Theses and Dissertations from UMD

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New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM

More information is available at Theses and Dissertations at University of Maryland Libraries.

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Subject: search.filters.subject.Membrane

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Now showing 1 - 5 of 5
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    Simulating membrane-bound cytoskeletal dynamics
    (2023) Ni, Haoran; Papoian, Garegin A.; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The cell membrane defines the shape of the cell and plays an indispensable role in bridging intra- and extra-cellular environments. The membrane, consisting of a lipid bilayer and various attaching proteins, mechanochemically interacts with the active cytoskeletal network that dynamically self-organizes, playing a vital role in cellular biomechanics and mechanosensing. Comprehensive simulations of membrane-cytoskeleton dynamics can bring insight in understanding how the cell mechanochemically responds to external signals, but a computational model that captures the complex cytoskeleton-membrane with both refined details and computational efficiency is lacking. To address this, we introduce in this thesis a triangulated membrane model and incorporate it with the active biological matter simulation platform MEDYAN ("Mechanochemical Dynamics of Active Networks"). This model accurately captures the membrane physical properties, showing how the membrane rigidity, the structure of actin networks and local chemical environments regulate the membrane deformations. Then, we present a new method for simulating membrane proteins, using stochastic reaction-diffusion sampling on unstructured membrane meshes. By incorporating a surface potential energy field into the reaction-diffusion sampling, we demonstrate rich membrane protein collective behaviors such as confined diffusion, liquid-liquid phase separation and membrane curvature sensing. Finally, in order to capture stretching, bending, shearing and twisting of actin filaments which are not all available with traditional actomyosin simulations, we introduce new finite-radius filament models based off Cosserat theory of elastic rods, with efficient implementation using finite-dimensional configurational spaces. Using the new filament models, we show that the filaments' torsional compliance can induce chiral symmetry breaking in a cross-linked actin bundle. All the new models are implemented in the MEDYAN platform, shedding light on whole cell simulations, paving way for a better understanding of the membrane-cytoskeleton system and its role in cellular dynamics.
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    PARAMETERIZATION OF THE CHARMM LIPID FORCE FIELD AND APPLICATIONS TO MEMBRANE MODELING
    (2022) Yu, Yalun; Klauda, Jeffery B.; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Computational modeling of lipids at the atomistic level provides insights into the chemical physics of biological membranes and opens the possibility to model membrane-protein interactions. This dissertation presents contributions to the CHARMM/Drude family of lipid force fields and applications of the CHARMM36 lipid force field to model membranes.Long-range Lennard-Jones interactions are critical for membrane simulations but were excluded from the CHARMM lipid force field for historical reasons. Re-parameterization of the CHARMM36 (C36) lipid force field for phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and ether lipids is performed to incorporate these interactions through the Lennard-Jones particle-mesh Ewald (LJ-PME) method. The resulting force field is denoted C36/LJ-PME. C36/LJ-PME is in excellent agreement with experimental structure data for lipid bilayers and reproduces the experimental compression isotherm of monolayers. A semi-automated protocol is developed and used during this parameterization and significantly accelerates the whole process. The same protocol is used for the optimization of the Drude polarizable lipid force field. The optimization of this force field focuses on the structural and mechanical properties of bilayers and ab initio results of model compounds representing the lipid headgroup. Long-range dispersion interactions are incorporated into the force field as well. The resulting force field is validated against more structural and dynamic properties of bilayers and the compression isotherm of monolayers and demonstrates significant improvements over the past versions of the force field. In addition to these fully atomistic models, this dissertation also discusses the update to the CHARMM36 united atom chain model. Both the original model (C36UA) and the revised model (C36UAr) adopt the all-atom C36 lipid force field parameters for the headgroup and a united atom representation for the chain. The update focuses on the Lennard-Jones parameters of the hydrocarbon chain and related dihedrals. Bulk liquid properties (density, heat of vaporization, isothermal compressibility, and diffusion constant) of linear alkanes and alkenes and ab initio torsional scans are used as initial fitting targets. Bilayer surface area is used to fine-tune the dihedral parameters. Bilayer simulations of various headgroups and tails using C36UAr demonstrate significant improvements over C36UA from a structural perspective. The last part of this dissertation presents the applications of the C36 lipid force field. The inner membrane of Pseudomonas aeruginosa (P. aeruginosa) is modeled in two modes (planktonic and biofilm) to study the influence of lipid composition on bilayer structural and mechanical properties. The hydrophobic thicknesses of the model membrane agree with the P. aeruginosa transmembrane proteins in the Orientations of Proteins in Membranes (OPM) database. Symmetric and asymmetric models for the Arabidopsis thaliana plasma membrane are modeled. Molecular dynamics (MD) simulations indicate that the outer leaflet is more rigid and tightly packed to the inner leaflet. The interplay between glycolipids and sterols is found to be critical in lipid clustering and a possible mechanism for lipid phase separation has been proposed.
