This thesis describes work designed to improve the resolution of Scanned Probe\r\nMicroscopy (SPM). The work falls into three main sections. Sections I and III are both\r\naimed towards making scanned probes with atomic resolution by attaching a single sharp\r\nmolecule to the end of a tip. Section II is aimed towards making a near-field \"optical\"\r\nprobe in the infrared wavelengths.
\r\n\r\nThe first section centers on the Touchdown Scheme, a path towards attachment of a\r\nsingle sharp molecule at the end of a conventional atomic force microscope (AFM) tip.\r\nThe ability to derivatize the tip with a good monolayer was required. Chapters 2 and 3\r\ndescribe the development and optimization of surface chemistry for this purpose.\r\nIncluded in this development were methods for making chemically patterned surfaces\r\nwith simple photolithography techniques. Chapter 1 describes mathematical methods to\r\nextract intermolecular pair potentials from AFM force measurements.
\r\n\r\nThe second section describes a technique for etching infrared-transmitting fibers to very\r\nsharp points. These sharpened fibers serve as probes in a Near-field Scanning Infrared\r\nMicroscope (NSIM). Making tips by chemical etching is far easier than heat-pulling, and\r\nthe etched probes have a power throughput several orders of magnitude higher than\r\npulled probes.
\r\n\r\nThe third section centers on attempts to attach a single molecule to the end of a single\r\ncarbon nanotube for use as an ultrasharp AFM tip. Bulk derivatization and labeling\r\nchemistry of carbon nanotubes was developed and successfully applied to single mounted\r\nnanotubes. Along the way, several new methods for handling nanotubes were developed.\r\nThese include methods for non-oxidative cleaning, making stable suspensions,\r\nfluorescence staining, and removal from solution without coalescence.
", "doi": "10.7907/xqdw-8009", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:3623", "collection": "thesis", "collection_id": "3623", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09182006-152253", "primary_object_url": { "basename": "Mislick_ka_1996.pdf", "content": "final", "filesize": 9355403, "license": "other", "mime_type": "application/pdf", "url": "/3623/1/Mislick_ka_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The role of proteoglycans in the delivery of cationic-DNA complexes and enhanced delivery by folate receptor-mediated endocytosis", "author": [ { "family_name": "Mislick", "given_name": "Kimberly Ann", "clpid": "Mislick-K-A" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Experiments were conducted to elucidate the mechanisms of polylysine-mediated transfection into mammalian cells in vitro. In the first chapter, the role of membrane-associated proteoglycans in transfection was investigated by testing transfection efficiency under a number of assay conditions. Cells were treated with sodium chlorate in order to desulfate glycosaminoglycan chains. Chlorate treatment inhibited expression of luciferase, the intracellular uptake of DNA, and binding of DNA to the cell surface. Expression, uptake, and binding of DNA was also inhibited by exogenous glycosaminoglycans and by glycosaminoglycan lyases. Similarly, each of the transfection steps was severely inhibited in CHO cell mutants, incapable of synthesizing proteoglycans. Transfection by certain cationic liposomes was also inhibited in the mutant cell line. The possible implications of these results for gene therapy of diseases affecting hematopoietic cells is described. In the second chapter, polylysine-mediated gene delivery via the folate receptor was developed. Gene delivery by folate receptor-mediated endocytosis was approximately 18 times higher than by nonspecific endocytosis of polylysine-DNA in the presence of chloroquine. A number of controls confirmed that the folate receptor was critical in the gene delivery mechanism. When chloroquine was removed from the media, transfection efficiency dropped approximately 30 fold, suggesting that gene delivery occurred via a lysosomal pathway. In the final chapter, transfection by folate receptor-mediated endocytosis was characterized by 2-photon laser scanning microscopy. KB cells were transfected with folate-polylysine-DNA complexes labeled with YOYO, a dimeric cyanine intercalator, and a single cell was examined over a two hour period. Although additional controls are required, preliminary evidence suggests that mitosis is not a strict requirement for delivery of DNA into the nucleus of cells.", "doi": "10.7907/7yx4-gh95", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:333", "collection": "thesis", "collection_id": "333", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01252005-092413", "primary_object_url": { "basename": "OConnor_sd_1995.pdf", "content": "final", "filesize": 10337823, "license": "other", "mime_type": "application/pdf", "url": "/333/1/OConnor_sd_1995.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Studying Material Properties on the Nanometer Scale: Instrumental Development and Applications", "author": [ { "family_name": "O'Connor", "given_name": "Stephen D.", "clpid": "O'Connor-Stephen-D" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" } ], "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 thesis describes experimental work designed to understand and manipulate material properties on the nanometer scale. Two strategies have been explored: instrument development and experimental applications.\r\n\r\nSection I describes work associated with atomic force microscopy, including application studies of human hair morphology and the surface microstructure of a bulk metallic glass [...]. Also included in this section are two instrumental advances. First, a mathematical algorithm to extract intermolecular potentials from experimental data is described. Second, a simple, robust method for reducing mechanical noise in these experiments is presented.\r\n\r\nSection II outlines early experiments aimed at applying Near-field Scanning Optical microscopy to gas-phase chemical analysis. Standard instruments were constructed and tested. Preliminary work aimed at using the near-field effect to desorb ionized particles from surfaces was also completed.\r\n\r\nSection III describes the construction of temperature and vibration sensors based on material properties in silicon. Unprecedented resolution has been obtained with a simple, inexpensive device. The vibration sensors take advantage of Schottky barrier reshaping while the junction is excited with optically induced charge carriers. In a similar manner, the temperature sensors monitor changes in electron mobility.", "doi": "10.7907/P0AA-7W43", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:1057", "collection": "thesis", "collection_id": "1057", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03222005-105400", "primary_object_url": { "basename": "Baselt_dr_1993.pdf", "content": "final", "filesize": 14972657, "license": "other", "mime_type": "application/pdf", "url": "/1057/1/Baselt_dr_1993.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "The Tip-Sample Interaction in Atomic Force Microscopy and its Implications for Biological Applications", "author": [ { "family_name": "Baselt", "given_name": "David Randall", "clpid": "Baselt-David-Randall" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Revel", "given_name": "Jean-Paul", "clpid": "Revel-J-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes the construction of an atomic force microscope and its application to the study of tip-sample interactions, primarily through the use of friction and hardness (elasticity) imaging.\r\n\r\nPart one describes the atomic force microscope, which consists of a scanned-cantilever stage (chapter 2); a versatile digital signal processor-based control system with self-optimizing feedback, lock-in amplifier emulation (for hardness imaging), and macro programmability (chapter 3); and image processing software (chapter 4).\r\n\r\nPart two describes a number of results that have helped to characterize the tip-sample interaction and the contact imaging modes used for its study. Meniscus forces act laterally as well as normally, and that they vary with position (chapter 5). Friction measurements couple with scanner position quid feedback, and the meniscus effects friction images (chapter 6). Sliding of the tip over the sample surface introduces slope-dependence into hardness measurements (chapter 7). Dull tips can create prominent topography artifacts even on very flat surfaces (chapter 8).