronectin and collagen IV, and were used for pancreatic cell culture in defined medium. When comparing this defined, protein-based medium to methylcellulose-Matrigel, we find that the growth of endocrine cells is promoted, as opposed to the ductal cells found in methylcellulose-Matrigel culture. We further find a difference in colony types observed based on whether the fibronectin or collagen IV cue is present. More interestingly, the protein-based culture material promotes the growth of endocrine progenitor cells, which may be useful for further studying the formation of the Islets of Langerhans. Finally, we observe that sorted populations of murine cells cultured in our protein hydrogels have a lower rate of colony formation, and this reduction in the number of colonies is not observed in methylcellulose-Matrigel culture. We believe that this might be evidence for a paracrine effect that promotes cell growth, particularly the growth of putative endocrine colonies, though further experiments are required to confirm this effect.
\r\n\r\nIn Chapter 2, I demonstrate how a self-associating protein can be used to change the fate of a cell culture, and give rise to multicellular colonies. However, for the purpose of constructing bioreactors, microbial fuel cells, or systems for environmental remediation, it may be advantageous to design tissue-like systems de novo, making multifunctional communities of bacteria that function as artificial tissues. In Chapter 3, I will discuss the construction of a synthetic microbial community of E. coli cells, whose quorum sensing response is governed by aggregation of the cells. This aggregation in turn is driven by the expression of surface-displayed self-associating proteins, and I will discuss methods developed to control the size, reversibility, and morphology of these aggregates. As the behavior of these aggregates is dependent on cell-cell communication facilitated by proximity, these consortia represent early examples of synthetically-designed artificial tissues that can be governed by engineered cell-cell signaling.
", "doi": "10.7907/3Z3B-V584", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11567", "collection": "thesis", "collection_id": "11567", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05302019-112215583", "type": "thesis", "title": "Effects of Branching on Conformation, Crystallization, and Self-Assembly of Polymers", "author": [ { "family_name": "Kim", "given_name": "Joey Dongjin", "orcid": "0000-0002-3359-4875", "clpid": "Kim-Joey-Dongjin" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "clpid": "Shapiro-M-G" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The central feature of bottlebrush polymers is the stiffening of the main-chain (MC) due to side-chain side-chain (SC-SC) repulsion, amplified by densely grafting long SCs, particularly in good solvent conditions. The expectation of stiffening has led most prior studies to refer to bottlebrush polymers as \"worm-like,\" \"cylindrical\" or a \"self-avoiding walk (SAW) of superblobs\". However, there is no direct evidence of stiffening of the main-chain and measurements of the overall segment distribution of the whole molecule have failed to discriminate between competing models. Here, we provide a set of measurements of the main-chain conformation (neutron scattering in a solvent that is contrast matched to the side chains) together with the overall conformation of the bottlebrush as a whole (light, X-ray, and neutron scattering) under conditions that highlight SC-SC repulsion: the side-chains are relatively long compared to prior literature, the concentration of bottlebrushes is low, and the solvent quality is good. Surprisingly, the main-chain has a conformation that does not conform to any prior models: all three main-chain lengths examined showed a window of length scales in which the scattering power increased less than linearly with length scale. In particular, the MC conformation is not worm-like. Direct observation of the main-chain conformation and the overall conformation discriminates among models more powerfully than the overall conformation alone. Inspired by the Paturej-Rubinstein tension blob model, we examined a conceptual model in which tension of the MC accumulates with distance from the ends of the MC and found that it can capture the salient features of both the MC- and whole bottlebrush scattering more gradually than previous theoretical models predicted. The conceptual model also explains our observation of a substantial increase in anisometry with increasing MC length, opposite to a worm-like chain. The results indicate that synthetically accessible bottlebrushes are not fractals; they cannot have self-similar (fractal) conformation because each increase in main-chain length accesses greater side-chain crowding than any of its shorter siblings. We expanded the work to understand the behavior in \u03b8 conditions and shorter side-chains expected to have reduced tension as well as the behavior at different concentrations.
\r\n\r\nIn addition, we characterized the interplay of self-assembly and polymer crystallization through analysis of three representative bottlebrush copolymer systems. Our results revealed a surprising number of unexpected behaviors ranging from unexpected morphologies, control of thermal properties even to complete suppression of phase transitions, and control of the orientation of crystal stem with respect to the morphological interface, which highlights the potential of the bottlebrush architecture.
", "doi": "10.7907/8AFE-YC54", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11695", "collection": "thesis", "collection_id": "11695", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06062019-082100687", "primary_object_url": { "basename": "omar_ahmad_2019.pdf", "content": "final", "filesize": 8647019, "license": "other", "mime_type": "application/pdf", "url": "/11695/1/omar_ahmad_2019.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Dynamics, Mechanics and Stability of Physical Gels", "author": [ { "family_name": "Omar", "given_name": "Ahmad Khalid", "orcid": "0000-0002-6404-7612", "clpid": "Omar-Ahmad-Khalid" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "From the commercial products that we encounter in our daily lives to the mucous that lines our gut, gels assembled by the reversible association of polymers or colloids are a ubiquitous, important and fascinating class of soft materials. The dual solid and fluid-like (viscoelastic) properties of associative polymer gels render them useful in a number of applications including as tissue-regeneration scaffolds, drug delivery vectors and organic electronics and batter technologies. However, there remains a number of open questions regarding the microscopic origins of many of the dynamical and mechanical properties that make these materials so appealing. The wide range of length and timescales in physical gels present a formidable challenge towards the formulation of a complete microscopic dynamical and rheological portrait. My work has focused on the development of microscopically-informed and experimentally verifiable explanations for some of the fundamental dynamical and mechanical properties of associative gels. I first present our viewpoint, informed by computer simulation and experiment, on the origin of the long-time self-diffusivity of telechelic polymer gels. Our perspective and resulting theory compare favorably with experiments. Shearing an associative polymer gel is found to result in the emergence of new diffusive modes with applied shear that are can destabilize homogeneous flow for gels sufficiently close to the two phase boundary. This finding motivates the idea that nonequilibrium forcing may promote the relaxation of arrested colloidal materials, such as a colloidal gel, closer to their thermodynamic ground state. The driving force need not be externally applied. The induced collective motion in colloidal gels subject to internal driving forces (such as the presence of a small fraction of self-propelling colloids) can drive the system from a state of arrested metastablity to a state of lower free energy. I conclude by showing that the internal stress generated by the self-propelling particles -- the active stress -- is not a \"true\" stress, but rather an equivalent stress analogous to the dynamic pressure of fluids in a gravitational field. The importance of this finding is demonstrated in resolving the perplexing finding of a negative surface tension in phase separated active materials.
", "doi": "10.7907/3F0A-4S95", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11474", "collection": "thesis", "collection_id": "11474", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04162019-155405091", "type": "thesis", "title": "How Polymers Shape the Physicochemical Environment of the Gut", "author": [ { "family_name": "Preska Steinberg", "given_name": "Asher Raphael", "orcid": "0000-0002-8694-7224", "clpid": "Preska-Steinberg-Asher-Raphael" } ], "thesis_advisor": [ { "family_name": "Ismagilov", "given_name": "Rustem", "clpid": "Ismagilov-R-F" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Ismagilov", "given_name": "Rustem F.", "clpid": "Ismagilov-R-F" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The gut is where food is digested and nutrients are absorbed, therapeutics are often delivered, and many infections take hold. The gut microbiota is in symbiosis with its host, and can influence host health and behavior. Though the gut holds these central roles, little is understood about the physics of how soft materials interact with and shape the physicochemical environment of the gut. Soft materials abound in the gut in the form of particulates (e.g., microbes, viruses, therapeutic particles, food granules) and polymers (e.g., dietary fibers, therapeutics, food additives). This thesis explores the soft matter physics of the gut and how physicochemical interactions can influence gut structure and function. This is studied through a combination of mouse experiments and numerical calculations. In the first part of this thesis, we investigate how particulates interact with polymers in the small intestine. We find that polymers from dietary fiber can aggregate particulates by a mechanism that is qualitatively consistent with depletion interactions. This mechanism is distinct from agglutination via specific chemical interactions. In the second part of this thesis, we investigate how polymers interact with the colonic mucus hydrogel. Colonic mucus is the nexus of host-microbe interactions. It is a barrier which protects against microbial infiltration, and alterations to its physical structure have been linked to changes in host health. Here, we find that polymers compress the colonic mucus hydrogel. For uncharged polymers, this mechanism can be described by a simple, mean-field model based on Flory-Huggins solution theory. Further, we find that microbes can modulate the extent of mucus compression by degrading polymers in the gut. In the last part of this thesis, we find that charged polymers (polyelectrolytes) compress mucus by a Donnan mechanism.
", "doi": "10.7907/XPEZ-G864", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:10972", "collection": "thesis", "collection_id": "10972", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05302018-104109274", "primary_object_url": { "basename": "AB Chang Thesis - Full Version.pdf", "content": "final", "filesize": 78455886, "license": "other", "mime_type": "application/pdf", "url": "/10972/19/AB Chang Thesis - Full Version.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Synthesis and Self-Assembly of Bottlebrush Block Polymers: Molecular Architecture and Materials Design", "author": [ { "family_name": "Chang", "given_name": "Alice B.", "orcid": "0000-0001-5036-2681", "clpid": "Chang-Alice-B" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Bottlebrush polymers represent a unique molecular architecture and a modular platform for materials design. However, the properties and self-assembly of bottlebrush polymers remain relatively unexplored, in large part due to the synthetic challenges imposed by the sterically demanding architecture. This thesis describes our work to close this gap, connecting (1) the synthesis of polymers with precisely tailored molecular architectures, (2) the study of fundamental structure-property relationships, and (3) the design of functional materials.
\r\n\r\nChapter 1 introduces key concepts related to polymer architecture and block polymer phase behavior. Recent developments in the synthesis and self-assembly of bottlebrush block polymers are highlighted in order to frame the work presented in Chapters 2\u20136.
\r\n\r\nChapter 2 introduces a versatile strategy to design polymer architectures with arbitrary side chain chemistry and connectivity. Simultaneous control over the molecular weight, grafting density, and graft distribution can be achieved via living ring-opening metathesis polymerization (ROMP). Copolymerizing a macromonomer and a small-molecule co-monomer provides access to well-defined polymers spanning the linear, comb, and bottlebrush regimes. This design strategy creates new opportunities for molecular and materials design.
\r\n\r\nChapter 3 explores the physical consequences of varying the grafting density and graft distribution in two contexts: block polymer self-assembly and linear rheological properties. The molecular architecture strongly influences packing demands and therefore the conformations of the backbone and side chains. Collectively, these studies represent progress toward a universal model connecting the chemistry and conformations of graft polymers.
\r\n\r\nChapter 4 discusses the phase behavior of ABA' and ABC bottlebrush triblock terpolymers. Low-χ interactions between the end blocks promote organization into a unique mixed-domain lamellar morphology, LAMP. X-ray scattering experiments reveal an unusual trend: the domain spacing strongly decreases with increasing total molecular weight. Insights into this behavior provide new opportunities for block polymer design with potential consequences spanning all self-assembling soft materials.
\r\n\r\nChapter 5 describes other physical consequences of low-χ block polymer design. The ternary phase diagrams for ABC, ACB, and BAC bottlebrush triblock terpolymers reveal the influences of low-χ A/C interactions, frustration, and the molecular architecture. Potential non-equilibrium effects and crystallization in these bottlebrush polymers will also be discussed.
\r\n\r\nChapter 6 describes applications of bottlebrush polymers as functional materials. Self-assembly enables mesoscale structural control over many materials properties, such as reflectivity, conductivity, and modulus. The synthetic methods (Chapter 2) and physical insights (Chapters 3\u22125) provided in previous chapters illustrate opportunities for materials design. We will discuss AB brush diblock polymers that self-assemble to photonic crystals and ABA brush triblock copolymers in solid polymer electrolytes.
\r\n", "doi": "10.7907/4xdv-9302", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10184", "collection": "thesis", "collection_id": "10184", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05182017-225415095", "primary_object_url": { "basename": "Thesis_Ho-Il_Ji_2017_v4_final.pdf", "content": "final", "filesize": 24616947, "license": "other", "mime_type": "application/pdf", "url": "/10184/1/Thesis_Ho-Il_Ji_2017_v4_final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Redox Kinetics of Nonstoichiometric Oxides", "author": [ { "family_name": "Ji", "given_name": "Ho-Il", "orcid": "0000-0002-6194-991X", "clpid": "Ji-Ho-Il" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Cerium oxide (CeO2-\u03b4) and its derivatives are the most attractive materials under consideration for solar-driven thermochemical production of chemical fuels. Understanding the rate-limiting factors in fuel production is essential for maximizing the efficacy of the thermochemical process.
\r\n\r\nThe rate of response of the porous ceria structured with architectural features typical of those employed in solar reactors was measured via electrical conductance relaxation methods. A transition from behavior controlled by material surface reaction kinetics to that controlled by sweep-gas supply rates is observed on increasing temperature, increasing volume specific surface area, and decreasing normalized gas flow rate. The transition behavior is relevant not only for optimal reactor operation and architectural design of material, but also for accurate measurement of material properties.
\r\n\r\nThe redox kinetics of undoped ceria, CeO2-\u03b4 at extreme high temperature (1400 \u00b0C) was investigated using the electrical conductivity relaxation method, and those of 10% Pr doped ceria at low temperature (700 \u00b0C) were done using the mass relaxation method. It was demonstrated under sufficiently high gas flow rates relative to the mass of the oxide, which is required in order to overcome gas phase limitations and access the material kinetic properties. Furthermore, the surface reaction rate constant of undoped ceria, ,kChem, was investigated at high temperature (1400 \u00b0C) in humidified gas atmosphere, in consideration of the operating conditions in thermochemical fuel production system. It was demonstrated that H2O potentially plays a role of oxidants as increasing temperature and/or decreasing oxygen partial pressure; thus in such thermodynamic conditions, pH2O, besides temperature and pO2, needs to be carefully considered in surface reaction study.
\r\n\r\nIn addition to relaxation experiments under small driving force for redox reaction, the kinetics of surface related oxidation reaction under large chemical driving force (large \u0394pO2 change) was investigated by mass relaxation method. Based on the normalized reaction rates of several possible rate determining steps, the relaxation behavior in oxygen concentration for all possible rate determining steps was computed. On the comparison with the experimental results, the most probable rate determining step was suggested (reduction of diatomic oxygen from neutral oxygen molecule to superoxide), and the oxidation kinetics under large driving force was explained.
\r\n", "doi": "10.7907/Z98913W2", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10288", "collection": "thesis", "collection_id": "10288", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06052017-162306037", "type": "thesis", "title": "An Investigation of Nonstoichiometric Oxides for Solar-Driven Thermochemical Fuel Production", "author": [ { "family_name": "Ignatowich", "given_name": "Michael Joseph", "orcid": "0000-0002-0097-664X", "clpid": "Ignatowich-Michael-Joseph" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Faber", "given_name": "Katherine T.", "clpid": "Faber-K-T" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In order to realize energy independence and substantially combat global climate change, renewable and sustainable energy technologies must be developed. Solar energy is the most readily abundant, and if converted into a chemical fuel, could be stored and transported easily. Solar-driven thermochemical cycling is a method of chemical fuel production that shows great promise, but current state-of-the-art systems have very low efficiencies. This work discusses new reactor designs and cycling techniques using nonstoichiometric oxides that will enable more efficient solar to fuel energy conversion. Practical aspects of the reactor design are explored \u2013 specifically, thermochemical expansion of the reactive oxide, and morphologies aimed at enhancing the reaction kinetics. Additionally, doped fluorite- and perovskite-structured materials are evaluated for thermodynamic behavior and in-situ thermochemical cycling performance. Oxide morphology and new doped compounds show little improvement over previously established neat ceria due to thermodynamic limitations. The thermodynamic limit is explored in new reactor geometries and is shown to demonstrate significantly more efficient fuel production. Finally, different nonstoichiometry thermodynamics are explored to provide guidance for further material exploration, as well as applicable methodologies.
", "doi": "10.7907/Z92805PM", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10270", "collection": "thesis", "collection_id": "10270", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06042017-233656614", "primary_object_url": { "basename": "Bilin_Zhuang_thesis_2016_v3.pdf", "content": "final", "filesize": 9028796, "license": "other", "mime_type": "application/pdf", "url": "/10270/1/Bilin_Zhuang_thesis_2016_v3.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Dipolar Liquids and Their Mixtures: Equilibrium and Nonequilibrium Properties with Field-Theoretic Approaches", "author": [ { "family_name": "Zhuang", "given_name": "Bilin", "orcid": "0000-0003-2934-4264", "clpid": "Bilin-Zhuang" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Liquid is a state of matter that is intermediate between the gas state and the solid state. Though it is an ordinary state of matter, the application of statistical mechanics for understanding its properties is far from complete. Compared to the solid state, the liquid state has molecules that can move around freely, and yet, unlike that in the gas state, the intermolecular correlations are significant in the liquid state. Therefore, the distance dependent correlations in a liquid need to be taken into account to properly describe a liquid. In particular, all molecules are polarizable. The polarizable nature allows the molecules to induce polarization in surrounding molecules, giving rise to van der Waals interactions that have important consequences on the properties of a liquid. In addition to polarizability, many molecules are intrinsically polar. The long-ranged dipole-dipole correlations contribute to the complexity of interactions and lead to a myriad of interesting properties special to a liquid.
\r\n\r\nIn recent years, field-theoretic technique has emerged as a convenient and systematic tool for deriving coarse-grained theories for a wide range of complex-fluid and soft-matter systems while preserving the essential physics. In this thesis, we present the application of field-theoretic approaches to two problems of liquids and their mixtures. The first problem is to describe the dielectric properties of an ordinary liquid or liquid mixture under equilibrium condition, where current field-theoretic methods are inadequate. In this problem, we apply a variational field-theoretic approach to develop a statistical field theory of the liquid, and predict the dielectric constant and the miscibility of liquids using the variational free energies derived. The second problem involves the nonequilibrium solvent composition and orientational polarization surrounding some charged solute in the context of electron transfer reactions. Using a self-consistent-field theory with constrained coarse-grained fields, we derive expressions for the nonequilibrium solvation energy, and apply it to compute the reorganization energy of electron transfer reactions. The theories presented in this thesis lead to simple analytical expressions for the equilibrium and the nonequilibrium free energies, making it possible to theoretically survey a wide range of liquids. In addition, our models involve only a few readily-available molecular parameters and avoid the use of any adjustable parameters, allowing one to make a priori predictions on the properties of liquids and their mixtures.
", "doi": "10.7907/Z9VQ30QR", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10172", "collection": "thesis", "collection_id": "10172", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05142017-141527247", "type": "thesis", "title": "Forces, Stresses, and the (Thermo?) Dynamics of Active Matter: The Swim Pressure", "author": [ { "family_name": "Takatori", "given_name": "Sho C.", "orcid": "0000-0002-7839-3399", "clpid": "Takatori-Sho-C" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Shapiro", "given_name": "Mikhail G.", "orcid": "0000-0002-0291-4215", "clpid": "Shapiro-M-G" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A core feature of many living systems is their ability to move, self-propel, and be active. From bird flocks to bacteria swarms, to even cytoskeletal networks, active matter systems exhibit collective and emergent dynamics owing to their constituents' ability to convert chemical fuel into mechanical activity. Active matter systems generate their own internal stress, which drives them far from equilibrium and thus frees them from conventional thermodynamic constraints, and by so doing they can control and direct their own behavior and that of their surrounding environment. This gives rise to fascinating behaviors such as spontaneous self-assembly and pattern formation, but also makes the theoretical understanding of their complex dynamical behaviors a challenging problem in the statistical physics of soft matter.
\r\n\r\nIn this thesis, I present a new principle that all active matter systems display---namely, through their self-motion they generate an intrinsic `swim pressure' that impacts their dynamic and collective behavior. I combine experimental and computational methods to demonstrate how intrinsic activity imparts new behaviors to soft materials that explain a variety of complex phenomena, including the collective motion of self-propelled particles and the complete loss of shear viscosity in fluid suspensions. These nonequilibrium phenomena are driven fundamentally by the active constituent's tendency to diffuse, undergo a random walk, and exert a mechanical force or a pressure on a confining wall. The swim pressure theory is conceptually similar to the kinetic theory of gases, where molecular collisions with the container walls exert a pressure, or to the Brownian osmotic pressure exerted by molecular or colloidal solutes in solution. In contrast to thermodynamic quantities such as the chemical potential and free energy, the mechanical pressure (or stress) is valid out of equilibrium because it comes directly from the micromechanical equations of motion. I apply this swim pressure framework in a broad context to interpret living matter as a material and understand its complex behavior using tools of hydrodynamics, kinetic theory, and nonequilibrium statistical mechanics. The present theory is applied to active systems that are driven by self-propulsion and motility, but there are other types of nonequilibrium driving work that may fit into this general theoretical framework, like driven autocatalytic reactions in electrochemical and biochemical systems.
", "doi": "10.7907/Z9RN35WF", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10242", "collection": "thesis", "collection_id": "10242", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012017-074605131", "primary_object_url": { "basename": "170531 Rapp_Thesis_May2017_Final.pdf", "content": "final", "filesize": 5582593, "license": "other", "mime_type": "application/pdf", "url": "/10242/1/170531 Rapp_Thesis_May2017_Final.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Diffusion and Molecular Association in Artificial Protein Hydrogels", "author": [ { "family_name": "Rapp", "given_name": "Peter Butterweck", "orcid": "0000-0002-9586-2126", "clpid": "Rapp-Peter-Butterweck" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "clpid": "Mazmanian-S-K" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Artificial proteins may be programmed to reversibly self-assemble into water-soluble networks, or \u201chydrogels\u201d, by encoding them with terminal coiled-coil forming domains. Such networks are model viscoelastic materials. The well-defined molecular structures adopted by proteins, combined with their facile preparation by recombinant synthesis, invite a careful exploration of the relationship between protein sequence and the resulting network properties.
\r\n\r\nThis work explores the relationship between network reorganization and diffusion from the perspective of single chains, using artificial elastin-like proteins as a model system. We make use of fluorescence recovery after photobleaching (FRAP), a classic biophysical technique, to measure chain mobilities as a function of network structure and probe architecture. Reversible network association is demonstrated to control the effective diffusivity of network-bound chains, and a novel mechanism of chain transport is proposed: the chains naturally partition into various bound states, and move by \u201chopping\u201d from site to site in between binding events.
\r\n\r\nA careful analysis of the equilibrium constants that control this partioning leads to the conclusion that the sequential binding of identical chain ends to the network is inherently asymmetric: the first association is always stronger than the second. This binding asymmetry is shown to arise from a strong entropic penalty for chain entry into the fully bound state due to local network structure. We derive a simple equation predicting the degree of binding asymmetry as a function of network geometry from equilibrium statistical mechanics. A large set of self-diffusivity measurements on a series of model telechelic proteins finds good agreement with this new theory. Generalized binding asymmetry for chains with many associative domains also holds.
\r\n\r\nFinally, the inherent viscoelasticity of the elastin-like network is found to couple with an entropically driven phase separation above a critical temperature set point. Relaxation of the viscoelastic stress throughout the process of phase domain segregation is found to induce highly dynamic phase patterns. The time evolution of these patterns illustrates that a delicate balance of surface tension and viscoelastic stress controls pattern formation in viscoelastic materials.
", "doi": "10.7907/Z9CV4FSF", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9982", "collection": "thesis", "collection_id": "9982", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11182016-183910155", "primary_object_url": { "basename": "MuWang2017Thesis.pdf", "content": "final", "filesize": 19537379, "license": "other", "mime_type": "application/pdf", "url": "/9982/67/MuWang2017Thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Constant Stress and Pressure Rheology of Dense Colloidal Suspensions", "author": [ { "family_name": "Wang", "given_name": "Mu", "orcid": "0000-0001-6090-6187", "clpid": "Wang-Mu" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis is a computational investigation on several aspects of the constant stress and pressure rheology of dense polydisperse colloidal suspensions. Using bidisperse suspensions as a model, we first study the influences of size polydispersity on short-time transport properties. The hydrodynamic interactions are calculated using a polydisperse implementation of Stokesian Dynamics (SD) via a Monte-Carlo approach. We carefully compare the SD computations with existing theoretical and numerical results, and critically assess the strengths and weaknesses of the SD algorithm. For suspensions, we find that the Pairwise Additive (PA) approximations with the Percus-Yevick structural input is valid up to volume fraction φ=0.1. We also develop an semi-analytical approximation scheme to predict the wavenumber-dependent partial hydrodynamic functions based on the δγ-scheme of Beenakker & Mazur [Physica 120A (1983) 388 & 126A (1984) 349], which is shown to be valid up to φ=0.4.
\r\n\r\nTo meet the computation requirements of dynamic simulations, we then developed the Spectral Ewald Accelerated Stokesian Dynamics (SEASD) based on the framework of SD with extension to compressible solvents. The SEASD uses the Spectral Ewald (SE) method [Lindbo & Tornberg, J. Comput. Phys. 229 (2010) 8994] for mobility computation with flexible error control, a novel block-diagonal preconditioner for the iterative solver, and the Graphic Processing Units (GPU) acceleration. For further speedup, we developed the SEASD-nf, a polydisperse extension of the mean-field Brownian approximation of Banchio & Brady [J. Chem. Phys. 118 (2003) 10323]. The SEASD and SEASD-nf are extensively validated with static and dynamic computations, and are found to scale as O(NlogN) with N the system size. The SEASD and SEASD-nf agree satisfactorily over a wide range of parameters for dynamic simulations.
\r\n\r\nNext, we investigate the colloidal film drying processes to understand the structural and mechanical implications when the constant pressure constraint is imposed by confining boundaries. The suspension is sandwiched between a stationary substrate and an interface moving either at a constant velocity or with constant imposed stress. Using Brownian Dynamics (BD) simulations without hydrodynamic interactions, we find that both fast and slow interface movement promote crystallization via distinct mechanisms. The most amorphous suspension structures occur when the interface moves at a rate comparable to particle Brownian motion. Imposing constant normal stresses leads to similar suspension behaviors, except that the interface stops moving when the suspension osmotic pressure matches the imposed stress. We also compare the simulation results with a continuum model. This work reveals the critical role of interface movement on the stress and structure of the suspension.
\r\n\r\nFinally, we study the constant shear stress and pressure rheology of dense colloidal suspensions using both BD and SEASD-nf to identify the role of hydrodynamic interactions. The constant pressure constraint is imposed by introducing a compressible solvent. We focus on the rheological, structural, and dynamical characteristics of flowing suspensions. Although hydrodynamic interactions profoundly affect the suspension structure and dynamics, they only quantitatively influence the behaviors of amorphous suspensions. The suspension becomes glassy, i.e., exhibits flow-arrest transitions, when the imposed pressure is high, and reveals the Shear Arrest Point (SAP) in the non-Brownian limit. From a granular perspective, we find that the suspensions move away from the arrested state in a universal fashion regardless of the imposed pressure, suggesting the critical role of the jamming physics. The hydrodynamic simulations quantitatively agree with the experiments of Boyer et al. [Phys. Rev. Lett. 107 (2011) 188301] with a volume fraction shift. The results at all imposed stresses and pressures reveal a generalized Stokes-Einstein-Sutherland relation with an effective temperature proportional to the pressure. We develop a model that accurately describes the rheology and diffusion of glassy suspensions. Our results show the critical role of pressure on the behaviors of dense colloidal suspensions.
", "doi": "10.7907/Z9BC3WHQ", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9899", "collection": "thesis", "collection_id": "9899", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08102016-154641607", "primary_object_url": { "basename": "Full_thesis_Final_version_HongYH.pdf", "content": "final", "filesize": 5228255, "license": "other", "mime_type": "application/pdf", "url": "/9899/1/Full_thesis_Final_version_HongYH.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Theory of Dynamical Processes in Semiconductor Quantum Dots", "author": [ { "family_name": "Hong", "given_name": "Yun-Hua", "orcid": "0000-0002-5868-8827", "clpid": "Hong-Yun-Hua" } ], "thesis_advisor": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" } ], "thesis_committee": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The focus of this dissertation is on the theory of the electronic dynamical processes in semiconductor quantum dots (QDs). The first part of the dissertation introduces the calculation method of electronic eigenstates used through the dissertation, the sp3s* tight-binding (TB) method, and the application of the symmetry-adapted linear combination (SALC) of atomic orbitals to the TB method. The combination of the SALC and TB method reduces the computational load, and generates reliable electronic eigenstates and eigenvalues of Wurtzite CdSe QDs. The second part of the dissertation uses the calculated eigenstates and eigenvalues of CdSe QDs, whose band gap states are removed by a passivation layer, to calculate various kinds of physical properties, such as the structure, the permanent dipole moment, the band gap, the molecular orbitals, the density of states (DOS), and the absorption spectrum. These calculated results are compared with the respective experimental measurements in further discussions. The last part of the dissertation focuses on the studies of the size-dependent trend of the Auger electron-hole recombination process that causes the semiconductor QDs to remain in the dark state, including the cases of a negative trion, a positive trion, and a biexciton, in semiconductor QDs. The rates of these Auger processes are expressed in the form of Fermi\u2019s golden rule, where the Coulombic interaction between the two electrons is the operator. Although the calculated results shows larger size dependence than that of the experimental findings, the literature of recent experiments and theories points out potential remedies to the discrepancy by modifying the current computational setting and theory in the dissertation.", "doi": "10.7907/Z99G5JT3", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10093", "collection": "thesis", "collection_id": "10093", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03092017-164905231", "type": "thesis", "title": "Modulating Biophysical Properties of Insulin with Non-Canonical Mutagenesis at Position B28", "author": [ { "family_name": "Fang", "given_name": "Katharine Yan", "clpid": "Fang-Katharine-Yan" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Ku", "given_name": "H. Teresa", "clpid": "Ku-H-T" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Non-canonical amino acids are tools for altering the chemical and physical properties of proteins, providing a facile strategy to engineer proteins with novel properties, especially where canonical amino acid mutagenesis has exhausted nearly all avenues for further optimization. Insulin, for example, is one of the most widely studied therapeutic proteins; however, non-canonical insulin engineering is a subfield that has been largely unexplored. To this end, my thesis research has focused on the use of non-canonical amino acids to understand and engineer the biophysical properties of insulin.
\r\n\r\nProtein structure and function are sensitive to the smallest of changes; even small differences such as a single atom substitution or change in stereo-orientation can cause large, unsuspected, and unpredictable global changes. Chapters 2 to 4 describe substitutions at the 4th position of proline at position 28 of insulin\u2019s B chain (ProB28) in a manner analogous to the structure-activity-relationships that are widely used in medicinal chemistry. Canonical mutagenesis at ProB28 has led to the discovery of rapid-acting insulins (RAIs): a class of therapeutic insulins with enhanced pharmacokinetic properties. Therefore, we chose to incorporate proline analogs with substitutions such as hydroxyl and fluoro groups, and different ring compositions to assess their effects on the biophysical properties (i.e. stability, dissociation rates and oligomerizations states) of insulin. Chapter 2 describes the discovery of a hydroxyinsulin variant with faster hexamer dissociation rates and enhanced stability compared to wild-type insulin in vitro. We find crystallographic evidence of a novel hydrogen bond in the insulin dimer interface which we hypothesize stabilizes the insulin dimer state. To complement the findings in chapter 2, chapters 3 and 4 detail an investigation of the importance of hydrophobic and nonpolar interactions for modulating the biophysical properties of insulin.
\r\n\r\nEstablishing structure-activity-relationships for insulin will create new opportunities for further engineering using non-canonical amino acids. In chapter 5, we describe progress towards a general, simple screening method to discover new aminoacyl-tRNA synthetases for the incorporation of non-canonical amino acids in E. coli. Implementing such a high-throughput screening system will allow scientists to perform medicinal chemistry on proteins and discover new or improved therapeutics to help manage human diseases.
", "doi": "10.7907/Z9V40S6J", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10093", "collection": "thesis", "collection_id": "10093", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03092017-164905231", "type": "thesis", "title": "Modulating Biophysical Properties of Insulin with Non-Canonical Mutagenesis at Position B28", "author": [ { "family_name": "Fang", "given_name": "Katharine Yan", "clpid": "Fang-Katharine-Yan" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Ku", "given_name": "H. Teresa", "clpid": "Ku-H-T" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Non-canonical amino acids are tools for altering the chemical and physical properties of proteins, providing a facile strategy to engineer proteins with novel properties, especially where canonical amino acid mutagenesis has exhausted nearly all avenues for further optimization. Insulin, for example, is one of the most widely studied therapeutic proteins; however, non-canonical insulin engineering is a subfield that has been largely unexplored. To this end, my thesis research has focused on the use of non-canonical amino acids to understand and engineer the biophysical properties of insulin.
\r\n\r\nProtein structure and function are sensitive to the smallest of changes; even small differences such as a single atom substitution or change in stereo-orientation can cause large, unsuspected, and unpredictable global changes. Chapters 2 to 4 describe substitutions at the 4th position of proline at position 28 of insulin\u2019s B chain (ProB28) in a manner analogous to the structure-activity-relationships that are widely used in medicinal chemistry. Canonical mutagenesis at ProB28 has led to the discovery of rapid-acting insulins (RAIs): a class of therapeutic insulins with enhanced pharmacokinetic properties. Therefore, we chose to incorporate proline analogs with substitutions such as hydroxyl and fluoro groups, and different ring compositions to assess their effects on the biophysical properties (i.e. stability, dissociation rates and oligomerizations states) of insulin. Chapter 2 describes the discovery of a hydroxyinsulin variant with faster hexamer dissociation rates and enhanced stability compared to wild-type insulin in vitro. We find crystallographic evidence of a novel hydrogen bond in the insulin dimer interface which we hypothesize stabilizes the insulin dimer state. To complement the findings in chapter 2, chapters 3 and 4 detail an investigation of the importance of hydrophobic and nonpolar interactions for modulating the biophysical properties of insulin.
\r\n\r\nEstablishing structure-activity-relationships for insulin will create new opportunities for further engineering using non-canonical amino acids. In chapter 5, we describe progress towards a general, simple screening method to discover new aminoacyl-tRNA synthetases for the incorporation of non-canonical amino acids in E. coli. Implementing such a high-throughput screening system will allow scientists to perform medicinal chemistry on proteins and discover new or improved therapeutics to help manage human diseases.
