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In this study, a versatile methodology for initiating polymerization from monomers in highly cross-linked materials is investigated. As polymerization progresses, force-field parameters undergo continuous modification due to the formation…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the…
Synthetic polymers are versatile and widely used materials. Similar to small organic molecules, a large chemical space of such materials is hypothetically accessible. Computational property prediction and virtual screening can accelerate…
Molecular modeling, a central topic in quantum mechanics, aims to accurately calculate the properties and simulate the behaviors of molecular systems. The molecular model is governed by physical laws, which impose geometric constraints such…
Several recently proposed semi--automatic and fully--automatic coarse--graining schemes for polymer simulations are discussed. All these techniques derive effective potentials for multi--atom units or super--atoms from atomistic…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
This document presents a combinatorial framework for analyzing assembly systems using generating functions. We explore the theory through concrete examples, such as linear polymers, and develop recursive equations to characterize valid…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
Some methods based on simple regularizing geometric element transformations have heuristically been shown to give runtime efficient and quality effective smoothing algorithms for meshes. We describe the mathematical framework and a…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
We present a new reduced-order computational method for the molecular dynamics simulation of entangled polymer systems. The polymer chains are modeled as continuous Gaussian chains. Our algorithm is based on the application of the molecular…
High-throughput computational screening of polymers offers a powerful way to address the imbalance between the vast number of polymers synthesised for diverse applications and the relatively small subset that can be studied using atomistic…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
We develop a Gromacs implementation of Dimer Metadynamics[JCTC 13, 425 (2017)] for enhanced sampling through artificial delocalization effects. This implementation is based entirely on a Plumed collective variable developed for this…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
Synthetic polymeric materials underpin fundamental technologies in the energy, electronics, consumer goods, and medical sectors, yet their development still suffers from prolonged design timelines. Although polymer informatics tools have…
We study surface effects in amorphous polymer systems by means of computer simulation. In the framework of molecular dynamics, we present two different methods to prepare such surfaces. {\em Free} surfaces are stabilized solely by…
One essential goal of constructing coarse-grained molecular dynamics (CGMD) models is to accurately predict non-equilibrium processes beyond the atomistic scale. While a CG model can be constructed by projecting the full dynamics onto a set…
Glycans are tree-like polymers made up of sugar monomer building blocks. They are found on the surface of all living cells, and distinct glycan trees act as identity markers for distinct cell types. Proteins called GTase enzymes assemble…