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Effects of static and temporally fluctuating tensions on semiflexible polymer looping

Jaeoh Shin, Wokyung Sung
2012 Journal of Chemical Physics  

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2011 pre-print arXiv:1112.0450v1 fatcat:l5wl62pvdffanitszwok6eqolm
We show a minute tension dramatically changes the looping time, especially for long chains.  ...  We study the dynamics of semiflexible polymer looping in the presence of such tensions by using Brownian dynamics simulation combined with an analytical theory.  ...  Acknowledgments This work was supported by Korea Research Foundation administered by Ministry of Education, Science and Technology, S. Korea.  ... 
doi:10.1063/1.3673439 pmid:22299917 fatcat:hpjxt2c3knd4daazqrmcgdrdqy
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Jaeoh Shin, Wokyung Sung. "Effects of static and temporally fluctuating tensions on semiflexible polymer looping." Journal of Chemical Physics 136.4 (2012) 045101

Buckling of semiflexible filaments under compression [article]

J.R. Blundell, E.M. Terentjev
2009 arXiv   pre-print

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2009 pre-print
arXiv:0902.2079v1 fatcat:lriuiguk2ralxnr5e7qb4heq4i
Using this formula we study the buckling transition of semiflexible filaments and find that kinetics plays an important role.  ...  Starting from the classical worm-like chain model under constant compression, we use a mean-field approach for filament inextensibility to find the complete partition function.  ...  Introduction There are a number of reasons for the current interest in semiflexible filaments under compression.  ... 
arXiv:0902.2079v2 fatcat:ibvz7vmtvbhthgur4rgaqeftum
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J.R. Blundell, E.M. Terentjev. "Buckling of semiflexible filaments under compression." arXiv (2009)

Collapse of a semiflexible polymer in poor solvent

Alberto Montesi, Matteo Pasquali, F. C. MacKintosh
2004 Physical Review E  

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2003 pre-print
arXiv:cond-mat/0308356v1 fatcat:a4zjnki6gvh7bcrb7ovbuh2ijy
We investigate the dynamics and the pathways of the collapse of a single, semiflexible polymer in a poor solvent via 3-D Brownian Dynamics simulations.  ...  The semiflexible chain collapse is studied as functions of the three relevant length scales of the phenomenon, i.e., the total chain length L, the persistence length L_p and the condensation length L_0  ...  Adam Horch for preparing the visualizations of the collapsing semiflexible molecules. This work was partially supported by the National Science Foundation under Grant No.  ... 
doi:10.1103/physreve.69.021916 pmid:14995500 fatcat:wdzct3xzrvdxveu2ffgn7awfyy
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Alberto Montesi, Matteo Pasquali, F. C. MacKintosh. "Collapse of a semiflexible polymer in poor solvent." Physical Review E 69.2 (2004)

Folding and unfolding kinetics of a single semiflexible polymer

Natsuhiko Yoshinaga
2008 Physical Review E  

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2008 pre-print arXiv:0804.2782v1 fatcat:6ox6cf5zszbchbvu3cs2nsa4xy
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer.  ...  We also propose the kinetics of the transitions in the presence of the hydrodynamic interaction.  ...  We would like to acknowledge the support of a fellowship from the JSPS (No. 7662). Part of the numerical calculations in this work was carried out on Altix3700 BX2 at YITP in Kyoto University.  ... 
doi:10.1103/physreve.77.061805 pmid:18643293 fatcat:x4mn3l7f2facljuoef6mn7uljq
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Natsuhiko Yoshinaga. "Folding and unfolding kinetics of a single semiflexible polymer." Physical Review E 77.6 (2008)

Dynamics of Folding in Semiflexible Filaments

P. Ranjith, P. B. Sunil Kumar
2002 Physical Review Letters  

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2002 pre-print arXiv:cond-mat/0203152v1 fatcat:y7l3svex3jexpclo5cx354hrw4
We investigate the dynamics of a single semiflexible filament, under the action of a compressing force, using numerical simulations and scaling arguments.  ...  It is shown that this behavior can be attributed to the exponentially falling tension profile in the filament.  ...  Seifert for discussions during a stay at MPIKG, Golm. We thank CSIR, India for financial support.  ... 
doi:10.1103/physrevlett.89.018302 pmid:12097074 fatcat:nb5e75ivczbnfnwanqnqhjdfzq
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P. Ranjith, P. B. Sunil Kumar. "Dynamics of Folding in Semiflexible Filaments." Physical Review Letters 89.1 (2002)

Binding of molecules to DNA and other semiflexible polymers

Haim Diamant, David Andelman
2000 Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics  

