Related papers: Molecular dynamics simulation with finite electric…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these…
Non-bonded potentials are included in most force fields and therefore widely used in classical molecular dynamics simulations of materials and interfacial phenomena. It is commonplace to truncate these potentials for computational…
We apply a temporal edge prediction model for weighted dynamic graphs to predict time-dependent changes in molecular structure. Each molecule is represented as a complete graph in which each atom is a vertex and all vertex pairs are…
Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic…
Predictive simulation of vibrational spectra of complex condensed-phase and interface systems with thousands of degrees of freedom has long been a challenging task of modern condensed matter theory. In this work, fourth-generation…
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
We develop a combined machine learning (ML) and quantum mechanics approach that enables data-efficient reconstruction of flexible molecular force fields from high-level ab initio calculations, through the consideration of fundamental…
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
Equilibration dynamics of hot oxygen atoms following O2 dissociation on Pd(100) and Pd(111) surfaces are investigated by molecular dynamics simulations based on a scalable neural network potential enabling first-principles description of O2…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
The local flow field and seepage induced drag obtained from Pore Network Models (PNM) is compared to Immersed Boundary Method (IBM) simulations, for a range of linear graded and bimodal samples. PNM were generated using a weighted Delaunay…
The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the…
To fully understand, analyze, and determine the behavior of dynamical systems, it is crucial to identify their intrinsic modal coordinates. In nonlinear dynamical systems, this task is challenging as the modal transformation based on the…
The transport of excess protons and hydroxide ions in water underlies numerous important chemical and biological processes. Accurately simulating the associated transport mechanisms ideally requires utilizing ab initio molecular dynamics…
Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
Cosmic-ray acceleration processes in astrophysical plasmas are often investigated with fully-kinetic or hybrid kinetic numerical simulations, which enable us to describe a detailed microphysics of particle energization mechanisms. Tracing…
The optical properties of molecules close to plasmonic nanostructures greatly differ from their isolated molecule counterparts. To theoretically investigate such systems in a Quantum Chemistry perspective, one has to take into account that…