Related papers: Irradiation driven molecular dynamics: A review

We show that an MHD-instability driven dynamo (IDD) operating in a hot accretion disk is capable of generating energetically adequate magnetic flux deposition rates above and below a mildly advective accretion disk structure. The dynamo is…

In most cases the ultrafast dynamics of resonantly excited molecules are considered, and almost always computed in the molecular frame, while experiments are carried out in the laboratory frame. Here we provide a formalism in terms of a lab…

Classical Molecular Dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational…

Molecular dynamics (MD) simulates the time evolution of atomic systems governed by interatomic forces, and the fidelity of these simulations depends critically on the underlying force model. Classical force fields (CFFs) rely on fixed…

In studying solidification process by simulations on the atomic scale, the modeling of crystal nucleation or amorphisation requires the construction of interatomic interactions that are able to reproduce the properties of both the solid and…

Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…

Molecular dynamics (MD) simulation is a powerful tool for studying biomolecular structural changes, molecular recognition, transmembrane transport, and functional mechanisms. However, its practical bottleneck lies not only in software…

Recently proposed non-adiabatic ring polymer molecular dynamics (NRPMD) approach has shown to provide accurate quantum dynamics by incorporating explicit electronic state descriptions and nuclear quantizations. Here, we present a rigorous…

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…

Field emission coupled with molecular dynamics simulation (FEcMD) software package is a computational tool for studying atomic structure evolution, structural deformation, phase transitions, recrystallization as well as electron emission…

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…

Dynamic Mode Decomposition (DMD) and its variants, such as extended DMD (EDMD), are broadly used to fit simple linear models to dynamical systems known from observable data. As DMD methods work well in several situations but perform poorly…

We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…

For 35 years, {\it ab initio} molecular dynamics (AIMD) has been the method of choice for modeling complex atomistic phenomena from first principles. However, most AIMD applications are limited by computational cost to systems with…

We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…

Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their…

Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for…

A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…

Dynamic Mode Decomposition (DMD) is a data-driven method related to Koopman operator theory that extracts information about dominant dynamics from data snapshots. In this paper we examine techniques to accelerate the application of DMD to…

Interfaces between molecules and 2D materials exhibit energy-driven functionalities, wherein charge transfer directs molecular motion. Unlike equilibrium systems, where molecular assemblies settle into static configurations, continuous…