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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…
Conformation-dependent design of polymer sequences can be considered as a tool to control macromolecular self-assembly. We consider the monomer unit sequences created via the modification of polymers in a homogeneous melt in accordance with…
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…
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…
The rapid growth of data-driven materials research has made it necessary to develop systematically designed, open databases of material properties. However, there are few open databases for polymeric materials compared to other material…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
In view of recent intense experimental and theoretical interests in the biophysics of liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
An innovative method is proposed to generate configurations of coarse grained models for polymer melts. This method, largely inspired by chemical ``radical polymerization'', is divided in three stages: (i) nucleation of radicals (reacting…
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
Polymer-Attenuated Coulombic Self-Assembly (PACS) is a flexible experimental approach for generating crystals from simple colloidal building blocks. The central components are charged spherical particles coated with a polymer brush that…
Atomistic (atom-scale) and coarse-grained (meso-scale) simulations of structure and dynamics of poly-isoprene melts are compared. The local structure and chain packing is mainly determined by the atomistic details of the polymer…
We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by…
Random sequential adsorption algorithm is a popular tool for modelling structure of monolayers built in irreversible adsorption experiments. However, this algorithm becomes very inefficient when the density of molecules in a layer rises.…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
We devise a method for designing materials that will have some desired structural characteristics. We apply it to multiblock copolymers that have two different types of monomers, A and B. We show how to determine what sequence of A's and…
Herein, we describe new methods to produce colloidal particle chains of three stiffness regimes that can be observed on a single-particle level, that is, on the level of the monomers that make up the chain; the chains can even be observed…
We use molecular dynamics simulations to study the static properties of a single linear multiblock copolymer chain under poor solvent conditions varying the block length $N$, the number of blocks $n$, and the solvent quality by variation of…
A two-step model for generating random polytopes is considered. For parameters $d$, $m$, and $p$, the first step is to generate a simple polytope $P$ whose facets are given by $m$ uniform random hyperplanes tangent to the unit sphere in…