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1999 pre-print
arXiv:cond-mat/9910162v2 fatcat:3b3qw2g3frdtxakkdmv4ttu4tu
1999 pre-print
arXiv:cond-mat/9910162v1 fatcat:pzs4jdamqfhjhh2hq2mva7oke4
2000 accepted
arXiv:cond-mat/9910162v3 fatcat:ii5r3uipwnesxoozsolbfv272q
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers.  ...  External tension exerted on the chain is found to significantly modify the binding by suppressing the fluctuation-induced interaction.  ...  II, we begin with the previously studied problem of a bare semiflexible chain, yet it is now a chain under tension ͓36,43͔.  ... 
doi:10.1103/physreve.61.6740 pmid:11088368 fatcat:tvrxzxrxlrgzxg3yymjjk47ozu
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Haim Diamant, David Andelman. "Binding of molecules to DNA and other semiflexible polymers." Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 61.6 (2000) 6740-6749

Morphological variation in a toroid generated from a single polymer chain

Y. Takenaka, K. Yoshikawa, Y. Yoshikawa, Y. Koyama, T. Kanbe
2005 Journal of Chemical Physics  

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2005 pre-print
arXiv:physics/0504054v1 fatcat:ny4ivvrbvvdsvaz4gjzrf5xe4e
A single semiflexible polymer chain folds into a toroidal object under poor solvent conditions.  ...  In this study, we examined the morphological change in such a toroidal state as a function of the width and stiffness of the chain together with the surface energy, which characterizes the segmental interaction  ...  Thus, the surface energy plays a significant role in determining the stable structure of a folded compact state in a single semiflexible chain.  ... 
doi:10.1063/1.1944007 pmid:16035864 fatcat:kevqznrbzff25pzfa5llzynr4q
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Y. Takenaka, K. Yoshikawa, Y. Yoshikawa, Y. Koyama, T. Kanbe. "Morphological variation in a toroid generated from a single polymer chain." Journal of Chemical Physics 123.1 (2005) 014902

Growth, microstructure, and failure of crazes in glassy polymers

Jörg Rottler, Mark O. Robbins
2003 Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics  

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2003 pre-print arXiv:cond-mat/0301447v1 fatcat:bmz7yehblfh2jlywgsbrbhnw44
, polymer chain length N, entanglement length N_e and strength of adhesive interactions between polymer chains.  ...  Molecular dynamics simulations of a coarse-grained bead-spring model were employed to investigate the molecular level processes during craze nucleation, widening, and breakdown for a wide range of temperature  ...  jams under tension.  ... 
doi:10.1103/physreve.68.011801 pmid:12935165 fatcat:s42fj67nmnbr7kb7wkj5l3yhly
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Jörg Rottler, Mark O. Robbins. "Growth, microstructure, and failure of crazes in glassy polymers." Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 68.1 (2003)

Fluctuations of Stiff Polymers and Cell Mechanics [chapter]

Jens Glaser, Klaus Kroy
2010 Biopolymers  

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And yet, this program of explaining the simple through the complex smacks suspiciously of the program of explaining atoms in terms of complex mechanical models.  ...  Indeed, the vista of the biochemist is one with an infinite horizon.  ...  Indeed, the model has recently been extended to account for bond kinetics with defined rates and under the influence of a force (Wolff et al., 2010) .  ... 
doi:10.5772/10276 fatcat:z4edlusogfca5f5dfighxfgimm
Citation

Jens Glaser, Klaus Kroy. "Fluctuations of Stiff Polymers and Cell Mechanics." Biopolymers (2010)

Dynamics of DNA: Experimental controversies and theoretical insights

Michael Hinczewski, Roland R. Netz
2010 Physica A: Statistical Mechanics and its Applications  

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The success of the theory makes it an excellent candidate for a variety of biophysical contexts where the internal fluctuations of semiflexible polymers play a role.  ...  However some of the first studies in this direction yielded conflicting results for the mean squared displacement of the tagged end-point of a DNA chain, deviating from traditional theories of polymer  ...  Acknowledgements Both authors express their deep gratitude to Nihat Berker on the occasion of his 60th birthday for his role as a wonderful teacher, relentless mentor and warm friend over the years.  ... 
doi:10.1016/j.physa.2010.02.012 fatcat:vcptwawanvaybnpon7t6jjuule
Citation

Michael Hinczewski, Roland R. Netz. "Dynamics of DNA: Experimental controversies and theoretical insights." Physica A: Statistical Mechanics and its Applications 389.15 (2010) 2993-2996

Elastic behavior of a semiflexible polymer in 3D subject to compression and stretching forces

