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dc.contributor.authorCook, Larry Jonathanen_US
dc.date.accessioned2014-03-14T20:20:46Z
dc.date.available2014-03-14T20:20:46Z
dc.date.issued2009-12-04en_US
dc.identifier.otheretd-12162009-145140en_US
dc.identifier.urihttp://hdl.handle.net/10919/30121
dc.description.abstractIn many situations in the world, the amount of resources available for use is limited. This statement is especially true in the cells of living organisms. During the translation process in protein synthesis, ribosomes move along the mRNA strand constructing proteins based on the sequence of codons that form a gene. The totally asymmetric simple exclusion process (TASEP) models well the translation process. However, these genes are constantly competing for ribosomes and other resources in the cell. To see how finite resources and competition affects such a system, we must construct a simple model to account for the limited resources.

We consider coupling multiple TASEPs to a finite reservoir of particles where the entry rate of particles into the TASEPs depends on the number of particles left in the reservoir. Starting with a single TASEP connected to the reservoir, we study the system using both Monte Carlo simulations and theoretical approaches. We explore how the average overall density, density profile, and current change as a function of the number of particles initially in the reservoir for various parameters. New features arise not seen in the ordinary TASEP model, even for a single TASEP connected to the pool of particles. These features include a localized shock in the density profile. To explain what is seen in the simulations, we use an appropriately generalized version of a domain wall theory.

The dynamics of the TASEPs with finite resources are also studied through the power spectra associated with the total particle occupancy of each TASEP and the reservoir. Again, we find new phenomena not seen in the power spectrum of the ordinary TASEP. For a single constrained TASEP, we find a suppression at low frequencies when compared to the power spectrum of the ordinary TASEP. The severity of this suppression is found to depend on how the entry rate changes with respect to the number of particles in the pool. For two TASEPs of different lengths, we find an enhancement of the power spectrum of the smaller TASEP when compared to the ordinary TASEP's power spectrum. We explain these findings using a linearized Langevin equation.

Finally, we model competition between ten genes found in Escherichia coli using a modified version of the TASEP. This modified version includes extended objects and inhomogeneous internal hopping rates. We use the insight gained from the previous studies of finite resources and competition as well as other studies to gain some insight into how competition affects protein production.

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dc.publisherVirginia Techen_US
dc.relation.haspartCook_LJ_D_2009.pdfen_US
dc.rightsI hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to Virginia Tech or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.en_US
dc.subjectpower spectraen_US
dc.subjectdomain wallen_US
dc.subjectprotein synthesisen_US
dc.subjectopen-boundaryen_US
dc.subjectTASEPen_US
dc.titleTotally Asymmetric Simple Exclusion Processes with Finite Resourcesen_US
dc.typeDissertationen_US
dc.contributor.departmentPhysicsen_US
dc.description.degreePh. D.en_US
thesis.degree.namePh. D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen_US
thesis.degree.disciplinePhysicsen_US
dc.contributor.committeechairZia, Royce K. P.en_US
dc.contributor.committeememberKulkarni, Rahul V.en_US
dc.contributor.committeememberPleimling, Michel J. F.en_US
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-12162009-145140/en_US
dc.contributor.committeecochairSchmittmann, Beateen_US
dc.date.sdate2009-12-16en_US
dc.date.rdate2012-08-07
dc.date.adate2009-12-22en_US


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