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Title: A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization

Abstract

We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models are not interchangeable. If the free parameters are properly selected, the reverse CG procedure also yields an effective potential. Furthermore, we explain how an aggressive coarse-graining procedure introduces many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can bemore » drawn.« less

Authors:
ORCiD logo [1]; ORCiD logo [1];  [2];  [1]
  1. Brown Univ., Providence, RI (United States)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division
OSTI Identifier:
1356514
Alternate Identifier(s):
OSTI ID: 1272642
Report Number(s):
PNNL-SA-116567
Journal ID: ISSN 0021-9606; KJ0401000
Grant/Contract Number:  
AC05-76RL01830; W911NF-12-2-0023; AC02-06CH11357; AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 145; Journal Issue: 4; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; Molecular dynamics; Polymers; Stochastic processes; Gyration radius; Many body problems; Newtonian mechanics; Nonequilibrium statistical mechanics; Static properties; Thermodynamic properties; Classical statistical mechanics

Citation Formats

Li, Zhen, Bian, Xin, Yang, Xiu, and Karniadakis, George Em. A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization. United States: N. p., 2016. Web. doi:10.1063/1.4959121.
Li, Zhen, Bian, Xin, Yang, Xiu, & Karniadakis, George Em. A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization. United States. https://doi.org/10.1063/1.4959121
Li, Zhen, Bian, Xin, Yang, Xiu, and Karniadakis, George Em. 2016. "A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization". United States. https://doi.org/10.1063/1.4959121. https://www.osti.gov/servlets/purl/1356514.
@article{osti_1356514,
title = {A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization},
author = {Li, Zhen and Bian, Xin and Yang, Xiu and Karniadakis, George Em},
abstractNote = {We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models are not interchangeable. If the free parameters are properly selected, the reverse CG procedure also yields an effective potential. Furthermore, we explain how an aggressive coarse-graining procedure introduces many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.},
doi = {10.1063/1.4959121},
url = {https://www.osti.gov/biblio/1356514}, journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 4,
volume = 145,
place = {United States},
year = {Mon Jul 25 00:00:00 EDT 2016},
month = {Mon Jul 25 00:00:00 EDT 2016}
}

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Works referenced in this record:

Simulating Microscopic Hydrodynamic Phenomena with Dissipative Particle Dynamics
journal, June 1992


Mori–Zwanzig formalism as a practical computational tool
journal, January 2010


Multiscale coarse graining of liquid-state systems
journal, October 2005


Rheology, Microstructure and Migration in Brownian Colloidal Suspensions
journal, January 2010


GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008


Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids
journal, June 1971


Hydrodynamics from dissipative particle dynamics
journal, August 1995


Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation
journal, September 1997


Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
journal, December 2005


Coarse-Graining Methods for Computational Biology
journal, May 2013


A uniqueness theorem for fluid pair correlation functions
journal, September 1974


High-Order Collocation Methods for Differential Equations with Random Inputs
journal, January 2005


Effective potentials for representing polymers in melts as chains of interacting soft particles
journal, September 2013


Direct construction of mesoscopic models from microscopic simulations
journal, February 2010


Static and dynamic properties of dissipative particle dynamics
journal, August 1997


Direct Molecular Dynamics Simulation of Branch Point Motion in Asymmetric Star Polymer Melts
journal, May 2007


Versatile Object-Oriented Toolkit for Coarse-Graining Applications
journal, November 2009


Obtaining fully dynamic coarse-grained models from MD
journal, January 2011


The fluctuation-dissipation theorem
journal, January 1966


Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems
journal, July 2015


Dynamics of entangled linear polymer melts:  A molecular‐dynamics simulation
journal, April 1990


Probing red blood cell mechanics, rheology and dynamics with a two-component multi-scale model
journal, August 2014

  • Li, Xuejin; Peng, Zhangli; Lei, Huan
  • Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 372, Issue 2021
  • https://doi.org/10.1098/rsta.2013.0389

Mesoscale modeling of phase transition dynamics of thermoresponsive polymers
journal, January 2015


Statistical Mechanics of Dissipative Particle Dynamics
journal, May 1995


Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
journal, October 1995


Interatomic Potentials from First-Principles Calculations: The Force-Matching Method
journal, June 1994


Equation of motion for coarse-grained simulation based on microscopic description
journal, May 2007


A Multiscale Coarse-Graining Method for Biomolecular Systems
journal, February 2005


The power of coarse graining in biomolecular simulations: The power of coarse graining in biomolecular simulations
journal, August 2013

  • Ingólfsson, Helgi I.; Lopez, Cesar A.; Uusitalo, Jaakko J.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 4, Issue 3
  • https://doi.org/10.1002/wcms.1169

Effective Interaction between Star Polymers
journal, June 1999


The Wiener--Askey Polynomial Chaos for Stochastic Differential Equations
journal, January 2002


Simulating flow of DNA suspension using dissipative particle dynamics
journal, January 2006


Uncertainty Quantification in MD Simulations. Part II: Bayesian Inference of Force-Field Parameters
journal, January 2012


Mesoscale modeling: solving complex flows in biology and biotechnology
journal, July 2013


The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
journal, June 2008


Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism
journal, December 2015


Reweighted minimization method for stochastic elliptic differential equations
journal, September 2013


Perspective: Coarse-grained models for biomolecular systems
journal, September 2013


The relative entropy is fundamental to multiscale and inverse thermodynamic problems
journal, October 2008


Simultaneous Iterative Boltzmann Inversion for Coarse-Graining of Polyurea
journal, May 2014


Enhancing sparsity of Hermite polynomial expansions by iterative rotations
journal, February 2016


Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations
journal, August 2003


No-go theorem in many-body dissipative particle dynamics
journal, April 2013


Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?
journal, January 2009


The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
journal, June 2008


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