", "doi": "10.7907/Z9V40S6J", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9761", "collection": "thesis", "collection_id": "9761", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252016-213050706", "primary_object_url": { "basename": "webb_michael_2016_thesis.pdf", "content": "", "filesize": 25730564, "license": "other", "mime_type": "application/pdf", "url": "/9761/1/webb_michael_2016_thesis.pdf", "version": "v1.0.0" }, "type": "thesis", "title": "Path-Integral and Coarse-Graining Strategies for Complex Molecular Phenomena", "author": [ { "family_name": "Webb", "given_name": "Michael Anthony", "orcid": "0000-0002-7420-4474", "clpid": "Webb-Michael-Anthony" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_chem" } ], "abstract": "Molecular simulation provides a powerful tool for connecting molecular-level processes to physical observables. However, the facility to make those connections relies upon the application and development of theoretical methods that permit appropriate descriptions of the systems or processes to be studied. In this thesis, we utilize molecular simulation to study and predict two phenomena with very different theoretical challenges, beginning with (1) lithium-ion transport behavior in polymers and following with (2) equilibrium isotope effects with relevance to position-specific and clumped isotope studies. In the case of ion transport in polymers, there is motivation to use molecular simulation to provide guidance in polymer electrolyte design, but the length and timescales relevant for ion diffusion in polymers preclude the use of direct molecular dynamics simulation to compute ion diffusivities in more than a handful of candidate systems. In the case of equilibrium isotope effects, the thermodynamic driving forces for isotopic fractionation are often fundamentally quantum mechanical in nature, and the high precision of experimental instruments demands correspondingly accurate theoretical approaches. Herein, we describe respectively coarse-graining and path-integral strategies to address outstanding questions in these two subject areas.", "doi": "10.7907/Z90Z7172", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9822", "collection": "thesis", "collection_id": "9822", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06022016-152749956", "primary_object_url": { "basename": "Complete Thesis.pdf", "content": "final", "filesize": 5766095, "license": "other", "mime_type": "application/pdf", "url": "/9822/73/Complete Thesis.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Programming Molecular Association and Viscoelastic Behavior in Protein Hydrogels", "author": [ { "family_name": "Dooling", "given_name": "Lawrence Joseph", "orcid": "0000-0002-1688-2066", "clpid": "Dooling-Lawrence-Joseph" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Recombinant artificial proteins contain genetically encoded information that specifies their assembly into higher order structures by physical or chemical cross-linking as well as elastic behavior and biological or chemical function. This thesis describes the use of artificial proteins to construct molecular networks containing covalent cross-links involving the thiol side chain of cysteine residues and physical cross-links involving the association of helical domains as coiled coils. The goal of this work was to demonstrate how the viscoelastic properties of protein hydrogels could be encoded within an artificial protein sequence.
\r\n\r\nUsing genetic engineering methods, a telechelic protein denoted ERE was designed from elastin- and fibronectin-derived repeating units and expressed in Escherichia coli. ERE was end-linked by the reaction of terminal cysteine residues with tetrakis-vinyl sulfone-functionalized 4-arm star PEG to form hydrogel networks. The effects of varying the precursor concentration and cross-linker stoichiometry on the swelling ratio and mechanical properties of the hydrogels were studied in detail in Chapter 2. The capacity for ERE hydrogels to serve as an artificial extracellular matrix was also assessed by the encapsulation of mouse fibroblasts, which survived the cross-linking reaction and exhibited a spread morphology within the gel.
\r\n\r\nChapter 3 describes a set of recombinant artificial proteins that can be cross-linked by covalent bonds, by association of helical domains, or by both mechanisms. These proteins were used to construct chemical, physical, and chemical-physical hydrogel networks in which the mechanism of cross-linking determines whether the material response to mechanical deformation is elastic or viscoelastic. In viscoelastic networks, stress relaxation and energy dissipation could be tuned by controlling the ratio of physical cross-linking to chemical cross-linking, and the physical cross-links could be disrupted either by protein denaturation or by mutation of the primary sequence.
\r\n\r\nNetwork dynamics control the viscoelasticity and erosion rate of materials and influence biological processes at multiple length scales.In Chapter 4, variation of the protein sequence was explored as a strategy to tune the characteristic relaxation timescale of protein networks. Single point mutations to coiled-coil physical cross-linking domains in chemical-physical hydrogels altered the characteristic relaxation time over five orders of magnitude. Using a pair of orthogonal coiled-coil physical cross-linking domains, networks with two distinct relaxation timescales were also engineered.
\r\n\r\nThe dynamic properties of protein hydrogels can also be controlled by interactions between protein domains and small molecule ligands. In Chapter 5, the viscoelastic behavior of chemical-physical protein gels was tuned by swelling the gels with small hydrophobic molecules including vitamin D3 and fatty acids. The proposed mechanism for this effect involves binding of the ligands within the hydrophobic pore or channel created by a coiled-coil physical cross-link. Exploiting natural and designed protein-ligand interactions represents a new approach to developing hydrogel \u201cformulations\u201d in which the viscoelastic properties of the material can be engineered to meet specific design criteria.
\r\n\r\nIn addition to exhibiting interesting dynamic properties, polymeric hydrogels containing permanent covalent cross-links and reversible physical cross-links often display enhanced toughness and extensibility. Protein hydrogels cross-linked by covalent thioether bonds and physical coiled coils could be extended further than control covalent hydrogels and exhibited a greater work of extension, which is considered a measure of material toughness. These results demonstrate progress toward engineering tougher, more extensible protein-based materials by the incorporation of coiled-coil physical cross-links within a covalent hydrogel network.
", "doi": "10.7907/Z9PK0D41", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9743", "collection": "thesis", "collection_id": "9743", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05242016-214836974", "type": "thesis", "title": "Dynamics of Chemically Active Suspensions", "author": [ { "family_name": "Yan", "given_name": "Wen", "orcid": "0000-0002-9189-0840", "clpid": "Yan-Wen" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" }, { "family_name": "Kochmann", "given_name": "Dennis M.", "clpid": "Kochmann-D-M" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Chemically active particles may swim by self-diffusiophoresis in a concentration gradient of chemical solutes they created themselves by patterned surface catalytic reactions. Those particles can also interact via normal diffusiophoresis in the same solute concentration field. The interaction can be attractive or repulsive. This 'field-driven' nature of the system makes its dynamics different from a thermodynamic system and is analyzed with a new simulation method. Simulations show that attractive active particles exhibit coexistence of dense and dilute regions, but it is different from a liquid-gas phase equilibrium. To explain the behavior, a continuum mechanics theory is developed based on the minimal Active Brownian Particles (ABP) model. In the continuum description, the surface force is found to be the swim stress, which can be anisotropic. The body force includes the average swim force as an internal contribution and an 'activity-gradient' force contribution. Further, behaviors of active matter at the sub-continuum scale are also analyzed. The continuum mechanics theory is shown to accurately describe the behaviors of chemically active particles. Particle clustering is explained with a linear stability analysis, and the steady state is explained with a sedimentation-like mechanical force balance.", "doi": "10.7907/Z9Z60M1V", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9733", "collection": "thesis", "collection_id": "9733", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05232016-092808469", "primary_object_url": { "basename": "WangConnie2016Thesis.pdf", "content": "final", "filesize": 8545528, "license": "other", "mime_type": "application/pdf", "url": "/9733/1/WangConnie2016Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Understanding Co-Translational Protein Targeting and Lithium Dendrite Formation through Free Energy Simulations and Coarse-Grained Models", "author": [ { "family_name": "Wang", "given_name": "Connie Yuan-Ying", "orcid": "0000-0003-2971-3971", "clpid": "Wang-Connie-Yuan-Ying" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Shan", "given_name": "Shu-ou", "orcid": "0000-0002-6526-1733", "clpid": "Shan-Shu-ou" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We describe the application of alchemical free energy methods and coarse-grained models to study two key problems: (i) co-translational protein targeting and insertion to direct membrane proteins to the endoplasmic reticulum for proper localization and folding, (ii) lithium dendrite formation during recharging of lithium metal batteries. We show that conformational changes in the signal recognition particle, a central component of the protein targeting machinery, confer additional specificity during the the recognition of signal sequences. We then develop a three-dimensional coarse-grained model to study the long-timescale dynamics of membrane protein integration at the translocon and a framework for the calculation of binding free energies between the ribosome and translocon. Finally, we develop a coarse-grained model to capture the dynamics of lithium deposition and dissolution at the electrode interface with time-dependent voltages to show that pulse plating and reverse pulse plating methods can mitigate dendrite growth.", "doi": "10.7907/Z97H1GHF", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:8655", "collection": "thesis", "collection_id": "8655", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09082014-140216721", "primary_object_url": { "basename": "CKY20140916-updatedversion.pdf", "content": "final", "filesize": 10704397, "license": "other", "mime_type": "application/pdf", "url": "/8655/7/CKY20140916-updatedversion.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "An Exploration of Perovskite Materials for Thermochemical Water Splitting", "author": [ { "family_name": "Yang", "given_name": "Chih-Kai", "clpid": "Yang-Chih-Kai" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Two-step thermochemical water splitting is a promising technology for the hydrogen production of solar energy. This process possesses the advantages of utilizing the full solar spectrum, producing flexible fuels, and requiring no precious metal catalysts. It furthermore temporally separates the oxygen release and hydrogen production steps, eliminating the possibility of O2 and H2 recombination. Ceria, which undergoes non-stoichiometric changes in oxygen content, has been demonstrated as an effective material for solar-driven thermochemical fuel production, but the process requires extremely high temperatures (~ 1600 degrees C), leading to efficiency penalties and challenges in reactor design and construction. Accordingly, the objective of this work is the development of new thermochemical reaction substrate materials which enable operation at lower temperatures and ideally increase fuel productivity and efficiency. Here we explore perovskite systems, specifically La1-xSrxMnO3-\u03b4, La0.8Sr0.2Mn1-yFeyO3-\u03b4, and La0.8Sr0.2Mn1-yAlyO3-\u03b4. The link between the solid-state chemistry, redox properties, hydrogen production, and reaction kinetic limitations will be discussed. This study aims to learn how to design and tailor the good catalytic oxides for solar-driven thermochemical water splitting application.", "doi": "10.7907/Z91834GB", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8650", "collection": "thesis", "collection_id": "8650", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08292014-092737024", "primary_object_url": { "basename": "Thesis_BG.pdf", "content": "final", "filesize": 11237115, "license": "other", "mime_type": "application/pdf", "url": "/8650/14/Thesis_BG.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Ab-Initio and Experimental Techniques for Studying Non-Stoichiometry and Oxygen Transport in Mixed Conducting Oxides", "author": [ { "family_name": "Balaji Gopal", "given_name": "Chirranjeevi", "clpid": "Balaji-Gopal-Chirranjeevi" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "van de Walle", "given_name": "Axel", "clpid": "van-de-Walle-A" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "van de Walle", "given_name": "Axel", "clpid": "van-de-Walle-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The ability of cerium oxide (CeO2-\u03b4, also called ceria), to vary its oxygen stoichiometry in response to changes in temperature or oxygen activity is key to many of its applications in catalysis and electrochemical energy storage and conversion. This thesis explores ab initio and experimental approaches to study the fundamental thermodynamic and oxygen transport properties of ceria (MxCe1-xOO2-\u03b4), but the methods are applicable to other mixed conducting oxides as well.
\r\n\r\nIn the first part of the thesis, a computational thermodynamics approach that integrates quantum mechanical and statistical ensemble-based simulations is used to calculate the reduction-oxidation thermodynamics of non-stoichiometric ceria entirely from first principles. This procedure is well understood and has been successfully implemented for metallic alloys, but has not been extended to correlated electron systems such as ceria, for which the physics of electronic structure calculations is significantly more complicated. Density functional calculations were used to obtain the ground state energies of ceria with vacancy concentrations ranging from fully stoichiometric up to \u03b4=0.25$. For each \u03b4, numerous vacancy configurations were sampled to capture the interactions between vacancies and other atoms. Using the frozen phonon method, lattice dynamical calculations of phonon density of states were performed for various \u03b4. Based on the ground state energies of nearly 40 structures, a cluster expansion Hamiltonian was used to parametrize the energy as a polynomial in occupation variables. The vibrational energies were used to make the Hamiltoninan temperature dependent. Lattice Monte Carlo (MC) simulations using the cluster expansion Hamiltonian were then used to study, for the first time, the effect of temperature and chemical potential on the vacancy concentration in ceria from first principles. The temperature composition phase diagram constructed from the MC simulations successfully reproduced the experimentally reported miscibility gap. The inclusion of vibrational and electronic contributions to the entropy made the agreement quantitative. Further, the partial molar enthalpy and entropy of reduction as a function of \u03b4 were extracted and found to deviate significantly from those of an ideally behaved system. The deviations were quantified by calculating the Warren-Cowley short range order parameters. This was the first demonstration of an ab initio approach being used to accurately model the defect thermodynamics of a correlated electron system without resorting to experimental inputs. Using ceria as benchmark material, this project lays the groundwork for a computational approach to screen new oxides for thermochemical cycling.
\r\n\r\nThe rest of the thesis describes experimental investigations of oxygen transport and non-stoichiometry in doped and undoped ceria. Oxygen transport studies were performed using electrical conductivity relaxation (ECR). In ECR, a small step change in pO2 forces the sample non-stoichiometry \u03b4, and other dependent properties such as electrical conductivity, to equilibrate to a new value. The rate of this re-equilibration is governed by the bulk oxygen diffusivity, DChem, and surface reaction rate constant, kS -- the two principal kinetic properties. By fitting the solution to Fick's second law, with the appropriate boundary conditions, to the conductivity relaxation profile, DChem and kS can be extracted. The instrumental capability for performing electrical conductivity relaxation experiments was set up and a systematic data analysis procedure was developed to reliably and accurately extract DChem and or kS. The experimental and data analytical methodologies were successfully benchmarked with 15 mol% Sm doped ceria, for which approximate values of the two principal transport properties, bulk oxygen diffusivity, DChem, and surface reaction rate constant, kS, can be found in the literature. An unexpectedly high p-type electronic transference number enabled ECR measurements under oxidizing conditions. A systematic data analysis procedure was developed to permit reliable extraction of the kinetic parameters even in the general case of simultaneous bulk and surface limitation. When the surface kinetics were too sluggish compared to bulk diffusion, Pt catalyst nanoparticles were sputtered to catalyze the surface reaction and enable extraction of DChem. The DChem from this study showed excellent qualitative and quantitative agreement with expected values, falling in the range from ~ 2 x 10-5 to 2 x 10-4 cm2/s. The surface reaction constant under H2/H2O mixtures also showed good agreement with literature results. Remarkably, this value increased by a factor of 40 under mixtures of CO/CO2 or O2/Ar. This observation suggests kinetic advantages for production of CO rather than H2 in a two-step solar-driven thermochemical process based on samarium doped ceria.
\r\n\r\nUsing ECR, the effect of 20% Zr addition on the electrical conductivity and oxygen transport properties of ceria as a function of pO2 and T was investigated. Under oxidizing conditions, both CeO2-\u03b4 and Zr0.2Ce0.8O2-\u03b4(ZDC20) showed n type, mixed conduction. The conductivity of ZDC20 was two orders of magnitude higher than that of undoped ceria. Contrary to previous studies, we found that Zr addition does not change the electronic mobility in this pO2 regime. The enhancement in conductivity is a consequence of higher vacancy concentration in ZDC20 under identical conditions compared to ceria. Under reducing conditions, while the n-type conductivity of ceria continued to increase with decreasing pO2, that of ZDC20 reached a broad maximum, eventually decreasing with pO2 (p-type) despite increasing carrier concentration. We show that the electronic mobility becomes strongly concentration dependent at high oxygen non-stoichiometry. This leads to a marked decrease in mobility with increase in \u03b4, causing the conductivity to roll over from n to p type. The chemical diffusion coefficient and surface reaction rate constant of both ceria and ZDC20 showed strong dependence on pO2 under oxidizing conditions, decreasing by nearly an order of magnitude between 10-2 atm and 10-5 atm. The unexpectedly high sensitivity to pO2 was ascribed to the effect of extrinsic vacancies generated by trace quantities of lower valence cation impurities, that dramatically increase both the absolute value of the thermodynamic factor and its sensitivity to pO2 close to stoichiometry. Overall, the addition of Zr lowers the DChem and kS of ceria in the temperature and oxygen partial pressure range of this study, the effect being more pronounced under reducing conditions. Beyond its relevance to ceria, this work demonstrates the potential of ECR to isolate the effect of kinetics from thermodynamics of the real thermochemical cycle, reveal the limiting transport parameters, and ultimately guide microstructure design for maximizing the rate of fuel production.
\r\n \r\nLastly, we improve upon an existing formalism to calculate the oxygen non-stoichiometry in thin films of mixed conducting oxides using AC impedance spectroscopy. Cerium oxide was once again chosen as the benchmarking material, since it shows both ideal and non-ideal thermodynamic behavior under different conditions, and has been well studied in its bulk form. In this method, the impedance response of dense, thin films of CeO2-\u03b4 deposited on a Y0.84Zr0.16O1.92> (YSZ) substrate was measured using AC impedance spectroscopy. To explore potential grain boundary effects on bulk thermodynamic properties. A physically derived equivalent circuit model was fit to the impedance response to extract a quantity called the 'chemical capacitance', which was subsequently related to the non-stoichiometry. Previous studies employing this method were restricted to systems that can be described using ideal solution thermodynamics, which allows simplifications to the theoretical treatment of their capacitance. Apart from extending this technique to a non-ideally behaved oxide, we report excellent agreement between the non-stoichiometry of single crystal and polycrystalline films and that of bulk ceria. By virtue of using thin films, equilibration times are dramatically decreased, enabling faster measurements compared to bulk techniques like thermogravimetry and coulometric titration. Further, the electrochemical method is ideal for thin films, for which the mass changes are below the detection limits of bulk techniques.
\r\n", "doi": "10.7907/Z9TT4NWZ", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8738", "collection": "thesis", "collection_id": "8738", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12102014-125310289", "primary_object_url": { "basename": "Rui Wang's thesis.pdf", "content": "final", "filesize": 2204287, "license": "other", "mime_type": "application/pdf", "url": "/8738/1/Rui Wang's thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Effects of Self Energy of the Ions on the Double Layer Structure and Properties at the Dielectric Interface", "author": [ { "family_name": "Wang", "given_name": "Rui", "clpid": "Wang-Rui" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Although numerous theoretical efforts have been put forth, a systematic, unified and predictive theoretical framework that is able to capture all the essential physics of the interfacial behaviors of ions, such as the Hofmeister series effect, Jones-Ray effect and the salt effect on the bubble coalescence remain an outstanding challenge. The most common approach to treating electrostatic interactions in the presence of salt ions is the Poisson-Boltzmann (PB) theory. However, there are many systems for which the PB theory fails to offer even a qualitative explanation of the behavior, especially for ions distributed in the vicinity of an interface with dielectric contrast between the two media (like the water-vapor/oil interface). A key factor missing in the PB theory is the self energy of the ion.
\r\n\r\nIn this thesis, we develop a self-consistent theory that treats the electrostatic self energy (including both the short-range Born solvation energy and the long-range image charge interactions), the nonelectrostatic contribution of the self energy, the ion-ion correlation and the screening effect systematically in a single framework. By assuming a finite charge spread of the ion instead of using the point-charge model, the self energy obtained by our theory is free of the divergence problems and gives a continuous self energy across the interface. This continuous feature allows ions on the water side and the vapor/oil side of the interface to be treated in a unified framework. The theory involves a minimum set of parameters of the ion, such as the valency, radius, polarizability of the ions, and the dielectric constants of the medium, that are both intrinsic and readily available. The general theory is first applied to study the thermodynamic property of the bulk electrolyte solution, which shows good agreement with the experiment result for predicting the activity coefficient and osmotic coefficient.
\r\n\r\nNext, we address the effect of local Born solvation energy on the bulk thermodynamics and interfacial properties of electrolyte solution mixtures. We show that difference in the solvation energy between the cations and anions naturally gives rise to local charge separation near the interface, and a finite Galvani potential between two coexisting solutions. The miscibility of the mixture can either increases or decreases depending on the competition between the solvation energy and translation entropy of the ions. The interfacial tension shows a non-monotonic dependence on the salt concentration: it increases linearly with the salt concentration at higher concentrations, and decreases approximately as the square root of the salt concentration for dilute solutions, which is in agreement with the Jones-Ray effect observed in experiment.
\r\n\r\nNext, we investigate the image effects on the double layer structure and interfacial properties near a single charged plate. We show that the image charge repulsion creates a depletion boundary layer that cannot be captured by a regular perturbation approach. The correct weak-coupling theory must include the self-energy of the ion due to the image charge interaction. The image force qualitatively alters the double layer structure and properties, and gives rise to many non-PB effects, such as nonmonotonic dependence of the surface energy on concentration and charge inversion. The image charge effect is then studied for electrolyte solutions between two plates. For two neutral plates, we show that depletion of the salt ions by the image charge repulsion results in short-range attractive and long-range repulsive forces. If cations and anions are of different valency, the asymmetric depletion leads to the formation of an induced electrical double layer. For two charged plates, the competition between the surface charge and the image charge effect can give rise to like- charge attraction.
\r\n\r\nThen, we study the inhomogeneous screening effect near the dielectric interface due to the anisotropic and nonuniform ion distribution. We show that the double layer structure and interfacial properties is drastically affected by the inhomogeneous screening if the bulk Debye screening length is comparable or smaller than the Bjerrum length. The width of the depletion layer is characterized by the Bjerrum length, independent of the salt concentration. We predict that the negative adsorption of ions at the interface increases linearly with the salt concentration, which cannot be captured by either the bulk screening approximation or the WKB approximation. For asymmetric salt, the inhomogeneous screening enhances the charge separation in the induced double layer and significantly increases the value of the surface potential.
\r\n\r\nFinally, to account for the ion specificity, we study the self energy of a single ion across the dielectric interface. The ion is considered to be polarizable: its charge distribution can be self-adjusted to the local dielectric environment to minimize the self energy. Using intrinsic parameters of the ions, such as the valency, radius, and polarizability, we predict the specific ion effect on the interfacial affinity of halogen anions at the water/air interface, and the strong adsorption of hydrophobic ions at the water/oil interface, in agreement with experiments and atomistic simulations.
\r\n\r\nThe theory developed in this work represents the most systematic theoretical technique for weak-coupling electrolytes. We expect the theory to be more useful for studying a wide range of structural and dynamic properties in physicochemical, colloidal, soft-matter and biophysical systems.
", "doi": "10.7907/Z9DN431P", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8774", "collection": "thesis", "collection_id": "8774", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02242015-173330087", "primary_object_url": { "basename": "thesis final revised.pdf", "content": "final", "filesize": 37069880, "license": "other", "mime_type": "application/pdf", "url": "/8774/1/thesis final revised.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Strength, Deformation and Fracture in Metallic Nanostructures", "author": [ { "family_name": "Gu", "given_name": "Xun Wendy", "clpid": "Gu-Xun-Wendy" } ], "thesis_advisor": [ { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" } ], "thesis_committee": [ { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Kochmann", "given_name": "Dennis M.", "clpid": "Kochmann-D-M" } ], "local_group": [ { "literal": "Kavli Nanoscience Institute" }, { "literal": "div_chem" } ], "abstract": "An understanding of the mechanics of nanoscale metals and semiconductors is necessary for the safe and prolonged operation of nanostructured devices from transistors to nanowire- based solar cells to miniaturized electrodes. This is a fascinating but challenging pursuit because mechanical properties that are size-invariant in conventional materials, such as strength, ductility and fracture behavior, can depend critically on sample size when materials are reduced to sub- micron dimensions. In this thesis, the effect of nanoscale sample size, microstructure and structural geometry on mechanical strength, deformation and fracture are explored for several classes of solid materials. Nanocrystalline platinum nano-cylinders with diameters of 60 nm to 1 \u03bcm and 12 nm sized grains are fabricated and tested in compression. We find that nano-sized metals containing few grains weaken as sample diameter is reduced relative to grain size due to a change from deformation governed by internal grains to surface grain governed deformation. Fracture at the nanoscale is explored by performing in-situ SEM tension tests on nanocrystalline platinum and amorphous, metallic glass nano-cylinders containing purposely introduced structural flaws. It is found that failure location, mechanism and strength are determined by the stress concentration with the highest local stress whether this is at the structural flaw or a microstructural feature. Principles of nano-mechanics are used to design and test mechanically robust hierarchical nanostructures with structural and electrochemical applications. 2-photon lithography and electroplating are used to fabricate 3D solid Cu octet meso-lattices with micron- scale features that exhibit strength higher than that of bulk Cu. An in-situ SEM lithiation stage is developed and used to simultaneously examine morphological and electrochemical changes in Si-coated Cu meso-lattices that are of interest as high energy capacity electrodes for Li-ion batteries.", "doi": "10.7907/Z91J97NV", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8028", "collection": "thesis", "collection_id": "8028", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11182013-104133647", "primary_object_url": { "basename": "Pirogovsky-Paul_PhD_Thesis_Final.pdf", "content": "final", "filesize": 8751475, "license": "other", "mime_type": "application/pdf", "url": "/8028/1/Pirogovsky-Paul_PhD_Thesis_Final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Intramolecular Conflict: Conformation and Self-Assembly of Architecturally Complex Macromolecules in Solution", "author": [ { "family_name": "Pirogovsky", "given_name": "Paul Peter", "clpid": "Pirogovsky-Paul-Peter" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The solution behavior of linear polymer chains is well understood, having been the subject of intense study throughout the previous century. As plastics have become ubiquitous in everyday life, polymer science has grown into a major field of study. The conformation of a polymer in solution depends on the molecular architecture and its interactions with the surroundings. Developments in synthetic techniques have led to the creation of precision-tailored polymeric materials with varied topologies and functionalities. In order to design materials with the desired properties, it is imperative to understand the relationships between polymer architecture and their conformation and behavior. To meet that need, this thesis investigates the conformation and self-assembly of three architecturally complex macromolecular systems with rich and varied behaviors driven by the resolution of intramolecular conflicts. First we describe the development of a robust and facile synthetic approach to reproducible bottlebrush polymers (Chapter 2). The method was used to produce homologous series of bottlebrush polymers with polynorbornene backbones, which revealed the effect of side-chain and backbone length on the overall conformation in both good and theta solvent conditions (Chapter 3). The side-chain conformation was obtained from a series of SANS experiments and determined to be indistinguishable from the behavior of free linear polymer chains. Using deuterium-labeled bottlebrushes, we were able for the first time to directly observe the backbone conformation of a bottlebrush polymer which showed self-avoiding walk behavior. Secondly, a series of SANS experiments was conducted on a homologous series of Side Group Liquid Crystalline Polymers (SGLCPs) in a perdeuterated small molecule liquid crystal (5CB). Monodomain, aligned, dilute samples of SGLCP-b-PS block copolymers were seen to self-assemble into complex micellar structures with mutually orthogonally oriented anisotropies at different length scales (Chapter 4). Finally, we present the results from the first scattering experiments on a set of fuel-soluble, associating telechelic polymers. We observed the formation of supramolecular aggregates in dilute (\u22640.5wt%) solutions of telechelic polymers and determined that the choice of solvent has a significant effect on the strength of association and the size of the supramolecules (Chapter 5). A method was developed for the direct estimation of supramolecular aggregation number from SANS data. The insight into structure-property relationships obtained from this work will enable the more targeted development of these molecular architectures for their respective applications. ", "doi": "10.7907/0DXJ-3H18", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8001", "collection": "thesis", "collection_id": "8001", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10192013-181502465", "primary_object_url": { "basename": "Ming-Hsin_Wei_2014_thesis.pdf", "content": "final", "filesize": 6936655, "license": "other", "mime_type": "application/pdf", "url": "/8001/1/Ming-Hsin_Wei_2014_thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Synthesis and Potency of Long End-Associative Polymers for Mist Control", "author": [ { "family_name": "Wei", "given_name": "Ming-Hsin", "clpid": "Wei-Ming-Hsin" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Sarohia", "given_name": "Virendra", "clpid": "Sarohia-V" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Long linear polymers that are end-functionalized with associative groups were studied as additives to hydrocarbon fluids to mitigate the fire hazard associated with the presence of mist in a crash scenario. These polymers were molecularly designed to overcome both the shear-degradation of long polymer chains in turbulent flows, and the chain collapse induced by the random placement of associative groups along polymer backbones. Architectures of associative groups on the polymer chain ends that were tested included clusters of self-associative carboxyl groups and pairs of hetero-complementary associative units.
\r\n\r\nLinear polymers with clusters of discrete numbers of carboxyl groups on their chain ends were investigated first: an innovative synthetic strategy was devised to achieve unprecedented backbone lengths and precise control of the number of carboxyl groups on chain ends (N). We found that a very narrow range of N allows the co-existence of sufficient end-association strength and polymer solubility in apolar media. Subsequent steady-flow rheological study on solution behavior of such soluble polymers in apolar media revealed that the end-association of very long chains in apolar media leads to the formation of flower-like micelles interconnected by bridging chains, which trap significant fraction of polymer chains into looped structures with low contribution to mist-control. The efficacy of very long 1,4-polybutadiene chains end-functionalized with clusters of four carboxyl groups as mist-control additives for jet fuel was further tested. In addition to being shear-resistant, the polymer was found capable of providing fire-protection to jet fuel at concentrations as low as 0.3wt%. We also found that this polymer has excellent solubility in jet fuel over a wide range of temperature (-30 to +70\u00b0C) and negligible interference with dewatering of jet fuel. It does not cause an adverse increase in viscosity at concentrations where mist-control efficacy exists.
\r\n\r\nFour pairs of hetero-complementary associative end-groups of varying strengths were subsequently investigated, in the hopes of achieving supramolecular aggregates with both mist-control ability and better utilization of polymer building blocks. Rheological study of solutions of the corresponding complementary associative polymer pairs in apolar media revealed the strength of complementary end-association required to achieve supramolecular aggregates capable of modulating rheological properties of the solution.
\r\n\r\nBoth self-associating and complementary associating polymers have therefore been found to resist shear degradation. The successful strategy of building soluble, end-associative polymers with either self-associative or complementary associative groups will guide the next generation of mist-control technology.
", "doi": "10.7907/Z91834FW", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8451", "collection": "thesis", "collection_id": "8451", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05302014-220000101", "type": "thesis", "title": "Density Functional Theory Embedding for Correlated Wavefunctions", "author": [ { "family_name": "Goodpaster", "given_name": "Jason Daniel", "clpid": "Goodpaster-Jason-Daniel" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Methods that exploit the intrinsic locality of molecular interactions show significant promise in making tractable the electronic structure calculation of large-scale systems. In particular, embedded density functional theory (e-DFT) offers a formally exact approach to electronic structure calculations in which the interactions between subsystems are evaluated in terms of their electronic density. In the following dissertation, methodological advances of embedded density functional theory are described, numerically tested, and applied to real chemical systems.
\r\n\r\nFirst, we describe an e-DFT protocol in which the non-additive kinetic energy component of the embedding potential is treated exactly. Then, we present a general implementation of the exact calculation of the non-additive kinetic potential (NAKP) and apply it to molecular systems. We demonstrate that the implementation using the exact NAKP is in excellent agreement with reference Kohn-Sham calculations, whereas the approximate functionals lead to qualitative failures in the calculated energies and equilibrium structures.
\r\n\r\nNext, we introduce density-embedding techniques to enable the accurate and stable calculation of correlated wavefunction (CW) in complex environments. Embedding potentials calculated using e-DFT introduce the effect of the environment on a subsystem for CW calculations (WFT-in-DFT). We demonstrate that WFT-in-DFT calculations are in good agreement with CW calculations performed on the full complex.
\r\n\r\nWe significantly improve the numerics of the algorithm by enforcing orthogonality between subsystems by introduction of a projection operator. Utilizing the projection-based embedding scheme, we rigorously analyze the sources of error in quantum embedding calculations in which an active subsystem is treated using CWs, and the remainder using density functional theory. We show that the embedding potential felt by the electrons in the active subsystem makes only a small contribution to the error of the method, whereas the error in the nonadditive exchange-correlation energy dominates. We develop an algorithm which corrects this term and demonstrate the accuracy of this corrected embedding scheme.
", "doi": "10.7907/RX3S-GH65", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:7320", "collection": "thesis", "collection_id": "7320", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12102012-132511810", "primary_object_url": { "basename": "Abrecht-PHDThesis.pdf", "content": "final", "filesize": 1819276, "license": "other", "mime_type": "application/pdf", "url": "/7320/1/Abrecht-PHDThesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Thermodynamic Properties of Organometallic Dihydrogen Complexes for Hydrogen Storage Applications", "author": [ { "family_name": "Abrecht", "given_name": "David Gregory", "clpid": "Abrecht-David-Gregory" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_chem" } ], "abstract": "The mechanism and thermodynamic properties of hydrogen binding to the solid-state complexes [M(CO)dppe2][BArF24] (M = Mn, Re, Tc) and [M'Hdppe2][NTf2] (M' = Fe, Ru, Os) were investigated experimentally and computationally over the temperature range 298K-373K and pressure range 0-2800 torr, based on the Sieverts method. The bulk absorption behavior was found to be accurately described by Langmuir isotherms. Enthalpy and entropy values of ΔH° = -52.2 kJ/mol and ΔS° = -99.6 J/mol-K were obtained experimentally for hydrogen absorption onto [Mn(CO)dppe2][BArF24] from the Langmuir equilibrium constant, and values obtained from electronic structure calculations using the LANL2DZ-ECP basis set were found to successfully reproduce both the pressure-temperature-composition behavior and the thermodynamic values to within 5% of those obtained through experiment. Results from simulations for all complexes yielded large enthalpy values similar to metal hydride formation enthalpies for all complexes studied, and the substitution of the metal center reproduced qualitative binding strength trends of 5d>3d>4d consistent with those previously reported for the group 6 metals.
\r\n\r\nX-ray diffraction patterns and Mössbauer spectra were taken to determine the thermal decomposition pathway for [FeH(η2-H2)dppe2][NTf2]. Simulations at the B3LYP/TZVP level of theory and experimental Mössbauer spectra confirmed the direct thermal decomposition from singlet-state [FeH(η2-H2)dppe2][NTf2] to triplet-state [FeHdppe2][NTf2] under vacuum conditions at 398K. Evaluation of the partial quadrupole splitting values of Q(H2) = -0.245 mm/s from Mössbauer spectroscopy significantly differ from typical values obtained for hydrides, indicating an underutilized mechanism for identification of dihydrogen ligands. Singlet-state thermodynamic values from simulation were consistent with experimental observations for Ru and Os, and ruthenium complexes were found to have thermodynamic properties within appropriate ranges for hydrogen storage applications. Simulated thermodynamic values for Fe complexes were found to significantly underestimate experimental behavior, demonstrating the importance of the magnetic spin state of the molecule to hydrogen binding properties.
