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Density functional theory (DFT) and machine learning potentials (MLPs) are essential for predicting and understanding materials properties, yet preparing, executing, and analyzing these simulations typically requires extensive scripting,…
In atomistic simulations, pseudo-dynamics relaxation schemes often exhibit better performance and accuracy in finding local minima than line-search-based descent algorithms like steepest descent or conjugate gradient. Here, an improved…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Modeling plasmas in terms of atoms or ions is theoretically appealing for several reasons. When it is relevant, the notion of atom or ion in a plasma provides us with an interpretation scheme of the plasma's internal functioning. From the…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
The open source ALPS (Algorithms and Libraries for Physics Simulations) project provides a collection of physics libraries and applications, with a focus on simulations of lattice models and strongly correlated systems. The libraries…
Modeling deformable objects - especially continuum materials - in a way that is physically plausible, generalizable, and data-efficient remains challenging across 3D vision, graphics, and robotic manipulation. Many existing methods…
We introduce a particle-based simulation method for granular material in interactive frame rates. We divide the simulation into two decoupled steps. In the first step, a relatively small number of particles is accurately simulated with a…
Molecular dynamics (MD) employing machine-learned interatomic potentials (MLIPs) serve as an efficient, urgently needed complement to ab initio molecular dynamics (aiMD). By training these potentials on data generated from ab initio…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
SALMON (Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience, http://salmon-tddft.jp) is a software package for the simulation of electron dynamics and optical properties of molecules, nanostructures, and crystalline solids…
Particle suspensions are ubiquitous in our daily life, but are not well understood due to their complexity. During the last twenty years, various simulation methods have been developed in order to model these systems. Due to varying…
ParticLS (\emph{Partic}le \emph{L}evel \emph{S}ets) is a software library that implements the discrete element method (DEM) and meshfree methods. ParticLS tracks the interaction between individual particles whose geometries are defined by…
Molecular dynamics (MD) enables the study of physical systems with excellent spatiotemporal resolution but suffers from severe time-scale limitations. To address this, enhanced sampling methods have been developed to improve exploration of…
Raman spectroscopy is a powerful experimental technique for characterizing molecules and materials that is used in many laboratories. First-principles theoretical calculations of Raman spectra are important because they elucidate the…
A GPU-accelerated version of the lattice Boltzmann method for efficient simulation of soft materials is introduced. Unlike standard approaches, this method reconstructs the distribution functions from available hydrodynamic variables…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…