Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates

Effects of alignment layer thickness on the pretilt angle of liquid crystals APL: Org. Electron. Photonics 3, 270 (2010) Effects of alignment layer thickness on the pretilt angle of liquid crystals Appl. Phys. Lett. 97, 243306 (2010) Field-theoretic model of inhomogeneous supramolecular polymer networks and gels J. Chem. Phys. 133, 174903 (2010) Origin of translocation barriers for polyelectrolyte chains JCP: BioChem. Phys Results of united atom molecular dynamics simulations of a n-C 120 H 242 melt at 450 K are presented. It is shown that the results of mean square displacement, dynamic structure factor, end-to-end vector autocorrelation, and shear relaxation modulus can consistently be described by the Rouse model with a single set of fit parameters, provided the length scales involved are larger than the statistical segment length bϷ1.2 nm. On smaller length scales the stiffness of the chain becomes prominent, and the results deviate increasingly from the Rouse predictions. The shear relaxation modulus G(t) is determined from the stress autocorrelation function from both atomic and molecular points of view. The integrals ͐G(t)dt are found to be identical after 1 ps and a Rouse description is shown to coincide for time scales larger than 0.4 ns. Compared to experimental values, the measured diffusion coefficient is overestimated by 63% and the viscosity is underestimated by 38%, consistent with molecular dynamics simulations of small molecules.

Section: Simulation Model and Methodologymentioning

confidence: 99%

Zero-shear stress relaxation and long time dynamics of a linear polyethylene melt: A test of Rouse theory

Padding

Briels

2001

“…One first way to tackle this, was to reduce the number of de-grees of freedom by a systematic coarse-graining, which retains only those degrees of freedom that are relevant for the particular property of interest. Examples of molecular systems where the coarsegraining approach has been used with much success are fluids [9], lipid bilayers [10,11,12,13,14], and polymer systems [15,16,17,18].…”

Section: Introductionmentioning

confidence: 99%

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly

Praprotnik

Site

Kremer

2005

372

514

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecule's atomic and coarse-grained level of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, the other containing only one particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The coarse-grained and the atomistically resolved systems have the same statistical properties at the same physical conditions.

“…Aside of this rigorous numerical analysis direction, entropy-based computational techniques were also developed and used for constructing approximations of coarse-grained (effective) potentials for models of large biomolecules and polymeric systems (fluids, melts). Optimal parametrization of effective potentials based on minimizing the relative entropy between equilibrium Gibbs states, e.g., 3,6,7 , extended previously developed inverse Monte Carlo methods, primarily based on force matching approaches, used in coarsegraining of macromolecules (see, e.g., 30,38 ). In 13 an extension to dynamics is proposed in the context of FokkerPlanck equations, by considering the corresponding relative entropy for discrete-time approximations of the transition probabilities.…”

Section: Introductionmentioning

confidence: 99%

Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems

Katsoulakis

Plecháč

2013

In this paper we focus on the development of new methods suitable for efficient and reliable coarse-graining of non-equilibrium molecular systems. In this context, we propose error estimation and controlled-fidelity model reduction methods based on Path-Space Information Theory, combined with statistical parametric estimation of rates for non-equilibrium stationary processes. The approach we propose extends the applicability of existing information-based methods for deriving parametrized coarse-grained models to Non-Equilibrium systems with Stationary States (NESS). In the context of coarse-graining it allows for constructing optimal parametrized Markovian coarse-grained dynamics within a parametric family, by minimizing information loss (due to coarse-graining) on the path space. Furthermore, we propose an asymptotically equivalent methodrelated to maximum likelihood estimators for stochastic processes-where the coarse-graining is obtained by optimizing the information content in path space of the coarse variables, with respect to the projected computational data from a fine-scale simulation. Finally, the associated path-space Fisher Information Matrix can provide confidence intervals for the corresponding parameter estimators. We demonstrate the proposed coarse-graining method in (a) non-equilibrium systems with diffusing interacting particles, driven by out-ofequilibrium boundary conditions, as well as (b) multi-scale diffusions and their well-studied corresponding stochastic averaging limits, comparing them to our proposed methodologies.