Abstract Several studies in Bioinformatics, Computational Biology and Systems Biology rely
on the definition of physico-chemical or mathematical models of biological systems at …

We describe a highly optimized implementation of MPI domain decomposition in a GPU-
enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer …

For a number of years, we have been exploring the underpinnings of algorithms for
simulating molecular dynamics from a mathematics perspective, ie as outsiders. We have …

HOOMD-blue is a particle simulation engine designed for nano-and colloidal-scale
molecular dynamics and hard particle Monte Carlo simulations. It has been actively …

The synthesis of binary nanocrystal superlattices (BNSLs) enables the targeted integration
of orthogonal physical properties, such as photoluminescence and magnetism, into a single …

GALAMOST [graphics processing unit (GPU)‐accelerated large‐scale molecular simulation
toolkit] is a molecular simulation package designed to utilize the computational power of …

Shape and morphology of polymeric particles are of great importance in controlling their
optical properties or self-assembly into unusual superstructures. Confinement of block …

A hierarchical (triple scale) simulation methodology is presented for the prediction of the
dynamical and rheological properties of high molecular-weight entangled polymer melts …

We introduce the software package ReaDDy for simulation of detailed spatiotemporal
mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with …

The self-assembly process, where molecules form complex structures through interaction
forces, has broad applications in various fields. However, controlling the dynamics of self …