\r\n\r\nIn an investigation of collagen fibrils, AFM has revealed die characteristic 65 nm banding pattern, a second, minor banding pattern, and microfibrils that run along the fibril axis. The distribution of proteoglycans along the fibrils creates a characteristic pattern in friction images. Although imaging in water reduces interaction forces, water can also make biological samples more sensitive to force. However, for robust biological samples imaged in air, tip shape presents a greater obstacle than tip-sample interaction forces to obtaining high-resolution images. Tip contamination increases tip-sample friction and can occasionally improve resolution (chapter 9).\r\n\r\nFor a separate project I have designed a general-purpose nearfield scanning optical microscope (chapter 10).", "doi": "10.7907/5ZMM-7Q64", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:5310", "collection": "thesis", "collection_id": "5310", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-102157942", "primary_object_url": { "basename": "Coley_tr_1993.pdf", "content": "final", "filesize": 19371467, "license": "other", "mime_type": "application/pdf", "url": "/5310/1/Coley_tr_1993.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Prediction of scanning tunneling microscope images by computational quantum chemistry: chemical models and software design", "author": [ { "family_name": "Coley", "given_name": "Terry Ronald", "clpid": "Coley-T-R" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We have created chemical models for predicting and interpreting STM images of several specific systems. Detailed studies are made of transition metal dichalcogenides (MoS_2 and MoTe_2), Xe on Ni (110), C_3H_4 on Ni (110) and n-butyl benzene on a graphite model (C_(42)O_6H_(12). In the case of MoS_2 we study the ambiguity in the STM images regarding the assignment of peaks to the subsurface metal or the surface chalcogenide. In the Ni models we study STM imaging mechanisms for cases where the adsorbate states lie far above and below the metal Fermi level. The large n-butyl on graphite system models a system where adsorbate states can play a direct role in the imaging. Results from the cluster studies are related to various STM imaging modes, including constant current mode, constant height mode, and barrier height imaging.\t\r\nTwo new procedures are developed to aid in computational prediction of STM images. First, we implement an algorithm for computing Bardeen-type tunneling matrix elements from ab initio wave functions in Gaussian basis sets. Second, we show how to obtain state densities as a function of energy for bulk substrate/adsorbate systems using only Fock matrix elements from cluster calculations. Initial results are presented for a linear chain of Ni atoms with a perturbing Xe atom.\r\nA software environment for computational chemistry developed in the course of performing these calculations is presented. Tools for creating computational servers to perform chemistry calculations are described. Embedded in each chemistry server is a public domain control language created by J. Ousterhout at the University of California, Berkeley. This allows the development of a variety of clients for controlling the servers using a common language. Clients can be simple text \"scripts\" that organize a calculation, graphical interfaces, or control streams from other programs. All software entities are designed in an object oriented fashion discussed in the text.\r\n", "doi": "10.7907/jey5-ex12", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:7395", "collection": "thesis", "collection_id": "7395", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01112013-110414331", "type": "thesis", "title": "Atomic-Scale Imaging and Spectroscopy Using Scanning Tunneling Microscopy", "author": [ { "family_name": "Youngquist", "given_name": "Michael George", "clpid": "Youngquist-Michael-George" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Kaiser", "given_name": "William J.", "clpid": "Kaiser-William-J" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Advances in scanning tunneling microscopy (STM) instrumentation\r\nand applications are presented. An ultrahigh vacuum (UHV) scanning\r\ntunneling microscope incorporating computer-controlled two-dimensional\r\nsample translation and in vacuo tip and sample transfer was developed. Its\r\nperformance is documented through large-area and atomic-resolution\r\nimaging of highly stepped Si(111) 7x7 reconstructed surfaces and physisorbed\r\nclusters on graphite. An STM with automated approach and intra-Dew\u00e4r\r\nspring suspension was developed for operation in cryogenic liquids. A high\r\nperformance digital signal processor (DSP) based control system was\r\nconstructed, and software with advanced spectroscopic imaging and data\r\nprocessing capabilities was developed.
\r\n\r\nThe feasibility of individual-molecule vibrational spectroscopy via\r\nSTM-detected inelastic electron tunneling is assessed. In preliminary\r\nexperiments, a low-temperature STM was used for energy gap and phonon\r\nspectroscopy of superconducting Pb films. The first STM observation of\r\nphonon density of states effects in a superconductor is reported.
\r\n\r\nA systematic UHV STM imaging and spectroscopy study of 2H-MoS_2\r\nwas conducted. Atom-resolved images from three distinct imaging modes\r\nare presented. Occasional appearance of negative differential resistance\r\n(NOR) in I vs. V measurements is traced to changing tip electronic structure\r\nrather than localized surface states. Other potential NOR mechanisms are\r\ndiscussed including electron trap charging and resonant tunneling through a\r\ndouble-barrier quantum well structure arising from layer separation in the\r\nMoS_2 crystal.
\r\n\r\nDNA was imaged at atomic resolution with a UHV STM. Images show\r\ndouble-helical structure, base pairs, and atomic-scale substructure.\r\nExperimental STM profiles have atom-for-atom correlation with the A-DNA\r\nvan der Waals surface. This work demonstrates the potential of the STM for\r\ncharacterization of large biomolecular structures.
\r\n\r\nImpurity-pinned steps on silicon and gold surfaces were imaged by\r\nSTM. Pinned gold steps have short linear coherence lengths and form step\r\nloops at impurities by an Orowan-type bypassing mechanism. Step loops\r\nwere not observed at Si(111) pinning sites; step contours seem to be correlated\r\nwith the degree of order in the Si surface reconstruction.
", "doi": "10.7907/0d6k-be86", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:7275", "collection": "thesis", "collection_id": "7275", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11192012-103302776", "primary_object_url": { "basename": "Clark_sm_1993.pdf", "content": "final", "filesize": 37671547, "license": "other", "mime_type": "application/pdf", "url": "/7275/1/Clark_sm_1993.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Advances in scanning force microscopy of biological structures", "author": [ { "family_name": "Clark", "given_name": "Steven Manning", "clpid": "Clark-Steven-Manning" } ], "thesis_advisor": [ { "family_name": "Revel", "given_name": "Jean-Paul", "clpid": "Revel-J-P" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Revel", "given_name": "Jean-Paul", "clpid": "Revel-J-P" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "A multifacted approach to the imaging of biological structures by scanning force microscopy is described. The major problems addressed are the distortion of biological samples by excessive forces applied by the cantilever stylus and sample motion relative to the imaging substrate.
\r\n\r\nThe first two chapters discuss the design of digital signal processor based scanning force microscope control electronics and a novel microscope head that eliminates the application of excessive forces to the sample caused\r\nby electronic or vibrational noise.
\r\n\r\nThe third chapter presents a novel use of chemical vapor deposition for application of heterofunctional alkoxysilanes to scanning force microscopy imaging subsrates. This technique provides imaging substrates which have chemical groups that can be used for sample immobilization without compromising substrate smoothness. The use of the chemically derivatized substrates for scanning force microscopy is also explored.
