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Non-adiabatic molecular dynamics (NAMD) simulations have become an indispensable tool for investigating excited-state dynamics in solids. In this work, we propose a general framework, N$^2$AMD which employs an E(3)-equivariant deep neural…
The DMD (Dynamic Mode Decomposition) method has attracted widespread attention as a representative modal-decomposition method and can build a predictive model. However, the DMD may give predicted results that deviate from physical reality…
Molecular dynamics (MD) simulations give access to equilibrium structures and dynamic properties given an ergodic sampling and an accurate force-field. The force-field parameters are calibrated to reproduce properties measured by…
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…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
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…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
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…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
Disordered molecular systems such as amorphous catalysts, organic thin films, electrolyte solutions, and water are at the cutting edge of computational exploration today. Traditional simulations of such systems at length-scales relevant to…
Machine-learning force fields (MLFF) should be accurate, computationally and data efficient, and applicable to molecules, materials, and interfaces thereof. Currently, MLFFs often introduce tradeoffs that restrict their practical…
Machine-learning interatomic potentials (MLPs) are fast, data-driven surrogate models of atomistic systems' potential energy surfaces that can accelerate ab-initio molecular dynamics (MD) simulations by several orders of magnitude. The…
Simulating liquid water to an accuracy that matches its wealth of available experimental data requires both precise electronic structure methods and reliable sampling of nuclear (quantum) motion. This is challenging because applying the…
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…
Accuracy of molecular dynamics simulations depends crucially on the interatomic potential used to generate forces. The gold standard would be first-principles quantum mechanics (QM) calculations, but these become prohibitively expensive at…
Markov state models (MSMs) have been successful in computing metastable states, slow relaxation timescales and associated structural changes, and stationary or kinetic experimental observables of complex molecules from large amounts of…
We describe the development of machine-learned potentials of atmospheric gases with flexible monomers for molecular simulations. A recently suggested permutationally invariant polynomial neural network (PIP-NN) approach is utilized to…
Molecular dynamics (MD) simulations of complex electrochemical systems, such as ionic liquid supercapacitors, are increasingly including the constant potential method (CPM) to model conductive electrodes at specified potential difference,…