", "doi": "10.7907/z9057cvb", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7443", "collection": "thesis", "collection_id": "7443", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01262013-020116009", "primary_object_url": { "basename": "Han Thesis.pdf", "content": "final", "filesize": 52470821, "license": "other", "mime_type": "application/pdf", "url": "/7443/1/Han Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Development of Targeted, Polymeric Delivery Vehicles for Camptothesin and siRNA Via Boronic Acid-Diol Complexation", "author": [ { "family_name": "Han", "given_name": "Han", "clpid": "Han-Han" } ], "thesis_advisor": [ { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "thesis_committee": [ { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Our research lab has developed polymer-based nanoparticle delivery systems for the anticancer drug, camptothecin (CPT), CRLX101; and for the small interfering RNA (siRNA), CALAA-01. CRLX101 has shown great success in both animal studies and clinical trials. However, it is incapable of achieving targeted delivery. CALAA-01 has demonstrated effectiveness in a phase I clinical trial. However, it suffers from its rapid in vivo clearance. To address the issues of targeting in the anticancer drug delivery system and the short circulation time in the siRNA delivery system, we have created a new delivery platform involving the use of boronic acid-diol complexation. This thesis is divided into two parts to discuss CPT delivery and siRNA delivery separately.
\r\n\r\nIn Part I, the targeted delivery of CPT via boronic acid-diol complexation is described. CPT was conjugated to a copolymer of mucic acid and PEG (MAP) and self-assembled into MAP-CPT nanoparticles. The targeting agent, Herceptin antibody was attached to boronic acid (BA), this was then complexed with the diol-containing MAP to form a targeted nanoparticle carrying ca. 60 CPT, with a 40 nm diameter and a slightly negative surface charge. The attachment of a single Herceptin per nanoparticle was sufficient to enhance cellular uptake of nanoparticles into BT-474, a HER2 overexpressing cell line by 70% compared to the non-targeted version. Nude mice bearing BT-474 xenograft tumors treated with targeted MAP-CPT nanoparticles resulted in all mice revealing complete tumor regression.
\r\n\r\nIn Part II, the boronic acid-diol complexation delivery platform is applied for the delivery of siRNA. First, the CALAA-01 delivery system for siRNA was further characterized and optimized. Then, a copolymer of mucic acid and dimethylsuberimidate (MAD) was synthesized and used in condensing the anionic siRNA into nanoparticles. Nanoparticles were stabilized by placing a surface PEG layer through boronic acid-diol complexation. Targeting was achieved by conjugating the distal end of the BA-PEG with a targeting agent, Herceptin antibody. MAD/siRNA nanoparticles effectively entered cells and demonstrated low cellular toxicity. MAD/siRNA nanoparticles stabilized with nitroPBA-PEG resulted in a diameter of 130 nm with a slightly negative surface charge. Pharmacokinetic studies in mice demonstrated improved circulation compared to CALAA-01.
\r\n\r\n", "doi": "10.7907/NWSP-0Y35", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7193", "collection": "thesis", "collection_id": "7193", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08282012-110955629", "type": "thesis", "title": "A Novel Method for Studying Nucleated Pathways in Membranes: Development and Applications for Gene Delivery", "author": [ { "family_name": "Ting", "given_name": "Christina Lei", "clpid": "Ting-Christina-Lei" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Clemons", "given_name": "William M.", "orcid": "0000-0002-0021-889X", "clpid": "Clemons-W-M" }, { "family_name": "Davis", "given_name": "Mark E.", "orcid": "0000-0001-8294-1477", "clpid": "Davis-M-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The development of a safe, selective, and efficient gene delivery system is key to the success of human gene therapy. In polymer-based gene delivery systems, biocompatible polymers electrostatically bind and condense the genetic material into protective nanoparticles. These nanoparticles must subsequently overcome several challenges, which remain poorly understood. In particular, once internalized by the cell, the nanoparticles are trapped inside a membrane-bound compartment called the endosome. In the proton sponge hypothesis, the buffering capacity of the polymers leads to an increase in osmotic pressure that eventually ruptures the endosomal membrane and releases the trapped nanoparticles.
\r\n\r\nTo obtain a mechanistic understanding of the endosomal escape, we first develop a coarse-grained model to study the equilibrium interaction between a positively charged nanoparticle and a lipid membrane. Results indicate the existence of a pore with an inserted particle, whose metastability depends on the membrane tension and particle properties (size and charge). These pores are subsequently shown to lower the critical tension necessary for membrane rupture, thus possibly enhancing the release of the trapped genetic material from the endosome.
\r\n\r\nNext, we address the actual escape pathway, which is likely a thermally nucleated process and cannot be simulated directly or studied by equilibrium methods. Hence, we develop a novel method for studying minimum free energy paths in membranes. Our results indicate that thermally nucleated rupture may be an important factor for the low rupture strains observed in lipid membranes. Under the moderate tensions found in this regime, there are multiple pathways for crossing the membrane: (1) particle-assisted membrane rupture, (2) particle insertion into a metastable pore followed by translocation and membrane resealing, and (3) particle insertion into a metastable pore followed by membrane rupture. This suggests a direct role of the nanoparticle in the endosomal escape not previously envisioned in the proton sponge hypothesis, and illustrates the importance of having an induced tension on the membrane.
\r\n\r\nFinally, the methodology developed in this work represents the most advanced theoretical technique for describing nucleation pathways in soft condensed matter systems that also include hard-particle degrees of freedom. We expect the method to be useful for studying a wide range of nucleation phenomena beyond membrane systems, for example, in nanoparticle polymer composites.
\r\n", "doi": "10.7907/8FTH-8H35", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7242", "collection": "thesis", "collection_id": "7242", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10172012-174905364", "primary_object_url": { "basename": "cit_thesis_Bin_Zhang_Chemistry2012_SUBMITTED.pdf", "content": "final", "filesize": 31212562, "license": "other", "mime_type": "application/pdf", "url": "/7242/1/cit_thesis_Bin_Zhang_Chemistry2012_SUBMITTED.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "Sec-facilitated Protein Translocation and Membrane Integration", "author": [ { "family_name": "Zhang", "given_name": "Bin", "clpid": "Zhang-Bin" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Clemons", "given_name": "William M.", "clpid": "Clemons-W-M" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The Sec translocon is a central component of the cellular machinery for targeting and delivering nascent proteins. Ubiquitous across all kingdoms of life, it is a protein-conducting channel that facilitates recognition of integral membrane protein domains and the establishment of integral membrane protein topology. Structural, biochemical, and biophysical studies have illuminated the role of the Sec translocon in both cotranslational and posttranslational protein targeting. In particular, quantitative assays have established the dependence of transmembrane domain (TM) stop-transfer efficiency and integral membrane protein topogenesis on the physicochemical properties of the translocon and protein nascent chain. These studies provide a valuable starting point for understanding the molecular regulation of the translocon and its sensitivity to mutations in protein sequence and external driving forces; however, complexities associated with the Sec machinery, including the role of collaborating molecular motors, the importance of large-scale conformational changes in the translocon, and the crowded molecular environment of the channel interior, obscure the mechanistic basis for many experimentally observed trends. My PhD research has focused on the development of a unified, mechanistic understanding of Sec-facilitated protein targeting.
\r\n\r\nUsing both atomistic and coarse-grained molecular simulations, we have investigated the conformational landscape for the Sec translocon. We found that inclusion of a hydrophobic peptide substrate in the translocon stabilizes an open conformation of the lateral gate (LG) that is necessary for membrane integration, whereas inclusion of a hydrophilic peptide substrate favors only the closed LG conformation. We demonstrated that the translocon plug moiety adopts markedly different conformations in the channel, depending on whether the substrate peptide is hydrophobic or hydrophilic in character. Finally, we showed that the energetics of the translocon LG opening in the presence of the substrate peptides can be modeled in terms of the energetics of the peptide interface with the membrane. The manuscript associated with this study is published in PNAS, 107, 5399 (2010).
\r\n\r\nWe further developed a novel computational protocol that combines nonequilibrium growth of the nascent protein with microsecond-timescale molecular dynamics trajectories. Analysis of multiple, long-timescale simulations elucidated molecular features of protein insertion into the translocon, including signal-peptide docking at the translocon LG, large-lengthscale conformational rearrangement of the translocon LG helices, and partial membrane integration of hydrophobic nascent-protein sequences. Furthermore, the simulations demonstrated the role of specific molecular interactions in the regulation of protein secretion, membrane integration, and integral membrane protein topology. Salt-bridge contacts between the nascent-protein N-terminus, cytosolic translocon residues, and phospholipid head groups were shown to favor conformations of the nascent protein upon early-stage insertion that are consistent with the Type II (Ncyt/Cexo) integral membrane protein topology; and extended hydrophobic contacts between the nascent protein and the membrane lipid bilayer were shown to stabilize configurations that are consistent with the Type III (Nexo/Ccyt) topology. These results provide a detailed, mechanistic basis for understanding experimentally observed correlations between integral membrane protein topology, translocon mutagenesis, and nascent-protein sequence. The manuscript associated with this study is published in J. Am. Chem. Soc., 134, 13700 (2012).
\r\n\r\nFinally, we introduced a coarse-grained modeling approach that spans the nanosecond to minute-timescale dynamics of cotranslational protein translocation. The method enabled direct simulation of both integral membrane protein topogenesis and TM stop-transfer efficiency. Simulations revealed multiple kinetic pathways for protein integration, including a mechanism in which the nascent protein undergoes slow-timescale reorientation, or flipping, in the confined environment of the translocon channel. Competition among these pathways gives rise to the experimentally observed dependence of protein topology on ribosomal translation rate and protein length. We further demonstrated that sigmoidal dependence of stop-transfer efficiency on TM hydrophobicity arises from local equilibration of the TM across the translocon LG, and it was predicted that slowing ribosomal translation yields decreased stop-transfer efficiency in long proteins. This work reveals the balance between equilibrium and nonequilibrium processes in protein targeting, and it provides new insight into the molecular regulation of the Sec translocon. The manuscript associated with this study is published in Cell Reports, in press.
\r\n\r\nThis research has significantly enriched the mechanistic understanding of Sec-facilitated protein translocation and membrane integration with ample molecular details. The unifying picture that we propose establishes fundamental connections between previously disparate experimental studies, and it lays down the foundation for future verification and refinement.
", "doi": "10.7907/6WWV-V190", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7871", "collection": "thesis", "collection_id": "7871", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072013-154128559", "primary_object_url": { "basename": "Thesis_Nicholas_J_Hoh_FINAL.pdf", "content": "final", "filesize": 9085254, "license": "other", "mime_type": "application/pdf", "url": "/7871/1/Thesis_Nicholas_J_Hoh_FINAL.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Effects of Particle Size Ratio on Single Particle Motion in Colloidal Dispersions", "author": [ { "family_name": "Hoh", "given_name": "Nicholas Jeffrey", "clpid": "Hoh-Nicholas-Jeffrey" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Andrade", "given_name": "Jose E.", "clpid": "Andrade-J-E" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The motion of a single Brownian particle of arbitrary size through a dilute colloidal dispersion of neutrally buoyant bath spheres of another characteristic size in a Newtonian solvent is examined in two contexts. First, the particle in question, the probe particle, is subject to a constant applied external force drawing it through the suspension as a simple model for active and nonlinear microrheology. The strength of the applied external force, normalized by the restoring forces of Brownian motion, is the P\u00e9clet number, Pe. This dimensionless quantity describes how strongly the probe is upsetting the equilibrium distribution of the bath particles. The mean motion and fluctuations in the probe position are related to interpreted quantities of an effective viscosity of the suspension. These interpreted quantities are calculated to first order in the volume fraction of bath particles and are intimately tied to the spatial distribution, or microstructure, of bath particles relative to the probe. For weak Pe, the disturbance to the equilibrium microstructure is dipolar in nature, with accumulation and depletion regions on the front and rear faces of the probe, respectively. With increasing applied force, the accumulation region compresses to form a thin boundary layer whose thickness scales with the inverse of Pe. The depletion region lengthens to form a trailing wake. The magnitude of the microstructural disturbance is found to grow with increasing bath particle size -- small bath particles in the solvent resemble a continuum with effective microviscosity given by Einstein's viscosity correction for a dilute dispersion of spheres. Large bath particles readily advect toward the minimum approach distance possible between the probe and bath particle, and the probe and bath particle pair rotating as a doublet is the primary mechanism by which the probe particle is able to move past; this is a process that slows the motion of the probe by a factor of the size ratio. The intrinsic microviscosity is found to force thin at low P\u00e9clet number due to decreasing contributions from Brownian motion, and force thicken at high P\u00e9clet number due to the increasing influence of the configuration-averaged reduction in the probe's hydrodynamic self mobility. Nonmonotonicity at finite sizes is evident in the limiting high-Pe intrinsic microviscosity plateau as a function of bath-to-probe particle size ratio. The intrinsic microviscosity is found to grow with the size ratio for very small probes even at large-but-finite P\u00e9clet numbers. However, even a small repulsive interparticle potential, that excludes lubrication interactions, can reduce this intrinsic microviscosity back to an order one quantity. The results of this active microrheology study are compared to previous theoretical studies of falling-ball and towed-ball rheometry and sedimentation and diffusion in polydisperse suspensions, and the singular limit of full hydrodynamic interactions is noted.
\r\n\r\nSecond, the probe particle in question is no longer subject to a constant applied external force. Rather, the particle is considered to be a catalytically-active motor, consuming the bath reactant particles on its reactive face while passively colliding with reactant particles on its inert face. By creating an asymmetric distribution of reactant about its surface, the motor is able to diffusiophoretically propel itself with some mean velocity. The effects of finite size of the solute are examined on the leading order diffusive microstructure of reactant about the motor. Brownian and interparticle contributions to the motor velocity are computed for several interparticle interaction potential lengths and finite reactant-to-motor particle size ratios, with the dimensionless motor velocity increasing with decreasing motor size. A discussion on Brownian rotation frames the context in which these results could be applicable, and future directions are proposed which properly incorporate reactant advection at high motor velocities.
", "doi": "10.7907/XN4G-TB33", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7024", "collection": "thesis", "collection_id": "7024", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05112012-140027276", "primary_object_url": { "basename": "ThesisSJohnson2012_FINAL.pdf", "content": "final", "filesize": 42153918, "license": "other", "mime_type": "application/pdf", "url": "/7024/1/ThesisSJohnson2012_FINAL.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "DNA Mechanics and Transcriptional Regulation in the E. coli lac Operon", "author": [ { "family_name": "Johnson", "given_name": "Stephanie Lynn", "clpid": "Johnson-Stephanie-Lynn" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Many gene regulatory motifs in both prokaryotes and eukaryotes involve physical manipulations of the genetic material, often on length scales short enough that the mechanical properties of the DNA significantly impact gene expression. One class of such manipulations, called \u201caction at a distance\u201d, includes transcription factor-mediated DNA looping, in which a binding site some distance away on the DNA is brought into close proximity with the transcription machinery at the promoter. DNA looping is a key component of several important regulatory systems in bacteria, and is crucial to the combinatorial control that is common at eukaryotic promoters regulated by more transcription factors than can physically bind adjacent to the promoter. Here we use a prototypical DNA looping protein, the Lac repressor from E. coli, to explore questions regarding the role of DNA mechanics in DNA looping and combinatorial control, particularly concerning the role of sequence flexibility in short-length-scale looping. We combine a statistical mechanical model of looping by the Lac repressor with a single-molecule technique called tethered particle motion that allows us to quantify this looping, and the systematic tuning of four biologically relevant and experimentally tractable parameters: loop length, loop sequence, repressor-DNA affinity, and repressor concentration. We show that this combination is a powerful approach to measuring repressor-DNA binding affinities and sequence-dependent DNA flexibilities in a way that is orthogonal, and therefore complementary, to conventional ensemble assays. Our results show that the sequence dependence to looping is more complicated than has been observed in other contexts, suggesting that \u201csequence flexibility\u201d as a general term is misleading, and, we argue, that the measurement of sequence flexibilities depend more strongly than previously appreciated on the shape of the deformation used to make the measurement. Finally, we present preliminary results with a more complicated system that is a case study for broader issues in combinatorial control, and a new hidden Markov model approach, based on variational Bayesian inference, to analyze these more complicated systems, which we hope will allow more precise dissections of, and more robust extraction of kinetic parameters from, tethered particle motion assays.", "doi": "10.7907/W40T-PD39", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6852", "collection": "thesis", "collection_id": "6852", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03172012-160452929", "primary_object_url": { "basename": "Romero_dissertation.pdf", "content": "final", "filesize": 6124840, "license": "other", "mime_type": "application/pdf", "url": "/6852/1/Romero_dissertation.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Statistical Models of the Protein Fitness Landscape: Applications to Protein Evolution and Engineering", "author": [ { "family_name": "Romero", "given_name": "Philip Anthony", "orcid": "0000-0002-2586-7263", "clpid": "Romero-Philip-Anthony" } ], "thesis_advisor": [ { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" } ], "thesis_committee": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Understanding the protein fitness landscape is important for describing how natural proteins evolve and for engineering new proteins with useful properties. This mapping from protein sequence to protein function involves an extraordinarily complex balance of numerous physical interactions, many of which are still not well understood. Directed evolution circumvents our ignorance of how a protein\u2019s sequence encodes its function by using iterative rounds of random mutation and artificial selection. The selection criteria is based on experimental measurements, which permits the optimization of protein sequence properties that are not understood. While directed evolution has been useful for exploring protein fitness landscapes, these searches have been relatively local in comparison to the vast space of possible protein sequences. Here, we present several classes of statistical models that map protein sequence space on a larger scale. We use these simple models to interpret data from SCHEMA recombination libraries, understand the evolutionary benefit of intragenic recombination, and design optimized protein sequences. By training on directly on experimental data, these models implicitly capture the numerous and possibly unknown factors that shape the protein fitness landscape. This provides an unrivaled quantitative accuracy across a massive number of protein sequences.
\r\n", "doi": "10.7907/7W9R-Y338", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6947", "collection": "thesis", "collection_id": "6947", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04192012-094254839", "primary_object_url": { "basename": "Thesis_Final.pdf", "content": "final", "filesize": 14140320, "license": "other", "mime_type": "application/pdf", "url": "/6947/1/Thesis_Final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Reshaping Elastomers with Light: First Principles Model of Diffusion-Induced Deformation", "author": [ { "family_name": "Turner", "given_name": "Ryan Matthew", "clpid": "Turner-Ryan-Matthew" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Selinger", "given_name": "Robin L. B.", "clpid": "Selinger-R-L-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Elastomeric photopolymers are a new class of materials originally developed at Caltech for use as intraocular lenses. These materials consist of a host network swollen with short-chain, photoreactive \"macromers.\" Using a light source for selective photopolymerization, gradients in free macromer molecules are created, driving diffusion-induced shape change. Although models exist for external flow of solvent into a swelling gel or for gel deswelling caused by externally imposed forces, no known model exists to account for reaction-induced diffusion-deformation for a force-free material in which solvent can neither enter nor leave. To predict this unique reaction-diffusion-induced shape change, we propose a simple \"two-component\" model which treats macromer as converting directly into network strands. This model is first shown to be in good agreement with experimental data on the equilibrium swelling of elastomeric photopolymers. We then use mixture theory to develop constitutive laws for the system stress and the flux of macromer by ensuring that the second law of thermodynamics holds. Finally, we implement the theory to a variety of problems - including a finite-element model of the light-adjustable lens - in each case systematically detailing the relative importance of the material parameters on the magnitude and rate of shape change. We determined that the shape change depends upon the rate of consumption of macromer (specified by the initial extent of reaction profile and the initial volume fraction of macromer) and is independent of the network modulus or the macromer molar mass. In addition, we found that the macromer molar mass serves only to determine the rate at which the deformation proceeds, whereas the network modulus serves to determine the magnitude of the internal forces experienced in the photopolymer.", "doi": "10.7907/RVVD-2J26", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6245", "collection": "thesis", "collection_id": "6245", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02162011-153857988", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 14305814, "license": "other", "mime_type": "application/pdf", "url": "/6245/1/thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Pharmacological Behavior of Systemically Administered Nanoparticles of Defined Properties: Mechanistic Investigations at the Organ, Tissue, and Cellular Levels", "author": [ { "family_name": "Choi", "given_name": "Chung Hang Jonathan", "clpid": "Choi-Chung-Hang-Jonathan" } ], "thesis_advisor": [ { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "thesis_committee": [ { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Webster", "given_name": "Paul", "clpid": "Webster-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The objective of this thesis is to establish design rules for nanoparticle properties that enable their in vivo transport to target destinations. Gold nanoparticles containing surface-engrafted polyethylene glycol (PEG) chains are prepared with controlled physicochemical properties (hydrodynamic size, surface charge, targeting ligand density). Upon systemic injection into mice, the transport of nanoparticles is monitored by blood pharmacokinetics as well as distribution at the organ, tissue, and subcellular levels from the same injection in an individual animal.
\r\n\r\nAt a constant, slightly negative surface charge (ca. -10 mV), most PEGylated gold nanoparticles (PEG-AuNPs) deposit in the liver, spleen, and kidney of normal mice 24 hours after injection. Increasing retention in the liver (Kupffer cells) and spleen correlate positively with increasing nanoparticle diameter over the range of 25-165 nm, largely due to phagocytic uptake. Accumulation in the kidney is size-dependent, but shows a maximum uptake at ca. 75 \u00b1 25 nm that also gives the highest deposition in the mesangium (uptake by mesangial cells).
\r\n\r\nTumor-bearing mice received injections of PEG-AuNPs of near-constant size (ca. 75 nm) and surface charge (ca. -10 mV) but with variable amounts of ligands that target cancer cells (0-144 ligands per nanoparticle). Independent of ligand content, nanoparticles accumulate in the tumor by the enhanced permeation and retention effect to the same magnitude, and adjacent to leukocytes. Nanoparticles only enter cancer cells in significant amounts when they contain targeting ligands above a threshold amount (between 18 and 144 ligands per nanoparticle).
\r\n\r\nMechanistic studies from model nanoparticles provide insights for the delivery of therapeutic nanoparticles. Systemic administrations of targeted, cyclodextrin-based, siRNA-containing nanoparticles are investigated in animals and humans (Phase I clinical trial). A fluorescent chemical stain with exposed adamantane molecules for binding into the cyclodextrin cups of the targeted nanoparticles is created, allowing for the examination of tumor tissue sections from animals and patient biopsies. Results from both animal and human tissues reveal intracellular, dose-dependent accumulation of targeted nanoparticles in cancer cells of the tumor.
", "doi": "10.7907/33C2-FY20", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6454", "collection": "thesis", "collection_id": "6454", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262011-141718914", "primary_object_url": { "basename": "PhDthesis_Hutchens-S-B_2011(embedded-movies).pdf", "content": "final", "filesize": 64256089, "license": "other", "mime_type": "application/pdf", "url": "/6454/2/PhDthesis_Hutchens-S-B_2011(embedded-movies).pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Deformation Behavior and Mechanical Analysis of Vertically Aligned Carbon Nanotube (VACNT) Bundles", "author": [ { "family_name": "Hutchens", "given_name": "Shelby Brooke", "orcid": "0000-0003-0349-1792", "clpid": "Hutchens-Shelby-Brooke" } ], "thesis_advisor": [ { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Daraio", "given_name": "Chiara", "orcid": "0000-0001-5296-4440", "clpid": "Daraio-C" }, { "family_name": "Flagan", "given_name": "Richard C.", "orcid": "0000-0001-5690-770X", "clpid": "Flagan-R-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Vertically aligned carbon nanotubes (VACNTs) serve as integral components in a variety of applications including MEMS devices, energy absorbing materials, dry adhesives, light absorbing coatings, and electron emitters, all of which require structural robustness. It is only through an understanding of VACNT\u2019s structural mechanical response and local constitutive stress-strain relationship that future advancements through rational design may take place. Even for applications in which the structural response is not central to device performance, VACNTs must be sufficiently robust and therefore knowledge of their microstructure-property relationship is essential. This thesis first describes the results of in situ uniaxial compression experiments of 50 micron diameter cylindrical bundles of these complex, hierarchical materials as they undergo unusual deformation behavior. Most notably they deform via a series of localized folding events, originating near the bundle base, which propagate laterally and collapse sequentially from bottom to top. This deformation mechanism accompanies an overall foam-like stress-strain response having elastic, plateau, and densification regimes with the addition of undulations in the stress throughout the plateau regime that correspond to the sequential folding events. Microstructural observations indicate the presence of a strength gradient, due to a gradient in both tube density and alignment along the bundle height, which is found to play a key role in both the sequential deformation process and the overall stress-strain response. Using the complicated structural response as both motivation and confirmation, a finite element model based on a viscoplastic solid is proposed. This model is characterized by a flow stress relation that contains an initial peak followed by strong softening and successive hardening. Analysis of this constitutive relation results in capture of the sequential buckling phenomenon and a strength gradient effect. This combination of experimental and modeling approaches motivates discussion of the particular microstructural mechanisms and local material behavior that govern the non-trivial energy absorption via sequential, localized buckle formation in the VACNT bundles.", "doi": "10.7907/BPW6-Z145", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6455", "collection": "thesis", "collection_id": "6455", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262011-141745737", "type": "thesis", "title": "Individual Particle Motion in Colloids: Microviscosity, Microdiffusivity, and Normal Stresses", "author": [ { "family_name": "Zia", "given_name": "Roseanna Nellie", "clpid": "Zia-Roseanna-Nellie" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "orcid": "0000-0003-2908-5469", "clpid": "Bhattacharya-K" }, { "family_name": "Colonius", "given_name": "Tim", "orcid": "0000-0003-0326-3909", "clpid": "Colonius-T" }, { "family_name": "Lauga", "given_name": "Eric", "orcid": "0000-0002-8916-2545", "clpid": "Lauga-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Colloidal dispersions play an important role in nearly every aspect of life, from paint to biofuels to nano-therapeutics. In the study of these so-called complex \ufb02uids, a connection is sought between macroscopic material properties and the micromechanics of the suspended particles. Such properties include viscosity, diffusivity, and the osmotic pressure, for example. But many such systems are themselves only microns in size overall; recent years have thus seen a dramatic growth in demand for exploring microscale systems at a much smaller length scale than can be probed with conventional macroscopic techniques. Microrheology is one approach to such microscale interrogation, in which a Brownian \u201cprobe\u201d particle is driven through a complex \ufb02uid, and its motion tracked in order to infer the mechanical properties of the embedding material. With no external forcing the probe and background particles form an equilibrium microstructure that \ufb02uctuates thermally with the solvent. Probe motion through the dispersion distorts the microstructure; the character of this deformation, and hence its in\ufb02uence on probe motion, depends on the strength with which the probe is forced, F ext , compared to thermal forces, kT/b, defining a P\u00b4eclet number, P e = F ext /(kT /b), where kT is the thermal energy and b the bath-particle size. Both the mean and the \ufb02uctuating motion of the probe are of interest. Recent studies showed that the reduction in mean probe speed gives the e\ufb00ective material viscosity. But the velocity of the probe also \ufb02uctuates due to collisions with the suspended particles, causing the probe to undergo a random walk process. It is shown that the long-time mean-square \ufb02uctuational motion of the probe is diffusive and the effective diffusivity of the forced probe is determined for the full range of P\u00b4eclet number. At small Pe Brownian motion dominates and the diffusive behavior of the probe characteristic of passive microrheology is recovered, but with an incremental \ufb02ow-induced \u201cmicro-diffusivity\u201d that scales as Dmicro \u223c Da P e 2 \u03c6b , where viii \u03c6b is the volume fraction of bath particles and Da is the self-diffusivity of an isolated probe. At the other extreme of high P\u00b4eclet number the fuctuational motion is still diffusive, and the diffusivity becomes primarily force-induced , scaling as (F ext /\u03b7)\u03c6b , where \u03b7 is the viscosity of the solvent. The force-induced \u201cmicrodiffusivity\u201d is anisotropic, with diffusion longitudinal to the direction of forcing larger in both limits compared to transverse diffusion, but more strongly so in the high-P e limit.
\r\n\r\nPrevious work in microrheology defined a scalar viscosity; however, a tensorial expression for the suspension stress in microrheology was still lacking. The notion that diffusive \ufb02ux is driven by gradients in particle-phase stress leads to the idea that the microdiffusivity can be related directly to the suspension stress. In consequence, the anisotropy of the diffusion tensor may re\ufb02ect the presence of normal stress differences in non-linear microrheology. While the particle-phase stress tensor can be determined as the second moment of the deformed microstructure, in this study a connection is made between diffusion and stress gradients, and an analytical expression for particle-phase stress as a function of the microdiffusivity and microviscosity is obtained. The two approaches agree, suggesting that normal stresses and normal stress differences can be measured in active microrheological experiments if both the mean and mean-square motion of the probe are monitored. Owing to the axisymmetry of the motion about a spherical probe, the second normal stress difference is zero, while the \ufb01rst normal stress difference is linear in P e for P e \u226b 1 and vanishes as P e 3 for P e \u226a 1. An additional important outcome is that the analytical expression obtained for stress-induced migration can be viewed as a generalized non-equilibrium Stokes-Einstein relation.
\r\n\r\nStudies of steady-state dispersion behavior reveal the hydrodynamic and microstructural mechanisms that underlie non-Newtonian behaviors (e.g. shear-thinning, shear-thickening, and normal stress differences). But an understanding of how the microstructures evolve from the equilibrium state, and how non-equilibrium properties develop in time is much less well understood. Transient suspension behavior in the near-equilibrium, linear response regime has been studied via its connection to low-amplitude oscillatory probe forcing and the complex modulus; at very weak forcing, the microstructural response that drives viscosity is indistinguishable from equilibrium \ufb02uctuations. But important information about the basic physical aspects of structural development and relaxation ix in a medium are captured by start-up and cessation of the imposed deformation in the non-linear regime, where the structure is driven far from equilibrium. Here we study the evolution of stress and microstructure in a colloidal dispersion by tracking transient probe motion during start-up and cessation of a strong \ufb02ow. For large P e, steady state is reached when a boundary layer (in which advection balances diffusion) forms at particle contact on the timescale of the \ufb02ow, a/U , where a is the probe size and U its speed. On the other hand, relaxation following cessation occurs over several timescales corresponding to distinct physical processes. For very short times, the timescale for relaxation is set by the diffusion over the boundary-layer thickness. Nearly all stress relaxation occurs during this process, owing to the dependence of the bath-particle drag on the contact value of the microstructure. At longer times the collective diffusion of the bath particles acts to close the wake. In this long-time limit as structural isotropy is restored, the majority of the microstructural relaxation occurs with very little change in suspension stress. Theoretical results are presented and compared with Brownian dynamics simulation. Two regimes of probe motion are studied: an externally applied constant force and an imposed constant velocity. The microstructural evolution is qualitatively different for the two regimes, with a longer transient phase and a thinner boundary layer and longer wake at steady state in the latter case. The work is also compared to analogous results for sheared suspensions undergoing start-up and cessation.
\r\n\r\nThe study moves next to investigations of dual-probe microrheology. Motivated by the phenomenon of equilibrium depletion interactions, we study the interaction between a pair of probe particles translating with equal velocity through a dispersion with their line of centers transverse to the external forcing. The character of the microstructure surrounding the probes is determined both by the distance R by which the two probes are separated and by the strength of the external forcing, P e = U a/Db , where U is the constant probe velocity and Db the diffusivity of the bath particles. Osmotic pressure gradients develop as the microstructure is deformed, giving rise to an interactive force between the probes. This force is studied for a range of P e and R. For all separations R > 2a, the probes attract when P e is small. As the strength of the forcing increases, a qualitative change in the interactive force occurs: the probes repel each other. The probe separation R at which the x attraction-to-repulsion transition occurs decreases as P e increases, because the entropic depletion attraction becomes weak compared to the force-induced osmotic repulsion. The non-equilibrium interactive force is strictly repulsive for two separated probes.
\r\n\r\nBut non-linear microrheology provides far more than a microscale technique for interrogating complex \ufb02uids. In 1906, Einstein published the famous thought experiment in which he proposed that if a liquid were indeed composed of atoms, then the motion of a small particle suspended in the \ufb02uid would move with the same random trajectories as the solvent atoms. Combining the theories of kinetics, diffusion, and thermodynamics, he showed that the diffusive motion of a small particle is indeed evidence of the existence of the atom. Perrin con\ufb01rmed the theory with measurement in 1909. This is a profound conclusion, drawn by simply watching a particle move in a liquid. Here, we follow this example and watch a particle move in a complex \ufb02uid\u2014but now for a system that is not at equilibrium. In equilibrium systems, the relationship between \ufb02uctuation and dissipation is fundamental to our understanding of colloid physics. By studying \ufb02uctuations away from equilibrium, we have discovered an analogous non-equilibrium relation between \ufb02uctuation and dissipation\u2014and that the balance between the two is stored in the material stress. A \ufb01nal connection can be made between this stress and energy storage.
", "doi": "10.7907/2743-8W26", "publication_date": "2011-06-10", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:5844", "collection": "thesis", "collection_id": "5844", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262010-132424180", "primary_object_url": { "basename": "thesis_jmueller_final.pdf", "content": "final", "filesize": 3921784, "license": "other", "mime_type": "application/pdf", "url": "/5844/1/thesis_jmueller_final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Structures, Energetics and Reactions of Hydrocarbons on Nickel", "author": [ { "family_name": "Mueller", "given_name": "Jonathan Edward", "orcid": "0000-0001-8811-8799", "clpid": "Mueller-Jonathan-Edward" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "To better understand and improve reactive processes on nickel surfaces such as the catalytic steam reforming of hydrocarbons, the decomposition of hydrocarbons at fuel cell anodes, and the growth of carbon nanotubes, we have performed atomistic studies of hydrocarbon adsorption and decomposition on low index nickel surfaces and nickel catalyst nanoparticles. Quantum mechanics (QM) calculations utilizing the PBE flavor of density functional theory (DFT) were performed on all CHx and C2Hy species to determine their structures and energies on Ni(111). In good agreement with experiments, we find that CH is the most stable form of CHx on Ni(111). It is a stable intermediate in both methane dehydrogenation and CO methanation, while CH(2,ad) is only stable during methanation. We also find that nickel surface atoms play an important catalytic role in C-H bond formation and cleavage. For the C2Hy species we find a low surface coverage decomposition pathway proceeding through CHCHad, the most stable intermediate, and a high surface coverage pathway which proceeds through CCH3,ad, the next most stable intermediate. Our enthalpies along these pathways are consistent with experimental observations.