\r\n\r\nThe final chapter presents high resolution images of bovine liver catalase micro-crystals. The images of the protein micro-crystals show resolution on the order of 2 to 3 nanometers allowing the visualization of individual catalase tetramers. To our knowledge this is the first report of images of protein micro-crystals taken by scanning force microscopy which have resolution comparable to that of electron microscopy.
\r\n", "doi": "10.7907/0vhp-pk35", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:7284", "collection": "thesis", "collection_id": "7284", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11262012-114541543", "primary_object_url": { "basename": "Fujiwara_m_1993.pdf", "content": "final", "filesize": 14388032, "license": "other", "mime_type": "application/pdf", "url": "/7284/1/Fujiwara_m_1993.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Characterization of pH-Dependent Poly(Acrylic Acid)-Vesicle Interaction and its Application in Cellular Drug Delivery", "author": [ { "family_name": "Fujiwara", "given_name": "Mitsuko", "clpid": "Fujiwara-Mitsuko" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Revel", "given_name": "Jean-Paul", "clpid": "Revel-J-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Polymers can be used to control drug targeting and drug release from phospholipid vesicles through changes in pH. Understanding the effect of polymers on vesicle properties is important in obtaining a better control over drug delivery using phospholipid vesicles. The pH-dependent interaction of poly(acrylic acid) (PAA) with phosphatidylcholine (PC) vesicles (bilayers) and monolayers was investigated to elucidate the mechanism of P AA-induced vesicle destabilization. PAA induced aggregation of vesicles below pH 4.6 and lipid intermixing of vesicles below pH 4.1. Mixing of aqueous contents was not observed, indicating that the process is not a true membrane fusion. An increase in the membrane permeability accompanied lipid intermixing of vesicles. Both the hydrocarbon chain and phospholipid headgroup packing was more disordered from\r\npolymer association as evidenced by the increase in the CH_2 asymmetric stretching peakwidth and peak position and by the increase in the binding of potential-sensitive dye to\r\nthe vesicle surface, respectively. Polymer binding to vesicles at pH 3.8 showed a negative cooperativity with a K_b of 1.5 x 10^6 M^(-1).The driving force for PAA adsorption on vesicles is the formation of hydrogen-bonds between the protonated carboxyl groups of the polymer and the phospholipid molecule. The polymer mobility was restricted upon complexation with vesicles as evidenced by the anisotropy measurements of polymerassociated fluorophore. The polymer-associated vesicles exhibited fused vesicles and tubular structures in freeze-fracture images. Formation of nonbihyer phases or phase separation was not detected in freeze-fracture images or ^(31)P-NMR powder spectra of PC vesicles. PAA induced expansion of PC monolayers at low pH, and the extent of expansion was dependent on the monolayer surface pressure and on the pH of the subphase. Polymer-induced expansion became more difficult at increasing monolayer packing density and increasing pH. Therefore PAA-induced destabilization of vesicles is believed to be initiated by partial penetration of PAA on vesicle surface. The stress on the membrane created by PAA association presumably resulted in the rupture of bilayer and lipid intermixing of vesicles.
\r\n", "doi": "10.7907/ky3h-q886", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:7294", "collection": "thesis", "collection_id": "7294", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11292012-090633873", "primary_object_url": { "basename": "Driscoll_rj_1993.pdf", "content": "final", "filesize": 36345789, "license": "other", "mime_type": "application/pdf", "url": "/7294/1/Driscoll_rj_1993.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Scanning Tunneling Microscopy and Spectroscopy: I. Semimetals and Semiconductors. II. Atom-Resolved Imaging of DNA", "author": [ { "family_name": "Driscoll", "given_name": "Robert James", "clpid": "Driscoll-Robert-James" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Revel", "given_name": "Jean-Paul", "clpid": "Revel-J-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The topographic and electronic structure of semiconductor and semimetal surfaces were investigated using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS), respectively. The longrange morphology and atomic-scale characteristics of cleaved materials such as highly oriented pyrolitic graphite (HOPG), boronated pyrolitic graphite (BPG), titanium disulfide, and gallium arsenide (GaAs) were revealed by STM performed under ultrahigh vacuum (UHV) conditions.
\r\n\r\nAtomic resolution constant-current and current-imaging data, as well as barrier height information obtained from tunneling gap modulation, are presented. Both point and line defects were observed on these surfaces; the origin and role of native and adsorbed surface defects are discussed. Visual evidence of coulombic screening caused by adsorption of charged species on n-type GaAs(110) is provided. The atomic corrugation of the GaAs surface was measured to be as little as 0.03 \u00c5 peak-to-valley, attesting to the stability of the microscope design. The BPG sample used in these studies consisted of up to 0.5% boron; boron is the only known substitutional impurity of graphite. Boron substituent atoms appeared as small protrusions approximately 3 \u00c5 in diameter, with an atom density consistent with the assumed concentration.The BPG surface exhibited frequent line defects, including large-angle grain\r\nboundaries, and monolayer-depth etch pits. Images of BPG in air using graphite tips showed similar results; the validity of the popular \"sliding-planes\" mechanism for graphite imaging is evaluated.
\r\n\r\nThe effects of anisotropic stress on the morphology and reconstruction of a thermally annealed Si(111) wafer were explored. The height and orientation of step bunches, as well as terrace widths, on the (7x7) surface were determined. Electromigration effects were also observed; although the overall surface slope was conserved, the step bunches were \"smeared out\" by reversal of the current direction during heating. Line fault defects at step\r\nkinks were observed; a theory for the origin and structure of these features based on stress relief is proposed. Current imaging tunneling spectroscopy (CITS) and localized STS revealed differences between the adatom sites of the\r\n(7x7) surface. Atom-resolved barrier height images were also obtained;comparison to constant-current images may in fact provide a means of differentiating between defects and adsorbed species on the surface. The local effective barrier height was seen to depend strongly on the \"cleanliness\" of the STM tip. The barrier height increased dramatically following voltage pulsing on the order of ten volts. The large height of the step bunches also provided a good test to evaluate the sharpness of the STM tip; examples of \"tip changes\" affecting image resolution and \"multiple-tipping\" are provided. Silicon samples annealed at temperatures below 1000\u00b0C revealed substantial\r\nsilicon carbide (SiC) contamination which effected step pinning. No SiC islands were observed on samples annealed above 1250\u00b0C.
\r\n\r\nIn addition, atom-resolved STM images of duplex DNA supported on a HOPG surface were obtained in UHV. These images revealed double-helical structure, major and minor groove alternation, base pairs, and atomic-scale substructure. Comparison of the DNA dimensions derived from the STM data were in agreement with those from x-ray crystallography for \"random-sequence\" A-form DNA. Cross sectional profiles of the experimental STM data showed excellent correlation with the atomic contours of the van der Waals surface of A-DNA. Barrier height cross-sections showed general correlation with the atomic-scale topography over the phosphate-sugar backbone but distinct anticorrelation (complementarity) over the base pair region. The problems of aggregation and deposition coverage are discussed in the context of possible future applications of STM to DNA sequencing. The use of alternate techniques of DNA deposition, including electrospray\r\nionization, for increased experimental reproducibility are described. The limitations of HOPG as a substrate for biomolecular adsorbates in STM experiments are evaluated.
