Related papers: Irradiation driven molecular dynamics: A review
Irradiation experiments (IE) are an essential step in the development of High-Energy Physics (HEP) particle accelerators and detectors. They assess the radiation hardness of materials used in HEP experimental devices by simulating, in a…
Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a…
A molecular dynamics (MD) simulation is used to quantitatively analyze the induced membrane potential for an applied external field varied between 0.4 V/nm to 2.0 V/nm. The change in the electrostatic potential in the DPPC is directly…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
We present a Data-Driven (DD) paradigm that enables molecular dynamics calculations to be performed directly from sampled force-field data such as obtained, e.g., from ab initio calculations, thereby eschewing the conventional step of…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
We push the boundaries of electronic structure-based \textit{ab-initio} molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise barely reachable with classical force-field methods or novel neural network and machine…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
For nearly the past 30 years, Centroid Molecular Dynamics (CMD) has proven to be a viable classical-like phase space formulation for the calculation of quantum dynamical properties. However, calculation of the centroid effective force…
A fully three-dimensional (3D) magnetohydrodynamical (MHD) model is applied to simulate the evolution of the large-scale magnetic field in cluster galaxies interacting with the intra-cluster medium (ICM). As the model input we use a time…
Infrared vibrational spectroscopy in the gas phase has emerged as a powerful tool to determine complex molecular structures with Angstrom accuracy. Among the different approaches IRMPD (InfraRed Multiple Photon Dissociation), which requires…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
-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…
High-dimensional data are often assumed to lie on lower-dimensional manifolds. We study how to construct diffusion processes on this data manifold using only point cloud samples and without access to charts, projections, or other geometric…
A new "on the fly" method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic orbitals are evolved by a Schroedinger-like…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Accurate prediction of energy and forces for 3D molecular systems is one of fundamental challenges at the core of AI for Science applications. Many powerful and data-efficient neural networks predict molecular energies and forces from…
An approximate approach to quantum vibrational dynamics, "Brownian Chain Molecular Dynamics (BCMD)", is proposed to alleviate the chain resonance and curvature problems in the imaginary time-based path integral (PI) simulation. Here the…
Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer hardware and software improvements. Given these advancements, MD simulations are…