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Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…
Designing polymers with high intrinsic thermal conductivity (TC) is critically important for the thermal management of organic electronics and photonics. However, this is a challenging task owing to the diversity of the chemical space and…
Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…
Machine learning (ML) offers a powerful path toward discovering sustainable polymer materials, but progress has been limited by the lack of large, high-quality, and openly accessible polymer datasets. The Open Polymer Challenge (OPC)…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
Particle-Mesh (PM) codes are still very useful tools for testing predictions of cosmological models in cases when extra high resolution is not very important. We release for public use a cosmological PM N-body code. We provide a complete…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
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…
Modeling the atomic structure of amorphous materials has long been a critical challenge in materials science. Recent advances in monolayer amorphous materials enable direct observation of their atomic structures, paving the way for a better…
We present a coarse-grained model for linear polymers with a tunable number of effective atoms (blobs) per chain interacting by intra- and inter-molecular potentials obtained at zero density. We show how this model is able to accurately…
The conformational and dynamical properties of active Brownian polymers embedded in a fluid depend on the nature of the driving mechanism, e.g., self-propulsion or external actuation of the monomers. Implementations of self-propelled and…
Industrial polymeric materials often rely on antioxidants to achieve long-term reliability. Previous studies have frequently discussed the stabilization effect in the presence of macroscopic additive migration. However, the micro- to…
We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are…
Machine learning (ML) models for predicting gas permeability through polymers have traditionally relied on experimental data. While these models exhibit robustness within familiar chemical domains, reliability wanes when applied to new…
Continuum Monte-Carlo simulations at constant pressure are performed on short chain molecules at surfaces. The rodlike chains, consisting of seven effective monomers, are attached at one end to a flat twodimensional substrate. It is found…
This article describes a volumetric approach for procedural shape modeling and a new Procedural Shape Modeling Language (PSML) that facilitates the specification of these models. PSML provides programmers the ability to describe shapes in…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…