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    Silane Cross-Linked Graphene Oxide Membrane Demonstrating Unique Transport Phenomena in Aqueous Phase Separation
    (2015) Zheng, Sunxiang; Mi, Baoxia; Civil Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Graphene oxide (GO) membranes are considered promising for water purification applications. We synthesized a novel GO membrane using inorganic silane as a cross linker. Briefly, a pH 3 GO solution was filtrated through polyethersulfone (PES) membrane supports by vacuum filtration. The GO layers deposited on the PES supports were subsequently soaked in a saturated sodium metasilicate solution for crosslinking and stabilization. As a final step, the readily stabilized GO membranes were transferred into a 10% H2SO4 solution for further stabilization. The GO membrane exhibits unique rejection properties to uncharged organic species (~ 85%) and ionic species (~6%). A high water flux of 39 L/m2/h and a reasonable back solute flux of 0.011 mol/m2/h were observed with 0.25M trisodium citrate dehydrate (TSC) as draw solution in forward osmosis (FO). The GO membrane also demonstrates some interesting Janus effects and enables directional water gating (by blocking the permeation in one direction while allowing the permeation in the other direction).
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    GRAPHENE OXIDE MEMBRANES FOR WATER PURIFICATION
    (2015) Hu, Meng; Mi, Baoxia; Civil Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Graphene oxide (GO) is a two-dimensional material with a single layer carbon lattice, which is decorated with oxygenated functional groups on the basal plane as well as on the edges. Due to its unique properties, GO has attracted many applications including electronics, energy, sensors, optics, etc. Recently, it has been demonstrated that the graphene surface of GO presents long slip lengths of water, thus allowing for an unimpeded water flow. It was anticipated that the ultrafast water transport would be translated into membrane separations, in order to address one of the major challenges for membrane technology—low performance. It was also expected that GO might provide solutions to other obstacles facing membrane technology, such as membrane fouling. These two overarching themes, the technical limitations for membrane technology and the potential of GO to overcome those restrictions, inspired the current study. The main objective of this dissertation was to develop highly efficient membranes for water purification based on GO. Also investigated were the transport mechanisms for the designed GO membranes, the potential of GO to mitigate membrane fouling, and the feasibility of GO membrane regeneration. Major achievements of the study include: (1) the development of high performance GO membranes for nanofiltration and forward osmosis by two facile and sustainable methods, (2) the elucidation of transport mechanisms to guide better GO membrane design, (3) the application of GO for fouling mitigation in pressure retarded osmosis processes, and (4) the validation for regenerable GO membranes. Collectively, not only do the findings provide the first experimental verification for the ultrafast water transport in GO membranes, they also suggest that the GO membrane could be a promising prototype of next generation membranes with high performance, low fouling propensity, and full regenerability. The work has already begun to show its profound impact in the membrane field, as seen in the publications it has prompted.
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    Temperature and Pressure Effects on Hydrogen Permeation in Palladium Based Membranes
    (2010) James, Ryan T.; Gupta, Ashwani K.; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Palladium based membranes offer a promising method for extracting hydrogen from multi-component synthetic gas (syngas) mixtures. Thin palladium and palladium alloy membranes supported on porous media combine both enhanced strength and durability with increased permeation. The syngas produced from waste and biomass contains several gases of different concentrations. The availability of clean hydrogen from syngas is novel since the hydrogen storage and transportation are amongst the major issues for the utilization of hydrogen. A lab scale experimental facility has been designed and built that allows one to examine different types of membranes for efficient and effective separation of hydrogen from syngas. Experimental results have been obtained from this facility using palladium membranes. The results show hydrogen permeation increased with both temperature and pressure, with the greatest increase occurring with rising temperature. Determination of the pressure exponent revealed that the reaction was limited by both the surface reaction and diffusion process.