\r\n\r\nTo extend our study to larger systems and longer time scales, we have developed the ReaxFF reactive force field to describe hydrocarbon decomposition and reformation on nickel catalyst surfaces. The ReaxFF parameters were fit to geometries and energy surfaces from DFT calculations involving a large number of reaction pathways and equations of state for nickel, nickel carbides, and various hydrocarbon species chemisorbed on Ni(111), Ni(110) and Ni(100). The resulting ReaxFF description was validated against additional DFT data to demonstrate its accuracy, and used to perform reaction dynamics (RD) simulations on methyl decomposition for comparison with experiment. Finally ReaxFF RD simulations were applied to the chemisorption and decomposition of six different hydrocarbons (methane, acetylene, ethylene, benzene, cyclohexane and propylene) on a 468 atom nickel nanoparticle. These simulations realistically model hydrocarbon feedstock decomposition and provide reaction pathways relevant to this part of the carbon nanotube growth process. They show that C-C \u03c0 bonds provide a low barrier pathway for chemisorption, and that the low energy of subsurface C is an important driving force in breaking C-C bonds.
", "doi": "10.7907/RVXX-Z341", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5845", "collection": "thesis", "collection_id": "5845", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262010-140604509", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 4664039, "license": "other", "mime_type": "application/pdf", "url": "/5845/1/thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Colloids in Confined Geometries: Hydrodynamics, Simulation and Rheology", "author": [ { "family_name": "Swan", "given_name": "James W.", "orcid": "0000-0002-4244-8204", "clpid": "Swan-James-W" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" }, { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The hydrodynamics of colloids in confined geometries is studied hierarchically beginning with the exact solutions for a spherical particle translating, rotating and deforming in the presence of a plane wall at low Reynolds number. The many-bodied hydrodynamic interactions among a collection of spherical particles near a plane wall are computed and used to study the Brownian motion of confined suspensions. The method of reflections is used to describe the motion of a single spherical particle embedded in the fluid constrained by two, parallel plane walls. From this, tables which are independent of the channel width are generated describing the particle\u2019s response to various force moments. This same approach is expanded to describe the hydrodynamic interactions among the particles comprising a colloidal dispersion confined in a channel. The simulations arising from this theory depict the short-time self-diffusivity, sedimentation rate and high frequency viscosity of suspensions of varying volume fractions in channels of varying widths. A theory for the scattering of evanescent waves by colloidal dispersions is developed and cast in the form of the diffusivity measured by classical light scattering. A series of simulations is conducted to predict the short- time self-diffusivity and the collective diffusivity measured by evanescent wave dynamic light scattering. The thesis concludes with a discussion of how the developed simulations and theories can be extended to make dynamic measurements as well as a brief consideration of some remaining, open questions.", "doi": "10.7907/JJ28-7641", "publication_date": "2010-06-11", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5874", "collection": "thesis", "collection_id": "5874", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05282010-012507201", "primary_object_url": { "basename": "Manuj_thesis.pdf", "content": "final", "filesize": 5067713, "license": "other", "mime_type": "application/pdf", "url": "/5874/1/Manuj_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Bulk Viscosity of Suspensions", "author": [ { "family_name": "Swaroop", "given_name": "Manuj", "clpid": "Swaroop-Manuj" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Seinfeld", "given_name": "John H.", "clpid": "Seinfeld-J-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Particles suspended in a fluid are known to undergo variations in the local concentration in many flow situations; essentially a compression or expansion of the particle phase. The modeling of this behavior on a macroscopic scale requires knowledge of the effective bulk viscosity of the suspension, which has not been studied before. The bulk viscosity of a pure compressible fluid is defined as the constant of proportionality that relates the difference between the mechanical pressure and the thermodynamic pressure to the rate of compression. The bulk viscosity of a suspension is defined analogous to that for a pure fluid as the constant of proportionality relating the deviation of the trace of the macroscopic stress from its equilibrium value to the average rate of compression. The compression flow drives the suspension microstructure out of equilibrium and the thermal motion of the particles tries to restore equilibrium. The Peclet number (Pe), defined as the expansion rate made dimensionless with the Brownian time-scale, governs the departure of the microstructure from equilibrium. The microstructural forcing in compression is monopolar for small Pe resulting in a significantly slower spatial and temporal response of the microstructure compared to shearing or diffusive motion.
\r\n\r\nWe have determined the effective suspension bulk viscosity for all concentrations and all rates of compression, accounting for the full thermodynamic and hydrodynamic interactions that particles experience at the micro-scale. Current simulation techniques were enhanced to enable the dynamic simulation of compression flows in a suspension. A 'compression thinning' of the suspension is observed at small rates of compression and there is some 'compression thickening' at large compression rates. The bulk viscosity diverges as the volume fraction nears maximum packing and is in fact larger than the shear viscosity. Existing models for multiphase flows must therefore include the bulk viscosity term to properly simulate variations in particle concentration.
\r\n\r\nAn understanding of bulk viscosity effects in suspensions will enable the modeling of certain aggregation and separation behavior and lead to more accurate models for multiphase flows where there are variations in the particle concentration, such as filtration or fluidization.
", "doi": "10.7907/HQGZ-DV22", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5815", "collection": "thesis", "collection_id": "5815", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05182010-213110299", "primary_object_url": { "basename": "thesis_dw.pdf", "content": "final", "filesize": 30060497, "license": "other", "mime_type": "application/pdf", "url": "/5815/6/thesis_dw.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Biomechanical Information Transfer: Maximum Caliber, \u03bb Genome Ejection Dynamics, and the Formation of Otoliths in Zebrafish", "author": [ { "family_name": "Wu", "given_name": "David Dah-wei", "clpid": "Wu-David-Dah-wei" } ], "thesis_advisor": [ { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Biology is inherently a non-equilibrium process - constantly battling or co-opting the entropic enemy in order to achieve its sine qua non: growth, development, and reproduction. Involved in these processes is the formation of temporal and spatial order from disorder, and the transfer of information in genomic content but also in the form of physical principles.
\r\n\r\nFirst, I will describe a different way to analyze dynamics called Maximum Caliber, a model-free application of the Principle of Maximum Entropy to trajectories or processes, based purely on information theorya. We apply Maximum Caliber to analyze particles diffusing on a dual-minima energy landscape and attempt to describe and predict the probability distribution of trajectories. Next, I will discuss our efforts in analyzing the literal transfer of information from one organism to the next: specifically, how phage lambda's DNA gets inside Escherichia coli. The use of counterions as a parameter to tune the force of in vitro ejections is clarified before performing suggestive in vivo injection experiments. Last, the process of building and shaping the otolith of the zebrafish (the accelerometer and hearing organ) is analyzed, with the conclusion that it is possible to generate said organ through purely physical mechanisms, suggesting that biological information transfer is not exclusively genetic.
\r\n", "doi": "10.7907/X454-MV52", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5715", "collection": "thesis", "collection_id": "5715", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04122010-145555532", "primary_object_url": { "basename": "WitmanThesisComplete.pdf", "content": "final", "filesize": 2039918, "license": "other", "mime_type": "application/pdf", "url": "/5715/10/WitmanThesisComplete.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "The T-Shaped Anisotropic Molecule Model: A Unique Perspective on the Glass Transition and Gelation in Low Valence, Directional, Network Forming Liquids", "author": [ { "family_name": "Witman", "given_name": "Jennifer Elisabeth", "clpid": "Witman-Jennifer-Elisabeth" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Glass and gel formers exhibit unusual mechanical characteristics and amorphous phases which are highly dependent on their thermal history. We introduce a lattice model with T-shaped molecules that exhibits glassy and gel-like states without introducing artificial frustration. This system has a large number of degenerate energy minima separated by small barriers leading to a broad, kinetically-explored landscape. It particularly replicates valence-limited materials, which can form self-assembled materials with highly controlled physical properties. Despite its remarkable simplicity, this model reveals some of the fundamental kinetic and thermodynamic properties of the glass transition and of gel formation.
\r\n\r\nA dearth of low temperature experimental and simulation measurements has inhibited investigation in this field. We overcome this difficulty by using a modified Metropolis Monte Carlo method to quickly provide equilibrium samples. Then kinetic Monte Carlo techniques are used to explore the properties of the equilibrium system, providing a touchstone for the non-equilibrium glassy states.
\r\n\r\nFully-dense simulation samples reveal a fragile-to-strong crossover (FSC) near the mean-field (MF) spinodal. At the FSC, the relaxation time returns to Arrhenius behavior with cooling. There is an inflection point in the configurational entropy. This behavior resolves the Kauzmann Paradox which is a result of extrapolation from above the inflection point. In contrast, we find that the configurational entropy remains finite as the temperature goes to zero. We also observe different kinetics as the system is quenched below the FSC, resulting in non-equilibrium, amorphous states with high potential energy persisting for long periods of time. Simulation samples remain at non-equilibrium conditions for observation times exceeding those permitting complete equilibration slightly above the FSC. This suggests the FSC would often be identified as the glass transition without indication that there is true arrest or a diverging length scale. Indeed, our simulations show these samples do equilibrate if sufficient time is allowed. To elucidate the complex, interdependent relation time and length scales at the FSC will require careful consideration of the spatial-dynamic heterogeneity.
\r\n\r\nDynamic mean-field simulations at high density and in the solvated regime reveal a rich range of morphological features. They are consistent with simulated and experimental results in colloidal systems. Stability limits of decreasing length scales beneath the phase separation bimodal coincide into a single curve, which terminates at the fully-dense MF spinodal, suggesting that gelation and vitrification are the same phenomena. Our work indicates that gelation is, therefore, a result of phase separation arrested by a glass transition.
", "doi": "10.7907/0XET-0H46", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:390", "collection": "thesis", "collection_id": "390", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01282008-150852", "primary_object_url": { "basename": "LinHan.pdf", "content": "final", "filesize": 15479140, "license": "other", "mime_type": "application/pdf", "url": "/390/1/LinHan.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "In vitro DNA Mechanics in Gene Regulation: One Molecule at a Time", "author": [ { "family_name": "Han", "given_name": "Lin", "clpid": "Han-Lin" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Guo", "given_name": "Chin-Lin", "clpid": "Guo-Chin-Lin" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The biological significance of DNA is primarily attributed to its sequence information. On the other hand, the mechanical properties of DNA can play a critical role in a wide variety of biological processes. One prime example is DNA looping in the context of transcriptional regulation. The emergence of single molecule tracking techniques in the last two decades presents an unprecedented opportunity for studying looping kinetics. One such powerful technique, tethered particle motion (TPM), harnesses the Brownian motion of a microsphere as a means of reporting on the excursion of its tethered molecule, such as DNA. The present work focuses on a looping system found in Escherichia coli, which is mediated by the Lac repressor (LacI) protein. TPM is used to measure individual, real-time looping/unlooping events in DNA of various length and sequence characteristics. By monitoring the magnitude, frequency, and time interval of these features while tuning different parameters, such as LacI concentration, DNA length and DNA sequence, one can survey a host of important information about looping kinetics. A measurement of the LacI concentration dependence of looping probability was found to be in quantitative agreement with a simple thermodynamic model, which also led to the measurement of free energy of LacI-mediated looping, the first such measurement in a single molecule, in vitro setting. A quantitative characterization of free energy was obtained under conditions of different inter-operator spacing, systematically varied from 300 to 310 base pairs in one-base-pair increments. An important conclusion from this study is that free energy is modulated by DNA\u2019s helical structure, yet the energy difference between the aligned and unaligned operator configurations is small compared to expectation from simple polymer physics. TPM measurements also revealed an additional looped state, lending support to the hypothesis that two distinct conformations of LacI, the closed and open forms, can coexist. This study also confirmed that the presence of certain DNA sequences, particularly TA pairs in the minor groove of the nucleosomal positioning sequence, makes DNA substantially softer than a corresponding random sequence. This provides direct support for the notion of sequence-dependent DNA elasticity. Finally, a surprising result is that loops as short as 100 base pairs-only two-thirds the persistence length of DNA-can form by LacI-DNA binding. Classical elasticity theory almost forbids this, suggesting that LacI itself plays a more direct role in the bending process, or classical understanding of DNA elasticity breaks down at length scales comparable to its persistence length.", "doi": "10.7907/7573-A922", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2173", "collection": "thesis", "collection_id": "2173", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05272008-194010", "primary_object_url": { "basename": "Combined_Files.pdf", "content": "final", "filesize": 5820979, "license": "other", "mime_type": "application/pdf", "url": "/2173/43/Combined_Files.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Associative Polymers as Antimisting Agents and Other Functional Materials via Thiol-ene Coupling", "author": [ { "family_name": "David", "given_name": "Ralph Leonard Ameri", "clpid": "David-Ralph-Leonard-Ameri" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Sarohia", "given_name": "Virendra", "clpid": "Sarohia-V" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Associating polymers of varying molecular design were studied as potential additives to aviation fuel, aimed to suppress misting and thereby reduce the fuel\u2019s fire hazard in crash scenarios. Molecular architectures investigated varied from random placement along polymer chains of associating groups (referred to throughout this work as \u201cstickers\u201d) to selective clustering of the stickers at chain ends. Linear chains possessing associating functional groups grafted at random positions along the entire chain were investigated first. Model polymers with matched backbone length were synthesized to examine the effects of degree of functionalization and type of interaction (self-associating or donor-acceptor) on shear and extensional rheology of both dilute and semi-dilute solutions in non-polar hydrocarbon solvents. We found that intramolecular associations dominate the behavior of self-associating chains even in semi-dilute concentrations, leading to chain collapse and reduced shear and extensional viscosities. Mixtures of donor-acceptor chains show much more favorable intermolecular pairing in dilute solutions (as evidenced by the formation of large aggregates), but nevertheless display reduced solution elasticity and extensional viscosity relative to unmodified homologues: sticker pairing interfered with the stretching of the chains in elongational flow. Molecular designs that overcome chain collapse by clustering stickers at the ends of polymer chains were studied next. We showed by theoretical modeling that symmetric linear chains displaying strongly associating endgroups suffer instead from loop formation, which traps the bulk of the polymer into small cyclic aggregates with low mist-control properties. Therefore, we suggest molecular architectures that preclude formation of cyclic supramolecules by employing several different donor-acceptor pairs that do not affect one another (\u201corthogonal\u201d pairs). This presents a synthetic challenge, i.e., the development of simple and rapid protocols for the preparation of functional polymer materials of controlled architecture and functionality. We developed such convenient protocols (fast, non-wasteful, and scalable procedures) for the functionalization of polybutadiene by thiol-ene addition to yield functional polymers of narrow polydispersity. These powerful, versatile synthetic tools can potentially be applied to add any side-group onto any polymer, copolymer, or block copolymer displaying pendant vinyl groups, with exciting potential applications in fields ranging from organic electronics to drug delivery.", "doi": "10.7907/9AHR-A213", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:1667", "collection": "thesis", "collection_id": "1667", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05072008-204627", "primary_object_url": { "basename": "mchale_thesis.pdf", "content": "final", "filesize": 4874716, "license": "other", "mime_type": "application/pdf", "url": "/1667/1/mchale_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Feedback Tracking and Correlation Spectroscopy of Fluorescent Nanoparticles and Biomolecules", "author": [ { "family_name": "McHale", "given_name": "Kevin L.", "clpid": "McHale-Kevin-L" } ], "thesis_advisor": [ { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" } ], "thesis_committee": [ { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" }, { "family_name": "Yang", "given_name": "Changhuei", "clpid": "Yang-Changhuei" }, { "family_name": "Mabuchi", "given_name": "Hideo", "clpid": "Mabuchi-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The best way to study dynamic fluctuations in single molecules or nanoparticles is to look at only one particle at a time, and to look for as long as possible. Brownian motion makes this difficult, as molecules move along random trajectories that carry them out of any fixed field of view. We developed an instrument that tracks the Brownian motion of single fluorescent molecules in three dimensions and in real-time while measuring fluorescence with nanosecond time resolution and single-photon sensitivity. The apparatus increases observation times by approximately three orders of magnitude while improving data-collecting efficiency by locking tracked objects to a high-intensity region of the excitation laser.
\r\n\r\nAs a first application of our technique, we tracked and studied the fluorescence statistics of semiconductor quantum dots. Our measurements were well resolved at 10ns correlation times, allowing measurement of photon anti-bunching on single particles in solution for the first time. We observed variations of (34 \u00b1 16)% in the fluorescence lifetimes and (23 \u00b1 18)% in the absorption cross-sections within an aqueous quantum dot sample, confirming that these variations are real, not artifacts of the immobilization methods previously used to study them. Additionally, we studied quantum dot fluorescence intermittency and its dependence on 2-mercaptoethanol, finding evidence that the chemical suppresses blinking on short time-scales (<1s) by reducing the lifetime of the dark state.
\r\n\r\nFinally, we studied the translational and intramolecular Brownian motion of \u03bb-phage DNA molecules. Our apparatus decouples these motions almost completely, and yielded a translational diffusion coefficient estimate D=(0.71 \u00b1 0.05)\u03bcm\u00b2/s lying between previous measurements for this molecule under identical solution conditions but with less precise techniques. Our measurements show clear evidence of intramolecular motion of the polymer chain in the form of statistical correlations on time-scales up to 1s, but we have not yet been able to determine the influence of solvent interactions on these dynamics.
\r\n", "doi": "10.7907/6YYA-9T10", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:390", "collection": "thesis", "collection_id": "390", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01282008-150852", "primary_object_url": { "basename": "LinHan.pdf", "content": "final", "filesize": 15479140, "license": "other", "mime_type": "application/pdf", "url": "/390/1/LinHan.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "In vitro DNA Mechanics in Gene Regulation: One Molecule at a Time", "author": [ { "family_name": "Han", "given_name": "Lin", "clpid": "Han-Lin" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967", "clpid": "Elowitz-M-B" }, { "family_name": "Guo", "given_name": "Chin-Lin", "clpid": "Guo-Chin-Lin" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The biological significance of DNA is primarily attributed to its sequence information. On the other hand, the mechanical properties of DNA can play a critical role in a wide variety of biological processes. One prime example is DNA looping in the context of transcriptional regulation. The emergence of single molecule tracking techniques in the last two decades presents an unprecedented opportunity for studying looping kinetics. One such powerful technique, tethered particle motion (TPM), harnesses the Brownian motion of a microsphere as a means of reporting on the excursion of its tethered molecule, such as DNA. The present work focuses on a looping system found in Escherichia coli, which is mediated by the Lac repressor (LacI) protein. TPM is used to measure individual, real-time looping/unlooping events in DNA of various length and sequence characteristics. By monitoring the magnitude, frequency, and time interval of these features while tuning different parameters, such as LacI concentration, DNA length and DNA sequence, one can survey a host of important information about looping kinetics. A measurement of the LacI concentration dependence of looping probability was found to be in quantitative agreement with a simple thermodynamic model, which also led to the measurement of free energy of LacI-mediated looping, the first such measurement in a single molecule, in vitro setting. A quantitative characterization of free energy was obtained under conditions of different inter-operator spacing, systematically varied from 300 to 310 base pairs in one-base-pair increments. An important conclusion from this study is that free energy is modulated by DNA\u2019s helical structure, yet the energy difference between the aligned and unaligned operator configurations is small compared to expectation from simple polymer physics. TPM measurements also revealed an additional looped state, lending support to the hypothesis that two distinct conformations of LacI, the closed and open forms, can coexist. This study also confirmed that the presence of certain DNA sequences, particularly TA pairs in the minor groove of the nucleosomal positioning sequence, makes DNA substantially softer than a corresponding random sequence. This provides direct support for the notion of sequence-dependent DNA elasticity. Finally, a surprising result is that loops as short as 100 base pairs-only two-thirds the persistence length of DNA-can form by LacI-DNA binding. Classical elasticity theory almost forbids this, suggesting that LacI itself plays a more direct role in the bending process, or classical understanding of DNA elasticity breaks down at length scales comparable to its persistence length.", "doi": "10.7907/7573-A922", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:5244", "collection": "thesis", "collection_id": "5244", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08022007-141737", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 4139235, "license": "other", "mime_type": "application/pdf", "url": "/5244/1/Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Quantitative Insights into Developmental Signals and Phenotypes in C. elegans", "author": [ { "family_name": "Giurumescu", "given_name": "Claudiu Adrian", "clpid": "Giurumescu-Claudiu-Adrian" } ], "thesis_advisor": [ { "family_name": "Asthagiri", "given_name": "Anand R.", "clpid": "Asthagiri-A-R" } ], "thesis_committee": [ { "family_name": "Asthagiri", "given_name": "Anand R.", "clpid": "Asthagiri-A-R" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Sternberg", "given_name": "Paul W.", "clpid": "Sternberg-P-W" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Design of biomaterials and cellular scaffolds for tissue-engineering applications and regenerative medicine requires a precise understanding of the principles underlying multicellular patterning. Adhesion, migration, division, differentiation, and apoptosis are characteristic cellular behaviors, the engineering of which has the potential to allow creation of custom, multicellular structures. These cellular events occur naturally during embryonic and postembryonic development of multicellular organisms. Development thus offers the opportunity to learn about the design principles and molecular mechanisms that guide cellular patterning.
\r\n\r\nA key finding in developmental biology is that a limited set of conserved molecular signaling pathways act at multiple times and locations throughout the embryo to introduce cell-fate asymmetries in homogenous populations of cells. In turn, these asymmetries serve as starting points for the patterning of new organs. These signaling pathways interact quantitatively at multiple levels, including signaling cues, post-translational regulation, and gene-regulatory networks, to guide multicellular patterning.
\r\n\r\nHow does the quantitative performance of these signaling networks ensure the intended phenotype pattern? How do changes in the quantitative performance of these networks, possibly over the course of evolution, give rise to new phenotypes? These are the central questions pursued in this thesis.
\r\n\r\nIn order to answer such questions, we used vulva formation in the nematode Caenorhabditis elegans as a model system of cellular patterning. We formulated a mathematical model of the molecular network underlying cellular-fate specification in this system. Computational analysis of this molecular network reveals that cell\u2013cell coupling through lateral LIN-12/Notch signaling amplifies the perception of the gradient in the epidermal-growth-factor-like soluble cue, LIN-3. Thus, the gradient in LIN-3 concentration produces an even steeper difference in LIN-3-mediated intracellular signals between adjoining cells. Such gradient amplification may be particularly important in converting a shallow, graded-specification signal into a spatial pattern of distinct fate choices.
\r\n\r\nThrough quantitative perturbations of interaction strengths between components of the vulval patterning network, we further show that our modeling approach can correctly predict phenotype patterns observed in C. elegans mutation studies. This study generated a framework for quantitative analysis of molecular networks that links quantitative molecular perturbations to patterning outcomes. This framework will prove useful in the analysis of other systems involving cellular fate decisions and in tissue engineering applications where the generation of precise cell patterns is needed. We demonstrate the generality of our approach through an application to evolutionary developmental biology. Since molecular connectivity of the vulva patterning network of several closely related Caenorhabditis species is preserved, we correctly predict the quantitative diversification that must have occurred in this network during species evolution.
", "doi": "10.7907/FVD0-R331", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:4377", "collection": "thesis", "collection_id": "4377", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11022007-232906", "primary_object_url": { "basename": "complete_thesis.pdf", "content": "final", "filesize": 1946299, "license": "other", "mime_type": "application/pdf", "url": "/4377/15/complete_thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Interplay Between Long-Range And Short-Range Interactions In Polymer Self-Assembly And Cell Adhesion", "author": [ { "family_name": "Zhang", "given_name": "Cheng-Zhong", "orcid": "0000-0001-8825-7158", "clpid": "Zhang-Cheng-Zhong" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Asthagiri", "given_name": "Anand R.", "orcid": "0000-0002-4925-7523", "clpid": "Asthagiri-A-R" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Interplay between long-range and short-range interactions is a common theme in soft and biological matter, which results in complicated self-assembly behaviors. We study two examples of this interplay: reversible gelation of associating polymers and ligand-receptor interactions in membrane adhesion. In associating polymer solutions, the competition between the conformation flexibility of polymer chains and the enthalpic monomer interactions results in phase-separated micro-structures at the mesoscopic scale; both gelation and the microphase order-disorder transition are manifestations of this self-assembly. We further establish that reversible gelation is similar to the glass transition: both are characterized by ergodicity breaking, aperiodic micro-structures, and non-equilibrium relaxations over a finite temperature range. In the study of ligand-receptor interactions between surfaces, we emphasize the interplay between specific ligand-receptor binding, and generic physical interactions. We find that both the finite spatial extension of receptors and their mobilities affect their binding affinity. As a special case of the interplay between receptor binding and generic interactions, we study the dynamics of membrane adhesion that is mediated by receptor binding but fulfilled through membrane deformations. We calculate the energy barrier of the adhesion as a result of membrane bending deformations and the double-well adhesion potential, and analyze the different scenarios according to the shape of the adhesion potential by scaling arguments.\r\n", "doi": "10.7907/GCH8-4A59", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2265", "collection": "thesis", "collection_id": "2265", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292008-200411", "primary_object_url": { "basename": "CordovaFigueroa_CaltechThesis2008.pdf", "content": "final", "filesize": 10222556, "license": "other", "mime_type": "application/pdf", "url": "/2265/1/CordovaFigueroa_CaltechThesis2008.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Directed Motion of Colloidal Particles via Chemical Reactions: Osmotic Propulsion", "author": [ { "family_name": "Cordova-Figueroa", "given_name": "Ubaldo M.", "orcid": "0000-0003-4891-5325", "clpid": "Cordova-Figueroa-Ubaldo-M" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Recent experiments showing reaction-driven propulsion at nanoscales have appeared as a possible mechanism for the transport of particles that may help us to not only understand chemo-mechanical transduction in biological systems, but also to create novel artificial motors that mimic living organisms and which can be harnessed to perform desired tasks. Reaction-driven propulsion consists of the generation of a localized potential gradient by an on-board surface chemical reaction. In this study, we propose and investigate a model for self-propulsion of a colloidal particle --- the osmotic motor --- immersed in a dispersion of ``bath\" particles. The non-equilibrium concentration of bath particles induced by a surface chemical reaction creates an osmotic pressure imbalance on the motor causing it to move. The departure of the bath particle concentration distribution from equilibrium is governed by the Damkohler number Da --- the ratio of the speed of reaction to that of diffusion --- which is employed to calculate the driving force on the motor, and from which the self-induced osmotic velocity is determined via application of Stokes drag law. To illustrate the significant physics in osmotic propulsion, a first-order surface reaction on a portion of the motor's surface is assumed, for the most part, in this work. The implications of these features for different bath particle concentrations and motor sizes are discussed. Furthermore, we investigate the role played by the distribution of reactions on the motor's surface. Different responses are expected depending on the amount of reactive surface in the limiting behaviors of the reaction speed. Lastly, we consider a motor with constant production of particles on a hemisphere as a model that resembles actin-based motility of biological cells and organelles.
\r\n\r\nThis research demonstrates that such an osmotic motor is possible and addresses such questions as: How fast can the motor move? How large of a force can it generate? What is the efficiency of such an osmotic motor? All motor behaviors discussed in this work are shown, after appropriate scaling, to be in good agreement with Brownian dynamics simulations.
\r\n", "doi": "10.7907/W8X1-FQ17", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:1037", "collection": "thesis", "collection_id": "1037", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03202008-163647", "primary_object_url": { "basename": "TOC.pdf", "content": "final", "filesize": 58738, "license": "other", "mime_type": "application/pdf", "url": "/1037/5/TOC.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Proteins of Novel Composition: Synthesis, Evolution, Dynamics", "author": [ { "family_name": "Yoo", "given_name": "Tae Hyeon", "orcid": "0000-0003-1448-3165", "clpid": "Yoo-Tae-Hyeon" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Recent efforts from several laboratories have expanded the repertoire of noncanonical amino acids that can be incorporated into recombinant proteins, either by amino acid replacement or by nonsense or frameshift suppression. The recruitment of new amino acid constituents endows the protein engineering field with powerful tools, and raises the prospects for creating novel proteins. In particular, global replacement of one of the canonical amino acids by a non-canonical analog would be expected to cause marked changes in protein structure, dynamics, and function.
\r\n\r\nRegardless of many possible advantages such as enhanced stability or reactivity, it seems likely that global replacement will in many cases compromise protein folding and function, since both protein structure and protein folding pathways have evolved in a context defined by the canonical amino acid side chains. In order to address the problem, we examined the laboratory re-evolution of the green fluorescent protein (GFP) following global replacement of its Leu residues by 5,5,5-trifluoroleucine (Tfl). The reduced fluorescence of bacterial cells expressing fluorinated GFP was recovered through eleven rounds of random mutagenesis of the GFP gene and screening via fluorescence-activated cell sorting. The mutant protein in fluorinated form showed improved photophysical properties, resistance to acid denaturation, and folding efficiency both in vivo and in vitro.
\r\n\r\nIn order to expand our understanding the roles of fluorinated constituents in protein environments, we studied the hydration dynamics at fluorinated protein surfaces by installing Tfl at surface-exposed positions of several coiled-coil proteins and monitoring the fluorescence Stokes shift of Trp with femtosecond resolution. Installing a Tfl residue near the Trp probe retarded the hydration dynamics. These results show that the strong but static dipole moment of the C-F bond interacts with water molecules in a quite different way from the C-H bond, and is instead more similar to polar (or charged) molecules.
\r\n\r\nThe ability of engineering aminoacyl-tRNA synthetases is critical in successful incorporation of analogues into proteins. We have developed a high-throughput method of screening methionyl-tRNA synthetase (MetRS) libraries for global incorporation of noncanonical amino acids. A variant of GFP was engineered to permit incorporation of analogues into its Met sites with minimal loss of fluorescence. Using this variant as a translational reporter, we screened a library of E coli MetRS variants for activity toward 6,6,6-trifluoronorleucine, and identified a MetRS mutant that enabled high-yield expression of recombinant proteins with quantitative replacement of Met with Tfn.
\r\n\r\nThe work explored in this thesis addresses three aspects of protein engineering using noncanonical amino acids: evolution of proteins with novel compositions, effects of unnatural chemical constituents on the protein hydration dynamics, and engineering aaRS for incorporation of new analogues. Even though the results shown here are restricted to fluorinated amino acids, we believe that these approaches can be applied to any noncanonical amino acid. These methodologies and the expanded understanding of noncanonical amino acids in protein environments will accelerate the creation of novel proteins with many copies of abiological constituents.
", "doi": "10.7907/MKAG-YJ31", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:1037", "collection": "thesis", "collection_id": "1037", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03202008-163647", "primary_object_url": { "basename": "TOC.pdf", "content": "final", "filesize": 58738, "license": "other", "mime_type": "application/pdf", "url": "/1037/5/TOC.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Proteins of Novel Composition: Synthesis, Evolution, Dynamics", "author": [ { "family_name": "Yoo", "given_name": "Tae Hyeon", "orcid": "0000-0003-1448-3165", "clpid": "Yoo-Tae-Hyeon" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Recent efforts from several laboratories have expanded the repertoire of noncanonical amino acids that can be incorporated into recombinant proteins, either by amino acid replacement or by nonsense or frameshift suppression. The recruitment of new amino acid constituents endows the protein engineering field with powerful tools, and raises the prospects for creating novel proteins. In particular, global replacement of one of the canonical amino acids by a non-canonical analog would be expected to cause marked changes in protein structure, dynamics, and function.
\r\n\r\nRegardless of many possible advantages such as enhanced stability or reactivity, it seems likely that global replacement will in many cases compromise protein folding and function, since both protein structure and protein folding pathways have evolved in a context defined by the canonical amino acid side chains. In order to address the problem, we examined the laboratory re-evolution of the green fluorescent protein (GFP) following global replacement of its Leu residues by 5,5,5-trifluoroleucine (Tfl). The reduced fluorescence of bacterial cells expressing fluorinated GFP was recovered through eleven rounds of random mutagenesis of the GFP gene and screening via fluorescence-activated cell sorting. The mutant protein in fluorinated form showed improved photophysical properties, resistance to acid denaturation, and folding efficiency both in vivo and in vitro.
\r\n\r\nIn order to expand our understanding the roles of fluorinated constituents in protein environments, we studied the hydration dynamics at fluorinated protein surfaces by installing Tfl at surface-exposed positions of several coiled-coil proteins and monitoring the fluorescence Stokes shift of Trp with femtosecond resolution. Installing a Tfl residue near the Trp probe retarded the hydration dynamics. These results show that the strong but static dipole moment of the C-F bond interacts with water molecules in a quite different way from the C-H bond, and is instead more similar to polar (or charged) molecules.
\r\n\r\nThe ability of engineering aminoacyl-tRNA synthetases is critical in successful incorporation of analogues into proteins. We have developed a high-throughput method of screening methionyl-tRNA synthetase (MetRS) libraries for global incorporation of noncanonical amino acids. A variant of GFP was engineered to permit incorporation of analogues into its Met sites with minimal loss of fluorescence. Using this variant as a translational reporter, we screened a library of E coli MetRS variants for activity toward 6,6,6-trifluoronorleucine, and identified a MetRS mutant that enabled high-yield expression of recombinant proteins with quantitative replacement of Met with Tfn.
\r\n\r\nThe work explored in this thesis addresses three aspects of protein engineering using noncanonical amino acids: evolution of proteins with novel compositions, effects of unnatural chemical constituents on the protein hydration dynamics, and engineering aaRS for incorporation of new analogues. Even though the results shown here are restricted to fluorinated amino acids, we believe that these approaches can be applied to any noncanonical amino acid. These methodologies and the expanded understanding of noncanonical amino acids in protein environments will accelerate the creation of novel proteins with many copies of abiological constituents.
