Dynamics of semiflexible polymers in a flow field

Munk, Tobias; Hallatschek, Oskar; Wiggins, Chris H.; Frey, Erwin

doi:10.1103/physreve.74.041911

Cited by 44 publications

(46 citation statements)

References 56 publications

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“…This, in turn, implies the importance of thermal fluctuation so that the Brownian forces cannot be neglected. However, to the best of our knowledge, only a few papers have addressed the thermal fluctuation effects 10–12,21,22 . Moreover, nonlinear response due to the thermal noise has become a central topic in studies of various dynamical systems.…”

Section: Introductionmentioning

confidence: 99%

Effects of thermal noise on the transitional dynamics of an inextensible elastic filament in stagnation flow

Deng

Grinberg²,

Caswell

et al. 2015

Soft Matter

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We investigate the dynamics of a single inextensible elastic filament subject to anisotropic friction in a viscous stagnation-point flow, by employing both a continuum model represented by Langevin type stochastic partial differential equations (SPDEs) and a Dissipative Particle Dynamics (DPD) method. Unlike previous works1, the filament is free to rotate and the tension along the filament is determined by the local inextensible constraint. The kinematics of the filament is recorded and studied with normal modes analysis. The results show that the filament displays an instability induced by negative tension, which is analogous to Euler buckling of a beam. Symmetry breaking of normal modes dynamics and stretch-coil transitions are observed above the threshold of the buckling instability point. Furthermore, both temporal and spatial noise are amplified resulting from the interaction of thermal fluctuations and nonlinear filament dynamics. Specifically, the spatial noise is amplified with even normal modes being excited due to symmetry breaking, while the temporal noise is amplified with increasing time correlation length and variance.

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Section: Introductionmentioning

confidence: 99%

Effects of thermal noise on the transitional dynamics of an inextensible elastic filament in stagnation flow

Deng

Grinberg²,

Caswell

et al. 2015

Soft Matter

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“…However, the decay ratio of the rotational time for 53 nm <p<2,650 nm was larger compared to both the p=53 nm and p≥2,650 nm cases. Munk et al 34 also predicted a similar behavior using their perturbation expansion method when L was comparable to p. Thus a critical p (p~2,650 nm) existed, and above this value, the polymer behaved like a rod, irrespective of the flow strength. If p was less than this critical p value, the polymer characteristics changes from rod-like to flexible with increasing flow strength.…”

Section: Resultsmentioning

confidence: 64%

Effect of stiffness on tumbling dynamics of short worm-like polymers under mixed flows

Lee¹,

Kim

2011

Macromol. Res.

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This study examined the effects of the stiffness on the tumbling dynamics of short semi-flexible polymers in mixed flows varying from simple shear to pure rotation, as an extension of a previous study on rod-like polymers. A multi bead-rod model with bending potential was adopted and represented the stiffness or persistence length of the polymers. The rotational time and angular distribution of the semi-flexible chains were examined in mixed flows. These results were compared with previous theoretical predictions and numerical simulations of rod-like polymers. Furthermore, the angular distribution of the short semi-flexible polymers was strongly dependent upon the stiffness of the polymers. These results are expected to be helpful in the development of lab-on-a-chip applications, such as the separation of short DNA molecules.

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“…The Rouse modes are easier to handle than, e.g., the eigenfunctions of the biharmonic operator, which are the modes used by Munk et al [20] for the IWLC [14]. The transformation (55) from positions to Rouse modes is an orthogonal transformation such that the Langevin equation in terms of Rouse modes reads…”

Section: Chains With Stiff Bondsmentioning

confidence: 99%

“…Note that detailed balance even holds if we were to include the O( τ ) term, which is omitted in Eq. (20). Detailed balance guarantees that the motion produces correct equilibrium averages.…”

Section: Equivalent Formulationmentioning

confidence: 99%

Efficient simulation of semiflexible polymers with stiff bonds

Barkema

Leeuwen

2017

Phys. Rev. E

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We investigate the simulation of stiff (extensible) and rigid (inextensible) semiflexible polymers in solution.In particular, we focus on polymers represented as chains of beads, interconnected by bonds with a low to zero extensibility, and significant persistence in the bond orientations along the chain, whose dynamical behavior is described by the Langevin equation. We review the derivation of the pseudopotential needed for rigid bonds. The efficiency of a number of routines for such simulations is determined. We propose a routine for handling rigid bonds which is, for longer chains, substantially more efficient than the existing ones. We also show that for extensible polymers, the Rouse modes can be exploited to achieve highly efficient simulations. At realistic values for the extensibility, e.g., that of double-stranded DNA, the simulations are orders of magnitude faster than those for rigid bonds. With increasing stiffness, however, the allowable time step and hence the efficiency decreases, until a crossover point is reached below which the routines with rigid bonds are more efficient; we present a numerical estimate of this crossover point.

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Dynamics of semiflexible polymers in a flow field

Cited by 44 publications

References 56 publications

Effects of thermal noise on the transitional dynamics of an inextensible elastic filament in stagnation flow

Effects of thermal noise on the transitional dynamics of an inextensible elastic filament in stagnation flow

Effect of stiffness on tumbling dynamics of short worm-like polymers under mixed flows

Efficient simulation of semiflexible polymers with stiff bonds

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