Jamming effects in glasses and biopolymers

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dc.contributor.advisorThirumalai, Devarajanen_US
dc.contributor.authorKang, Hongsuken_US
dc.contributor.departmentChemical Physicsen_US
dc.contributor.publisherDigital Repository at the University of Marylanden_US
dc.contributor.publisherUniversity of Maryland (College Park, Md.)en_US
dc.date.accessioned2014-10-11T05:41:05Z
dc.date.available2014-10-11T05:41:05Z
dc.date.issued2014en_US
dc.description.abstractIn this dissertation, jamming effects in highly packed systems are studied in two specific materials: glasses and biopolymers in cellular environments. Suspensions consisting of highly charged colloids, which are well-known glass-forming systems, are investigated using molecular dynamics simulations in order to test Random First Order Transition (RFOT) theory. I found that there is a critical volume fraction at which ergodic-to-nonergodic transitions for three dynamic observables take place in accordance with RFOT. Based on numerical observations, it is also proposed that the dynamic heterogeneity can be attributed to the violation of law of large numbers. In addition, the bond orientational order of colloidal suspensions and soft-spheres is discussed in the context of liquid-glass transitions. The response of biopolymers to a crowded environment is another interesting issue because 20-40% volume of a cell is occupied by various cellular components such as ribosomes and proteins in vivo. In this work, using low-friction langevin dynamics simulations with explicit crowding particles, I examined the conformational change of biopolymers in the presence of crowders of various sizes and shapes. The simulation results reveal that cylindrical crowders induce much greater compaction of the polymers than spherical ones at low volume fractions and the stronger crowding effects disappear at higher volume fractions due to local nematic ordering of cylindrical particles. The reduction in the size of polymer is even more dramatic in a mixture of spherical and cylindrical shapes because of cooperative crowding effects explained by the phase separation of spheres and rodlike particles. Finally, the crowding effects of cellular components on bacterial chromosomes are estimated using a mixture of spherical crowders with the composition found in bacterial cytoplasms.en_US
dc.identifierhttps://doi.org/10.13016/M28W2V
dc.identifier.urihttp://hdl.handle.net/1903/15723
dc.language.isoenen_US
dc.subject.pqcontrolledBiophysicsen_US
dc.subject.pqcontrolledPhysical chemistryen_US
dc.subject.pqcontrolledPhysicsen_US
dc.subject.pquncontrolledbond orientational orderen_US
dc.subject.pquncontrolledcolloidal glassesen_US
dc.subject.pquncontrolledDNAen_US
dc.subject.pquncontrolledintrinsically disordered proteinsen_US
dc.subject.pquncontrolledmacromolecular crowdingen_US
dc.subject.pquncontrolledRFOTen_US
dc.titleJamming effects in glasses and biopolymersen_US
dc.typeDissertationen_US

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