", "doi": "10.7907/MKAG-YJ31", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2032", "collection": "thesis", "collection_id": "2032", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05242007-211446", "primary_object_url": { "basename": "thesis_electronic.pdf", "content": "final", "filesize": 2659724, "license": "other", "mime_type": "application/pdf", "url": "/2032/1/thesis_electronic.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Analysis of Interacting Nucleic Acids in Dilute Solutions", "author": [ { "family_name": "Bois", "given_name": "Justin S.", "orcid": "0000-0001-7137-8746", "clpid": "Bois-Justin-S" } ], "thesis_advisor": [ { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Smolke", "given_name": "Christina D.", "clpid": "Smolke-C-D" }, { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" }, { "family_name": "Pierce", "given_name": "Niles A.", "clpid": "Pierce-N-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Motivated by the growing demand for analysis tools for diverse natural and engineered DNA and RNA systems, we develop a general theory and set of computational algorithms to perform thermodynamic analysis of dilute reactive solutions and then apply these techniques to interacting nucleic acids. The theory correctly accounts for the effects of indistinguishability in partition function calculations for complexes of interacting strands. With partition functions in hand, the unique complex concentrations corresponding to thermodynamic equilibrium are obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base-pairing observables corresponding to experimentally measurable properties. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality.
\r\n\r\nTo make these analysis tools available to researchers worldwide, we present NUPACK, a web-based software suite for thermodynamic analysis of nucleic acids. Its efficacy is demonstrated in example calculations and the results are shown to be in agreement with experiment.
\r\n\r\nFinally, the thermodynamic properties of a DNA-based triggered self-assembly device [1] are analyzed using NUPACK and extensions of its tools. The computational results complement experimental studies, exposing novel properties about the system and dictating further research.
", "doi": "10.7907/2JCJ-SX75", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1554", "collection": "thesis", "collection_id": "1554", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04302007-164103", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 3123632, "license": "other", "mime_type": "application/pdf", "url": "/1554/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The Self-Replication and Evolution of DNA Crystals", "author": [ { "family_name": "Schulman", "given_name": "Rebecca Beth", "orcid": "0000-0003-4555-3162", "clpid": "Schulman-Rebecca-Beth" } ], "thesis_advisor": [ { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" } ], "thesis_committee": [ { "family_name": "Abu-Mostafa", "given_name": "Yaser S.", "clpid": "Abu-Mostafa-Y-S" }, { "family_name": "Yurke", "given_name": "Bernard", "clpid": "Yurke-B" }, { "family_name": "Winfree", "given_name": "Erik", "clpid": "Winfree-E" }, { "family_name": "Joyce", "given_name": "Gerald", "clpid": "Joyce-G" }, { "family_name": "Bruck", "given_name": "Jehoshua", "clpid": "Bruck-J" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "How life began is still a mystery. While various theories suggest that life began in deep sea volcanic vents or that a world where life consisted predominantly of RNA molecules preceded us, there is no hard evidence to give shape to the chain of events that led to cellular life.
\r\n\r\nPerhaps the fundamental enigma of our origins is how life began to self-replicate in such a way that evolution could produce Earth's \"endless forms most beautiful.\" With the exception of biological organisms, we have no examples of self-replicating, evolving chemical systems, despite an extensive research program with the goal of identifying them.
\r\n\r\nIn this thesis, I construct a chemical system that is capable of the most basic self-replication and evolution. The system uses no enzymes or biological sequences, can support and replicate a combinatorial genome, and is completely autonomous. There are no fundamental obstacles to the replication by this system of much more complex sequences or to open-ended evolution.
\r\n\r\nThe design of the system is inspired by the work of Graham Cairns-Smith, who has proposed that life began with clay. Clays are tiny layered crystals; some clay crystals can contain one of several different patterns of atoms or molecules in each layer. The choice of patterns for the layers could be viewed as a sort of genome: it would be copied as the clay grew, and if the crystal broke, each new piece would inherit its pattern from the old piece and could replicate it in the same manner. If some patterns of layers could grow and reproduce faster than other patterns, crystals with faster-growing patterns would be selected for.
\r\n\r\nInstead of the atoms or small molecules of which clay consists, I use molecules consisting of 4-6 interwoven, synthetic DNA strands called DNA tiles to construct crystals that replicate and evolve as Cairns-Smith imagined. While the choice of construction material was influenced by ease of use -- in contrast to clay crystals, DNA tile crystals have been previously characterized and are easy to crystallize and image in the laboratory -- the choice was fundamentally made because DNA tile monomers are programmable, allowing us to create novel crystal morphologies rationally.
\r\n\r\nThe crystals I construct, termed \"zig-zag ribbons\", contain a sequence of information (\"a genome\") in each row. Growth of the ribbon adds rows, one at time, each of which contain an arrangement of DNA tiles that encode the same information sequence as the previous row. Altering the set of \"tiles\" used to assemble ribbons allows us to alter the alphabets for and the permitted lengths of sequences that can be copied.
\r\n\r\nI describe how to design tile sets that can replicate genomes with different alphabets and the kind of sequence evolution that is in theory possible with some simple tile sets. Altering the tile set can not only change the kinds of sequences that may be replicated, it can also make growth and splitting more robust. I show how to make changes to the crystals' design to prevent errors during growth and splitting and to reduce the rate of spontaneous generation of new crystals.
\r\n\r\nIt has been previously shown that DNA tile crystallization can be used to perform universal computation; I show that in theory crystals that can compute can undergo open-ended evolution as they try to produce more and more complex programs to take advantage of available growth resources. This mechanism is simple enough to potentially observe in the laboratory in the near future. In experiments, I demonstrate a much more basic kind of replication and evolution, in which zig-zag ribbons maintain a preference for a certain width into a second generation.
\r\n\r\nThis work suggests that the concept of a self-replicating chemistry is closely related to the concept of a chemistry that can store information and compute. It is only by clearly understanding how chemistry can perform these latter tasks that we can hope to understand how self-replication and evolution can occur, and by implication, understand how life might have begun.
", "doi": "10.7907/3F8C-9D50", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1681", "collection": "thesis", "collection_id": "1681", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05082007-152644", "primary_object_url": { "basename": "LFB_thesis_final_04may2007.pdf", "content": "final", "filesize": 3010267, "license": "other", "mime_type": "application/pdf", "url": "/1681/1/LFB_thesis_final_04may2007.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Formation of Oriented Precursors in Flow-Induced Polymer Crystallization: Experimental Methods and Model Materials", "author": [ { "family_name": "Fern\u00e1ndez-Ballester", "given_name": "Lucia", "orcid": "0000-0001-6956-5104", "clpid": "Fern\u00e1ndez-Ballester-Ballester-Lucia" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis presents new insights into the early events of formation of oriented precursors in flow-induced crystallization of polymers, specifically isotactic polypropylene. Experimental approaches are developed to follow the creation of thread-like precursors during flow. The use of model bimodal polymers provides insight on the role of long chains in the mechanism of formation of oriented precursors. The addition of very long chains (3500 kg/mol) at low concentration (< 1% wt) dramatically reduced the stress required to trigger formation of thread-like precursors, which opened a wide range of conditions in which to discover how oriented precursors form. The combination of powerful new methods and model materials exposed a kinetic and mechanistic step prior to propagation of oriented precursors that had not been addressed in prior literature. Furthermore, the present model systems provide a bridge to the flow-induced crystallization phenomena that occur in commercial resins, making it very likely that these well-defined polymers will reveal the underlying physics that governs the effects of flow on morphology and final properties of polymers, and providing a rational basis for molecular design of polyolefins to expand the envelope of accessible properties.
\r\n\r\nThe phenomenological effects of flow on polymer crystallization have been known for decades, manifested dramatically in most processing techniques due to the high stresses imposed onto the polymer melt. Processing flows can accelerate the kinetics of crystallization by orders of magnitude, and can induce the formation of highly oriented crystallites that, in turn, impact the final material properties in the solid state. The formation of oriented thread-like precursors is at the heart of these effects of flow on polymer crystallization; however, the fundamental mechanisms underlying their development remain elusive. This lack of understanding frustrates the formulation of a predictive model that relates the polymer molecular characteristics and the imposed processing conditions to the ensuing crystallization kinetics, the final morphology, and hence, the ultimate material properties. Here, we develop experimental approaches that provide insight into the physics of formation of the oriented precursors, which identify the essential elements required in a truly predictive model of flow-induced crystallization.
\r\n\r\nIn this work, we build on experimental capabilities of imposing well-defined flow and thermal histories onto a polymer melt, and of utilizing small quantities of material so that model polymers can be investigated, which allows us to isolate the effect of specific molecular characteristics and flow conditions. Our apparatus provides us with real-time measurements that probe a range of shear stresses throughout a slit flow channel; thus, we develop a \"depth sectioning method\" as a strategy to isolate the contribution to the real-time signal that arises from a specific level of shear stress. This method is of utmost importance since the formation of thread-like precursors depends strongly on stress. To separate the development of oriented precursors during flow from the growth of oriented crystallites on them, we develop an experimental approach, the \"temperature-jump,\" inspired by classical nucleation studies.
\r\n\r\nWe use a small concentration of ultra-high molecular weight isotactic polypropylene in a matrix of shorter chains to examine the role of long chains in the creation of thread-like precursors. The use of such high molecular weight chains has revealed a richer behavior than could be observed in earlier studies, indicating that there are two stages in thread formation, kick-off and propagation, and that the stress requirement for the first step is more stringent than for the second. The data are consistent with the hypothesis that the interaction of long chains with the tip of a shish creates a local orientation that is not found elsewhere in the flowing melt.
\r\n\r\nFinally, we combine the two experimental approaches to perform measurements that capture the development of the threads during flow. For intermediate shearing times, our results are well described by the most promising model currently available, the \"recoverable strain model,\" and lay the groundwork for determining the velocity of propagation of threads at different shearing stresses. Also, it suggests that some modifications to the recoverable strain model should be included to correctly capture kick-off and saturation of the formation of threads. The experimental tools described here can be extended to other model materials, for example, to expose the effects of long chain length > 3500 kg/mol and of the stereo-regularity of the long chains. A larger parameter space can be surveyed in the future to provide additional data to test predictive models that connect molecular characteristics of a resin to structure formation under processing conditions.
", "doi": "10.7907/HMNK-HP78", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:685", "collection": "thesis", "collection_id": "685", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02202007-131552", "primary_object_url": { "basename": "00_Scruggs_Thesis_Full.pdf", "content": "final", "filesize": 10731416, "license": "other", "mime_type": "application/pdf", "url": "/685/1/00_Scruggs_Thesis_Full.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Coupling Polymer Thermodynamics and Viscoelasticity to Liquid Crystalline Order: Self-Assembly and Relaxation Dynamics of Block Copolymers in a Nematic Solvent", "author": [ { "family_name": "Scruggs", "given_name": "Neal Robert", "orcid": "0000-0003-1329-4506", "clpid": "Carty-Neal-Robert-Scruggs" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The discontinuous change in solvent quality of a liquid crystal (LC) solvent, 5CB, at the nematic-isotropic phase transition produces abrupt changes in the phase behavior of solutions of coil and LC-polymers and in the self-assembly of coil-LC block copolymers. Nematic 5CB is strongly selective for a side-group liquid crystal polymer (SGLCP) and isotropic 5CB is a good solvent for both SGLCP and a random coil (polystyrene, PS). In nematic 5CB, unfavorable LC-PS interactions drive phase separation in SGLCP-PS-LC ternary solutions and drive micellization of PS-SGLCP diblocks. In isotropic 5CB, rich phase behavior occurs in both ternary solutions and block copolymer solutions. Despite the fact that isotropic 5CB is a good solvent for both SGLCP and PS, segregation can occur due to the asymmetric solvent effect (i.e., the preference of the solvent for the SGLCP). In concentrated isotropic solutions, unfavorable SGLCP-PS interactions become dominant.
\r\n\r\nIn binary solutions of SGLCP and 5CB, the delicate thermodynamic balance between LC order and polymer entropy manifests itself in a non-monotonic concentration dependence of the solutions' clearing points. The frustration between LC order and polymer entropy in an SGLCP melt is partially relieved by the addition of small molecule LC, greatly increasing the polymer's configurational freedom and stabilizing the nematic phase. In dilute solutions, the polymer adopts an anisotropic conformation because of its coupling to the LC solvent's prevailing director field; the sense and the magnitude of the anisotropy depend on the architecture of the SGLCP (end-on or side-on mesogens).
\r\n\r\nCoil-SGLCP-coil triblock copolymers self-assemble in 5CB to form liquid crystalline gels in which nematic order is coupled to an associative polymer network. The network's dynamic restructuring couples to fluctuations in the LC's local order to provide an additional relaxation process that is not present in SGLCP solutions or LC elastomers, and the importance of this process is highly dependent on the underlying anisotropy of the SGLCP-based network. The network furthermore provides a memory of the LC orientation state: when the LC is reoriented by electric-magnetic fields or mechanical shear, the network structure prevents the orientation from relaxing back to a random distribution when the aligning force is removed.
", "doi": "10.7907/68XG-G726", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2069", "collection": "thesis", "collection_id": "2069", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05252007-103551", "primary_object_url": { "basename": "paul-20070524-7.pdf", "content": "final", "filesize": 3301325, "license": "other", "mime_type": "application/pdf", "url": "/2069/1/paul-20070524-7.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The DNA Ejection Process in Bacteriophage \u03bb", "author": [ { "family_name": "Grayson", "given_name": "Paul Daniel", "clpid": "Grayson-Paul-Daniel" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Politzer", "given_name": "Hugh David", "orcid": "0000-0002-4983-6621", "clpid": "Politzer-H-D" }, { "family_name": "Bertani", "given_name": "Giuseppe", "clpid": "Bertani-G" }, { "family_name": "Kondev", "given_name": "Jane", "clpid": "Kondev-J" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "Bacteriophages have long served as model systems through which the nature of life may be explored. From a physical or mechanical point of view, phages are excellent examples of natural nanotechnology: they are nanometer-scale systems which depend critically on forces, pressures, velocities, and other fundamentally physical quantities for their biological functions. The study of the physical properties of phages has therefore provided an arena for application of physics to biology. In particular, recent studies of the motor responsible for packaging a phage gnome into a capsid showed a buildup of pressure within the capsid of tens of atmospheres. This thesis reports a combined theoretical and experimental study on various aspects of the genome ejection process, so that a comparison may be drawn with the packaging experiments. In particular, we examine various theoretical models of the forces within a phage capsid, deriving formulas both for the force driving genome ejection and for the velocity at which the genome is translocated into a host cell. We describe an experiment in which the force was measured as a function of the amount of genome within the phage capsid, and another where the genome ejection velocity was measured for single phages under the microscope. We make direct quantitative comparisons between the theory and experiments, stringently testing the extent to which we are able to model the genome ejection process.", "doi": "10.7907/A7ED-4044", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:613", "collection": "thesis", "collection_id": "613", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02122007-130627", "primary_object_url": { "basename": "Khair_thesis.pdf", "content": "final", "filesize": 6449685, "license": "other", "mime_type": "application/pdf", "url": "/613/1/Khair_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Particle Motion in Colloidal Dispersions: Applications to Microrheology and Nonequilibrium Depletion Interactions", "author": [ { "family_name": "Khair", "given_name": "Aditya Satish", "orcid": "0000-0001-6076-2910", "clpid": "Khair-Aditya-Satish" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Seinfeld", "given_name": "John H.", "clpid": "Seinfeld-J-H" }, { "family_name": "Squires", "given_name": "Todd M.", "clpid": "Squires-T-M" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Over the past decade, microrheology has burst onto the scene as a technique to interrogate and manipulate complex fluids and biological materials at the micro- and nano-meter scale. At the heart of microrheology is the use of colloidal 'probe' particles embedded in the material of interest; by tracking the motion of a probe one can ascertain rheological properties of the material. In this study, we propose and investigate a paradigmatic model for microrheology: an externally driven probe traveling through an otherwise quiescent colloidal dispersion. From the probe's motion one can infer a 'microviscosity' of the dispersion via application of Stokes drag law. Depending on the amplitude and time-dependence of the probe's movement, the linear or nonlinear (micro-)rheological response of the dispersion may be inferred: from steady, arbitrary-amplitude motion we compute a nonlinear microviscosity, while small-amplitude oscillatory motion yields a frequency-dependent (complex) microviscosity. These two microviscosities are shown, after appropriate scaling, to be in good agreement with their (macro)-rheological counterparts. Furthermore, we investigate the role played by the probe's shape --- sphere, rod, or disc --- in microrheological experiments.
\r\n\r\nLastly, on a related theme, we consider two spherical probes translating in-line with equal velocities through a colloidal dispersion, as a model for depletion interactions out of equilibrium. The probes disturb the tranquility of the dispersion; in retaliation, the dispersion exerts a entropic (depletion) force on each probe, which depends on the velocity of the probes and their separation. When moving 'slowly' we recover the well-known equilibrium depletion attraction between probes. For 'rapid' motion, there is a large accumulation of particles in a thin boundary layer on the upstream side of the leading probe, whereas the trailing probe moves in a tunnel, or wake, of particle-free solvent created by the leading probe. Consequently, the entropic force on the trailing probe vanishes, while the force on the leading probe approaches a limiting value, equal to that for a single translating probe.
", "doi": "10.7907/RWKF-E288", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:5192", "collection": "thesis", "collection_id": "5192", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05212007-164114", "primary_object_url": { "basename": "Alvizo_Thesis_052307.pdf", "content": "final", "filesize": 6107269, "license": "other", "mime_type": "application/pdf", "url": "/5192/1/Alvizo_Thesis_052307.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Computational Protein Design Force Field Optimization: A Negative Design Approach", "author": [ { "family_name": "Alvizo", "given_name": "Oscar", "orcid": "0000-0002-3545-1317", "clpid": "Alvizo-Oscar" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "An accurate force field is essential to computational protein design and protein folding studies. Proper force field tuning is problematic, however, due in part to the incomplete modeling of the unfolded state. The first part of this thesis discusses the optimization of a protein design force field by constraining the amino acid composition of the designed sequences to that of the wild-type protein. According to the random energy model, the unfolded state energies of amino acid sequences with the same composition are identical. Under these constraints, unfolded state energies are inconsequential and any discrepancies between computational predictions and experimental results can be directly attributed to flaws in the force field\u2019s ability to properly account for folded state sequence energies. This aspect of fixed composition design allows for force field optimization by focusing solely on the interactions in the folded state. In addition, the fixed composition requirement imposes a large negative design constraint that is used to ensure fold specificity. Several rounds of fixed composition optimization of the beta-1 domain of protein G yielded force field parameters with significantly greater predictive power: optimized sequences exhibited higher wild-type sequence identity in critical regions of the structure and the wild-type sequence showed an improved Z score. Experimental studies revealed a 24-fold mutant to be stably folded with a melting temperature comparable to that of the wild-type protein.
\r\n\r\nThe second part of the thesis discusses the optimization of HIV protease substrate specificity using a combination of positive and negative design. HIV protease is a homodimeric protein with a symmetrical binding region that recognizes and cleaves asymmetrical substrates that exhibit little sequence homology. The designs attempt to increase specificity towards one of HIV protease\u2019s wild-type targets by optimizing hydrogen bonds and electrostatic interactions using a positive design approach. Explicit negative design is incorporated by modeling predicted mutations on multiple substrates. A scoring function that selects for mutations that pack favorably with the target substrate but result in large steric clashes in alternate substrates is used. A three point mutant was designed and experimentally shown to have increased specificity towards the target substrate.
", "doi": "10.7907/NYVY-7Z76", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2069", "collection": "thesis", "collection_id": "2069", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05252007-103551", "primary_object_url": { "basename": "paul-20070524-7.pdf", "content": "final", "filesize": 3301325, "license": "other", "mime_type": "application/pdf", "url": "/2069/1/paul-20070524-7.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The DNA Ejection Process in Bacteriophage \u03bb", "author": [ { "family_name": "Grayson", "given_name": "Paul Daniel", "clpid": "Grayson-Paul-Daniel" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Politzer", "given_name": "Hugh David", "orcid": "0000-0002-4983-6621", "clpid": "Politzer-H-D" }, { "family_name": "Bertani", "given_name": "Giuseppe", "clpid": "Bertani-G" }, { "family_name": "Kondev", "given_name": "Jane", "clpid": "Kondev-J" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "Bacteriophages have long served as model systems through which the nature of life may be explored. From a physical or mechanical point of view, phages are excellent examples of natural nanotechnology: they are nanometer-scale systems which depend critically on forces, pressures, velocities, and other fundamentally physical quantities for their biological functions. The study of the physical properties of phages has therefore provided an arena for application of physics to biology. In particular, recent studies of the motor responsible for packaging a phage gnome into a capsid showed a buildup of pressure within the capsid of tens of atmospheres. This thesis reports a combined theoretical and experimental study on various aspects of the genome ejection process, so that a comparison may be drawn with the packaging experiments. In particular, we examine various theoretical models of the forces within a phage capsid, deriving formulas both for the force driving genome ejection and for the velocity at which the genome is translocated into a host cell. We describe an experiment in which the force was measured as a function of the amount of genome within the phage capsid, and another where the genome ejection velocity was measured for single phages under the microscope. We make direct quantitative comparisons between the theory and experiments, stringently testing the extent to which we are able to model the genome ejection process.", "doi": "10.7907/A7ED-4044", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:558", "collection": "thesis", "collection_id": "558", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02082007-153627", "primary_object_url": { "basename": "Verduzcothesis.pdf", "content": "final", "filesize": 7365378, "license": "other", "mime_type": "application/pdf", "url": "/558/13/Verduzcothesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Self-Assembled Liquid Crystal Polymer Gels", "author": [ { "family_name": "Verduzco", "given_name": "Rafael", "orcid": "0000-0002-3649-3455", "clpid": "Verduzco-Rafael" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The combination of liquid crystals (LCs) with polymer networks results in fascinating materials in which the elasticity of the polymer network is coupled to LC order, and they hold promise for a variety of applications which depend on an optical or a mechanical response to external stimuli. Unfortunately, the methods for preparing LC networks are limited. In this work, we present two types of LC gels with novel network architectures: a physical gel made by polymer self-assembly in an LC solvent and a chemical gel made by crosslinking telechelic side-group liquid crystalline polymers (SGLCPs). The physical gel thermoreversibly transitions to a liquid on heating, and it can be uniformly aligned using electric, magnetic, or flow fields. The gel exhibits a fast electro-optical response, making it potentially viable for display applications. The physical gel also reveals novel equilibrium and dynamic properties that arise due the coupling between LC order and the polymer network. When confined between cell substrates prohibiting macroscopic shape change, it exhibits a temperature-sensitive striped texture transition. We provide a theoretical model that captures the striped texture by accounting for the compromise between nematic rubber elasticity and LC elasticity. Dynamic light scattering studies reveal two distinct director relaxation modes, in contrast to covalent gels, which show a single relaxation mode. We argue that the slower dynamics arise from the coupling between the director and the physically associated network which restructures on long time scales. We also investigate the self-assembled micellar structure of the gel via neutron scattering and rheometry studies, and these studies reveal that the gels' structure changes dramatically across the nematic-to-isotropic phase transition. Finally, we investigate model LC networks made by crosslinking telechelic SGLCPs using \"click\" chemistry. These chemical networks can be swollen in a small-molecule LC, and they exhibit a low-threshold electro-optic response and a temperature dependent size. These novel physical and chemical LC gels provide insight into the role of network structure in determining the material properties of liquid crystalline elastomers and gels.\r\n", "doi": "10.7907/VAAF-0809", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1165", "collection": "thesis", "collection_id": "1165", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03272006-142956", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 36843578, "license": "other", "mime_type": "application/pdf", "url": "/1165/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Dissipative Nanomechanics", "author": [ { "family_name": "Inamdar", "given_name": "Mandar Mukund", "orcid": "0000-0001-8549-8490", "clpid": "Inamdar-Mandar-Mukund" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "orcid": "0000-0003-2908-5469", "clpid": "Bhattacharya-K" }, { "family_name": "Dill", "given_name": "Ken A.", "clpid": "Dill-K-A" }, { "family_name": "Gelbart", "given_name": "William", "clpid": "Gelbart-W" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Due to thermal fluctuations, systems at small length scales are remarkably different than their large length scale counterparts. For example, bacterial viruses (phages) have thousands of nanometers of DNA packed inside a hollow capsid of tens of nanometers. This tight compaction leads to large forces on the phage DNA (tens of piconewtons). These forces can be subsequently utilized to instigate the DNA ejection during the infection phase. Developments in optics, biochemistry, microfluidics, etc., have enabled the experimental quantification of these forces, and the rate of DNA packing and ejection. Similarly, eukaryotic genome is compacted into nanometer size structures called nucleosomes. The conformational changes in the nucleosome due to the thermal fluctuations of the DNA are instrumental in making the DNA accessible for key genomic processes. Developments in FRET, gel electrophoresis, spectroscopy etc. have made it possible to quantify the equilibrium constant and the rates of these fluctuations. The first part of the thesis involves formulation of simple models for the phage and nucleosome to respond to the existing experimental data and predict results to stimulate further experimentation.
\r\n\r\nOne of the next frontiers in biology is to understand the \"small numbers\" problem: how does a biological cell function given that most of its proteins and nucleotide polymers are present in numbers much smaller than Avogadro's number? For example, one of the most important molecules, a cell's DNA, occurs in only a single copy. Also, it is the flow of matter and energy through cells that makes it possible for organisms to maintain a relatively stable form. Hence, cells must be in this stable state far from equilibrium to function. Many problems of current interest thus involve small systems that are out of equilibrium. Unfortunately, there is no general theoretical frame-work to model these dissipative systems. E. T. Jaynes suggested the use of dynamical microtrajectories to write down the trajectory entropy, or caliber, for such systems. Maximization of this trajectory entropy, subject to the external constraints, provides one with the probabilities of the underlying microtrajectories. Jaynes calls this the \"principle of maximum caliber.\" Advances in optics, video-microscopy, etc. have made it possible to experimentally measure these microtrajectories for various systems. In the second part of the thesis we develop simple microtrajectory models for small systems like molecular motors, ion-channels, etc., and apply the maximum caliber principle to obtain the probabilities of the underlying microtrajectories. Our goal is to respond to these experiments and make new predictions.
", "doi": "10.7907/P5K9-BD68", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:1756", "collection": "thesis", "collection_id": "1756", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05122006-102528", "primary_object_url": { "basename": "Santiago_Solares_PhD_Dissertation_2006.pdf", "content": "final", "filesize": 10261219, "license": "other", "mime_type": "application/pdf", "url": "/1756/1/Santiago_Solares_PhD_Dissertation_2006.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Multi-Scale Simulations of Single-Walled Carbon Nanotube Atomic Force Microscopy and Density Functional Theory Characterization of Functionalized and Non-Functionalized Silicon Surfaces", "author": [ { "family_name": "Solares", "given_name": "Santiago de Jesus", "orcid": "0000-0003-0895-8160", "clpid": "Solares-Santiago-de-Jesus" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Collier", "given_name": "C. Patrick", "clpid": "Collier-C-P" }, { "family_name": "Giapis", "given_name": "Konstantinos P.", "clpid": "Giapis-K-P" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation focuses on two theoretical research topics: Multiscale Simulations of Single-Walled Carbon Nanotube Atomic Force Microscopy (AFM, chapters 1 through 3) and Density Functional Theory Characterization of Functionalized and non-functionalized Silicon Surfaces (chapters 4 through 8). The first topic presents the development of an AFM simulation methodology, based on first principles, which incorporates the atomistic details of probe, sample, and impurities in the construction of the images. It also includes studies of the influence of common artifacts (such as elastic deformations and imaging multistability) and probe structure (tilt angle and number of walls in the carbon nanotube probe) on image quality. The second topic concerns the structure and energetics of reconstructed and unreconstructed silicon (111) surfaces (either functionalized with groups such as methoxy and methyl or without functionalization) and non-functionalized copper-silicon surfaces and crystals. These studies lead to novel findings such as the formation of a full stacking fault on the methylated Si(111) surface in the presence of large etch pits and the quantification of the surface energy path of the Si(111) 1x1 \u2192 DAS 7x7 reconstruction. Most of this work was done in collaboration with experimental groups and is in agreement with the most current experimental results.", "doi": "10.7907/XZR1-C472", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2111", "collection": "thesis", "collection_id": "2111", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262006-133416", "primary_object_url": { "basename": "APOThesis.pdf", "content": "final", "filesize": 3586495, "license": "other", "mime_type": "application/pdf", "url": "/2111/1/APOThesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Scanning Activity Gravimetric Analysis (SAGA) of Aqueous Polyethylene Oxide", "author": [ { "family_name": "Olsen", "given_name": "Adam Paul", "clpid": "Olsen-Adam-Paul" } ], "thesis_advisor": [ { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Seinfeld", "given_name": "John H.", "clpid": "Seinfeld-J-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis introduces a new technique\u2014scanning activity gravimetric analysis (SAGA)\u2014for investigating phase transitions in semicrystalline polymers. Isothermal growth and dissolution of polymer crystallites within picogram to milligram samples are manifested by mass changes in response to changes in the activity of sorbed solvent vapor. Single charged particles are levitated and weighed in an electrostatic field, providing access to highly supersaturated states. Phase transitions are inferred from simultaneous equilibrium sorption and light scattering measurements. Analogous to differential scanning calorimetry, scanning solvent activity up and down exposes broad transitions between the semicrystalline solid state and the dissolved state, which are influenced by sample history. We demonstrate dissolution and crystallization of nanogram samples of polyethylene oxide by controlling the activity of sorbed water vapor and observe self-nucleation of crystallites from partially states and fully dissolved states.
\r\n\r\nMemory effects in semicrystalline polymers have been documented for a variety of systems in which the rate of crystallization depends on the temperature and duration of a prior melting step. We report analogous observations of memory effects in aqueous solution droplets of polyethylene oxide. Remnants of the crystalline phase\u2014clusters of chain folded molecules\u2014that are too small to be detected by gravimetric or optical means persist for long times in solution after macroscopic crystals have been dissolved, and they then serve as athermal nuclei when the concentration of the polymer solution droplet is increased. These remnants evolve under certain conditions toward increasing or decreasing thickness, as indicated by a shift in the conditions at which they effectively catalyze crystal growth. Although memory effects in semicrystalline polymers have usually been attributed exclusively to sluggish kinetics of melting or dissolution, thermodynamic considerations may also play an important role. A simple model describing the free energy of a lamellar crystal based on insights of Janeschitz-Kriegl captures the metastability of lamellar remnants and their evolution in thickness. The qualitative successes of the model lend support to the thermodynamic rationalization of memory effects in semicrystalline polymers.
", "doi": "10.7907/5X91-2F81", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:1165", "collection": "thesis", "collection_id": "1165", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03272006-142956", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 36843578, "license": "other", "mime_type": "application/pdf", "url": "/1165/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Dissipative Nanomechanics", "author": [ { "family_name": "Inamdar", "given_name": "Mandar Mukund", "orcid": "0000-0001-8549-8490", "clpid": "Inamdar-Mandar-Mukund" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "orcid": "0000-0003-2908-5469", "clpid": "Bhattacharya-K" }, { "family_name": "Dill", "given_name": "Ken A.", "clpid": "Dill-K-A" }, { "family_name": "Gelbart", "given_name": "William", "clpid": "Gelbart-W" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Due to thermal fluctuations, systems at small length scales are remarkably different than their large length scale counterparts. For example, bacterial viruses (phages) have thousands of nanometers of DNA packed inside a hollow capsid of tens of nanometers. This tight compaction leads to large forces on the phage DNA (tens of piconewtons). These forces can be subsequently utilized to instigate the DNA ejection during the infection phase. Developments in optics, biochemistry, microfluidics, etc., have enabled the experimental quantification of these forces, and the rate of DNA packing and ejection. Similarly, eukaryotic genome is compacted into nanometer size structures called nucleosomes. The conformational changes in the nucleosome due to the thermal fluctuations of the DNA are instrumental in making the DNA accessible for key genomic processes. Developments in FRET, gel electrophoresis, spectroscopy etc. have made it possible to quantify the equilibrium constant and the rates of these fluctuations. The first part of the thesis involves formulation of simple models for the phage and nucleosome to respond to the existing experimental data and predict results to stimulate further experimentation.
\r\n\r\nOne of the next frontiers in biology is to understand the \"small numbers\" problem: how does a biological cell function given that most of its proteins and nucleotide polymers are present in numbers much smaller than Avogadro's number? For example, one of the most important molecules, a cell's DNA, occurs in only a single copy. Also, it is the flow of matter and energy through cells that makes it possible for organisms to maintain a relatively stable form. Hence, cells must be in this stable state far from equilibrium to function. Many problems of current interest thus involve small systems that are out of equilibrium. Unfortunately, there is no general theoretical frame-work to model these dissipative systems. E. T. Jaynes suggested the use of dynamical microtrajectories to write down the trajectory entropy, or caliber, for such systems. Maximization of this trajectory entropy, subject to the external constraints, provides one with the probabilities of the underlying microtrajectories. Jaynes calls this the \"principle of maximum caliber.\" Advances in optics, video-microscopy, etc. have made it possible to experimentally measure these microtrajectories for various systems. In the second part of the thesis we develop simple microtrajectory models for small systems like molecular motors, ion-channels, etc., and apply the maximum caliber principle to obtain the probabilities of the underlying microtrajectories. Our goal is to respond to these experiments and make new predictions.
", "doi": "10.7907/P5K9-BD68", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2395", "collection": "thesis", "collection_id": "2395", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06022005-192548", "primary_object_url": { "basename": "thesis_final.pdf", "content": "final", "filesize": 774897, "license": "other", "mime_type": "application/pdf", "url": "/2395/1/thesis_final.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Design and Analysis of Combinatorial Protein Libraries Created by Site-Directed Recombination", "author": [ { "family_name": "Endelman", "given_name": "Jeffrey B.", "orcid": "0000-0003-0957-4337", "clpid": "Endelman-Jeffrey-B" } ], "thesis_advisor": [ { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" } ], "thesis_committee": [ { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "For many protein design problems, limited understanding of the relationship between sequence and function necessitates searching through a library of proteins to find the properties of interest. To accelerate this process, molecular models and optimization algorithms can be combined to design diverse libraries enriched in folded proteins. I apply this strategy to site-directed recombination, in which an alignment of p homologs is partitioned into f blocks, and the resulting gene fragments are combinatorially assembled to create a library with p^f chimeric sequences. To design the fragments, I present a dynamic programming algorithm that minimizes the average energy of the library, subject to constraints on fragment length. This algorithm works for any pairwise residue potential, several of which are compared for their ability to predict which chimeras retain the parental function and/or fold. The alignments of folded and unfolded chimeras are used to generate sequence-function relationships via logistic regression, a technique for fitting models to binary data. Compared to methods developed for alignments of naturally occurring proteins, logistic regression more readily distinguishes true interactions from correlations between strongly stabilizing but non-interacting residues.", "doi": "10.7907/GF35-Q269", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2388", "collection": "thesis", "collection_id": "2388", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06022005-131439", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 1519061, "license": "other", "mime_type": "application/pdf", "url": "/2388/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Studies of Suspension Behavior: I. Instabilities of Non-Brownian Suspensions. II. Microrheology of Colloidal Suspensions", "author": [ { "family_name": "Carpen", "given_name": "Ileana Cristina", "clpid": "Carpen-Ileana-Cristina" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Squires", "given_name": "Todd M.", "clpid": "Squires-T-M" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Complex fluids are present in a multitude of forms: polymers, foods, paints, inks, biological materials, pharmaceuticals, cosmetics, etc. Many of these are suspensions, which have a particulate phase suspended in a solvent phase. This multiphase character gives a rich variety of behaviors, making suspensions interesting and useful materials but difficult to process. We investigate two different aspects of suspension behavior: instabilities in suspension flows and the use of microrheology in colloidal suspensions.