Christina Kurzthaler
2018 Soft Matter  

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2019 pre-print
arXiv:1911.03438v1 fatcat:hhub7laavzdopolknpai47clku
We elucidate the elastic behavior of a wormlike chain in 3D under compression and provide exact solutions for the experimentally accessible force–extension relation in terms of generalized spheroidal wave  ...  The content of this RSS Feed (c) The Royal Society of Chemistry Entangled chain polymer liquids under continuous shear deformation: consequences of a microscopically anharmonic confining tube Soft Matter  ...  Access This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.  ... 
doi:10.1039/c8sm01403e pmid:30168558 fatcat:s4pow5pe3jg2hg5vxheujy7jri
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Christina Kurzthaler. "Elastic behavior of a semiflexible polymer in 3D subject to compression and stretching forces." Soft Matter 14.37 (2018)

Refolding dynamics of stretched biopolymers upon force quench

C. Hyeon, G. Morrison, D. L. Pincus, D. Thirumalai
2009 Proceedings of the National Academy of Sciences of the United States of America  

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2009 pre-print
arXiv:0911.3530v1 fatcat:rdpphgkf6fblhbiynt2o7fmdsu
An analytical solution of the de Gennes model under tension reproduces the multistage stage kinetics in R(t).  ...  The prediction that the initial stages of collapse should also be a generic feature of polymers is validated by simulation of the kinetics of toroid (globule) formation in semiflexible (flexible) homopolymers  ...  Collapse of semiflexible chain. In the absence of force, the thermodynamically stable state of a semiflexible chain in a poor solvent is a toroid (see Fig. 5A ).  ... 
doi:10.1073/pnas.0905764106 pmid:19915145 pmcid:PMC2787142 fatcat:af5inccusbdz5dsjysdhlxfjv4
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C. Hyeon, G. Morrison, D. L. Pincus, D. Thirumalai. "Refolding dynamics of stretched biopolymers upon force quench." Proceedings of the National Academy of Sciences of the United States of America 106.48 (2009) 20288-20293

Competition between compaction of single chains and bundling of multiple chains in giant DNA molecules

Toshio Iwataki, Satoru Kidoaki, Takahiro Sakaue, Kenichi Yoshikawa, Sergey S. Abramchuk
2004 Journal of Chemical Physics  

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When the concentration of DNA is increased to 10 M, a thick fiberlike assembly of multiple chains appears.  ...  AFM measurements of this thick fiber revealed that more than tens of DNA molecules form a bundle structure with parallel ordering of the chains.  ...  By denoting the surface tension ϭd and the bending modulus ϭk B T, the surface energy and bending energy are U sur ϷrR, U bend Ϸ L R 2 . ͑9͒ The optimization of U sur ϩU bend under the constraint Rr 2  ... 
doi:10.1063/1.1642610 pmid:15268566 fatcat:bxyrmmoigzhotfbrd4yoye5d7a
Citation

Toshio Iwataki, Satoru Kidoaki, Takahiro Sakaue, Kenichi Yoshikawa, Sergey S. Abramchuk. "Competition between compaction of single chains and bundling of multiple chains in giant DNA molecules." Journal of Chemical Physics 120.8 (2004) 4004-4011

Developments in Polymer Theory and Simulation

Martin Kröger
2019 Polymers  

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Polymer theory and simulation are topics that are still growing (Figure 1), highlighting the need for an understanding of microscopic mechanisms influencing material properties of systems containing macromolecules  ...  Unrealistic tension is alleviated by pairing the slip links on one chain with those on a second chain, and allowing some of the large tension on one of the two to be transferred to the second chain, producing  ...  The ends of the slip springs undergo thermally activated hops between adjacent beads along the chain backbones, which are tracked by kinetic Monte Carlo simulation.  ... 
doi:10.3390/polym12010030 pmid:31877990 pmcid:PMC7023532 fatcat:e7sdvsoqrjh7dnuw43oh5ig2t4
DOAJ
Citation

Martin Kröger. "Developments in Polymer Theory and Simulation." Polymers 12.1 (2019) 30

Global cross-over dynamics of single semiflexible polymers

M. Hinczewski, R. R. Netz
2009 Europhysics letters  

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2009 pre-print
arXiv:0907.3891v1 fatcat:3js4kkteevb2dkjjpq4uhubqmm
2009 accepted
arXiv:0907.3891v2 fatcat:kyhfu3cnufhqpaba4u4cu5hdgi
kinetics of DNA strands in solution.  ...  We present a mean-field dynamical theory for single semiflexible polymers which can precisely capture, without fitting parameters, recent fluorescence correlation spectroscopy results on single monomer  ...  While these limitations are not relevant to modeling the FCS results for ∆ end (t) of a freely diffusing chain, they would be significant for an anisotropic experimental setup, i.e. a chain under tension  ... 
doi:10.1209/0295-5075/88/18001 fatcat:lywvrpxl3betvcgrhc2zed7pzy
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M. Hinczewski, R. R. Netz. "Global cross-over dynamics of single semiflexible polymers." Europhysics letters 88.1 (2009) 18001

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