Efficient simulation of noncrossing fibers and chains in a hydrodynamic solvent.

@article{Padding2009EfficientSO,
  title={Efficient simulation of noncrossing fibers and chains in a hydrodynamic solvent.},
  author={Johan T. Padding},
  journal={The Journal of chemical physics},
  year={2009},
  volume={130 14},
  pages={
          144903
        }
}
  • J. Padding
  • Published 24 February 2009
  • Physics, Engineering
  • The Journal of chemical physics
An efficient simulation method is presented for Brownian fiber suspensions, which includes both uncrossability of the fibers and hydrodynamic interactions between the fibers mediated by a mesoscopic solvent. To conserve hydrodynamics, collisions between the fibers are treated such that momentum and energy are conserved locally. The choice of simulation parameters is rationalized on the basis of dimensionless numbers expressing the relative strength of different physical processes. The method is… 
7 Citations

Figures and Tables from this paper

Hydrodynamic interactions in rod suspensions with orientational ordering
The effect of hydrodynamic interactions on the diffusion of rods in the nematic phase is studied, both experimentally by time-resolved fluorescence video microscopy and theoretically by
Brownian dynamics simulations of single polymer chains with and without self-entanglements in theta and good solvents under imposed flow fields
The effects of self-entanglements (spring-spring uncrossability) and solvent quality on the static and dynamic properties of a polymer chain in shear and extensional flows are investigated using
Review of multi-scale particulate simulation of the rheology of wormlike micellar fluids
We provide a review of our recent work on the development of a multi-scale simulation methodology to calculate the rheology and flow of wormlike micelles. There is a great need for understanding the
Hybrid molecular dynamics simulations of living filaments.
TLDR
A hybrid molecular dynamics/multi-particle collision dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers is proposed and a Monte Carlo scheme to deal with single monomer addition or removal is introduced, satisfying the detailed balance condition within a proper statistical mechanical framework.
Systematic coarse-graining of the dynamics of entangled polymer melts: the road from chemistry to rheology.
  • J. Padding, W. Briels
  • Materials Science
    Journal of physics. Condensed matter : an Institute of Physics journal
  • 2011
TLDR
Current and past computer simulation techniques are reviewed and critically assess their ability to provide a rigorous link between chemistry and rheology and super-coarse-grained methods in which an entire polymer is represented by a single particle are reviewed.
Multiscale modeling and mechanics of filamentous actin cytoskeleton
TLDR
Every temporal and spatial scale of actin cytoskeletal structure is considered, and it is expected that discrete and continuum dynamics ranging from functional expression at the molecular level to macroscopic functionalexpression at the whole cell level will be developed and applied to multiscale modeling and simulation.

References

SHOWING 1-10 OF 174 REFERENCES
Screening of hydrodynamic interactions in Brownian rod suspensions.
TLDR
These results confirm the validity of the hydrodynamic "screening" hypothesis and ratify the neglect of hydrodynamical stresses in quantifying the linear rheology of Brownian rod suspensions.
Dynamic simulations of the inhomogeneous sedimentation of rigid fibres
We have simulated the dynamics of suspensions of fibres sedimenting in the limit of zero Reynolds number. In these simulations, the dominant inter-particle force arises from hydrodynamic interactions
A numerical study of the sedimentation of fibre suspensions
The sedimentation of fibre suspensions at low Reynolds number is studied using two different, but complementary, numerical simulation methods: (1) Monte Carlo simulations, which consider
Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods.
TLDR
This theory for the dynamics of suspensions of long thin rigid rods is put to the test by comparing it against computer simulations and shows that, for the currently accessible volume fractions, the decay times in both cases are virtually identical.
Brownian dynamics simulations of a flexible polymer chain which includes continuous resistance and multibody hydrodynamic interactions.
TLDR
A Brownian dynamics algorithm with multibody hydrodynamic interactions for simulating the dynamics of polymer molecules is developed and a difference in the apparent scaling of diffusivity with polymer length for the multibODY versus two-body level of approximation is indicated.
Effect of flexibility on the shear-induced migration of short-chain polymers in parabolic channel flow
We use Brownian dynamics to investigate the effect of chain flexibility on the cross-streamline migration of short polymers in a pressure-driven flow between two infinite flat plates. A simulation
Lattice-Boltzmann simulations of the dynamics of polymer solutions in periodic and confined geometries.
TLDR
It is shown that hydrodynamic interactions in large polymers can be systematically coarse-grained to substantially reduce the computational cost of the simulation, and the results support the qualitative conclusions of recent Brownian dynamics simulations of confined polymers.
Rod-like colloids and polymers in shear flow: a multi-particle-collision dynamics study
The effect of the hydrodynamic interaction on the dynamics of flexible and rod-like polymers in solution is investigated. The solvent is simulated by the multi-particle-collision dynamics (MPCD)
The hydrodynamic stress in a suspension of rods
A theory is presented to describe the momentum transport properties of suspensions containing randomly placed, slender fibers. The theory is based on a diagrammatic representation of the multiple
...
...