\r\n\r\nWe look at two different mechanisms that generate instabilities and pattern formation in suspension flows. In the first, a jump in normal stresses at the interface between two fluids may lead to growing perturbations of the interface that ultimately give rise to migration of the particle phase into enriched regions. Fluids with a negative second normal stress difference, such as suspensions, can be unstable with respect to transverse or spanwise perturbations. The mechanism appears to be generic, although the details will depend on the specific system. The second mechanism may affect suspensions whose particle phase is not density-matched to the fluid. In this case, a flow can be unstable to spanwise perturbations of the particle phase when the shearing motion generates a density profile that increases with height. This is a Rayleigh--Taylor-like instability, due to having heavier material over light. As with the first instability, this mechanism may play an important role in pattern formation in multiphase flows.
\r\n\r\nThe second aspect of suspension behavior we examine is the application of microrheology to colloidal suspensions. Microrheology has great promise for the study of soft, heterogeneous materials, but is not as well understood as traditional rheology. Most methods use tracer particles to investigate a medium, sometimes passively---tracking random motion (well established but restricted to the linear viscoelastic regime)---and more rarely actively---applying an external force to drive the tracers and access the medium's nonlinear response. Active microrheology is not well understood, and we study it by simulating a prototypical example, the motion of a particle due to an imposed force through a colloidal suspension. The deformation of the microstructure results in resistance to the tracer\u2019s motion. This system displays 'force-thinning', analogous to the 'shear-thinning' in a macrorheologically sheared suspension, but the comparison is not exact, and care needs to be taken in the use and application of microrheological results. Comparable length scales between the measurement device (the tracer) and the medium lead to interesting effects and distinctions between types of microrheological methods.
", "doi": "10.7907/857a-gg43", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:1774", "collection": "thesis", "collection_id": "1774", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05132005-114413", "primary_object_url": { "basename": "Title.pdf", "content": "final", "filesize": 107165, "license": "other", "mime_type": "application/pdf", "url": "/1774/7/Title.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Structure, Dynamics, and Properties of Artificial Protein Hydrogels Assembled Through Coiled-Coil Domains", "author": [ { "family_name": "Shen", "given_name": "Wei", "clpid": "Shen-Wei" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The structure-property relationships of an artificial protein hydrogel, which was constructed from a triblock protein (designated AC10A) that contained two associative leucine-zipper endblocks and a water-soluble random coil midblock, were investigated to provide guidelines for the rational design of new generations of artificial protein hydrogels. The leucine zipper A domain is composed of six heptad repeating units designated as abcdefg, where the a and d positions are occupied by hydrophobic residues, and the e and g positions are mainly occupied by glutamic acid residues. In contrast to hydrogels formed from synthetic hydrophobically modified polymers, the normalized plateau storage modulus G/nkT of the AC10A gel was below 13% at all concentrations examined. This indirect evidence that AC10A tends to form a substantial fraction of looped configurations was supported by a fluorescence quenching experiment: significant quenching occurred in labeled d-AC10A-a (d=tryptophan at the N-terminus, a=coumarin at the C terminus) chains mixed with a great excess of unlabelled AC10A chains in a solution. The strong tendency to form loops originates in large part from the compact size of the random coil midblock domain (mean RH, C10~20 A, determined from quasi-elastic light scattering of C10). Despite the small aggregation number of the leucine zipper domains (tetrameric aggregates, determined from multi-angle static light scattering of AC10 diblock), the average center-to-center distance between aggregates in a 7% w/v AC10A solution is roughly 3 times the radius of gyration and 1.5 times the average end-to-end distance of the C10 domain. To avoid the energy penalty for stretching the C10 domain to form bridges, the chains tend to form loops. The importance of loops explains the nonmonotonic effect of pH on modulus and the decrease in modulus with increasing ionic strength. It also led to the design concept of increasing the midblock length or charge density to increase storage modulus.
\r\n \r\nDynamic properties of the AC10A hydrogel show correlation between network relaxation behavior and molecular exchange kinetics of the associative domain. The longest stress relaxation time changes from ca. 70 seconds at pH 8.0 to ca. 1000 seconds at pH 7.0, determined by creep measurements on 7% w/v gels. In a parallel manner, the characteristic time of the leucine zipper strand exchange varies from ca. 200 seconds at pH 8.0 to ca. 4500 seconds at pH 7.0, determined by fluorescence de-quenching after mixing a fluorescein-labeled leucine zipper solution (in which fluorescence was quenched) with a great excess of an unlabeled leucine zipper solution. Both time scales vary strongly with pH due to the associated change in charge on the e and g residues of the leucine zipper.
\r\n\r\nThe observed structure-property relationships suggest that the rapid dissolution that occurs with AC10A hydrogels in open systems originates from the tendency of the protein to form loops, the small aggregation number of the associative domains, and the transient nature of association. For applications in which materials are surrounded by excess fluids, we demonstrated two molecular design approaches to avoid the rapid dissolution. One way to slow dissolution is to suppress loops by engineering a triblock protein with dissimilar associative endblocks, PC10A, such that P associates only with P and A associates only with A. A PC10A gel erodes 500 times more slowly and exhibits a 5-fold increase in modulus compared to an AC10A gel at the same concentration. Alternatively, hydrogel stability in open systems can be improved by engineering a cysteine residue into each leucine zipper domain to allow covalent bond formation following physical association of leucine zippers. Asymmetric placement of the cysteine residue in each leucine zipper domain suppresses locking-in loops and creates linked \"multichains\". The increased valency of the building units stabilizes the hydrogels in open systems, while the physical nature of their association retains the reversibility of gelation. The gel networks dissolve at pH 12.2, where the helicity of the leucine zipper domains is reduced by ca. 90%, and re-form upon acidification.
\r\n\r\nThe ability to form robust artificial protein hydrogels in open systems opens the way to biomedical applications. Therefore, we examined their toxicity and incorporated an RGD cell-binding domain into the midblock backbone. Viability assays for mammalian 3T3 fibroblast cells cultured in the presence of the AC10A protein revealed no evidence of toxicity. Anchorage-dependent epithelial cells spread well on hydrogel films bearing an RGD cell-binding domain. In contrast, cells remained round on films without the cell-binding domain; significant apoptosis was induced. Encapsulated 3T3 fibroblast cells remained viable inside the hydrogel for at least 12 hours, suggesting that these materials have proper permeability for transferring oxygen, nutrients, and metabolic waste. The hydrogel containing the RGD domain was micropatterned on a PEG-modified glass surface and limited cell adhesion to the hydrogel region.
\r\n", "doi": "10.7907/NXST-MZ65", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2094", "collection": "thesis", "collection_id": "2094", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262005-134552", "primary_object_url": { "basename": "thesis_pdf.pdf", "content": "final", "filesize": 12280333, "license": "other", "mime_type": "application/pdf", "url": "/2094/1/thesis_pdf.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Biology Beyond Biochemistry:The Mechanics of Life", "author": [ { "family_name": "Wiggins", "given_name": "Paul Alexander", "clpid": "Wiggins-Paul-Alexander" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Politzer", "given_name": "Hugh David", "orcid": "0000-0002-4983-6621", "clpid": "Politzer-H-D" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" }, { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "In the last half century, biologists have made great strides towards understanding the intricate structure of the cell and the relation between this structure and cellular function. Single-molecule techniques and advances in microscopy have also significantly changed the way in which biologists ask and answer questions. As biological measurements and techniques have become increasingly quantitative, they have allowed biologists to ask ever more quantitative questions: How do the molecular machines, which comprise the cell function microscopically? Can we understand the design principles that govern the structure and function of biological systems on a microscopic scale? One outcome of this new generation of quantitative biological questions is the need to greet quantitative experiments with models at a higher level of abstraction than the traditional cartoons of molecular biology. In this thesis, I present two such quantitative models.
\r\n\r\nIn the first half of this thesis, I present a physical model for mechanotransduction. Mechanosensitive channels are the central agents employed by cells to transduce mechanical stimuli. Our senses of hearing and touch are both examples of this functional motif. The Mechanosensitive Channel of Large conductance (MscL) is arguably the simplest and best studied mechanosensitive channel. I present analytic estimates for the forces and free energy generated by bilayer deformation which reveal a compelling and intuitive model for the function of the MscL channel, analogous to the nucleation of a second phase. The competition between hydrophobic mismatch of the protein with the surrounding membrane and tension results in a surprisingly rich story which can provide both a quantitative comparison to measurements of the opening tension for MscL when reconstituted in bilayers of different thickness and qualitative insights into the function of the MscL channel and other transmembrane proteins.
\r\n\r\nIn the second half of this thesis, I examine models for the mechanics of DNA. DNA bending, on length scales shorter than a persistence length, plays a central role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a renewed interest in the short-contour-length polymer statistics relevant for describing the conformational free energy of DNA bending induced by protein-DNA complexes. The recent DNA cyclization studies of Cloutier and Widom have questioned the applicability of the canonical semiflexible polymer theory, the wormlike chain model, to DNA bending on biological length scales. We describe a new class of polymer models that can resolve the proposed discrepancy between short and long-contour-length bending. These models explain the spectacular success of the wormlike chain model in describing many traditional DNA mechanics experiments, as well as its failure to describe the short-contour-length mechanics of DNA. In particular, I present two toy models for DNA bending which capture the short-contour-length behavior observed by Cloutier and Widom. These toy models make quantitative predictions for chain statistics of DNA, observable in DNA mechanics experiments and of central importance to the qualitative description of cellular function, from chromosomal DNA packaging to transcription and gene regulation to viral packaging.
", "doi": "10.7907/015B-JA11", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:4584", "collection": "thesis", "collection_id": "4584", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11162004-120143", "primary_object_url": { "basename": "AJS-dissertation-9-4-04.pdf", "content": "final", "filesize": 12556205, "license": "other", "mime_type": "application/pdf", "url": "/4584/1/AJS-dissertation-9-4-04.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Semiflexible Polymers: Fundamental Theory and Applications in DNA Packaging", "author": [ { "family_name": "Spakowitz", "given_name": "Andrew James", "orcid": "0000-0002-0585-1942", "clpid": "Spakowitz-Andrew-James" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Much is understood about the behavior of perfectly flexible and perfectly rigid polymer chains; however, many polymers, for example DNA, are somewhere in between these two limiting cases. Such polymers are termed semiflexible, and their molecular elasticity can play a significant role in single-chain behavior as well as contribute to collective effects. Using analytical theory and numerical methods, we address several problems that focus on the equilibrium and dynamic behavior of semiflexible polymers to gain a deeper understanding of their fundamental physics. We consider the equilibrium statistical behavior of semiflexible polymers under the influence of external fields, confinement, and the collective influence of a nematic liquid-crystal phase. We then turn to the dynamics of a deformed elastic thread, addressing instances of instability and the subsequent nonlinear relaxation. Once we establish an understanding of these physical effects, we discuss the role that they play in DNA packaging, specifically focusing on the role of twist in DNA packaging in chromatin and the formation of an ordered conformation within a viral capsid.", "doi": "10.7907/GGY2-SZ67", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:4822", "collection": "thesis", "collection_id": "4822", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12072004-021118", "primary_object_url": { "basename": "YouyongLi_Thesis.pdf", "content": "final", "filesize": 3996304, "license": "other", "mime_type": "application/pdf", "url": "/4822/1/YouyongLi_Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Atomistic Simulation of Macromolecules", "author": [ { "family_name": "Li", "given_name": "Youyong", "orcid": "0000-0002-5248-2756", "clpid": "Li-Youyong" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis focuses on the atomistic simulation of polymers/dendrimers material properties and development/applications of Monte Carlo methods for macromolecules. The main topics and their outlines are listed as following.
\r\n\r\n1) Structures and properties of crystalline polymers from theory. Although crystalline polymers such as nylon are important industrial materials, it is difficult to get the details of the various structures/properties and the conversion between them from the experiment. Using molecular modeling, we successfully predicted the complicated structures/properties and illustrated the process of forming the polymer crystal and conversion mechanism among those structures.
\r\n\r\n2) Packing mechanism of self-assembly dendrimer balls with soft coronas. Using the vibrational density of state (DoS) derived from molecular dynamic simulations, we investigate the free energy of the liquid crystal formed by soft dendrimer balls. We find that the preferred lattice for soft balls is different from the hard balls and illustrate the mechanism.
\r\n\r\n3) Development of CCBTX Monte Carlo method for polymer and dendrimer. Although computer simulation has developed as a powerful research tool to study polymer/dendrimer materials properties recently, it has been hampered by the difficulties of sampling amorphous polymer/dendrimer configurations efficiently. We develop the efficient Continuous Configurational Biased TX (CCBTX) method to generate high-quality amorphous polymer and dendrimer atomistic structures directly. The code is implemented in C++ and ported in python environment, which provides friendly interface.
\r\n\r\n4) Thermodynamic functions, critical exponents, and theta temperatures of polymer chains from CCBB Monte Carlo method. We examine the thermodynamic properties (entropy, energy, end-to-end distance) of isolated polymer chains with the Monte Carlo method.
", "doi": "10.7907/NW1Q-1E81", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2094", "collection": "thesis", "collection_id": "2094", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262005-134552", "primary_object_url": { "basename": "thesis_pdf.pdf", "content": "final", "filesize": 12280333, "license": "other", "mime_type": "application/pdf", "url": "/2094/1/thesis_pdf.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Biology Beyond Biochemistry:The Mechanics of Life", "author": [ { "family_name": "Wiggins", "given_name": "Paul Alexander", "clpid": "Wiggins-Paul-Alexander" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "thesis_committee": [ { "family_name": "Politzer", "given_name": "Hugh David", "orcid": "0000-0002-4983-6621", "clpid": "Politzer-H-D" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" }, { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "In the last half century, biologists have made great strides towards understanding the intricate structure of the cell and the relation between this structure and cellular function. Single-molecule techniques and advances in microscopy have also significantly changed the way in which biologists ask and answer questions. As biological measurements and techniques have become increasingly quantitative, they have allowed biologists to ask ever more quantitative questions: How do the molecular machines, which comprise the cell function microscopically? Can we understand the design principles that govern the structure and function of biological systems on a microscopic scale? One outcome of this new generation of quantitative biological questions is the need to greet quantitative experiments with models at a higher level of abstraction than the traditional cartoons of molecular biology. In this thesis, I present two such quantitative models.
\r\n\r\nIn the first half of this thesis, I present a physical model for mechanotransduction. Mechanosensitive channels are the central agents employed by cells to transduce mechanical stimuli. Our senses of hearing and touch are both examples of this functional motif. The Mechanosensitive Channel of Large conductance (MscL) is arguably the simplest and best studied mechanosensitive channel. I present analytic estimates for the forces and free energy generated by bilayer deformation which reveal a compelling and intuitive model for the function of the MscL channel, analogous to the nucleation of a second phase. The competition between hydrophobic mismatch of the protein with the surrounding membrane and tension results in a surprisingly rich story which can provide both a quantitative comparison to measurements of the opening tension for MscL when reconstituted in bilayers of different thickness and qualitative insights into the function of the MscL channel and other transmembrane proteins.
\r\n\r\nIn the second half of this thesis, I examine models for the mechanics of DNA. DNA bending, on length scales shorter than a persistence length, plays a central role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a renewed interest in the short-contour-length polymer statistics relevant for describing the conformational free energy of DNA bending induced by protein-DNA complexes. The recent DNA cyclization studies of Cloutier and Widom have questioned the applicability of the canonical semiflexible polymer theory, the wormlike chain model, to DNA bending on biological length scales. We describe a new class of polymer models that can resolve the proposed discrepancy between short and long-contour-length bending. These models explain the spectacular success of the wormlike chain model in describing many traditional DNA mechanics experiments, as well as its failure to describe the short-contour-length mechanics of DNA. In particular, I present two toy models for DNA bending which capture the short-contour-length behavior observed by Cloutier and Widom. These toy models make quantitative predictions for chain statistics of DNA, observable in DNA mechanics experiments and of central importance to the qualitative description of cellular function, from chromosomal DNA packaging to transcription and gene regulation to viral packaging.
", "doi": "10.7907/015B-JA11", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2937", "collection": "thesis", "collection_id": "2937", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07202003-103429", "primary_object_url": { "basename": "Thesis_Mike_Kempe.pdf", "content": "final", "filesize": 5162032, "license": "other", "mime_type": "application/pdf", "url": "/2937/1/Thesis_Mike_Kempe.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Rheology and Dynamics of Side-Group Liquid Crystalline Polymers in Nematic Solvents", "author": [ { "family_name": "Kempe", "given_name": "Michael David", "orcid": "0000-0003-3312-0482", "clpid": "Kempe-Michael-David" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "To form a liquid crystalline (LC) gel that retains the ability to respond rapidly to applied fields, it is necessary to work with low polymer concentrations. In turn, to form a dilute polymer network it is necessary to use very long polymers that are soluble in the small molecule LC. This research focuses on the synthesis of ultra-long side-group liquid crystalline polymers (SGLCPs), their properties when dissolved in nematic hosts, and the self-assembly of a nematic gel using an ABA triblock with an SGLCP midblock and LC-phobic end-blocks. Typically, LCs are made from small molecules that can be quickly reoriented. In applications such as artificial muscles, flexible displays, or compensating films, a more robust LC gel is desired. Prior routes to LC gels, typically using in situ polymerization, suffer from director misorientation, lack of control over cross-link density, polymer network inhomogeneity, undesired phase separation, and slow responses to applied fields. The present research (at the intersection of block copolymers, gels, and LCs) has demonstrated that an optically uniform LC gel with fast reorientational response can be achieved using a self-assembling ABA triblock copolymer.
\r\n\r\nTo provide the fundamental underpinning for the design of a self-assembling gel, we first advanced the synthesis of model SGLCPs that have well-defined length even at high degrees of polymerization. The polymerization method must provide narrow length distribution, be applicable to block copolymers, and preferably enable chains of varied side-group structure to be prepared. These requirements were met by starting from an anionically produced prepolymer and attaching the mesogen in a second step (a ?polymer analogous? approach). Homopolymers were made and characterized to determine how polymer structure affects solubility, rheological response, electro-optic response and chain conformation. This showed that cyanobiphenyl (CB) side-groups provide excellent solubility in CB-based small molecule LCs even for SGLCPs an order of magnitude longer than those investigated in solution previously; that ultra-long SGLCPs have unprecedented effects on the flow behavior of LC solutions, and that the anisotropy (R^/R?1.6) is insensitive to spacer length and degree of polymerization.
\r\n\r\nThe size of a polymer is related to the concentration necessary to form a gel network; however, there have been few studies of SGLCP dimensions in LC solvents. Since it is the polymer backbone conformation that is of interest, researchers use polymers labeled on the backbone to avoid scattering from the side groups. Unfortunately in a dilute solution this provides unacceptably low scattered intensity. Therefore, we demonstrate a method for measuring the dimensions of an unlabeled SGLCP in a perdeuterated nematic solvent, in which scattering originates from both the backbone and the pendant side groups. Since it is the backbone conformation that is of interest, we developed a method to mathematically account for scattering due to the side groups.
\r\n\r\nInformation gained from homopolymer studies guided the design of ABA block copolymers for nematic gels. We demonstrated that an optically uniform nematic gel can form in a small molecule LC even at low polymer concentrations using a triblock composed of an SGLCP center block and end-blocks that microphase separate to form physical cross-links. The key to making a dilute gel was using well-solvated, very long SGLCP midblocks. The necessity of cross-linking very dilute chain ends is prohibitive using covalent linking, but facile using end-blocks that spontaneously aggregate. In contrast to prior LC gels, these dilute gels maintain both the optical uniformity and fast reorientational responses of the small molecule LC host.
", "doi": "10.7907/W41E-KB03", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:2196", "collection": "thesis", "collection_id": "2196", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282004-161503", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 13394896, "license": "other", "mime_type": "application/pdf", "url": "/2196/1/Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Computation Aided Design in Molecular Nanotechnology", "author": [ { "family_name": "Deng", "given_name": "Wei-Qiao", "orcid": "0000-0002-3671-5951", "clpid": "Deng-Wei-Qiao" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We use multi-scale simulation strategy to understand, improve and rationally design novel materials with desired properties in molecular nanotechnology. The areas we have studied cover from molecular electronics, nano-structured materials to carbon nanotube technology.
\r\n\r\nIn term of molecular and nano-electronics, first we used quantum mechanics to characterize the structure and current-voltage (I-V) performance of the Stoddart-Heath rotaxane-based programmable electronic switch. This methodology established a basis for iterative experimental-theoretical efforts to optimize systems for molecule-based electronics. We extended this switch principle and rationally designed an ultrafast molecular switch, proton-hopping molecular switch. Second we developed a kinetic model to study the hole mobility in organic semiconductor. After screening several designs, we presented a nano-bracelet as a competitive organic semiconductor.
\r\n\r\nWe studied several topics related to the applications of nano-structured materials in fuel cell technology. Based on our simulation, we proposed a new kind of carbon-based materials for hydrogen storage. It can satisfy the target set up by the Department of Energy, USA. We develop a kinetic model to study the proton diffusion in proton exchange membrane of hydrogen fuel cell. We validated our proposed system, fluorinated imidazole impregnated nafion, as the candidate that can transfer proton above 100 0C at water-free media.
\r\n\r\nIn term of carbon nanotube technology, we explored the reason why bimetallic catalysts are 10-100 times better than mono-metals at assisting single wall carbon nanotube growth. Based on our proposed two-stage growth mechanism, we screened and designed a better catalysis.
", "doi": "10.7907/3EKY-3J53", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:3169", "collection": "thesis", "collection_id": "3169", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08192002-161141", "primary_object_url": { "basename": "voigt_thesis.pdf", "content": "final", "filesize": 45686480, "license": "other", "mime_type": "application/pdf", "url": "/3169/1/voigt_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Computationally Optimizing the Directed Evolution of Proteins", "author": [ { "family_name": "Voigt", "given_name": "Christopher Ashby", "orcid": "0000-0003-0844-4776", "clpid": "Voigt-Christopher-Ashby" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Roberts", "given_name": "Richard W.", "orcid": "0000-0002-8587-5097", "clpid": "Roberts-R-W" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Fontana", "given_name": "Walter", "clpid": "Fontana-Walter" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Directed evolution has proven a successful strategy for protein engineering. To accelerate the discovery process, we have developed several computational methods to optimize the mutant libraries by targeting specific residues for mutagenesis, and subunits for recombination. In achieving this goal, a statistical model was first used to study the dynamics of directed evolution as a search algorithm. These simulations improved our understanding of the relationship between parameters describing the search space (e.g., interactions between amino acids) and experimental search parameters (e.g., mutation rate and library size). Based on these simulations, a more detailed model was used to calculate the structural tolerance of each residue to amino acid substitutions. Further, a computational model was developed to optimize recombination experiments, based on the three-dimensional structure. Together, these computational techniques represent a major step towards information-driven combinatorial protein design. ", "doi": "10.7907/E4GF-EQ41", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:3169", "collection": "thesis", "collection_id": "3169", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08192002-161141", "primary_object_url": { "basename": "voigt_thesis.pdf", "content": "final", "filesize": 45686480, "license": "other", "mime_type": "application/pdf", "url": "/3169/1/voigt_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Computationally Optimizing the Directed Evolution of Proteins", "author": [ { "family_name": "Voigt", "given_name": "Christopher Ashby", "orcid": "0000-0003-0844-4776", "clpid": "Voigt-Christopher-Ashby" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Roberts", "given_name": "Richard W.", "orcid": "0000-0002-8587-5097", "clpid": "Roberts-R-W" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Fontana", "given_name": "Walter", "clpid": "Fontana-Walter" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Directed evolution has proven a successful strategy for protein engineering. To accelerate the discovery process, we have developed several computational methods to optimize the mutant libraries by targeting specific residues for mutagenesis, and subunits for recombination. In achieving this goal, a statistical model was first used to study the dynamics of directed evolution as a search algorithm. These simulations improved our understanding of the relationship between parameters describing the search space (e.g., interactions between amino acids) and experimental search parameters (e.g., mutation rate and library size). Based on these simulations, a more detailed model was used to calculate the structural tolerance of each residue to amino acid substitutions. Further, a computational model was developed to optimize recombination experiments, based on the three-dimensional structure. Together, these computational techniques represent a major step towards information-driven combinatorial protein design. ", "doi": "10.7907/E4GF-EQ41", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:2934", "collection": "thesis", "collection_id": "2934", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07192007-103729", "primary_object_url": { "basename": "Tae_g_2002.pdf", "content": "final", "filesize": 5606627, "license": "other", "mime_type": "application/pdf", "url": "/2934/1/Tae_g_2002.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "In situ Forming Hydrogels Using Self-Assembly of Fluoroalkyl-Ended Poly(ethylene Glycol)s", "author": [ { "family_name": "Tae", "given_name": "Giyoong", "clpid": "Tae-Giyoong" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Hubbell", "given_name": "Jeffrey A.", "clpid": "Hubbell-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Davis", "given_name": "Mark E.", "orcid": "0000-0001-8294-1477", "clpid": "Davis-M-E" }, { "family_name": "Hubbell", "given_name": "Jeffrey A.", "clpid": "Hubbell-J-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Telechelic polymers with hydrophilic midblocks (poly(ethylene glycol), PEG) and hydrophobic end groups (fluoroalkyl, Rf) are synthesized and explored as candidates for in situ forming hydrogels for biomedical applications. Relevant physical properties, including phase behavior, rheology and erosion kinetics, are characterized to guide rational design of polymers for specific applications, including controlled release of therapeutic proteins and deposition of biocompatible surface layers. Disruption of the aggregation of the end groups using biocompatible complexing agents or solvents produces a low viscosity liquid that is injectable; self-assembly of the gel once inside the body can be achieved gently by diffusion of the complexing agent or solvent out into the surrounding tissue. By modulating molecular structure, the mechanical and erosion properties of these hydrogels can be systematically varied over a wide range for desired applications.
\r\n\r\nWith increasing fluoroalkyl length relative to PEG length, the phase behavior of these fluoroalkyl-ended PEGs (Rf-PEGs) polymers in aqueous solution changes from singlephase behavior (continuous transition in properties from solution-like to gel-like with increasing concentration), to sol-gel coexistence, to an insoluble precipitate (Chapter 2). For sol-gel coexisting polymers, the equilibrium gel concentration and the modulus of the gel phase are governed by the length of the PEG midblock, whereas the relaxation time is determined by the hydrophobe length. The erosion characteristics of these hydrogels correlate with their phase behavior: the gels of sol-gel coexisting species exhibit surface erosion in an open system with slow dissolution rate controlled by the end-group length, whereas gels showing single-phase behavior exhibit bulk erosion that is relatively fast.
\r\n\r\nAqueous solutions of Rf-PEGs exhibit ordering transitions, with increasing concentration (Chapter 3). The hydrophobic cores of the micelle-like aggregates order into a body-centered-cubic (BCC) structure. The aggregated state of the hydrophobic core is determined by the length of the hydrophobic end group, and is insensitive to the concentration of the polymer solution or the temperature. A shorter PEG length for a given end group produces a much enhanced ordering compared to a longer one. This micelle packing effect is manifested in changes in the viscoelastic properties: the single-relaxation behavior evolves to the appearance of a new low frequency elastic plateau in the dynamic moduli, and a linear response changes to a yielding behavior in creep.
\r\n\t\r\nThe gel phase of sol-gel coexisting polymers can be transformed into an injectable state by the addition of a bio-tolerable organic solvent, such as N-methyl pyrrolidone (NMP), and this solution can be restored to a hydrogel state quickly after injection by removal of the organic solvent by diffusion. Release of Human growth hormone (hGH) using this injectable formulation (Chapter 4) reveals that hGH remains stable inside the hydrogel formed, and more than 2 weeks of prolonged release of hGH pretreated with zinc is obtained using the injectable formulation without irreversible aggregation. For the Rf-PEGs examined here, the release rate of hGH is determined by the rate of diffusion through the hydrogel.
\r\n\r\nThe telechelic Rf-PEGs that exhibit sol-gel equilibrium or precipitated gel phase behavior provide a facile route to hydrophilic modification of poly(tetrafluoroethylene) (PTFE) surfaces that are frequently encountered in biomedical devices (Chapter 5). Dip coating of PTFE into 1 wt % Rf-PEGs in ethanol, followed by immersing into water, converts the surface of PTFE from hydrophobic to hydrophilic. The lifetime of this modification is correlated to the phase behavior of the bulk gel state, and stable in the various ranges of shear rates. An Rf-PEG that is insoluble in water gave a stable modification over a period of weeks in the absence of shear, and persisted for days when subjected to the highest shear stresses encountered in arteries (3-4Pa). Telechelic Rf-PEGs are effective, while monofunctional PEGs with a single fluoroalkyl group are not.
\r\n\r\nThe swelling and drying behaviors of thin films of RfPEGs (~0.1 [mu]m) show abnormalities relative to glassy and semi-crystalline films (Chapter 6). In a humidity ramp test starting from a dry state, thin films of Rf-PEGs show a distinctive hysteresis behavior; as humidity increases, little swelling occurs until ~ 85% humidity, then the film swells rapidly; as the humidity decreases, a rapid deswelling occurs near ~75% humidity. In a humidity step test, following a step-up the mass increase shows an overshoot, followed by a gradual approach to the equilibrium value, whereas the film tracks the equilibrium state very rapidly and monotonically following a step down from high to low humidity.
", "doi": "10.7907/xrnv-yh71", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:2808", "collection": "thesis", "collection_id": "2808", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07042002-114141", "primary_object_url": { "basename": "mythesis_susp.pdf", "content": "final", "filesize": 6323591, "license": "other", "mime_type": "application/pdf", "url": "/2808/1/mythesis_susp.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Inertial Effects in Suspension Dynamics", "author": [ { "family_name": "Subramanian", "given_name": "Ganesh", "clpid": "Subramanian-Ganesh" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Campbell", "given_name": "Charles Soutter", "clpid": "Campbell-Charles-Soutter" }, { "family_name": "Hunt", "given_name": "Melany L.", "orcid": "0000-0001-5592-2334", "clpid": "Hunt-M-L" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This work analyses the role of small but finite particle inertia on the microstructure of suspensions of heavy particles subjected to an external flow. The magnitude of particle inertia is characterized by the Stokes number, St, defined as the ratio of the inertial relaxation time of a particle to the flow time scale. Fluid inertia is neglected so that the fluid motion satisfies the quasi-steady Stokes equations. The statistics of the particles is governed by a Fokker-Planck equation in position and velocity space. For small St, a multiple scales formalism is developed to solve for the phase-space probability density of a single spherical Brownian particle in a linear flow. Though valid for an arbitrary flow field, the method fails for a spatially varying mass and drag coefficient. In all cases, however, a Chapman-Enskog-like formulation provides a valid multi-scale description of the dynamics both for a single Brownian particle and a suspension of interacting particles. For long times, the leading order solution simplifies to the product of a local Maxwellian in velocity space and a spatial density satisfying the Smoluchowski equation. The higher order corrections capture both short-time momentum relaxations and long-time deviations from the Maxwellian. The inertially corrected Smoluchowski equation includes a non-Fickian term at O(St).
\r\n\r\nThe pair problem is solved to O(St) for non-Brownian spherical particles in simple shear flow. In contrast to the zero inertia case, the relative trajectories of two particles are asymmetric. Open trajectories in 'repels' nearby trajectories that spiral out onto a new stable limit cycle in the shearing plane. This limit cycle acts as a local attractor; in-plane trajectories from an initial offset of O(St\u00b9/\u00b2) or less approach the limit cycle. The topology of the off-plane trajectories is more complicated because the gradient displacement changes sign away from the plane of shear. The 'neutral' off-plane trajectory with zero net gradient displacement acts to separate trajectories spiralling onto contact from those that go off to infinity. The aforementioned asymmetry leads to a non-Newtonian rheology and self-diffusivities in the gradient and voriticity directions that scale as St\u00b2 ln St and St2, respectively.
", "doi": "10.7907/DSMP-HV88", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:257", "collection": "thesis", "collection_id": "257", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01202009-160503", "primary_object_url": { "basename": "Sierou_a_2002.pdf", "content": "final", "filesize": 7782769, "license": "other", "mime_type": "application/pdf", "url": "/257/1/Sierou_a_2002.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Accelerated Stokesian Dynamics: Development and Application to Sheared Non-Brownian Suspensions", "author": [ { "family_name": "Sierou", "given_name": "Asimina", "clpid": "Sierou-Asimina" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Hunt", "given_name": "Melany L.", "orcid": "0000-0001-5592-2334", "clpid": "Hunt-M-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A new implementation of the conventional Stokesian Dynamics (SD) algorithm, called Accelerated Stokesian Dynamics (ASD), is presented. The equations governing the motion of N particles suspended in a viscous fluid at low particle Reynolds number are solved accurately and efficiently, including all hydrodynamic interactions, but with a significantly lower computational cost of O(N ln N). The main differences from the conventional SD method lie in the calculation of the many-body long-range interactions, where the Ewald-summed wave-space contribution is calculated as a Fourier Transform sum, and in the iterative inversion of the now sparse resistance matrix. The ASD method opens up an entire new class of suspension problems that can be investigated, including particles of non-spherical shape and a distribution of sizes, and can be readily extended to other low-Reynolds-number flow problems. The new method is applied to the study of sheared non-Brownian suspensions.