\r\n", "doi": "10.7907/fp55-ng98", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:7361", "collection": "thesis", "collection_id": "7361", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01022013-133723062", "primary_object_url": { "basename": "Male_r_1993.pdf", "content": "final", "filesize": 36335985, "license": "other", "mime_type": "application/pdf", "url": "/7361/1/Male_r_1993.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Development of an Effective Drug Delivery System Using Loaded Platelets", "author": [ { "family_name": "Male", "given_name": "Roxanne", "clpid": "Male-Roxanne" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Liposomes have been used to deliver diagnostic and therapeutic drugs\r\nwith moderate success. Current applications include targeting to tumors\r\n(1), where the vasculature is leaky and allows liposome penetration, and\r\nKupffer cells in the liver (2). Reticuloendothelial system (RES) uptake and\r\nlack of targeting specificity of the liposomes have been the major problems\r\nencountered. Several groups including Allen et al. (3) and Liu et al. (4)\r\nhave increased the circulation times by attaching polyethylene glycol (PEG)\r\nor the ganglioside GM_1 to the liposome surface; the circulation half-lives\r\nfor disteroylphosphatidylcholine (DSPC):cholesterol:PEG and GM_1\r\nliposomes are 20.0 \u00b1 3.5 and 16.4 \u00b1 3.1 hours, respectively as compared to\r\n6.7 \u00b1 4.5 hours for DSPC:cholesterol (2:1 mole ratio) liposomes (3). In\r\naddition, some attempts have been made to target specific areas by the\r\naddition of ligands, such as human gamma globulin or aminomannose;\r\nhowever this increased targeting has been largely limited to increased\r\nKupffer cell and RES uptake (5,6). Addition of antibodies to the liposomes\r\nincreases targeting specificity, but has met with limited success since the\r\nliposomes are still prone to RES uptake (7).
\r\n\r\nReconstituted Sendai virus envelopes (RSVE) are essentially liposomes\r\nwith binding and fusogenic glycoproteins on their surface. These vesicles\r\nhave been used as vehicles for delivering molecules into cells in vitro\r\nand for the transfer of membrane proteins into the cells' plasma\r\nmembranes. Similar to intact viruses, RSVE attach preferentially to cells\r\nhaving the appropriate receptors, usually gangliosides, and fuse with the\r\ncellular membranes, thus emptying their contents into the cell cytoplasm.\r\nThis also results in the implantation of the viral envelope components\r\ninto the recipient cell plasma membrane.
\r\n\r\nWe have studied the in vitro interactions of small unilamellar\r\nvesicles (SUV) and reconstituted Sendai virus (RSVE) with platelets with\r\nthe objective of developing new drug delivery systems. Specifically, we\r\nhave examined the kinetics and mechanisms of uptake of SUV, with and\r\nwithout covalently attached proteins, and RSVE. Liposomes that have\r\nbeen studied include: DSPC:cholesterol (2:1 mole ratio) liposomes\r\n(control) (8) and aminomannose (Am), human gamma globulin (HgG)\r\nand transferrin (Tf) labeled control liposomes (9). From our data we\r\nconclude that the mechanisms and kinetics of uptake and subsequent\r\nspecific localization of the lipid and aqueous components of the liposomes\r\nwithin the cells are dependent on the type of liposome used.
\r\n\r\nPlatelets have the unique ability to target to specific areas in vivo\r\nincluding areas of infection and inflammation, tumors and clots.\r\nTherefore we hoped to combine this in vivo targeting ability with the\r\nplatelets' ability to take up liposomes and RSVE in vitro to create new\r\ndrug delivery systems to deliver diagnostic and therapeutic reagents.\r\nHaving a variety of systems from which to choose should offer the ability\r\nto optimize drug delivery parameters.
\r\n\r\nIn vitro functional assays, including microaggregation, serotonin\r\nrelease and membrane integrity, conclude that platelet function is not\r\ninhibited by liposome uptake (8, 9). However, uptake of intact and\r\nreconstituted Sendai virus particles induce platelet aggregation and\r\nsecretion. In vivo organ distribution studies in Sprague-Dawley rats\r\nindicate that circulation times and RES uptake of liposome-loaded rat\r\nplatelets are identical to control rat platelets (10).
\r\n", "doi": "10.7907/1q2y-nz07", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:6644", "collection": "thesis", "collection_id": "6644", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09012011-151648229", "primary_object_url": { "basename": "Baker_sm_1992.pdf", "content": "final", "filesize": 52406562, "license": "other", "mime_type": "application/pdf", "url": "/6644/1/Baker_sm_1992.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Scanning Tunneling Microscopy and Spectroscopy of Silicon and Carbon Surfaces", "author": [ { "family_name": "Baker", "given_name": "Shenda Mary", "orcid": "0000-0002-9985-473X", "clpid": "Baker-Shenda-Mary" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Rossman", "given_name": "George Robert", "orcid": "0000-0002-4571-6884", "clpid": "Rossman-G-R" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Scanning Tunneling Microscopy (STM) investigations and additional surface analyses were performed on carbon and silicon surfaces. A number of anomalies have been observed on highly oriented pyrolytic graphite (HOPG), including large corrugations, distorted images, large range of tip motion and the absence of defects. A mechanism involving direct contact between tip and sample or contact through a contamination layer to provide an additional conduction pathway is proposed. This model of point-contact imaging provides an explanation for added stability of the STM system, a mechanism for producing multiple tips or sliding graphite planes and an explanation for the observed anomalies. These observations indicate that the use of HOPG for testing and calibration of STM instrumentation may be misleading. Designs for the atmospheric STM used in this study are also presented.
\r\n\r\nThe conditions necessary for preparing a dean silicon(111) (7x7) surface are discussed. The design and analysis of heaters necessary to prepare the silicon reconstructed surface at ultrahigh vacuum (UHV) are described. Results from both radiatively and resistively heated samples are shown in addition to a comparision of topographic and barrier height images of the boron (\u221a3 x\u221a3) reconstructed surfaces. A spectroscopic distinction between sites of boron, silicon or contaminants is demonstrated.
\r\n\r\nA synthetic boron-doped diamond was examined by a number of analytical techniques in order to determine its composition and surface morphology. Current-voltage spectroscopy taken with the STM indicates that the diamond Fermi level can be pinned in atmospheric conditions. In ultrahigh vacuum, band bending is observed, but the strength of the electric field experienced by the diamond semiconductor is less than expected; introduction of surface charges is shown to account for the field screening.
\r\n\r\nPresentation of an STM study of a protein-antibody complex on a gold surface illustrates the requirements for and difficulties of imaging large biomolecules. A flat, conducting substrate and sample stability on the surface\r\nare shown and discussed. Molecular manipulation by the STM tip is also presented. Although routine imaging of large adsorbates on surfaces is not yet possible, this study presents the obstacles and the potential afforded by the STM in attaining this goal.
