Related papers: Monte Carlo SImulation of Polymers: Coarse-Grained…
By means of sophisticated Monte Carlo methods, we investigate the conformational phase diagram of a simple model for flexible polymers with explicit thickness. The thickness constraint, which is introduced geometrically via the global…
We investigate the conformations of a semiflexible polymer confined to a square box. Results of Monte Carlo simulations show the existence of a shape transition when the persistence length of the polymer becomes comparable to the dimensions…
We explain a method, inspired by control theory model reduction and interpolation theory, that rigorously establishes the types of coarse graining that are appropriate for systems with quadratic, generalized Hamiltonians. For such systems,…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
Polymers consisting of more than one type of monomer, known as copolymers, are vital to both living and synthetic systems. Copolymerisation has been studied theoretically in a number of contexts, often by considering a Markov process in…
We simulate structural phase behavior of polymer-grafted colloidal particles by molecular Monte Carlo technique. Interparticle potential, which has a finite repulsive square-step outside a rigid core of the colloid, was previously confirmed…
Based on the wormlike chain model, a coarse-grained description of the nonlinear dynamics of a weakly bending semiflexible polymer is developed. By means of a multiple scale perturbation analysis, a length-scale separation inherent to the…
Understanding the structure and dynamics of liquids is pivotal for the study of larger spatiotemporal processes, especially in glass-forming materials at low temperatures. Density scaling, observed in many molecular systems through…
The dynamics of real magnets is often governed by several interacting processes taking place simultaneously at different length scales. For dynamical simulations the relevant length scales should be coupled, and the energy transfer…
We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called Deep Coarse-Grained Potential…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
Mesoscopic particle based fluid models, such as dissipative particle dynamics, are usually assumed to be coarse-grained representations of an underlying microscopic fluid. A fundamental question is whether there exists a map from…
We present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often…
Large-scale Monte Carlo simulations of a phase-separating colloid-polymer mixture are performed and compared to recent experiments. The approach is based on effective interaction potentials in which the central monomers of self-avoiding…
Differentiable physics modeling combines physics models with gradient-based learning to provide model explicability and data efficiency. It has been used to learn dynamics, solve inverse problems and facilitate design, and is at its…
Graphity models are characterized by configuration spaces in which states correspond to graphs and Hamiltonians that depend on local properties of graphs such as the degrees of vertices and numbers of short cycles. As statistical systems,…
The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of…
In many numerical schemes, the computational complexity scales non-linearly with the problem size. Solving a linear system of equations using direct methods or most iterative methods is a typical example. Algebraic multi-grid (AMG) methods…
We present few ordering mechanisms in block copolymer melts in the coarse-graining approach. For chemically homogeneous or modulated confining surfaces, the surface ordering is investigated above and below the order-disorder temperature. In…
As a complementary tool to laboratory experiments, discrete numerical simulation, applied to granular materials, provides valuable information on the grain and contact scale microstructure, thereby enabling one to better understand the…