Literature DB >> 15836206

From molecular dynamics to hydrodynamics: a novel Galilean invariant thermostat.

Simeon D Stoyanov1, Robert D Groot.   

Abstract

This paper proposes a novel thermostat applicable to any particle-based dynamic simulation. Each pair of particles is thermostated either (with probability P) with a pairwise Lowe-Andersen thermostat [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] or (with probability 1-P) with a thermostat that is introduced here, which is based on a pairwise interaction similar to the Nosé-Hoover thermostat. When the pairwise Nosé-Hoover thermostat dominates (low P), the liquid has a high diffusion coefficient and low viscosity, but when the Lowe-Andersen thermostat dominates, the diffusion coefficient is low and viscosity is high. This novel Nosé-Hoover-Lowe-Andersen thermostat is Galilean invariant and preserves both total linear and angular momentum of the system, due to the fact that the thermostatic forces between each pair of the particles are pairwise additive and central. We show by simulation that this thermostat also preserves hydrodynamics. For the (noninteracting) ideal gas at P = 0, the diffusion coefficient diverges and viscosity is zero, while for P > 0 it has a finite value. By adjusting probability P, the Schmidt number can be varied by orders of magnitude. The temperature deviation from the required value is at least an order of magnitude smaller than in dissipative particle dynamics (DPD), while the equilibrium properties of the system are very well reproduced. The thermostat is easy to implement and offers a computational efficiency better than (DPD), with better temperature control and greater flexibility in terms of adjusting the diffusion coefficient and viscosity of the simulated system. Applications of this thermostat include all standard molecular dynamic simulations of dense liquids and solids with any type of force field, as well as hydrodynamic simulation of multiphase systems with largely different bulk viscosities, including surface viscosity, and of dilute gases and plasmas.

Entities:  

Year:  2005        PMID: 15836206     DOI: 10.1063/1.1870892

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  8 in total

1.  Thermostatic and rheological responses of DPD fluid to extreme shear under modified Lees-Edwards boundary condition.

Authors:  Abouzar Moshfegh; Goodarz Ahmadi; Ahmad Jabbarzadeh
Journal:  Eur Phys J E Soft Matter       Date:  2015-12-28       Impact factor: 1.890

2.  Study of critical dynamics in fluids via molecular dynamics in canonical ensemble.

Authors:  Sutapa Roy; Subir K Das
Journal:  Eur Phys J E Soft Matter       Date:  2015-12-23       Impact factor: 1.890

3.  Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes.

Authors:  Brian A Camley; Michael G Lerner; Richard W Pastor; Frank L H Brown
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

4.  Spatially resolved simulations of membrane reactions and dynamics: multipolar reaction DPD.

Authors:  R M Füchslin; T Maeke; J S McCaskill
Journal:  Eur Phys J E Soft Matter       Date:  2009-08-21       Impact factor: 1.890

5.  Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.

Authors:  Christopher Maffeo; Han-Yi Chou; Aleksei Aksimentiev
Journal:  Adv Theory Simul       Date:  2019-02-12

6.  The fusion of membranes and vesicles: pathway and energy barriers from dissipative particle dynamics.

Authors:  Andrea Grafmüller; Julian Shillcock; Reinhard Lipowsky
Journal:  Biophys J       Date:  2009-04-08       Impact factor: 4.033

7.  Hydrodynamic cavitation in Stokes flow of anisotropic fluids.

Authors:  Tillmann Stieger; Hakam Agha; Martin Schoen; Marco G Mazza; Anupam Sengupta
Journal:  Nat Commun       Date:  2017-05-30       Impact factor: 14.919

8.  On the effect of the thermostat in non-equilibrium molecular dynamics simulations.

Authors:  José Ruiz-Franco; Lorenzo Rovigatti; Emanuela Zaccarelli
Journal:  Eur Phys J E Soft Matter       Date:  2018-07-02       Impact factor: 1.890

  8 in total

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