\r\n", "doi": "10.7907/5JGQ-4X60", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:6602", "collection": "thesis", "collection_id": "6602", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08192011-093115822", "primary_object_url": { "basename": "Garyantes_tk_1992.pdf", "content": "final", "filesize": 62436603, "license": "other", "mime_type": "application/pdf", "url": "/6602/1/Garyantes_tk_1992.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "The Effect of Electrical Stimulation on Neuronal Outgrowth and the Development of a New Method for Chronic Long-Term Stimulation and Recording from Groups of Neurons in Culture", "author": [ { "family_name": "Garyantes", "given_name": "Tina Kramer", "clpid": "Garyantes-Tina-Kramer" } ], "thesis_advisor": [ { "family_name": "Pine", "given_name": "Jerome", "clpid": "Pine-J" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Berg", "given_name": "Howard C.", "clpid": "Berg-Howard-C" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "In this dissertation, I shall examine the response of neurite outgrowth from cultured rat superior cervical ganglion (SCG) neurons to electrical stimulation and to changes in cytoplasmic calcium. Previous studies have shown that suprathreshold electrical stimulation arrests axonal growth from mouse dorsal root ganglion (DRG) and Helisoma neurons (Fields et al., 1990; Cohan and Kater, 1986). Cohan and collaborators (1987) have attributed the arrest of neurite outgrowth from Helisoma neurons to a rise in the growth-cone calcium concentration, [Ca]gc. In the experiments presented in this dissertation, neurite outgrowth from neonatal rat SCG neurons continued unabated during continuous suprathreshold electrical stimulation at 10 Hz for up to one hour. As in previous studies, the internal calcium concentration rose during stimulation. Fura-2 measurements showed that growth cone calcium levels rose from about 100 nM to greater than 500 nM, before settling at about 350 nM during stimulation. Despite this increase, neurite outgrowth continued. My results suggest that electrical activity is not a universal signal for neurons to stop growing and that a rise in internal calcium does not always arrest the migration of growth cones.
\r\n\r\nI was also able to record from and stimulate rat SCG neurons using a new device that allows maintained two-way communication between neurons and electronic circuitry. The new device or \"neuron well array\" holds individual neurons in surface micromachined holes. A self-supporting overhanging grillwork restrains the neurons in the holes. Each hole has an electrical contact which allows recording from and stimulation of the cell trapped therein. Neurons that grow in the holes appeared to suffer no observable ill effects of entrapment. Future neuronal development studies are planned with the wells.
\r\n", "doi": "10.7907/4CQ9-7F40", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:6665", "collection": "thesis", "collection_id": "6665", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09132011-085913260", "primary_object_url": { "basename": "Di_simone_c_1992.pdf", "content": "final", "filesize": 33456897, "license": "other", "mime_type": "application/pdf", "url": "/6665/1/Di_simone_c_1992.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Membrane Fusion Activities of Native and Reconstituted Mumps and Sendai Viruses", "author": [ { "family_name": "Di Simone", "given_name": "Christopher", "clpid": "Di-Simone-Christopher" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Strauss", "given_name": "James H.", "clpid": "Strauss-J-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The structure and activities of whole and reconstituted Sendai and mumps viruses were examined using a number of physical and biological techniques: electron microscopy, photon correlation spectroscopy, perturbed angular\r\ncorrelation spectroscopy, gel electrophoresis, hemagglutination assays, plaque assays, fluorescence microscopy and fluorescent assays of membrane fusion. The fluorescent probe octadecyl rhodamine (RIB) was found to have a proximal transfer behavior which reduced usage of the probe as a membrane fusion indicator to short time periods. Simple bireactant and mass action kinetic models were sufficent to fit the data provided by the fluorescent assays on viral fusion with cell membranes. The\r\nreconstitution of mumps virus was optimized by using the detergent Triton X-IOO. Reconstituted virus envelopes which were the same size as whole virus and which were active in binding and fusing to cells were produced. The reconstituted Sendai and mumps virus accumulated in the reticuloendothelial system when injected into mice and hamsters, respectively. The kinetics of the membrane fusion activity of mumps with ghost erythrocytes and CV-I cells was measured and analysed. A general rate of reaction of 3 (\u00b11) x 10^9 M^-l sec^-1 was found. The membrane fusion activity of reconstituted Sendai with HL60, U937, Cos, H9\r\nand PBL cell lines was also measured and analyzed. The fusion activity was utilized to deliver plasmids for transfection to the interiors of the HL60 and Cos cells. Luciferase expression was found in the Cos cells but not in the HL60 cells. Loading of plasm ids into the vesicle interiors was enhanced by a factor of ten by complexing the DNA with the positive proteins polylysine, lysozyme and protamine.\r\n", "doi": "10.7907/rr73-5d56", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:8609", "collection": "thesis", "collection_id": "8609", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07252014-124055207", "primary_object_url": { "basename": "Novick-sl-1990.pdf", "content": "final", "filesize": 25152660, "license": "other", "mime_type": "application/pdf", "url": "/8609/1/Novick-sl-1990.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Chemical Studies of Viral Entry Mechanisms: I. Hydrophobic Protein-Lipid Interactions During Sendai Virus Membrane Fusion. II. Kinetics of Bacteriophage \u03bb DNA Injection", "author": [ { "family_name": "Novick", "given_name": "Steven Louis", "clpid": "Novick-Steven-Louis" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Strauss", "given_name": "James H.", "clpid": "Strauss-J-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Viruses possess very specific methods of targeting and entering cells. These methods would be extremely useful if they could also be applied to drug delivery, but little is known about the molecular mechanisms of the viral entry process. In order to gain further insight into mechanisms of viral entry, chemical and spectroscopic studies in two systems were conducted, examining hydrophobic protein-lipid interactions during Sendai virus membrane fusion, and the kinetics of bacteriophage \u03bb DNA injection.
\r\n\r\nSendai virus glycoprotein interactions with target membranes during the early stages of fusion were examined using time-resolved hydrophobic photoaffinity labeling with the lipid-soluble carbene generator3-(trifluoromethyl)-3-(m-^(125\r\n)I] iodophenyl)diazirine (TID). The probe was incorporated in target membranes prior to virus addition and photolysis. During Sendai virus fusion with liposomes composed of cardiolipin (CL) or phosphatidylserine (PS), the viral fusion (F) protein is preferentially labeled at early time points, supporting the hypothesis that hydrophobic interaction of the fusion peptide at the N-terminus of the F_1 subunit with the target membrane is an initiating event in fusion. Correlation of the hydrophobic interactions with independently monitored fusion kinetics further supports this conclusion. Separation of proteins after labeling shows that the F_1 subunit, containing the putative hydrophobic fusion sequence, is exclusively labeled, and that the F_2 subunit does not participate in fusion. Labeling shows temperature and pH dependence consistent with a need for protein conformational mobility and fusion at neutral pH. Higher amounts of labeling during fusion with CL vesicles than during virus-PS vesicle fusion reflects membrane packing regulation of peptide insertion into target membranes. Labeling of the viral hemagglutinin/neuraminidase (HN) at low pH indicates that HN-mediated fusion is triggered by hydrophobic interactions, after titration of acidic amino acids. HN labeling under nonfusogenic conditions reveals that viral binding may involve hydrophobic as well as electrostatic interactions. Controls for diffusional labeling exclude a major contribution from this source. Labeling during reconstituted Sendai virus envelope-liposome fusion shows that functional reconstitution involves protein retention of the ability to undergo hydrophobic interactions.
