Literature DB >> 19894934

Implicit and explicit solvent models for the simulation of a single polymer chain in solution: Lattice Boltzmann versus Brownian dynamics.

Tri T Pham1, Ulf D Schiller, J Ravi Prakash, Burkhard Dünweg.   

Abstract

We present a comparative study of two computer simulation methods to obtain static and dynamic properties of dilute polymer solutions. The first approach is a recently established hybrid algorithm based on dissipative coupling between molecular dynamics and lattice Boltzmann (LB), while the second is standard Brownian dynamics (BD) with fluctuating hydrodynamic interactions. Applying these methods to the same physical system (a single polymer chain in a good solvent in thermal equilibrium) allows us to draw a detailed and quantitative comparison in terms of both accuracy and efficiency. It is found that the static conformations of the LB model are distorted when the box length L is too small compared to the chain size. Furthermore, some dynamic properties of the LB model are subject to an L(-1) finite-size effect, while the BD model directly reproduces the asymptotic L-->infinity behavior. Apart from these finite-size effects, it is also found that in order to obtain the correct dynamic properties for the LB simulations, it is crucial to properly thermalize all the kinetic modes. Only in this case, the results are in excellent agreement with each other, as expected. Moreover, Brownian dynamics is found to be much more efficient than lattice Boltzmann as long as the degree of polymerization is not excessively large.

Entities:  

Year:  2009        PMID: 19894934     DOI: 10.1063/1.3251771

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


  4 in total

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Authors:  Subhra Sarkar; Shawn Witham; Jie Zhang; Maxim Zhenirovskyy; Walter Rocchia; Emil Alexov
Journal:  Commun Comput Phys       Date:  2013-01       Impact factor: 3.246

2.  Effects of nanopore size on the flow-induced star polymer translocation.

Authors:  Qiaoyue Chen; Lili Zhang; Mingming Ding; Xiaozheng Duan; Yineng Huang; Tongfei Shi
Journal:  Eur Phys J E Soft Matter       Date:  2016-11-21       Impact factor: 1.890

3.  DelPhi: a comprehensive suite for DelPhi software and associated resources.

Authors:  Lin Li; Chuan Li; Subhra Sarkar; Jie Zhang; Shawn Witham; Zhe Zhang; Lin Wang; Nicholas Smith; Marharyta Petukh; Emil Alexov
Journal:  BMC Biophys       Date:  2012-05-14       Impact factor: 4.778

4.  Modelling realistic microgels in an explicit solvent.

Authors:  F Camerin; N Gnan; L Rovigatti; E Zaccarelli
Journal:  Sci Rep       Date:  2018-09-26       Impact factor: 4.379

  4 in total

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