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:17268", "collection": "thesis", "collection_id": "17268", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05232025-215105217", "primary_object_url": { "basename": "Stewart_Christopher_2025.pdf", "content": "final", "filesize": 2698906, "license": "other", "mime_type": "application/pdf", "url": "/17268/1/Stewart_Christopher_2025.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Dynamics of Charged Polyionic Liquids", "author": [ { "family_name": "Stewart", "given_name": "Christopher Jenkins", "orcid": "0009-0001-0280-2336", "clpid": "Stewart-Christopher-Jenkins" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "None", "given_name": "None" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Polymerized ionic liquids (PILs) exhibit complex ion transport dynamics that are central to advancing technology in energy storage and efficient energy conversion. In this work, we probe the behavior of charged polymer systems in the solvent\u2010free limit using a coarse\u2010grained Gaussian core model that explicitly incorporates long\u2010range electrostatic interactions. Our simulations span a wide range of chain lengths, from monomeric units to highly entangled polymers, revealing how both intrachain and interchain interactions govern key properties such as the radius of gyration, relaxation time, and diffusivity. Notably, charged polymers adhere to classical reptation scaling, indicating that electrostatic forces do not inhibit standard polymer melt scaling behavior. We quantify these effects by evaluating both the Onsager transport coefficients and the direct drift response under applied electric fields, thereby linking molecular trajectories to macroscopic ion conductivity.
\r\n\r\nOur findings show that as the chain length increases, the motion of polymerized ions becomes increasingly correlated, a trend that stabilizes ion conductivity despite decreasing diffusivity. This study demonstrates that the complex interplay between correlated motion and cooperative chain dynamics results in a relatively stable conductivity that increases over short chain length, plateaus in the transition regime, before decreasing in the fully entangled regime \u2014 contrary to idealized predictions based solely on diffusivity. By explicitly modeling the microscopic interactions and accounting for both hydrodynamic and electrostatic effects, we provide a physically grounded framework that captures the emergent behavior of these charged systems. In doing so, our work offers a robust platform for the rational design of next-generation PIL electrolytes, distinguishing itself from phenomenological models through clear, simulation-based insights.
", "doi": "10.7907/6js0-8r29", "publication_date": "2025", "thesis_type": "masters", "thesis_year": "2025" }, { "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: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: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: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: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: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: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: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: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: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: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: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: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: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: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:1452", "collection": "thesis", "collection_id": "1452", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04222005-131237", "primary_object_url": { "basename": "Zheng_w_1997.pdf", "content": "final", "filesize": 6422106, "license": "other", "mime_type": "application/pdf", "url": "/1452/1/Zheng_w_1997.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Novel aspects in the microphase separation of block copolymers", "author": [ { "family_name": "Zheng", "given_name": "Wei", "clpid": "Zheng-Wei" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "Several novel aspects of the microphase separation transition of block copolymers have been studied. These aspects are exemplified by the following three systems:\r\n\r\n(1) ABC triblock copolymers;\r\n(2) Weakly charged diblock copolymers;\r\n(3) Diblock copolymers in confined geometries.\r\n\t\r\nFor ABC triblock copolymers, results from theoretical calculations of the morphological phase diagrams in the strong segregation limit are presented. The chain conformation free energy is approximated following an approach proposed by Ohta and Kawasaki. Our study focuses on two unique features of the ABC triblock copolymers, namely, the dependence of the morphology on the sequence of the triblock chain and the relative strength of the various interaction parameters. Our results compare favorably with experimental observations. In addition, we predict the existence of some new structures that have yet to be observed experimentally.\r\n\r\nFor weakly charged diblock copolymers, a theoretical framework is developed. This framework combines the Random Phase Approximation and the Poisson-Boltzmann equation in order to consistently treat the electrostatic interactions between all charged species and the free energy contributions from the connectivity of the diblock copolymers. A Landau-Ginzburg effective free energy is derived and is used to study the microphase separation of charged-neutral block copolymers with an arbitrary amount of added salt in the weak segregation limit. Study of the spinodal limit of the system shows not only greatly enhanced compatibility between A and B blocks in comparison with the corresponding neutral system, but also inhibition of microphase separation under certain conditions. A criterion for microphase separation is derived and phase diagrams under various conditions are presented. Study of concentration fluctuation near the order-disorder transition demonstrates that the breaking of the interchange symmetry leads to new scaling of fluctuation corrections at a fixed value of monomer charge density [alpha].\r\n\r\nThe morphology of diblock copolymer melt confined between two solid walls in the strong segregation limit is studied by extending the method developed by Ohta and Kawasaki to include surface effects. We focus on two new features which are absent in simple diblock copolymers: the competition between the surface interactions and the confinement effects, and the breaking of the rotational and translational symmetry. The first new feature is demonstrated by studying the equilibrium properties of symmetric/nearly symmetric diblock copolymers confined between two identical walls with a small preferential surface affinity. The second feature is illustrated by studying the phase behavior of diblock copolymers with arbitrary value of volume fraction. For phase transition involves morphologies with three dimensional structure, the broken rotational and translational symmetry leads to the dependence of the transition volume fraction on the distance between the two plates. The influence of surface effects on diblock copolymers confined between two distinct plates is also studied by presenting phase diagrams for two special cases.\r\n", "doi": "10.7907/N3Z2-AV91", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" } ]