\r\n\r\nExamination of Sendai virus fusion with erythrocyte membranes indicates that hydrophobic interactions also trigger fusion between biological membranes, and that HN binding may involve hydrophobic interactions as well. Labeling of the erythrocyte membranes revealed close membrane association of spectrin, which may play a role in regulating membrane fusion. The data show that hydrophobic fusion protein interaction with both artificial and biological membranes is a triggering event in fusion. Correlation of these results with earlier studies of membrane hydration and fusion kinetics provides a more detailed view of the mechanism of fusion.
\r\n\r\nThe kinetics of DNA injection by bacteriophage \u03bb. into liposomes bearing reconstituted receptors were measured using fluorescence spectroscopy. LamB, the bacteriophage receptor, was extracted from bacteria and reconstituted into liposomes by detergent removal dialysis. The DNA binding fluorophore ethidium bromide was encapsulated in the liposomes during dialysis. Enhanced fluorescence of ethidium bromide upon binding to injected DNA was monitored, and showed that injection is a rapid, one-step process. The bimolecular rate law, determined by the method of initial rates, revealed that injection occurs several times faster than indicated by earlier studies employing indirect assays.
\r\n\r\nIt is hoped that these studies will increase the understanding of the mechanisms of virus entry into cells, and to facilitate the development of virus-mimetic drug delivery strategies.
\r\n", "doi": "10.7907/k40w-2z72", "publication_date": "1990", "thesis_type": "phd", "thesis_year": "1990" }, { "id": "thesis:2503", "collection": "thesis", "collection_id": "2503", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06072007-091301", "type": "thesis", "title": "Modification of Membrane Surfaces with Carbohydrates: An Approach for Stabilization During Freezing and Drying", "author": [ { "family_name": "Goodrich", "given_name": "Raymond Paul, Jr.", "orcid": "0000-0002-5945-4571", "clpid": "Goodrich-Raymond-Paul-Jr" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Revel", "given_name": "Jean-Paul", "clpid": "Revel-J-P" }, { "family_name": "Imperiali", "given_name": "Barbara", "orcid": "0000-0002-5749-7869", "clpid": "Imperiali-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A new class of molecules possessing amphipathic character was prepared. These compounds possessed a hydrophobic region capable of intercalation into a lipid bilayer, a hydrophilic linker group capable of extending beyond the surface of a membrane, and a carbohydrate attached at the end of this linker group. These features of this class of compounds permitted their direct incorporation into vesicle formulations and hence the direct examination of interactions occuring in the dry state between carbohydrates and lipid groups in such vesicle membrane systems.
\r\n\r\nSamples of treated vesicle preparations were subjected to freezing and thawing as well as to direct dehydration via lyophilization. Under these conditions, the stability and integrity of the membrane was examined via several spectroscopic techniques.
\r\n\r\nThrough these studies of systems in which a carbohydrate is directly bound to a membrane surface, it was possible to determine a defined ratio, independent of solution and concentration effects, at which carbohydrates can afford protection to dehydrated membranes. In addition, the interactions responsible for conferring the protection were determined. It was found that direct intercalation of the carbohydrates into a membrane interface preserves the membrane structure and organization that is normally observed in the presence of water. This behavior prevents the phase transitions, lipid phase separations, and fusion phenomena that normally compromise dehydrated membrane systems. This phenomena is directly related to the amount of carbohydrate that is present and the structure of the carbohydrate that is used. These results indicate that the partitioning behavior of the carbohydrates at the interface is of prime importance in determining the effectiveness in this regard.
", "doi": "10.7907/ff9e-th51", "publication_date": "1990", "thesis_type": "phd", "thesis_year": "1990" }, { "id": "thesis:2576", "collection": "thesis", "collection_id": "2576", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06132007-103520", "primary_object_url": { "basename": "Kramar_ja_1990.pdf", "content": "final", "filesize": 12143834, "license": "other", "mime_type": "application/pdf", "url": "/2576/1/Kramar_ja_1990.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Scanning Tunneling Microscopy and Spectroscopy of Molybdenum Disulfide", "author": [ { "family_name": "Kramar", "given_name": "John Adam", "orcid": "0000-0001-6038-637X", "clpid": "Kramar-John-Adam" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Scanning tunneling microscopy (STM) is a recently developed surface analysis technique that is capable of atomic resolution imaging in real space. In STM, a sharp electrically conducting tip is brought near the sample and a tunneling current is established between the two. For topographical imaging, the tip is then raster-scanned over the surface while a feedback control system maintains constant current by adjusting the position of the tip in the surface normal. The trajectory that the tip follows is displayed as the surface topography. The unique geometry of the STM has also allowed the electronic nature of surfaces to be probed with unprecedented spatial resolution. This can be implemented, for example, by posing the probe tip over a specific surface location and examining the current-versus-voltage characteristics.\r\n\r\nCareful consideration must be given in the design of an STM system. The crucial elements of vibration isolation and microscope rigidity must be optimized within the constraints of allowing coarse positioning of the tip and sample and permitting high-resolution scanning. A stable feedback control system must also be designed with flexibility to allow for different operating conditions.\r\n\r\nWe have built an ultrahigh vacuum (UHV) STM that is similar to the familiar pocket STM design. The UHV system includes a separate sample preparation chamber and vacuum-transfer load lock to facilitate in studies of clean, carefully prepared surfaces. The instrument is interfaced with a microprocessor for control of scanning, data acquisition, and coarse tip-sample approach and positioning. A high-resolution graphics monitor is also included for displaying the topographic images and the current-voltage spectra during acquisition and for reviewing previously stored images.\r\n\r\nStudies of the basal cleavage plane of MoS2 have been performed with this instrument. Large area images up to 360 x 360 nm reveal a high degree of variability in surface morphology, ranging from atomically smooth planes, to islands or mounds ranging from 1 to 10 nm in diameter, to areas of complete surface roughness. Many unusual imaging phenomena were also observed in these scans, including bias-dependent images and surface modifications that were due to tip-sample interactions.\r\n\r\nAtomic-resolution images revealing the trigonal symmetry of the surface plane were obtained in both the constant-current and current-imaging modes on the smooth areas of the surface. Two distinct sites can be seen, corresponding to the known molybdenum and sulfur atomic positions.