\r\n\r\nThe rheological behavior of a monodisperse suspension of non-Brownian particles in simple shear flow in the presence of a weak interparticle force is studied first. The availability of a faster numerical algorithm permits the investigation of larger systems (typically of N = 512 \u2014 1000 particles), and accurate results for the suspension viscosity, first and second normal stress differences and the particle pressure are determined as a function of the volume fraction. The system microstructure, expressed through the pair-distribution function, is also studied and it is demonstrated how the resulting anisotropy in the microstructure is correlated with the suspension non-Newtonian behavior. The ratio of the normal to excess shear stress is found to be an increasing function of the volume fraction, suggesting different volume fraction scalings for different elements of the stress tensor. The relative strength and range of the interparticle force is varied and its effect on the shear and normal stresses is analyzed. Volume fractions above the equilibrium freezing volume fraction (\u00f8 \u2248 0.494) are also studied, and it is found that the system exhibits a strong tendency to order under flow for volume fractions below the hard-sphere glass transition; limited results for \u00f8 = 0.60, however, show that the system is again disordered under shear.
\r\n\r\nSelf-diffusion is subsequently studied and accurate results for the complete tensor of the shear-induced self-diffusivities are determined. The finite, and oftentimes large, auto-correlation time requires the mean-square displacement curves to be followed for longer times than was previously thought necessary. Results determined from either the mean-square displacement or the velocity autocorrelation function are in excellent agreement. The longitudinal (in the flow direction) self-diffusion coefficient is also determined, and it is shown that the finite autocorrelation time introduces an additional coupled term to the longitudinal self-diffusivity, a term which previous theoretical and numerical results omitted. The longitudinal self-diffusivities for a system of non-Brownian particles are calculated for the first time as a function of the volume fraction.
\r\n", "doi": "10.7907/SX3A-8M59", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:2934", "collection": "thesis", "collection_id": "2934", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07192007-103729", "primary_object_url": { "basename": "Tae_g_2002.pdf", "content": "final", "filesize": 5606627, "license": "other", "mime_type": "application/pdf", "url": "/2934/1/Tae_g_2002.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "In situ Forming Hydrogels Using Self-Assembly of Fluoroalkyl-Ended Poly(ethylene Glycol)s", "author": [ { "family_name": "Tae", "given_name": "Giyoong", "clpid": "Tae-Giyoong" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Hubbell", "given_name": "Jeffrey A.", "clpid": "Hubbell-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Davis", "given_name": "Mark E.", "orcid": "0000-0001-8294-1477", "clpid": "Davis-M-E" }, { "family_name": "Hubbell", "given_name": "Jeffrey A.", "clpid": "Hubbell-J-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Telechelic polymers with hydrophilic midblocks (poly(ethylene glycol), PEG) and hydrophobic end groups (fluoroalkyl, Rf) are synthesized and explored as candidates for in situ forming hydrogels for biomedical applications. Relevant physical properties, including phase behavior, rheology and erosion kinetics, are characterized to guide rational design of polymers for specific applications, including controlled release of therapeutic proteins and deposition of biocompatible surface layers. Disruption of the aggregation of the end groups using biocompatible complexing agents or solvents produces a low viscosity liquid that is injectable; self-assembly of the gel once inside the body can be achieved gently by diffusion of the complexing agent or solvent out into the surrounding tissue. By modulating molecular structure, the mechanical and erosion properties of these hydrogels can be systematically varied over a wide range for desired applications.
\r\n\r\nWith increasing fluoroalkyl length relative to PEG length, the phase behavior of these fluoroalkyl-ended PEGs (Rf-PEGs) polymers in aqueous solution changes from singlephase behavior (continuous transition in properties from solution-like to gel-like with increasing concentration), to sol-gel coexistence, to an insoluble precipitate (Chapter 2). For sol-gel coexisting polymers, the equilibrium gel concentration and the modulus of the gel phase are governed by the length of the PEG midblock, whereas the relaxation time is determined by the hydrophobe length. The erosion characteristics of these hydrogels correlate with their phase behavior: the gels of sol-gel coexisting species exhibit surface erosion in an open system with slow dissolution rate controlled by the end-group length, whereas gels showing single-phase behavior exhibit bulk erosion that is relatively fast.
\r\n\r\nAqueous solutions of Rf-PEGs exhibit ordering transitions, with increasing concentration (Chapter 3). The hydrophobic cores of the micelle-like aggregates order into a body-centered-cubic (BCC) structure. The aggregated state of the hydrophobic core is determined by the length of the hydrophobic end group, and is insensitive to the concentration of the polymer solution or the temperature. A shorter PEG length for a given end group produces a much enhanced ordering compared to a longer one. This micelle packing effect is manifested in changes in the viscoelastic properties: the single-relaxation behavior evolves to the appearance of a new low frequency elastic plateau in the dynamic moduli, and a linear response changes to a yielding behavior in creep.
\r\n\t\r\nThe gel phase of sol-gel coexisting polymers can be transformed into an injectable state by the addition of a bio-tolerable organic solvent, such as N-methyl pyrrolidone (NMP), and this solution can be restored to a hydrogel state quickly after injection by removal of the organic solvent by diffusion. Release of Human growth hormone (hGH) using this injectable formulation (Chapter 4) reveals that hGH remains stable inside the hydrogel formed, and more than 2 weeks of prolonged release of hGH pretreated with zinc is obtained using the injectable formulation without irreversible aggregation. For the Rf-PEGs examined here, the release rate of hGH is determined by the rate of diffusion through the hydrogel.
\r\n\r\nThe telechelic Rf-PEGs that exhibit sol-gel equilibrium or precipitated gel phase behavior provide a facile route to hydrophilic modification of poly(tetrafluoroethylene) (PTFE) surfaces that are frequently encountered in biomedical devices (Chapter 5). Dip coating of PTFE into 1 wt % Rf-PEGs in ethanol, followed by immersing into water, converts the surface of PTFE from hydrophobic to hydrophilic. The lifetime of this modification is correlated to the phase behavior of the bulk gel state, and stable in the various ranges of shear rates. An Rf-PEG that is insoluble in water gave a stable modification over a period of weeks in the absence of shear, and persisted for days when subjected to the highest shear stresses encountered in arteries (3-4Pa). Telechelic Rf-PEGs are effective, while monofunctional PEGs with a single fluoroalkyl group are not.
\r\n\r\nThe swelling and drying behaviors of thin films of RfPEGs (~0.1 [mu]m) show abnormalities relative to glassy and semi-crystalline films (Chapter 6). In a humidity ramp test starting from a dry state, thin films of Rf-PEGs show a distinctive hysteresis behavior; as humidity increases, little swelling occurs until ~ 85% humidity, then the film swells rapidly; as the humidity decreases, a rapid deswelling occurs near ~75% humidity. In a humidity step test, following a step-up the mass increase shows an overshoot, followed by a gradual approach to the equilibrium value, whereas the film tracks the equilibrium state very rapidly and monotonically following a step down from high to low humidity.
", "doi": "10.7907/xrnv-yh71", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:5374", "collection": "thesis", "collection_id": "5374", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-112545862", "type": "thesis", "title": "First Principles Based Multiscale Modeling of Single Crystal Plasticity: Application to BCC Tantalum", "author": [ { "family_name": "Wang", "given_name": "Guofeng", "orcid": "0000-0001-8249-4101", "clpid": "Wang-Guofeng" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Cagin", "given_name": "Tahir", "clpid": "Cagin-Tahir" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Haile", "given_name": "Sossina M.", "orcid": "0000-0002-5293-6252", "clpid": "Haile-S-M" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In principle, the macroscopic plasticity properties of crystalline materials are derivable from the physical processes involving dislocations and interactions between dislocations with other defects. However, a quantitative theory of plasticity based on the dislocation mechanism requires crossing multiple length and time scales. To accommodate these requirements, we developed a multiscale approach for modeling crystalline solids. In this thesis, to establish the connections between simulations in different length and time scales, I mainly focus on identifying and determining the importance and influence of various unit processes involving the dislocations through atomic level simulations. These unit processes in turn play a major role in modeling the single crystal plasticity.
\r\n\r\nKey Results from Atomistic Simulations
\r\n\r\nDislocation core structure and core energy: Using the first-principles qEAM force field (FF), we determine the core energy for 1/2a<111> screw dislocation and 1/2a<111> edge dislocation in bcc Ta. We find that the core energy of edge dislocation is 1.77 times higher than that of screw dislocation. This ratio (1.77) is a fundamental material property used as input to the macroscopic model. Furthermore, we find that the central 12 atoms closest to the 1/2a<111> screw dislocation line have distinguishably higher atomistic strain energy than the other atoms. Thus, we arrive at a physical definition of dislocation core.
\r\n\r\nScrew dislocation mobility: In this thesis, we proposed a new method to investigate dislocation mobility by analyzing the process of migration of a screw dislocation dipole. The new method is based on the energy distribution at the atomistic scale and is used to calculate the Peierls potential barrier and Peierls stress for dislocation continuous motion. The calculated Peierls stress is in good agreement with results obtained using other method. Simulating dislocation motion at finite temperatures (from 20 K to 300 K), we find that the activation energy for dislocation motion is about 6 times lower than computed at 0.001 K. Our results suggest that the decrease in the correlation between neighboring segments in the dislocation line accounts for the decrease of activation energy. We observe that the formation of kink pair along the dislocation line enhances the dislocation mobility. This verifies the traditional belief that the screw dislocation in bcc metals moves by first kink pair nucleation and subsequently lateral movements of kinks along the dislocation.
\r\n\r\nKinks in screw dislocations: To bridge the atomistic process of dislocation motion with continuum model, we accurately calculate the material properties, such as kink pair formation energy and effective kink pair length, using atomic level simulations. In detailed structural analysis, we discover the substructures of different kinks when the screw dislocation core is asymmetric. There are only two kinds of elementary kinks in the dislocation and the others are the composite kinks consisting of an elementary kink and one or two flips. Based on these findings, we further explain the observed trend of the formation energy and mobility of different classes of kinks. (Note: Similar trend and conclusion could have been found in earlier studies but not mentioned by the authors of those papers.)
\r\n\r\nIn summary, we have used quantum mechanics based interaction potentials to investigate the unit processes that play important role in single crystal plasticity and verified the findings using the quantitative results obtained from the atomic level simulation in a macroscopic model for single crystal plasticity.
", "doi": "10.7907/5nyn-ct36", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:5374", "collection": "thesis", "collection_id": "5374", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-112545862", "type": "thesis", "title": "First Principles Based Multiscale Modeling of Single Crystal Plasticity: Application to BCC Tantalum", "author": [ { "family_name": "Wang", "given_name": "Guofeng", "orcid": "0000-0001-8249-4101", "clpid": "Wang-Guofeng" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Cagin", "given_name": "Tahir", "clpid": "Cagin-Tahir" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Haile", "given_name": "Sossina M.", "orcid": "0000-0002-5293-6252", "clpid": "Haile-S-M" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In principle, the macroscopic plasticity properties of crystalline materials are derivable from the physical processes involving dislocations and interactions between dislocations with other defects. However, a quantitative theory of plasticity based on the dislocation mechanism requires crossing multiple length and time scales. To accommodate these requirements, we developed a multiscale approach for modeling crystalline solids. In this thesis, to establish the connections between simulations in different length and time scales, I mainly focus on identifying and determining the importance and influence of various unit processes involving the dislocations through atomic level simulations. These unit processes in turn play a major role in modeling the single crystal plasticity.
\r\n\r\nKey Results from Atomistic Simulations
\r\n\r\nDislocation core structure and core energy: Using the first-principles qEAM force field (FF), we determine the core energy for 1/2a<111> screw dislocation and 1/2a<111> edge dislocation in bcc Ta. We find that the core energy of edge dislocation is 1.77 times higher than that of screw dislocation. This ratio (1.77) is a fundamental material property used as input to the macroscopic model. Furthermore, we find that the central 12 atoms closest to the 1/2a<111> screw dislocation line have distinguishably higher atomistic strain energy than the other atoms. Thus, we arrive at a physical definition of dislocation core.
\r\n\r\nScrew dislocation mobility: In this thesis, we proposed a new method to investigate dislocation mobility by analyzing the process of migration of a screw dislocation dipole. The new method is based on the energy distribution at the atomistic scale and is used to calculate the Peierls potential barrier and Peierls stress for dislocation continuous motion. The calculated Peierls stress is in good agreement with results obtained using other method. Simulating dislocation motion at finite temperatures (from 20 K to 300 K), we find that the activation energy for dislocation motion is about 6 times lower than computed at 0.001 K. Our results suggest that the decrease in the correlation between neighboring segments in the dislocation line accounts for the decrease of activation energy. We observe that the formation of kink pair along the dislocation line enhances the dislocation mobility. This verifies the traditional belief that the screw dislocation in bcc metals moves by first kink pair nucleation and subsequently lateral movements of kinks along the dislocation.
\r\n\r\nKinks in screw dislocations: To bridge the atomistic process of dislocation motion with continuum model, we accurately calculate the material properties, such as kink pair formation energy and effective kink pair length, using atomic level simulations. In detailed structural analysis, we discover the substructures of different kinks when the screw dislocation core is asymmetric. There are only two kinds of elementary kinks in the dislocation and the others are the composite kinks consisting of an elementary kink and one or two flips. Based on these findings, we further explain the observed trend of the formation energy and mobility of different classes of kinks. (Note: Similar trend and conclusion could have been found in earlier studies but not mentioned by the authors of those papers.)
\r\n\r\nIn summary, we have used quantum mechanics based interaction potentials to investigate the unit processes that play important role in single crystal plasticity and verified the findings using the quantitative results obtained from the atomic level simulation in a macroscopic model for single crystal plasticity.
", "doi": "10.7907/5nyn-ct36", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:2808", "collection": "thesis", "collection_id": "2808", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07042002-114141", "primary_object_url": { "basename": "mythesis_susp.pdf", "content": "final", "filesize": 6323591, "license": "other", "mime_type": "application/pdf", "url": "/2808/1/mythesis_susp.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Inertial Effects in Suspension Dynamics", "author": [ { "family_name": "Subramanian", "given_name": "Ganesh", "clpid": "Subramanian-Ganesh" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Campbell", "given_name": "Charles Soutter", "clpid": "Campbell-Charles-Soutter" }, { "family_name": "Hunt", "given_name": "Melany L.", "orcid": "0000-0001-5592-2334", "clpid": "Hunt-M-L" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This work analyses the role of small but finite particle inertia on the microstructure of suspensions of heavy particles subjected to an external flow. The magnitude of particle inertia is characterized by the Stokes number, St, defined as the ratio of the inertial relaxation time of a particle to the flow time scale. Fluid inertia is neglected so that the fluid motion satisfies the quasi-steady Stokes equations. The statistics of the particles is governed by a Fokker-Planck equation in position and velocity space. For small St, a multiple scales formalism is developed to solve for the phase-space probability density of a single spherical Brownian particle in a linear flow. Though valid for an arbitrary flow field, the method fails for a spatially varying mass and drag coefficient. In all cases, however, a Chapman-Enskog-like formulation provides a valid multi-scale description of the dynamics both for a single Brownian particle and a suspension of interacting particles. For long times, the leading order solution simplifies to the product of a local Maxwellian in velocity space and a spatial density satisfying the Smoluchowski equation. The higher order corrections capture both short-time momentum relaxations and long-time deviations from the Maxwellian. The inertially corrected Smoluchowski equation includes a non-Fickian term at O(St).
\r\n\r\nThe pair problem is solved to O(St) for non-Brownian spherical particles in simple shear flow. In contrast to the zero inertia case, the relative trajectories of two particles are asymmetric. Open trajectories in 'repels' nearby trajectories that spiral out onto a new stable limit cycle in the shearing plane. This limit cycle acts as a local attractor; in-plane trajectories from an initial offset of O(St\u00b9/\u00b2) or less approach the limit cycle. The topology of the off-plane trajectories is more complicated because the gradient displacement changes sign away from the plane of shear. The 'neutral' off-plane trajectory with zero net gradient displacement acts to separate trajectories spiralling onto contact from those that go off to infinity. The aforementioned asymmetry leads to a non-Newtonian rheology and self-diffusivities in the gradient and voriticity directions that scale as St\u00b2 ln St and St2, respectively.
", "doi": "10.7907/DSMP-HV88", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:3274", "collection": "thesis", "collection_id": "3274", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08292008-110129", "primary_object_url": { "basename": "Zhou_w_2001.pdf", "content": "final", "filesize": 7877319, "license": "other", "mime_type": "application/pdf", "url": "/3274/1/Zhou_w_2001.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Dynamics and Shear Alignment Behavior of a Model Thermotropic Liquid Crystalline Polymer", "author": [ { "family_name": "Zhou", "given_name": "Weijun", "clpid": "Zhou-Weijun" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Gavalas", "given_name": "George R.", "orcid": "0000-0003-1468-6835", "clpid": "Gavalas-G-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Although liquid crystalline polymers (LCPs) emerged as important engineering materials in the early 1970s, the current level of understanding still falls short of allowing deliberate manipulation of macroscopic orientation, leading to poor control of morphology and material properties. The flow behavior of rod-like LCP solutions (lyotropic) are fairly well understood, yet little progress has been made on LCP melts (thermotropic) because of the formidable experimental difficulties with commercial thermotropes. A simple extension of the knowledge obtained from rod-like LCP solutions to thermotropic LCPs is unlikely to hold due to the enhanced molecular flexibility and intimate molecular contact in LCP melts.
\r\n\r\nThe primary concern of this thesis is therefore the flow behavior of thermotropic LCPs, with an emphasis on how flow influences orientation and morphology and how this depends on molecular structure. For this purpose we synthesized a model thermotropic LCP selected for its chemical stability, wide nematic range and optical transparency. This main-chain LCP, designated as DHMS-7,9, has alternating mesogen and spacer structure with dihydroxy-[alpha]-methylstilbene as mesogen and two different lengths of alkyl spacers (-C\u2087H\u2081\u2084- and -C\u2089H\u2081\u2088-). A range of molecular weights were prepared to probe the effects of chain flexibility (ratio of chain length of persistence length). Synthesis was scaled up to provide adequate quantities for physical studies (rheology, rheo-conoscopy and rheo-WAXS).
\r\n\r\nThe director response of a monodomain during shear flow is followed by in situ optical conoscopy using a custom-made shear cell. We observe that the director rotates opposite to the vorticity in shear for DHMS-7,9 using planar monodomain samples, demonstrating conclusively that it is flow aligning throughout its nematic temperature range. Director rotation is solely a function of applied strain, independent of shear rate, showing that the Leslie-Ericksen theory is applicable to polymeric nematics for shear rates that are low relative to their molecular relaxation. Comparisons of the observed tumbling parameter of DHMS-7,9 with predictions from available molecular models lead us to infer that molecular flexibility produces shear alignment for this class of thermotropic LCPs. To identify the effect of chain flexibility on the dynamics of this LCP, the rotational viscosity and shear viscosity were measured as functions of molecular weight. Both viscosities showed weaker sensitivity to molecular weight above a characteristic molecular weight, suggesting a crossover to semiflexible character at high molecular weight.
\r\n\r\nRheology and shear orientation behavior of DHMS-7,9 are markedly different from that of nematic lyotropic LCPs. Synchrotron WAXS measurements in steady shear show that molecular orientation is relatively high and nearly independent of shear rate. In transient shear during flow inception, flow reversal, and step up/down shear rate, neither shear stress nor orientation parameter shows multiple oscillations. Thus, both steady and transient responses of DHMS-7,9 are characteristic of flow-aligning liquid crystals, in contrast to tumbling rod-like LCPs, which show complex shear rate dependence in steady shear and oscillatory response to these transient flows.
\r\n\r\nAn interesting feature of DHMS-7,9 is the existence of a mysterious liquid crystalline phase--Phase X. The flow behavior of Phase X is completely different from that of the nematic phase. A striking flip of the orientation from the flow direction to the vorticity direction occurs below a critical shear rate. This orientational flipping is reversible in response to step changes of temperature and/or shear rate. In addition, we found that oscillatory shear flow also induces a similar type of orientational flipping. Examination of the linear viscoelastic properties as a function of orientation in Phase X suggests rheological similarity to layered fluids.
", "doi": "10.7907/dv2d-w145", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:3783", "collection": "thesis", "collection_id": "3783", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09262005-074935", "primary_object_url": { "basename": "Kumaraswamy_g_2000.pdf", "content": "final", "filesize": 10060303, "license": "other", "mime_type": "application/pdf", "url": "/3783/1/Kumaraswamy_g_2000.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The effect of flow history on the crystallization of semicrystalline polymers", "author": [ { "family_name": "Kumaraswamy", "given_name": "Guruswamy", "clpid": "Kumaraswamy-G" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Semicrystalline polymers constitute well over half of all the polymers produced worldwide. Their material properties depend sensitively on the thermal and flow history experienced during processing which strongly influences the kinetics of phase change and the morphology of the final crystalline microstructure. Therefore, it is of considerable interest to understand the mechanisms of flow effects on the rate and geometry of nucleation and crystal growth.\r\n\r\nMicrostructural development under the influence of flow is controlled by the interplay between melt relaxation processes and crystallization processes: the thermodynamic and kinetic aspects give rise to rich physics that are not well understood. This thesis elucidates key fundamentals of this process. We develop novel instrumentation that improves over prior approaches by examining the development of order at all the length scales of interest (in-situ rheo-optics, synchrotron small angle X-ray scattering (SAXS), and wide angle X-ray diffraction (WAXD), and ex-situ electron and optical microscopy); and by reducing the sample requirement by about three orders of magnitude, opening the way to study of model materials. We investigate a polydisperse, commercial Ziegler-Natta isotactic polypropylene (iPP) using the short term shearing protocol pioneered by the group of Janeschitz-Kriegl which imposes a well defined thermal and flow history on the polymer.\r\n\r\nRheo-optical investigations reveal that imposition of brief intervals of shear (less than a thousandth of the quiescent crystallization time) reduces the crystallization time by two orders of magnitude at a crystallization temperature of 141\u00b0C. Above a critical value of the shear stress, there is a transition to highly oriented growth with increase in shearing duration. This transition is correlated with changes in the transient behavior during flow and the semicrystalline morphology observed exsitu. During flow, we observe the generation of long-lived, highly oriented structures (evident in the transient birefringence) under all conditions that induce subsequent growth of highly oriented crystallites. In turn, the development of oriented crystallites observed in-situ after cessation of flow correlates with development of a \"skin-core\" morphology observed ex-situ.\r\n\r\nThe transient structures that develop during flow are identified as oriented [alpha]-phase crystals by WAXD, and show an unexpected temperature dependence for their time of formation: with increase in temperature, they occur at shorter times after startup of flow. This very unusual temperature dependence is strikingly similar to that for rheological processes, and is in contrast to the exponential increase expected for crystallization time-scales. Thus, the transition to anisotropic nucleation in polymers subjected to flow follows a non-classical kinetic pathway controlled by the formation of a transient, highly oriented metastable melt state.\r\n\r\nIn-situ synchrotron SAXS and WAXD reveal that for shearing conditions that lead to anisotropic morphologies, crystals that are highly oriented in the flow direction develop during shear, templating the formation of crystallites after flow cessation. In the densely nucleated skin regions, ex-situ TEM shows lamellae growing radially from oriented central \"shish\" structures until they impinge to form the \"shish-kebab\" or row-nucleated structures. Under milder shear conditions, the rate of crystallization is gradual compared to strong shearing, and less oriented morphologies develop. Interestingly the ratio of parent to the crosshatched, epitaxial daughter lamellae for the oriented crystallites increases with increase in shearing time, imposed wall shear stress and temperature.\r\n\r\nOur data suggests a mechanistic model for shear-enhanced crystallization: the rheologically-controlled formation of a critical anisotropic distribution of chain segments in the melt upon imposition of flow nucleates oriented crystallites. For intense shearing conditions, these line-nuclei are long and dense. Row nucleated structures develop from these line nuclei as lamellae grow radially to form fully impinged structures. For milder shearing conditions, lower nucleation densities lead to the development of less oriented structures.\r\n", "doi": "10.7907/8SJ5-HM09", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:17544", "collection": "thesis", "collection_id": "17544", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07212025-050343265", "primary_object_url": { "basename": "Chu_J_1999.pdf", "content": "final", "filesize": 33433151, "license": "other", "mime_type": "application/pdf", "url": "/17544/1/Chu_J_1999.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Computational Explorations of Life", "author": [ { "family_name": "Chu", "given_name": "Johan", "clpid": "Chu-Johan" } ], "thesis_advisor": [ { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" } ], "thesis_committee": [ { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Adami", "given_name": "Christoph Carl", "orcid": "0000-0002-2915-9504", "clpid": "Adami-C-C" }, { "family_name": "Peck", "given_name": "Charles W.", "clpid": "Peck-C-W" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "Artificial Life, the creation and study of man-made systems that exhibit the characteristics\r\nof life, is a young and still emerging field. The goals of Artificial Life\r\nare two-fold; to gain knowledge about and from biology. The Artificial Life system\r\nsanda, which extends upon previous systems tierra and avida, was designed to help in\r\ninvestigations into the statistical nature of evolution. As such, it is a model of the\r\nsimplest living, evolving organisms. Experiments involving tierra, avida, and sanda\r\nwere the inspiration for investigations into the causes of apparently scale-free dynamics\r\nfound in these systems. These investigations lead to identification of a branching\r\nprocess that explains the scale-free dynamics of not only these Artificial Life systems,\r\nbut also those manifested in the taxon rank-frequency distributions of biology and in\r\nthe size distributions of avalanches in \"self-organized critical\" sandpile models. This\r\nbranching process can quantitatively predict-with no free parameters-the pattern\r\nof the observed distributions, including their divergence from a true power law. Further,\r\nthe branching process gives insight into the universal mechanisms involved in\r\nthe creation of, and divergence from, scale-free dynamics in these systems, including\r\na definition of order and control parameters reminiscent of those from second-order\r\nphase transit ions in statistical physics.", "doi": "10.7907/vkq7-ng96", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:17544", "collection": "thesis", "collection_id": "17544", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07212025-050343265", "primary_object_url": { "basename": "Chu_J_1999.pdf", "content": "final", "filesize": 33433151, "license": "other", "mime_type": "application/pdf", "url": "/17544/1/Chu_J_1999.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Computational Explorations of Life", "author": [ { "family_name": "Chu", "given_name": "Johan", "clpid": "Chu-Johan" } ], "thesis_advisor": [ { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" } ], "thesis_committee": [ { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Adami", "given_name": "Christoph Carl", "orcid": "0000-0002-2915-9504", "clpid": "Adami-C-C" }, { "family_name": "Peck", "given_name": "Charles W.", "clpid": "Peck-C-W" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "Artificial Life, the creation and study of man-made systems that exhibit the characteristics\r\nof life, is a young and still emerging field. The goals of Artificial Life\r\nare two-fold; to gain knowledge about and from biology. The Artificial Life system\r\nsanda, which extends upon previous systems tierra and avida, was designed to help in\r\ninvestigations into the statistical nature of evolution. As such, it is a model of the\r\nsimplest living, evolving organisms. Experiments involving tierra, avida, and sanda\r\nwere the inspiration for investigations into the causes of apparently scale-free dynamics\r\nfound in these systems. These investigations lead to identification of a branching\r\nprocess that explains the scale-free dynamics of not only these Artificial Life systems,\r\nbut also those manifested in the taxon rank-frequency distributions of biology and in\r\nthe size distributions of avalanches in \"self-organized critical\" sandpile models. This\r\nbranching process can quantitatively predict-with no free parameters-the pattern\r\nof the observed distributions, including their divergence from a true power law. Further,\r\nthe branching process gives insight into the universal mechanisms involved in\r\nthe creation of, and divergence from, scale-free dynamics in these systems, including\r\na definition of order and control parameters reminiscent of those from second-order\r\nphase transit ions in statistical physics.", "doi": "10.7907/vkq7-ng96", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:2684", "collection": "thesis", "collection_id": "2684", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06222005-110302", "primary_object_url": { "basename": "Yurkovetsky_Y_1998.pdf", "content": "final", "filesize": 11158780, "license": "other", "mime_type": "application/pdf", "url": "/2684/1/Yurkovetsky_Y_1998.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. Statistical mechanics of bubbly liquids. II. Behavior of sheared suspensions of non-Brownian particles", "author": [ { "family_name": "Yurkovetsky", "given_name": "Yevgeny", "clpid": "Yurkovetsky-Y" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Brennen", "given_name": "Christopher E.", "clpid": "Brennen-C-E" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Hunt", "given_name": "Melany L.", "clpid": "Hunt-M-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nI. Statistical mechanics of bubbly liquids. The dynamics of bubbles at high Reynolds numbers is studied from the viewpoint of statistical mechanics. Individual bubbles are treated as dipoles in potential flow. A virtual mass matrix of the system of bubbles is introduced, which depends on the instantaneous positions of the bubbles, and is used to calculate the energy of the bubbly flow as a quadratic form of the bubbles' velocities. The energy is shown to be the system's Hamiltonian and is used to construct a canonical ensemble partition function, which explicitly includes the total impulse of the suspension along with its energy. The Hamiltonian is decomposed into an effective potential due to the bubbles' collective motion and a kinetic term due to the random motion about the mean. An effective bubble temperature - a measure of the relative importance of the bubbles' relative to collective motion--is derived with the help of the impulse-dependent partition function. Two effective potentials are shown to operate: one, due to the mean motion of the bubbles, dominates at low bubble temperatures where it leads to their grouping in flat clusters normal to the direction of the collective motion, while the other, temperature invariant, is due to the bubbles' position-dependent virtual mass and results in their mutual repulsion. Numerical evidence is presented for the existence of the effective potentials, the condensed and dispersed phases and a phase transition.\r\n\r\nII. Behavior of sheared suspensions of non-Brownian particles. Suspensions of non-Brownian particles in simple shear flow of a Newtonian solvent in the range of particle phase concentration, [...], from 0.05 to 0.52, are studied numerically by Stokesian Dynamics. The simulations are a function of [...] and the dimensionless shear rate, [...], which measures the relative importance of the shear and short-ranged interparticle forces. The pair-distribution functions, shear viscosity, normal stress differences, suspension pressure, long-time self-diffusion coefficients, and mean square of the particle velocity fluctuations in the velocity-gradient and vorticity directions are computed, tabulated and plotted. In concentrated suspensions ([...] > 0.45), two distinct microstructural patterns are shown to exist at the highest and lowest shear rates. At [...] = 0.1 the particles form hexagonally packed strings in the flow direction. As [...] increases, the strings are gradually being replaced by non-compact clusters of particles kept together by strong lubrication forces while the particle pair-distribution displays a broken fore-aft symmetry. These changes in the microstructure are accompanied by increases in the shear viscosity, normal stress differences, suspension pressure, longtime self-diffusion coefficients, and fluctuational motion. Agreement is found between the simulation results and the theoretical predictions of Brady and Morris (1997).\r\n", "doi": "10.7907/NMJQ-2X32", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:325", "collection": "thesis", "collection_id": "325", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01242008-095827", "type": "thesis", "title": "I. Dynamics of Block Copolymer Nanostructures. II. Polymerizability of Cyclic Olefins and Ring-Closing Metathesis", "author": [ { "family_name": "Chen", "given_name": "Zhong-Ren", "orcid": "0000-0002-2929-9566", "clpid": "Chen-Zhong-Ren" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Ko", "given_name": "Chan U.", "clpid": "Ko-Chan-U" }, { "family_name": "Doi", "given_name": "Masao", "clpid": "Doi-Masao" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Self-assembly of block copolymers provide versatile means to create nanostructures with potential applications in nanotechnologies. The form and size of these structures are controlled by the type and the length of each block, and the number of blocks. Active processing using symmetry-breaking fields such as flow can extend self-assembled order into the macroscopic dimensions, thus gain desired directional properties, such as transport, optical, and electrical properties.
\r\n\r\nTowards the integrated synthesis and processing of functional block copolymer nanostructures, dynamics and thermodynamics of block copolymer nanostructures must be understood. The dynamics of flow-induced alignment of block copolymers will provide the basis to predict the direction, rate, and degree of alignment, while defect dynamics and thermodynamics will give insight into the possibilities of formation of desired nanostructures. In chapter 1, I will overview key issues of flow-induced alignment based on literature and new results from the first two chapters of the thesis. A three-dimensional mapping summarizes the flow behavior of diblock copolymers in terms of molecular characteristics and processing conditions. Various mechanisms that had been proposed since two decades ago are reviewed and re-evaluated.
\r\n\r\nIn chapter 2, I will present detailed results revealed by a powerful experimental method, which combines in-situ rheo-optical measurements and ex-situ structural characterization by electron microscopy and x-ray scattering. A PS-PI (10K-10K) diblock is used as a model system. Three different trajectories of alignment are investigated: perpendicular alignment and two qualitatively different routes to parallel alignment. At the highest frequencies, symmetry arguments explain the transient development of a bimodal texture en route to alignment of layers parallel to the planes of shear. At lower frequencies, larger scale relaxations introduce rearrangements out of the deformation plane that permit formation of lamellae perpendicular to the shear plane. These explain the change in character of the pathway to parallel alignment and the emergence of perpendicular alignment with decreasing frequency. For each trajectory in general, the initial 'fast' process enhances not only the projection of the orientation distribution that corresponds to the final state, but also increases other projections of the distribution; the late-stage 'slow' process eliminates these other projections and perfects a single alignment.
\r\n\r\nABC triblock copolymer can form a fascinating array of nanostructures. Phase behavior, dynamics of oscillatory-shear alignment, and other issues raised by ABC triblock copolymers, such as dynamics of lamellar perforation in three-nanophase-separated states will be discussed in chapter 3. Both thermotropical and shear-induced phase transitions are observed. Dramatic changes of morphology and alignment behavior are induced simply by switching the permutation of the blocks, molecular size, shear condition, and temperature. In three-nanophase-separated lamellar materials, a new type of defect is found: correlated perforation. As these defects annihilate upon annealing, long range correlations produce striking patterns, including those that resemble a ship's wake. The creation and evolution of these defect structures present challenge and opportunities in developing novel nanostructures.
