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Title: Computer simulation of two polymers confined to a box-like cavity
Date: 2021
Author: Rehel, Desiree
Genre: Honours
Abstract: In this study, we use computer simulations to examine the behaviour of systems of two polymers confined to a box-like cavity, with strong...
Publisher: University of Prince Edward Island
Publication Status: PUBLISHED




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Title: Free-energy cost of localizing a single monomer of a confined polymer
Source: Physical Review E
Date: 2019
Author: Polson, James M.; McLure, Zakary R. N.
Genre: Journal Article
Volume: 99
Issue: 6
Start Page: 062503
DOI: 10.1103/PhysRevE.99.062503




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Title: Polymer translocation into cavities: Effects of confinement geometry, crowding, and bending rigidity on the free energy
Source: Physical Review E
Date: 2019
Author: Polson, James M.; Heckbert, David R.
Genre: Journal Article
Volume: 100
Issue: 1
Start Page: 012504




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Title: Segregation of polymers under cylindrical confinement: effects of polymer topology and crowding
Source: Soft Matter
Date: 2018
Author: Polson, James M.; Kerry, Deanna R.-M.
Genre: Journal Article
Volume: 14
Start Page: 6360
DOI: 10.1039/C8SM01062E




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Title: Segregation of polymers under cylindrical confinement: Effects of polymer topology and crowding
Source: ArXiv
Date: 2018
Author: Polson, James M.; Kerry, Deanna R.-M.
Genre: Journal Article
Abstract: Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple...
Volume: 1805.09270
DOI: 10.1039/c8sm01062e




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Title: Free energy of a folded semiflexible polymer confined to a nanochannel of various geometries
Source: arXiv
Date: 2018
Author: Polson, James M.
Genre: Journal Article
Abstract: Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the...
Volume: 1805.12497
DOI: 10.1021/acs.macromol.8b01148



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Title: Simulation study of the confinement free energy of folded polymers
Date: 2017
Author: Tremblett, Aidan
Genre: Honours
Publisher: University of Prince Edward Island
Publication Status: PUBLISHED



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Title: Crowding effects on the segregation of cylindrically confined ring polymers
Date: 2017
Author: Kerry, Deanna Rita-Mae
Genre: Honours
Abstract: In the cell cycle, chromosome segregation occurs during anaphase, the process where original and replicated chromosomes move towards opposite sides...
Publisher: University of Prince Edward Island
Publication Status: PUBLISHED




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Title: Free energy of a folded polymer under cylindrical confinement
Source: ArXiv
Date: 2017
Author: Polson, James M.; Tremblett, Aidan F.; McLure, Zakary R. N.
Genre: Journal Article
Abstract: Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The...
Volume: 1710.00203
DOI: 10.1021/acs.macromol.7b02114




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Title: Polymer translocation into and out of an ellipsoidal cavity
Source: arXiv
Date: 2015
Author: Polson, J.M.
Genre: Journal Article
Abstract: Monte Carlo simulations are used to study the translocation of a polymer into and out of a ellipsoidal cavitythrough a narrow pore. We measure the...
Volume: 1303.5483v3
DOI: 10.1063/1.4919642



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Title: Evaluating the applicability of the Fokker-Planck equation in polymer translocation
Subtitle: A Brownian dynamics study
Source: Journal of Chemical Physics
Date: 2014
Author: Polson, James M.; Dunn, Taylor R.
Genre: Journal Article
Volume: 140
Issue: 18
Start Page: 184904
DOI: 10.1063/1.4874976
Publication Status: PUBLISHED




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Title: Polymer segregation under confinement: Free energy calculations and segregation dynamics simulations
Source: arXiv
Date: 2014
Author: Polson, James M.; Montgomery, Logan G.
Genre: Journal Article
Abstract: Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain...
Volume: 1408.4766v1
DOI: 10.1063/1.4898714




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Title: Discontinuous molecular dynamics (DMD) study of heteropolymer collapse in an explicit solvent
Source: Cell Biochemistry And Biophysics
Date: 2013
Author: Opps , S.B.; Rilling , K.M.; Polson , J.M.
Genre: Journal Article
Abstract: In this study, we employ the discontinuous molecular dynamics simulation method to investigate the collapse properties of a single heteropolymer...
Volume: 66
Issue: 1
Start Page: 29
DOI: 10.1007/s12013-012-9394-6



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Title: Polymer translocation dynamics in the quasi-static limit
Source: Journal of Chemical Physics
Date: 2013
Author: Polson, James M.; McCaffrey, Anthony C. M.
Genre: Journal Article
Abstract: Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate...
Volume: 138
Issue: 17
Start Page: 174902
DOI: 10.1063/1.4803022
Publication Status: PUBLISHED



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Title: Simulation study of the polymer translocation free energy barrier
Source: Journal of Chemical Physics
Date: 2013
Author: Polson, J.M.; Hassanabad, M.F.; McCaffrey, A.
Genre: Journal Article
Volume: 138
Start Page: 024906
DOI: 10.1063/1.4774118
Publication Status: PUBLISHED



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Title: Dynamics of a polymer in a Brownian ratchet
Source: Physical Review.E, Statistical, Nonlinear, and Soft Matter Physics
Date: 2010
Author: Polson, J. M.; Bylhouwer, B.; Zuckermann, M. J.; Horton, A. J.; Scott, W. M.
Genre: Journal Article
Abstract: We have used Brownian dynamics simulations to study the dynamics of a bead-and-spring polymer subject to a flashing ratchet potential. To elucidate...
Volume: 82
Issue: 5 Pt 1
Start Page: 051931
DOI: 10.1103/physreve.82.051931
Publication Status: PUBLISHED




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Title: A Monte Carlo simulation study of polymer translocation through a nanopore
Source: Physics in Canada / La Physique au Canada
Date: 2009
Author: Hassanabad, Mostafa Fatehi; Polson, James
Genre: Journal Article
Volume: 65
Issue: 3
Start Page: 126



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Title: Theoretical study of solvent effects on the coil-globule transition
Source: Journal of Chemical Physics
Date: 2009
Author: Polson, J. M.; Opps, S. B.; Abou Risk, N.
Genre: Journal Article
Abstract: The coil-globule transition of a polymer in a solvent has been studied using Monte Carlo simulations of a single chain subject to intramolecular...
Volume: 130
Issue: 24
Start Page: 244902
DOI: 10.1063/1.3153350
Publication Status: PUBLISHED



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Title: Discontinuous molecular dynamics simulation study of polymer collapse
Source: Journal of Chemical Physics
Date: 2006
Author: Opps, Sheldon B.; Polson, James M.; Abou Risk, N.
Genre: Journal Article
Abstract: Discontinuous molecular dynamics simulations were used to study the coil-globule transition of a polymer in an explicit solvent. Two different...
Volume: 125
Issue: 19
Start Page: 194904
DOI: 10.1063/1.2388270
Publication Status: NO_OBJ



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Title: Equilibrium conformational dynamics of a polymer in a solvent
Source: Journal of Chemical Physics
Date: 2006
Author: Polson, James M.; Gallant, J. P.
Genre: Journal Article
Abstract: Molecular dynamics simulations were used to study the conformational dynamics of a bead-spring model polymer in an explicit solvent under good...
Volume: 124
Issue: 18
Start Page: 184905
DOI: 10.1063/1.2194903
Publication Status: NO_OBJ

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