\r\n\r\nA simple description of the distance dependence of tunneling between the STM tip and an ideal semiconductor surface (no surface Fermi level pinning) is presented, based on conventional metal-insulator-semiconductor (MIS) theories. The current conduction mechanism involves thermionic emission over the semiconductor diffusion-potential barrier, which is a decreasing function of the tip-sample separation, followed by tunneling through the vacuum gap. The competition between the decreased vacuum-tunneling probability and the increased carrier population at the semiconductor surface for increasing separation gives rise to a predicted peak in the I-s curves at small separations, and a lowering of the apparent tunneling barrier height out to separations of more than 1 nm. The normally rectified current-voltage characteristics are also found to be a function of the tip-sample spacing, showing a weakening and then a reversal of rectification as the separation is increased. These predicted effects are substantiated by means of a detailed numerical calculation for the passivated n-type Si(111) surface.\r\n\r\nThe current-voltage spectroscopy of MoS2, which is expected to behave as an ideal semiconductor, was examined. The surface-averaged spectra show a high degree of variability, with different data sets showing rectification in opposite polarities for the same physical tip and sample. The results are shown to be qualitatively different from known mechanisms for rectification in STM, including tip-curvature-induced field gradient effects and effects that are due to the separation dependence of rectification in ideal MIS structures. The results are best explained as doping inhomogeneities in our mineralogical samples.\r\n", "doi": "10.7907/Q36A-AW73", "publication_date": "1990", "thesis_type": "phd", "thesis_year": "1990" }, { "id": "thesis:2518", "collection": "thesis", "collection_id": "2518", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06082007-081855", "type": "thesis", "title": "Disulphide Polymerizeable Phosphatidylcholines: Characterization of Membrane Physical Properties and Investigations of in vivo Behavior", "author": [ { "family_name": "Handel", "given_name": "Tracy Marie", "orcid": "0000-0002-2558-6138", "clpid": "Handel-Tracy-Marie" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In the past ten years, polymerizeable amphiphiles have been recognized as an important class of synthetic phospholipids due to their ability to modify the mechanical and chemical stability of membranes. The motivation behind studies of polymerizeable phospholipids is based on the potential importance of stable membranes in a wide variety of applications including reactivity control, encapsulation technologies and drug delivery. However, compared to nonpolymerizeable lipids, there is a relative paucity of information correlating membrane physical properties with the structure of the polymeric lipid. The present investigation involves the synthesis of a series of disulfide polymerizeable phosphatidylcholines, the characterization of the physical properties of membranes formed from these lipids, and an investigation of the biodistributions, vascular clearance rates and degradation rates of these liposomes in vivo.
\r\n\r\nThe structures of the lipids under investigation are analogous to saturated phosphayitdylcholines but with a thiol either alpha to the carbonyl of the acyl chain (\u03b1-THIOL) or at the chain terminus (\u03c9-THIOL). It is found that the presence and position of the polymerizeable moiety drastically alters the physical characteristics of the membranes. A variety of physical techniques have been utilized to understand both the bulk properties of the lipids such as morphology and permeability, as well as the molecular details of the lipid conformation and dynamics. On the basis of such studies including Raman, FT-IR and DSC, it appears that the presence of the polymerizeable group at the interfacial region (\u03b1-THIOLS) causes a reduction in the lipid packing and an increase in chain disorder compared to nonpolymerizeable analogs. For the monomeric form of the \u03b1-THIOLS, the decreased interlipid interaction may be ascribed to the presence of an additional hydrophilic pendant group at the interface that interferes with tight crystalline packing, most likely by a combination of steric and hydration effects. In contrast to the general expectations for polymerized versus nonpolymerized phospholipids, upon polymerization, the membrane disorder is augmented even further. We believe this to be a consequence of the conformational restrictions of polymerization which inhibit the ability of the polymeric lipids to adopt a highly ordered and uniform packing state. Instead it is suspected that the reduced conformational freedom of polymerized lipids promotes the formation of surface defects between unlinked polymer chains. As a morphological consequence, the polymeric \u03b1-THIOLS tend to form smaller and largely unilamellar vesicles on dispersion in water. Furthermore because of the disorder in the hydrocarbon chain region, they are quite permeable to entrapped solutes and when administered in vivo, are cleared rapidly from the circulatory system. The latter effect is likely the result of facilitated absorption of opsonizing proteins into the disordered membrane surface which subsequently accelerates vascular clearance and uptake by the cells of the reticuloendothelial system (RES).
\r\n\r\nOn the basis \u00b3\u00b9P NMR relaxation measurements, it was observed that the motion of the headgroups in polymeric \u03b1-THIOLS was reduced relative to nonpolymerizeable analogs. Furthermore a reduced chemical shift anisotropy of polymeric \u03b1-THIOLS in the liquid-crystalline state relative to nonpolymerizeable lipids was observed and suggests an alteration in the average orientation of the headgroup for the polymer. Because the headgroup of phosphatidylcholines is zwitterionic, changes in the average orientation can have marked effects on the electrostatic properties of the membrane surface, which in turn can affect membrane morphology and interactions with cell-surfaces and proteins.
\r\n\r\nFor \u03c9-THIOLS, a distinctly different behavior was observed compared to the \u03b1-THIOLS. For the monomers and especially the polymers, results from vibrational spectroscopy and DSC suggest that the membrane conformational order and rigidity is increased relative to nonpolymerizeable phosphatidylcholine analogues. However, in contrast to the \u03b1-THIOLS that form normal self-sealed liposomal structures in both the monomeric and polymeric state, polymerization induces the transformation of \u03c9-THIOLS into bilayer fragments lacking an internal aqueous compartment. The most likely explanation for this was derived from \u00b9\u00b3C NMR relaxation experiments, which indicated that the mobility at the bilayer midplane of polymeric \u03c9-THIOLS is as restricted as the interfacial region. This contrasts to nonpolymerizeable phospholipids and \u03b1-THIOLS, which have the bilayer interior as the most fluid portion of the membrane. The rigidity at the midplane may prohibit the ability of the polymeric \u03c9-THIOLS to form curved or continuous multilamellar sheets or to respond to transient defects in the membrane without fragmentation.
\r\n\r\nAn interesting and unexpected result concerning the \u03c9-THIOLS was retention of a phase transition after polymerization. For most polymeric lipids that have the polymerizeable moiety at the chain terminus, polymerization has resulted in the disappearance of the transition due to crosslinking of the hydrocarbon chains. The presence of the transition in polymerized \u03c9-THIOLS may be evidence for the fact that polymerization results in a predominance of intra- rather than inter-leaflet coupled chains.
