Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions

We examine the collective dynamics of polarizable, Brownian, sedimenting rods of high aspect ratio. Previous work of Koch and Shaqfeh (J. Fluids Mech., vol. 209, 1989 pp. 521–542) has shown that in the absence of Brownian motion, sedimenting suspensions of rods are unstable to concentration fluctuations and form dense streamers via interparticle hydrodynamic interactions. Recently, Saintillan, Shaqfeh & Darve (Phys. Fluids, vol. 18 (121701), 2006b p. 1) demonstrated that electric fields can act to stabilize these non-Brownian suspensions of polarizable rods through induced-charge electrokinetic rotation, which forces particle alignment. In this paper, we employ a mean-field linear stability analysis as well as Brownian dynamics simulations to study the effect of thermal motion on the onset of instability. We find that in the absence of electric fields, Brownian motion consistently suppresses instability formation through randomization of particle orientation. However, when electric fields are applied, thermal motion can act to induce instability by counteracting the stabilizing effect of induced-charge orientation.

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Magnetic Polymer Models for Epigenetics-Driven Chromosome Folding

10.1101/831412 ◽

2019 ◽

Author(s):

Davide Coli ◽

Davide Michieletto ◽

Davide Marenduzzo ◽

Enzo Orlandini

Keyword(s):

Brownian Dynamics ◽

Regulatory Networks ◽

Mean Field ◽

Thermal Fluctuations ◽

First Order Phase Transition ◽

Polymer Models ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations ◽

First Order Phase

Epigenetics is a driving force of important and ubiquitous phenomena in nature such as cell differentiation or even metamorphosis. Oppositely to its widespread role, understanding the biophysical principles that allow epigenetics to control and rewire gene regulatory networks remains an open challenge. In this work we study the effects of epigenetic modifications on the spatial folding of chromosomes -- and hence on the expression of the underlying genes -- by mapping the problem to a class of models known as magnetic polymers. In this work we show that a first order phase transition underlies the simultaneous spreading of certain epigenetic marks and the conformational collapse of a chromosome. Further, we describe Brownian Dynamics simulations of the model in which the topology of the polymer and thermal fluctuations are fully taken into account and that confirm our mean field predictions. Extending our models to allow for non-equilibrium terms yields new stable phases which qualitatively agrees with observations in vivo. Our results show that statistical mechanics techniques applied to models of magnetic polymers can be successfully exploited to rationalize the outcomes of experiments designed to probe the interplay between a dynamic epigenetic landscape and chromatin organization.

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Mean-field hydrodynamics brownian dynamics simulations of stabilized colloidal liquids under shear

Journal of Non-Newtonian Fluid Mechanics ◽

10.1016/s0377-0257(96)01501-7 ◽

1997 ◽

Vol 68 (1) ◽

pp. 101-124 ◽

Cited By ~ 5

Author(s):

D.M. Heyes ◽

P.J. Mitchell

Keyword(s):

Brownian Dynamics ◽

Mean Field ◽

Colloidal Liquids ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations

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Thermally Fluctuating, Semiflexible Sheets in Simple Shear Flow

Soft Matter ◽

10.1039/d1sm01510a ◽

2022 ◽

Author(s):

Kevin S. Silmore ◽

Michael Strano ◽

James W. Swan

Keyword(s):

Shear Flow ◽

Simple Shear ◽

Brownian Dynamics ◽

Thermal Fluctuations ◽

Hydrodynamic Interactions ◽

Simple Shear Flow ◽

Bending Rigidity ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations ◽

Shear Energy

We perform Brownian dynamics simulations of semiflexible colloidal sheets with hydrodynamic interactions and thermal fluctuations in shear flow. As a function of the ratio of bending rigidity to shear energy...

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