Molecular-dynamics simulations with explicit hydrodynamics I: on the friction coefficients of deformed polymers

The European Physical Journal. E, Soft Matter
M Kenward, G W Slater

Abstract

We implement large-scale Molecular-Dynamics (MD) simulations which incorporate hydrodynamic interactions via the inclusion of explicit Lennard-Jones solvent to examine the behaviour of polymer chains in sieving media. We begin by examining the friction coefficients of polymers in long-lived states responsible for inducing length-dependent mobility, i.e., allowing separation of polymers (or polyelectrolytes) by molecular weight. In particular, the conformations we examine occur in devices which utilize arrays of molecular obstacles or dilute solutions of polymers. We compare the results from our MD simulations with expressions from macroscopic hydrodynamics for four specific cases: i) a random coil excluded-volume Zimm polymer, ii) a rigid polymer moving perpendicular to its major axis iii) a rigid polymer moving parallel to its major axis and iv) a rigid polymer, folded at different points along its contour. We also examine the behaviour of the friction coefficient of a fully flexible molecule pulled by its middle monomer as a function of an applied force F and show that there are several distinct frictional regimes.

References

Dec 1, 1994·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·G I Nixon, G W Slater
Aug 1, 1988·Physical Review Letters·K KremerI Carmesin
Jan 14, 2000·Electrophoresis·C F ChouS Turner
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Apr 1, 2002·The European Physical Journal. E, Soft Matter·Motohiko Tanaka, A Yu Grosberg

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Citations

Aug 30, 2008·Critical Reviews in Food Science and Nutrition·Christina KriegelJochen Weiss
Sep 1, 2005·The European Physical Journal. E, Soft Matter·Y Gratton, G W Slater
Jun 17, 2006·The European Physical Journal. E, Soft Matter·M Kenward, G W Slater
Jun 11, 2005·The Journal of Chemical Physics·M A Webster, J M Yeomans
Dec 31, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Martin Kenward, Gary W Slater
Aug 11, 2005·Physical Review Letters·Nicolas MincKevin D Dorfman
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Martin Bertrand, Béla Joós

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