", "doi": "10.7907/x0z5-ef38", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:10756", "collection": "thesis", "collection_id": "10756", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03062018-123026017", "primary_object_url": { "basename": "Reimer_JA_1981.pdf", "content": "final", "filesize": 67599808, "license": "other", "mime_type": "application/pdf", "url": "/10756/1/Reimer_JA_1981.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The Development of Novel Nuclear Magnetic Resonance Techniques for the Study of Solids, Thin Films and Surfaces with Particular Application to Amorphous Semiconducting Silicon-Hydrogen Films", "author": [ { "family_name": "Reimer", "given_name": "Jeffrey Allen", "clpid": "Reimer-Jeffrey-Allen" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Cole", "given_name": "Terry", "clpid": "Cole-Terry" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part 1
\r\n\r\nProton magnetic resonance data are presented for twenty different plasma-deposited amorphous silicon-hydrogen films. The two phase compositional inhomogeneity observed in these films is found to be independent of film thickness down to less than 1\u03bc. Models for various structural configurations show that these films contain heavily monohydride clustered regions such as divacancies and voids, as well as (SiH2)n and SiH3 local bonding configurations. The presence of the divacancies in films showing predominantly monohydride vibrational modes provides some insight into the controversy over the assignment of the 2090 cm-1 vibrational mode. The films also contain regions in which monohydride groups are distributed at random. Based on changes in a film whose proton NMR lineshapes are metastable as deposited, a model based on strain relief is proposed for film development which explains the ubiquitous presence of the two phase inhomogeneity. Examination of the changes in proton NMR data as a function of deposition conditions furnishes new insight on the role SiH2 and SiH+x groups have in models for the gas phase reactions involved in the developing films. Finally, p- or n-type doping is found to increase the the hydrogen content of the films, and, under heavy p-type doping with diborane, boron clustering may occur within the films. Proton NMR lineshapes are also presented as a function of annealing temperature up to 650\u00b0C. The data indicate that hydrogen diffuses internally before major evolution occurs, that transfer of hydrogen occurs from a heavily clustered phase to a dilute phase coincident with evolution and that evolution occurs initially from the heavily clustered phase. Internal hydrogen diffusion is found to be concomitant with the reduction in paramagnetic center density.
\r\n\r\nSilicon-29 and hydrogen magic angle sample spinning experiments on amorphous silicon-hydrogen films (involving cross-polarization and homonuclear multiple pulse techniques respectively) fail to yield quantitative determinations of local silicon-hydrogen bonding environments. However, the 29Si data are qualitatively consistent with infra-red assignments of (SiH2)n groups. Furthermore, the lack of significant line narrowing for the 29Si spectra upon magic angle sample spinning shows that there are large chemical shift dispersions, indicative of the disorder in the amorphous lattice.
\r\n\r\nProton spin-lattice relaxation data are presented for several plasma deposited amorphous silicon-hydrogen films when (i), homonuclear dipolar interactions are suppressed, (ii), deuterium is isotopically substituted for hydrogen, and (iii), films are annealed. These data are consistent with a model in which proton nuclei are relaxed by hydrogen-containing disorder modes. Analysis of these data shows that the density of disorder modes is ~30% higher in the low hydrogen density domain and that more than one hydrogen nucleus is associated with each disorder mode. The behavior of T1 upon annealing indicates that a small fraction of unpaired spins or \"dangling bonds\" may be associated with the disorder modes. These results suggest that the role of hydrogen in amorphous silicon is more complex than passivation of \"dangling bond\" intrinsic defects.
\r\n\r\nFinally, proton magnetic resonance data are presented for the hydrogen alloys of plasma-deposited amorphous boron, carbon, silicon carbide and silicon nitride. Linewidth and lineshape analysis leads to the conclusion that hydrogen nuclei are clustered in a-Si/C:H, a-C:H, and a-Si/N:H. Both a-Si/C:H and a-C:H data show hydrogen exists in two phases. Modeling of linewidths in a-Si/C:H indicates that the two phases are heavily hydrogenated carbon clusters imbedded in a weakly hydrogenated a-Si lattice. In addition, evidence is presented for the presence of motionally narrowed hydrogen spectra in a-Si/N:H, a-B:H, and a-C:H. It is suggested that the hydrogen nuclei giving rise to these spectra are associated with disorder modes.
\r\n\r\nPart 2
\r\n\r\nThe production of heteronuclear dipolar modulated chemical shift spectra of specific protons within polycrystalline solids is described by consideration of explicit double resonance pulse schemes which remove both heteronuclear and homonuclear dipolar interactions. These spectra furnish an accurate method of determining bond distances in local environments of complicated chemical systems. When used in conjunction with selectively observed chemical shift spectra, these schemes present a means for characterization of both geometrical and electronic properties in the solid state. To demonstrate the utility of these experiments, selective proton observed NMR results are presented for the carbonyl protons of adsorbed formic acid on ammonium-Y zeolite and the hydrogen bonded proton in polycrystalline acetanilide. Chemical shift information for the adsorbed formic acid shows a chemisorbed species consistent with formate ions. The data for the amide bond in polycrystalline acetanilide show a hydrogen bond with a chemical shift anisotropy of 17.7 ppm and a N-H distance of 1.05 \u00b1 0.01 \u00c5.
", "doi": "10.7907/c2h9-0m19", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:18529", "collection": "thesis", "collection_id": "18529", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04302026-160335841", "type": "thesis", "title": "I. Methods for Restriction Endonuclease Studies of DNA Structure. II. Restriction Endonucleolytic Characterization of Animal Mitochondrial DNAs and Human Globin Genes", "author": [ { "family_name": "Parker", "given_name": "Richard Carl", "clpid": "Parker-Richard-Carl" } ], "thesis_advisor": [ { "family_name": "Vinograd", "given_name": "Jerome Rubin", "clpid": "Vinograd-J-R" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Maniatis", "given_name": "Tom", "orcid": "0000-0002-2722-8633", "clpid": "Maniatis-T" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "An initial approach to the structural organization of DNA is restriction\r\nendonuclease site mapping and gel electrophoretic analysis. This is true for genomes\r\nof the simplest or greatest complexities.
\r\n\r\nTwo techniques are presented in this thesis that facilitate this approach.\r\nThe first uses ethidium bromide to limit the action of a restriction endonuclease\r\non a closed circular DNA in order to derive a set of circularly permuted linear\r\nmolecules. These molecules, after appropriate treatment, can be used to orient\r\nthe restriction endonuclease sites and to calibrate the relationship between\r\nelectrophoretic mobility and DNA fragment size without the introduction of\r\nexternal standards.
\r\n\r\nThe second technique utilizes a low melting temperature agarose. It\r\nprovides a simple system for two-dimensional electrophoretic analysis of DNA\r\nmolecules with restriction endonuclease digestion of the DNA occurring after\r\nthe first electrophoretic separation and before the second.
\r\n\r\nThese techniques and others were used to study mitochondrial DNA from\r\nmice and rats. Some of these data explore the evolutionary divergence of the\r\nmtDNA in these animals. This information can be compared to evolutionary\r\nstudies with nuclear DNA.
\r\n\r\nAdditionally, chromosomal DNA from patients with normal hemoglobin\r\nand hemoglobin Lepore was studied. Using this type of analysis we were able\r\nto demonstrate that a change in the amino acid sequence of some of the \u03b2-related\r\nglobin chains in hemoglobin Lepore is associated with a change in DNA structure.
", "doi": "10.7907/pphq-jv67", "publication_date": "1979", "thesis_type": "phd", "thesis_year": "1979" } ]