\r\n\r\nOlefin metathesis by transition metal complex has been a powerful method in polymer and organic synthesis. In chapter 4, I will present a model to predict the ring-chain equilibria in ring-opening-closing reaction. Statistical mechanics and molecular mechanics provide the basic tools in problem formulation and parameter determination. Polymerizability of cyclic olefins are predicted by this model, and agree well with ring-opening metathesis polymerization experiments. We have extended this model to assist ring-closing metathesis of eight-member rings, which can be a useful starting material for drug synthesis.
", "doi": "10.7907/xd1r-aj40", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:17585", "collection": "thesis", "collection_id": "17585", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08012025-174712767", "primary_object_url": { "basename": "Martin_JI_1998.pdf", "content": "final", "filesize": 35602016, "license": "other", "mime_type": "application/pdf", "url": "/17585/1/Martin_JI_1998.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Statistical Mechanics of End-Attached Polymer Interfaces", "author": [ { "family_name": "Martin", "given_name": "Jeremy Isaac", "orcid": "0000-0001-7233-7217", "clpid": "Martin-Jeremy-Isaac" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation discusses several closely related problems involving end attached polymers\r\nat interfaces. The studies share a numerical self-consistent field approach which is described\r\nin detail in Chapter 1.
\r\n\r\nIn Chapter 2, we consider irreversible polymer brushes (polymers densely end tethered\r\nto a surface). First, we discuss the adequacy of second virial treatments of interchain\r\ninteractions. Next we examine the extent of interbrush penetration between compressed\r\npolymer brushes, and its effect on the interactions between them. Then we identify scaling\r\nvariables which control the behavior of polymer brushes in polymeric solvents. Finally we\r\ninvestigate brush configurations and interactions in mixed solvents, where nonmonotonic\r\ninteraction profiles are predicted with a longer range weak attraction, and strong repulsion\r\nat shorter separations.
\r\n\r\nIn Chapter 3, we discuss the modification of spreading properties of a liquid on a solid\r\nsurface by the addition of end-adsorbing polymers. An end-adsorption polymer additive\r\ncan lead an otherwise non-spreading liquid to spread. A phase diagram for spreading of a\r\nliquid drop of fixed volume as a function of the concentration of end-adsorbing polymers\r\nand the energy of end-adsorption to the surface is obtained. The equilibrium thickness of\r\na spread film is also calculated, and is shown to be closely related to the thickness of a\r\nself-assembled polymer brush in an unbounded fluid and relatively insensitive to the bare\r\nspreading power of the liquid or the Hamaker constant, which determine the equilibrium\r\nthickness of a film of a simple liquid.
\r\n\r\nFinally, in Chapter 4, we study the interaction forces between two plates in a semi-dilute\r\nsolution of polymers each having one weakly adsorbing end-group. This system exhibits\r\nboth repulsive and attractive interactions of comparable magnitude and well-separated\r\nlength scales. The repulsion has a length scale of the end-to-end distance of the endadsorbed\r\npolymer, and a magnitude which is proportional to the end-adsorption energy\r\nand the volume fraction of the polymer, and inversely proportional the chain molecular\r\nweight. At plate separations of order the correlation length of the solution, a depletion\r\nattraction sets in with a magnitude that scales with the bulk osmotic pressure.
", "doi": "10.7907/4pc9-vz14", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:323", "collection": "thesis", "collection_id": "323", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01242008-085938", "primary_object_url": { "basename": "Kusaka_i_1998.pdf", "content": "final", "filesize": 6819732, "license": "other", "mime_type": "application/pdf", "url": "/323/1/Kusaka_i_1998.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Molecular Theory of Vapor Phase Nucleation", "author": [ { "family_name": "Kusaka", "given_name": "Isamu", "clpid": "Kusaka-Isamu" } ], "thesis_advisor": [ { "family_name": "Seinfeld", "given_name": "John H.", "orcid": "0000-0003-1344-4068", "clpid": "Seinfeld-J-H" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Seinfeld", "given_name": "John H.", "orcid": "0000-0003-1344-4068", "clpid": "Seinfeld-J-H" }, { "family_name": "Gavalas", "given_name": "George R.", "orcid": "0000-0003-1468-6835", "clpid": "Gavalas-G-R" }, { "family_name": "Flagan", "given_name": "Richard C.", "orcid": "0000-0001-5690-770X", "clpid": "Flagan-R-C" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "An attempt has been made to establish the foundation of molecular level theory of vapor phase nucleation. We have focused on evaluating the reversible work of cluster formation and followed two major trends in this direction, namely, statistical mechanical density functional theory and molecular level simulation.\r\n\r\nWe applied density functional theory to heterogeneous nucleation onto an ion. Our prime interest is to predict a sign preference of nucleation rate, which has been experimentally observed yet remained inexplicable in the classical framework. The theory indicates that asymmetry in ion-molecule interaction is directly responsible for the sign preference. The predicted sign dependence decreases as the supersaturation is increased. Our results from density functional theory agree well with the existing experimental observations.\r\n\r\nMolecular simulation offers an alternative to molecular level approach. A long-standing issue of fundamental importance in cluster simulation is the precise definition of a cluster. Thus far, all attempts of defining a cluster had introduced ad hoc criteria to determine unambiguously whether a given molecule in the system belongs to vapor or to a cluster for any instantaneous configuration of molecules. From a careful examination of the context in which a cluster should be introduced into nucleation theory, we conclude that such a criterion is unnecessary. Then, we present a new approach to cluster simulation which is free of any arbitrariness involved in the definition of a cluster. Instead, it preferentially and automatically generates the physical clusters, defined as the density fluctuations that lead to nucleation, and determines their equilibrium distribution in a single simulation. The latter feature permits one to completely bypass the computationally demanding free energy evaluation that is necessary in a conventional simulation. The method is applied first to water using the SPC/E model. We then turn to H2SO4/H2O binary system to obtain a large section of the reversible work surface. The resulting surface is markedly different from that in classical theory and indicates that the rate limiting step of stable particle formation in this system is the binary collision of the sulfuric acid hydrates.\r\n", "doi": "10.7907/jwwk-0n13", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:17585", "collection": "thesis", "collection_id": "17585", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08012025-174712767", "primary_object_url": { "basename": "Martin_JI_1998.pdf", "content": "final", "filesize": 35602016, "license": "other", "mime_type": "application/pdf", "url": "/17585/1/Martin_JI_1998.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Statistical Mechanics of End-Attached Polymer Interfaces", "author": [ { "family_name": "Martin", "given_name": "Jeremy Isaac", "orcid": "0000-0001-7233-7217", "clpid": "Martin-Jeremy-Isaac" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation discusses several closely related problems involving end attached polymers\r\nat interfaces. The studies share a numerical self-consistent field approach which is described\r\nin detail in Chapter 1.
\r\n\r\nIn Chapter 2, we consider irreversible polymer brushes (polymers densely end tethered\r\nto a surface). First, we discuss the adequacy of second virial treatments of interchain\r\ninteractions. Next we examine the extent of interbrush penetration between compressed\r\npolymer brushes, and its effect on the interactions between them. Then we identify scaling\r\nvariables which control the behavior of polymer brushes in polymeric solvents. Finally we\r\ninvestigate brush configurations and interactions in mixed solvents, where nonmonotonic\r\ninteraction profiles are predicted with a longer range weak attraction, and strong repulsion\r\nat shorter separations.
\r\n\r\nIn Chapter 3, we discuss the modification of spreading properties of a liquid on a solid\r\nsurface by the addition of end-adsorbing polymers. An end-adsorption polymer additive\r\ncan lead an otherwise non-spreading liquid to spread. A phase diagram for spreading of a\r\nliquid drop of fixed volume as a function of the concentration of end-adsorbing polymers\r\nand the energy of end-adsorption to the surface is obtained. The equilibrium thickness of\r\na spread film is also calculated, and is shown to be closely related to the thickness of a\r\nself-assembled polymer brush in an unbounded fluid and relatively insensitive to the bare\r\nspreading power of the liquid or the Hamaker constant, which determine the equilibrium\r\nthickness of a film of a simple liquid.
\r\n\r\nFinally, in Chapter 4, we study the interaction forces between two plates in a semi-dilute\r\nsolution of polymers each having one weakly adsorbing end-group. This system exhibits\r\nboth repulsive and attractive interactions of comparable magnitude and well-separated\r\nlength scales. The repulsion has a length scale of the end-to-end distance of the endadsorbed\r\npolymer, and a magnitude which is proportional to the end-adsorption energy\r\nand the volume fraction of the polymer, and inversely proportional the chain molecular\r\nweight. At plate separations of order the correlation length of the solution, a depletion\r\nattraction sets in with a magnitude that scales with the bulk osmotic pressure.
", "doi": "10.7907/4pc9-vz14", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:4493", "collection": "thesis", "collection_id": "4493", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11102005-141042", "primary_object_url": { "basename": "Yan_y_1997.pdf", "content": "final", "filesize": 17311051, "license": "other", "mime_type": "application/pdf", "url": "/4493/1/Yan_y_1997.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Preparation of zeolite ZSM-5 membranes", "author": [ { "family_name": "Yan", "given_name": "Yushan", "clpid": "Yan-Yushan" } ], "thesis_advisor": [ { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "thesis_committee": [ { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Giapis", "given_name": "Konstantinos P.", "clpid": "Giapis-K-P" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nZeolite ZSM-5 membranes were prepared on porous [...] disks by in-situ crystallization using a clear solution of optimized composition [...]. During the synthesis, the disk was fixed horizontally at the air-liquid interface and a continuous polycrystalline zeolite film of about 10 \u00b5m thickness formed on the bottom surface of disk. Extensive experimentation was carried out to find the optimal composition. Pure gas permeation measurements of the most successful preparation yielded hydrogen:isobutane and n-butane:isobutane ratios of 151 and 18 at room temperature and 54 and 31 at 185\u00b0C, respectively.\r\n\r\nElectron probe microanalysis of the cross section of a membrane prepared on a bare alumina disk revealed a layer of crystalline or amorphous silica extending 80 \u00b5m inside the pores of the support. It is believed that this internal layer adds resistance to permeation and degrades selectivity. To limit the excessive penetration of siliceous species into the support pores, a diffusion barrier was introduced into the pores of the support prior to zeolite crystallization by impregnating the disk with a 1:1 molar mixture of furfuryl alcohol and tetraethylorthosilicate, polymerizing the mixture retained in the disk, and carbonizing the resulting polymer. Following carbonization, a partial carbon burnoff was carried out to generate a carbon-free region near the surface of the support. Membranes synthesized using barriers have n-butane flux and n-butane:isobutane selectivity 2.7 x [...] and 45 at 185\u00b0C which are, respectively, about 1.6 and 4 times as large as those of membranes prepared without the use of barriers.\r\n\r\nThe n-butane:isobutane selectivity of ZSM-5 membranes was substantially improved (e.g. 322 vs. 45 at 185\u00b0C) by a post-synthetic coking treatment which was accomplished by impregnating the membranes with liquid 1,3,5-triisopropylbenzene (TIPB) for 24 hours at room temperature and then calcining them in air at 500\u00b0C for 2 hours. Calcination at 500\u00b0C for up to 30 hours does not destroy the high n-butane:isobutane selectivity. Thermogravimetric analysis experiments suggest that microdefects in the zeolite membranes were selectively eliminated by the TIPB coking treatment while the intracrystalline pore space of the ZSM-5 was not affected.\r\n\r\nA model of surface-induced nucleation, crystal growth, and crystal adhesion was proposed for the aforementioned heterogeneous hydrothermal synthesis system. During the synthesis, aluminosilicates in the aged solution interact favorably with and travel toward the [...] surface, resulting in concentration and nucleation in the vicinity of the surface. Some of the nuclei become attached to the surface and grow into a zeolite film while others settle and produce loose zeolite crystals at the bottom of the autoclave. The nutrients for crystal growth is supplied by active gel particles and the synthesis solution. Surface -OH groups on the substrate appear important for crystal adhesion via condensation. As for zeolite membrane formation on a surface of certain area, the location and orientation of the surface as well as the amount of synthesis liquid accessible to the surface are critical for the quality of the zeolite membrane.\r\n", "doi": "10.7907/05FZ-JS07", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:17603", "collection": "thesis", "collection_id": "17603", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08072025-210544236", "primary_object_url": { "basename": "Baxter-Drayton_YV_1997.pdf", "content": "final", "filesize": 36191781, "license": "other", "mime_type": "application/pdf", "url": "/17603/1/Baxter-Drayton_YV_1997.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "The Dynamics of Flocculated Dispersions", "author": [ { "family_name": "Baxter-Drayton", "given_name": "Yvette Valencia", "clpid": "Baxter-Drayton-Yvette-Valencia" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Gavalas", "given_name": "George R.", "orcid": "0000-0003-1468-6835", "clpid": "Gavalas-G-R" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The rheological behavior of Brownian electrorheological (ER) fluids is studied\r\nas a model for flocculated colloidal dispersions. The ER fluid has the advantages\r\nthat the interparticle potential energy can be varied by simply changing the applied\r\nfield strength, and the microstructure consists of essentially linear chains of particles\r\naligned with the field direction. Studies of the quiescent suspension structure find a\r\ndispersed region, an equilibrium flocculated region, and a kinetically flocculated region\r\nfor low, moderate, and large attractive potential well depths, Umin/kT, respectively.\r\nUnder simple shear flow, the suspension has a high-shear-rate Newtonian viscosity\r\nand a shear thinning viscosity at lower shear rates. For moderate attractive potential\r\nwell depths the suspension has a low-shear viscosity that scales as exp(Umin/kT).\r\nFurthermore, the low-shear limiting behavior is seen at shear rates that scale as\r\nexp(-Umin/kT). The first normal stress difference is also presented. It was found\r\nthat due to the electric field the suspension structure is anisotropic with respect to\r\nthe compressional axis, and the first normal stress difference does not decay with the\r\nshear rate as it does for Brownian hard-spheres, but approaches a low-shear limiting\r\nvalue.
\r\n\r\nA theory is proposed that makes use of the time scale of diffusion for aggregated\r\nparticles out of their mutual potential well, \u03c4 ~ (a2/D)(kT/Umin)exp(Umin/kT),\r\nmuch in the spirit of the Eyring theory, to describe the rheology of the flocculated\r\ndispersion. Here a is the particle radius and D is the diffusivity of an isolated particle.\r\nWhen the shear rate is non-dimensionalized by \u03c4, the reduced viscosity data for all\r\nfield strengths collapse onto a single universal curve. Although we use a relatively\r\nsmall monolayer suspension, our simulation results compare well to the limited experimental\r\nand theoretical work on Brownian ER suspensions. The scaling relationship\r\nfor the low-shear viscosity has also been evidenced in other studies of flocculated\r\ndispersions.
\r\n\r\nThe model is tested for its general applicability by a study of the rheology of\r\na three-dimensional flocculated dispersion with an isotropic potential by molecular\r\ndynamics simulation and by analysis of experimental data obtained independently by\r\nBuscall, McGowan and Morton-Jones for a depletion flocculated dispersion. In both\r\ncases the suspension has a low-shear viscosity that scales exponentially with the pair\r\npotential well depth, and the low-shear limiting behavior was observed at a shear rate\r\nthat scales inverse exponentially with the pair potential well depth, Umin/kT. The\r\nreduced viscosity data collapse onto a single curve when plotted as a function of the\r\nshear rate non-dimensionalized by the escape time scale, and the model was found to\r\npredict the reduced curves.
\r\n\r\n", "doi": "10.7907/vqnw-np85", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:109", "collection": "thesis", "collection_id": "109", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01102008-085702", "primary_object_url": { "basename": "Morris_jf_1996.pdf", "content": "final", "filesize": 9844570, "license": "other", "mime_type": "application/pdf", "url": "/109/1/Morris_jf_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Suspensions: microstructure, diffusion, and inhomogeneous flow", "author": [ { "family_name": "Morris", "given_name": "Jeffrey Franklin", "clpid": "Morris-J-F" } ], "thesis_advisor": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA theory of self-diffusivity in sheared suspensions valid for any particle volume fraction [phi], Peclet number Pe, and lengthscale of disturbance in [phi] is developed. The theory is applied to the determination of the full tensor self-diffusivity in a weakly- sheared (Pe << 1) suspension of hydrodynamically-interacting hard spheres and a strongly-sheared (Pe >> 1) suspension of hard spheres without hydrodynamic interactions, both at [phi] << 1.\r\n\r\nThe influence of weak Brownian motion alone and in conjunction with a repulsive interparticle force of hard-sphere type upon the pair-distribution function, g(r) where r is the separation vector of a pair of particles, is analyzed for a suspension of spheres at Pe >> 1 and [phi] << 1. At large Pe, the radial fluxes of pair probability due to advection and Brownian diffusion balance in a thin [...] boundary layer at contact, with a the sphere radius. The boundary-layer analyses demonstrate that Brownian diffusion renders g finite at contact in the absence of interparticle forces, and that within the boundary layer there is generally a large excess of pair probability along the compressional axes. By calculation of the bulk normal stress differences in the case with repulsive forces, it is shown how this asymmetry of the microstructure yields non-Newtonian constitutive behavior in the limit Pe[superscript -1] = 0.\r\n\r\nHydrodynamic resistance functions relating the particle and bulk motions to the bulk isotropic stress are developed. Application of these functions is demonstrated by calculations of the shear-induced correction to the osmotic pressure and the particle contribution to the pressure in a sheared lattice.\r\n\r\nPressure-driven flow in a channel at vanishing Reynolds number of a suspension of particles denser than the suspending fluid has been dynamically simulated by Stokesian Dynamics over ranges of the particle fraction, channel width, and a buoyancy parameter characterizing the relative strength of the buoyancy to shearing forces. The predictions of the flow by the suspension-balance model are in good agreement with simulation results.\r\n", "doi": "10.7907/069F-Z696", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:15", "collection": "thesis", "collection_id": "15", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01032008-082416", "primary_object_url": { "basename": "Rubin_sf_1996.pdf", "content": "final", "filesize": 12348211, "license": "other", "mime_type": "application/pdf", "url": "/15/1/Rubin_sf_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Viscoelasticity and dynamics of alignment in side-group liquid crystalline polymers", "author": [ { "family_name": "Rubin", "given_name": "Susan Felicia", "clpid": "Rubin-S-F" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Hubbell", "given_name": "Jeffrey A.", "clpid": "Hubbell-J-A" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nSide-group liquid-crystalline polymers (SG-LCPs) consist of a flexible polymeric backbone and rigid mesogens (molecules forming LC phases), attached laterally to the backbone via flexible spacers. Since the dynamics of the mesogen field and polymeric backbone are partially decoupled, uniformly-aligned SG-LCP materials show promise in a variety of applications such as non-linear optical materials, optical data storage media, and stress sensors, which require switching of the mesogen orientation. Recent work has shown that uniform alignment of SG-LCP materials can be accomplished using flow-fields. However, the mechanisms of alignment, which are essential for the development of effective and rational processing strategies for the SG-LCP materials, remain poorly understood. To address this need, we focus on the viscoelastic properties of nematic and smectic SG-LCPs and the dynamics of field-induced alignment of SG-LCPs.\r\n\r\nWe have investigated the dynamic mechanical response of SG-LCPs having methacrylate backbone, hexamethylene spacer, and phenyl benzoate mesogens as a function of molecular weight in the isotropic, nematic, and smectic phases [...], and have discovered a unique molecular-weight dependence of the sensitivity of the dynamic modulus to nematic order of the melt. Nematic order produced a profound change in the dynamics of the entangled SG-LPCs relative to the isotropic phase; however, this effect was absent in the unentangled SG-LCPs. In SGLCPs with smectic order, there was increase in the elastic character of the fluid with smectic ordering, but the incremental effect in a system that was entangled was relatively small. Oscillatory shear with large amplitude [...] induced macroscopic alignment in the nematic phase for all the SG-LCPs studied and could be used to alter the microstructure in the smectic liquid. Shearing the smectic phase produced a decrease in modulus, whereas shearing in the nematic phase followed by cooling into the smectic phase produced an increase in modulus.\r\n\r\nTo assess the effect of the coupling between the mesogen and the backbone on field- induced orientation of nematic SG-LCPs, we have compared magnetically aligned and flow-aligned nematic SG-LCPs. Magnetic forces act primarily on the mesogens, and the backbone conformation changes to accommodate the torques on its pendant mesogens. In contrast, oscillatory shear can couple to the relaxation modes of both the director field and backbone. We have discovered that while the flow-aligned material exhibits distinct low-frequency relaxation dynamics, the relaxation of magnetically- aligned monodomains is indistinguishable from that of polydomain nematic melts. This suggests that flow alignment and magnetic alignment produce qualitatively distinct changes in the fluid miscostructure. We have further compared the processes of shear- and magnetic-alignment by monitoring the evolution of director orientation in nematic SG-LCP melts, in-situ, through visible transmittance (related to the liquid-crystalline domain size) and visible birefringence (related to the molecular orientation).", "doi": "10.7907/bdjk-n270", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:18", "collection": "thesis", "collection_id": "18", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01032008-092017", "primary_object_url": { "basename": "Shnek_dr_1996.pdf", "content": "final", "filesize": 14591522, "license": "other", "mime_type": "application/pdf", "url": "/18/1/Shnek_dr_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Targeting of Proteins and Protein Analogs to Metal-Chelating Lipid Vesicles", "author": [ { "family_name": "Shnek", "given_name": "Deborah Rebecca", "clpid": "Deborah Rebecca" } ], "thesis_advisor": [ { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" } ], "thesis_committee": [ { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Chan", "given_name": "David C.", "orcid": "0000-0002-0191-2154", "clpid": "Chan-D-C" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis investigation demonstrates that new metal-chelating lipids formed into mixed vesicles can bind to a variety histidine-rich ligands through metal coordination. Our results show the feasibility of metal-chelating lipids as a method for targeting histidine-rich compounds to lipid interfaces. Interesting metal chelating lipid materials for protein orientation studies, matching the surface distribution of surface residues, protein drug delivery, and for two-dimensional protein crystallization could be made with chelating-lipids. Engineered proteins containing a histidine \"tag\" or proteins with natural surface histidine residues are easily targeted to the interface using metal binding.\r\n\r\nBoth metal binding and histidine-rich ligand binding were investigated with mixed metal-chelating lipid vesicles. New metal-chelating lipids containing an iminodiacetate (IDA) chelating-moiety were formed into mixed vesicles and shown to bind transition metal ions through the lipid headgroup. Metal binding was characterized through calorimetry, freeze-etch microscopy, light scattering, ESR, and fluorescence studies. Fluorescently-labeled lipids containing iminodiacetate showed a large change in the fluorescence emission spectra upon metal binding, behavior which has proven useful for a vesicle-based metal sensor.\r\n\r\nMetal-loaded vesicles bound a model protein specifically through surface-accessible histidines, as shown using ESR studies. Equilibrium binding measurements showed at least an order of magnitude increase in binding affinity of the protein for the membrane when metal was present. The association constants determined through isothermal titration calorimetry for a model bivalent histidine compound binding to metal-chelating lipid bilayers were of the order of [...], while monovalent binding constants were of the order [...].\r\n\r\nLipid re-organization upon ligand binding was probed with model histidine compounds and histidine polymers using fluorescently-labeled metal-chelating lipid vesicles. The ability of lipids to form multivalent ligand-lipid complexes was investigated using the formation of lipid excimers, as demonstrated by fluorescence measurements of the E/M intensity ratio. Histidine content of model compounds determines the magnitude of the effect on the fluorescence emission spectra. Histidine polymers showed a larger increase of the E/M ratio than the smaller bivalent or monovalent compounds. Combining equilibrium binding results obtained with model complexes and results from fluorescence experiments, studies with metal-chelating vesicles support multivalent coordination and reorganization of the lipids by histidine-rich ligands.", "doi": "10.7907/ctnn-4057", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:4988", "collection": "thesis", "collection_id": "4988", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12132007-085351", "primary_object_url": { "basename": "Gupta_vk_1996.pdf", "content": "final", "filesize": 8373125, "license": "other", "mime_type": "application/pdf", "url": "/4988/1/Gupta_vk_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Controlling molecular and microstructural alignment in anisotropic polymer systems", "author": [ { "family_name": "Gupta", "given_name": "Vinay Kumar", "clpid": "Gupta-V-K" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Molecular and microstructural orientation plays a key role in determining the useful mechanical, optical and electrical properties of a large class of polymeric materials. Realization of the technological promise of these materials requires rational control of the microstructure and understanding of the processing-structure-property relationships. Towards this end, we focus on the material properties and dynamical processes that affect molecular order of two complex polymeric systems (a) Ultra-thin Langmuir-Blodgett films of a hairy-rodlike polymer, and (b) Lamellar diblock copolymer melts of polystyrene and polyisoprene (PS-PI).\n\nWe accomplish our objective by improving and tying together existing analytic techniques into instruments extremely effective for measuring molecular orientation and order. For fundamental insights into the nature of alignment in ultra-thin (~ few nanometers thick) LB films, we integrate laser scanning microscopy (LSM) with polarization-modulation (PM) polarimetry. PM-LSM possesses high spatial resolution, sensitivity and speed, and allows us to image the anisotropy in films as thin as two molecular layers. To monitor the dynamics of flow alignment in diblock copolymers, in situ and in real time, we combine polarization-modulation polarimetry with rheometry. This rheo-optical technique enables us to monitor the evolution of microstructure by measuring the optical anisotropy, and correlate it with changes in macroscopic mechanical observables, such as stress and strain.\n\nUsing PM-LSM we have investigated the interplay of molecular weight, layer thickness and thermal annealing in controlling molecular order in rodlike polymer LB films. Upon investigating two different molecular weights of the polymer, we find lowering of molecular order in deposited films with increase in molecular weight. Furthermore, thermal annealing improves alignment only for films of shorter rodlike polymers (~ lower molecular weight). We believe that the underlying cause for these results is a difference in the structure of the deposited films for the longer polymer because of the relative changes in timescales for the macromolecular relaxation and the monolayer deformation during deposition. We also find that for both molecular weights, the substrate exerts an anchoring effect on the first two layers adjacent to it and suppresses improvement in alignment on annealing. This inability to improve alignment has important consequences for applications such as molecular electronics where monolayers or bilayers having a high degree of orientation are required.\n\nIn-situ measurement of flow birefringence during oscillatory shear alignment, clarifies the evolution of the lamellar orientation distribution for a diblock copolymer melt. Shearing results in \"parallel\" or \"perpendicular\" alignment i. e. layers normal to either the velocity gradient or the vorticity axis, respectively (Figure 1.1). Both states of alignment occur via an initial \"fast\" process followed by a \"slow\" one. The fast process is dominated by the depletion of the projection of the orientation distribution along either the perpendicular direction or the \"transverse\" direction (layers normal to the flow). This resulting biaxial distribution is then transformed into a well-aligned uniaxial one during the slow process. Surprisingly, at particular frequencies, the projection along the perpendicular direction can disappear faster than the projection along the transverse direction. In both the fast and the slow processes the time evolution of birefringence follows a highly non-linear scaling with strain; the scaling being different for the fast and slow processes. A systematic study of the effects of strain on shear alignment in block copolymers led to the discovery that strain affects not only the dynamics of alignment, but also the direction. This phenomenon expands the range of parameters that can be used to flip the direction of alignment. In relation to previous studies that examined the regimes of alignment only in terms of temperature and frequency, this phenomenon necessitates consideration of a third dimension - strain.", "doi": "10.7907/xb3f-3a10", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:3471", "collection": "thesis", "collection_id": "3471", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09112007-131436", "type": "thesis", "title": "Rational Approaches to Regulating Polymer Properties in Ring-Opening Metathesis Polymerization", "author": [ { "family_name": "Benedicto", "given_name": "Alto D.", "clpid": "Benedicto-Alto-D" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The molecular weight distribution of a living polymerization when chain-transfer agents are intentionally added were computed numerically. Results showed that traditional expressions for number-average degree of polymerization (X\u0305n) and polydispersity index (PDI) of chain-growth polymerization cannot be used. The well-known Mayo equation fails even when the system has achieved steady-state polymerization. Although the behavior of the system is complex, an analytical expression for X\u0305n was derived. Plots based on the analytical expression showed excellent agreement with that from numerical solutions. The implications of the calculations were discussed. The kinetics of living ring-opening metathesis polymerization (ROMP) of norbornene in the presence of neohexene catalyzed by Mo was investigated.
\r\n\r\nThe living ROMP of norbornene (n\u0332) and bicyclo[3.2.0]hept-2-ene (c\u0332) by Cl\u2082(PPh\u2083)\u2082Ru(=CHCHCPh\u2082) was demonstrated. The molecular weight varied linearly with conversion. Discrete propagating species showed that PPh\u2083 ligand dissociated during polymerization of c\u0332, and that CuCl (abstracts PPh\u2083) enhanced the rate of polymerization of n\u0332. The specific propagation rate constants (kn\u0332n\u0332 and kc\u0332c\u0332, respectively) of homopolymerization of n\u0332 and c\u0332 were measured, respectively. Block copolymers were easily prepared. From reactivity ratio studies, the ordering of the specific propagation rate constants are kn\u0332c\u0332 >> kkn\u0332n\u0332 > kc\u0332c\u0332 > kc\u0332n\u0332. The effect of styrene as chain-transfer agent on the molecular weight was examined.
\r\n\r\nThe hitherto unassigned (and unknown) microstructure of polymers prepared from 7-oxabicyclo[2.2.1]hept-2-ene derivatives have finally been unambiguously assigned. Polymers catalyzed by W(CH-t-Bu)(NAr)(OCMe(CF\u2083)\u2082)\u2082 have all cis double bonds and highly syndiotactic, while those from RuCl\u2083\u20223H\u20820 and [RuCl(\u03bc-Cl)(\u03bc\u00b3:\u03bc\u00b3-C\u2081\u2080H\u2081\u2086)]\u2082 {C\u2081\u2080H\u2081\u2086= 2,7-dimethyloctadienediyl} have high trans double bond content and highly isotactic.
\r\n\r\nStudies on the olefin isomerization catalyzed by Ru(H\u2082O)\u2086tos\u2082 revealed that the presence of hydroxyl functionality on the terminal olefin resulted in formation of 1:1 ratio of cis : trans double bonds on the isomerized internal olefin product, in contrast with near exclusive isomerization of double bond to trans when no hydroxyl group was present.
\r\n\r\nA numerical algorithm was developed for the evaluation of a chirality function for triangles on a plane, showing that such algorithm may be easily extended into the case of tetrahedron in 3-dimensional space.
\r\n", "doi": "10.7907/BC47-7W20", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:4305", "collection": "thesis", "collection_id": "4305", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10292007-104923", "primary_object_url": { "basename": "Wang_n_1995.pdf", "content": "final", "filesize": 1237235, "license": "other", "mime_type": "application/pdf", "url": "/4305/1/Wang_n_1995.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Studies in dynamics", "author": [ { "family_name": "Wang", "given_name": "Neng E.", "clpid": "Wang-Neng-E" } ], "thesis_advisor": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nIn this thesis, three parts of my work are reported. The first part of the work was done with Prof. Rudy Marcus, the second and third parts of the work were done with Prof. Bill Goddard. Here I would like to summarize the results from each part briefly.\r\n\r\nIn the first part, we propose doing Scanning Tunneling Microscopy(STM) current calculations with a new model in the spheroidal coordinate system. The tip is modeled as a hyperboloid. The electrostatic potential part of this model is solved exactly. The free electron model of the whole system is also solved exactly.\r\n\r\nIn the second part, we found that the Nose Canonical Molecular Dynamics, the most commonly used CMD method, leads to the wrong heat capacity for the system and hence is inconsistent with the thermodynamics. To solve this problem, we propose Two Nose variable Dynamics by changing the dimensionality of the Nose variable s and its conjugate [...] from one- to two-dimension.\r\n\r\nIn the third part, The exact expression for the quantum statistical partition function in the canonical ensemble is given. The physical interpretation of each term for N-particle system is discussed. The new formula is applied to the weakly degenerate quantum ideal case. By analyzing each term in the expansion, it is possible that this canonical partition function can be applied to cases where both quantum correlation effects and particle interactions are important.\r\n", "doi": "10.7907/j1ch-3v41", "publication_date": "1995", "thesis_type": "masters", "thesis_year": "1995" }, { "id": "thesis:4039", "collection": "thesis", "collection_id": "4039", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10112007-104204", "primary_object_url": { "basename": "Kannan_r_1995.pdf", "content": "final", "filesize": 7865566, "license": "other", "mime_type": "application/pdf", "url": "/4039/1/Kannan_r_1995.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Flow-induced alignment in intrinsically anisotropic polymeric materials", "author": [ { "family_name": "Kannan", "given_name": "Rangaramanujam Mudumbai", "clpid": "Kannan-R-M" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Brady", "given_name": "John F.", "clpid": "Brady-J-F" }, { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "To understand the processing behavior of complex polymeric materials, it is imperative that we understand the distinct underlying molecular and microstructural contributions to macroscopic mechanical response. We have developed rheo-optical methods to isolate the dynamics at such length scales, by combining conventional mechanical testing with polarimetry. The rheology and flow-induced alignment in side-group liquid-crystalline polymers (SG-LCPs) and lamellar diblock copolymers (BCPs) have been investigated using the rheo-optical apparatus.\r\n\r\nThe rheology of SG-LCPs arises from a combination of the polymeric nature of the backbone, the ordering tendency of the mesogens, and the coupling between the two introduced by the spacer. Contrary to previous studies, we find that the nematic order can significantly affects the macroscopic viscoelastic response in SG-LCP melts. In the nematic state, we have discovered that oscillatory shear is effective in inducing macroscopic orientation of the sample. Shear flow may prove to be an economical, efficient way to obtain macroscopically aligned SGLCPs, which have potential as optical data storage media and nonlinear optical materials. In contrast to magnetic field induced alignment, the mechanism of shear induced alignment appears to bedriven by the distortion of the polymer backbone.\r\n\r\nWe study the mechanisms of flow-induced alignment in a poly(ethylenepropylene)-poly(ethylethylene) lamellar diblock copolymer, which produce macroscopic alignment with lamellae normal along the shear gradient direction ('parallel' alignment), or along the vorticity direction ('perpendicular' alignment). We accomplish this by monitoring the evolution of the microstructure and viscoelasticity in situ during the alignment process. Our results suggest that 'parallel' alignment occurs due to irreversible 'rocking' of grains which tends to align the grains along the shear direction, whereas 'perpendicular' alignment occurs at conditions where the microscale deformation is nearly homogeneous.", "doi": "10.7907/ZDCX-2W89", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" } ]