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Effects of static and temporally fluctuating tensions on semiflexible polymer looping

Jaeoh Shin, Wokyung Sung
2012 Journal of Chemical Physics  
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

Buckling of semiflexible filaments under compression [article]

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

Collapse of a semiflexible polymer in poor solvent

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

Folding and unfolding kinetics of a single semiflexible polymer

Natsuhiko Yoshinaga
2008 Physical Review E  
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

Dynamics of Folding in Semiflexible Filaments

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

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  
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

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  
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

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  
, 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

Fluctuations of Stiff Polymers and Cell Mechanics [chapter]

Jens Glaser, Klaus Kroy
2010 Biopolymers  
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

Dynamics of DNA: Experimental controversies and theoretical insights

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

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

Christina Kurzthaler
2018 Soft Matter  
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

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  
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

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  
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

Developments in Polymer Theory and Simulation

Martin Kröger
2019 Polymers  
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

Global cross-over dynamics of single semiflexible polymers

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