相关论文: Averaging Molecular Dynamics simulations to study …

Refractory complex concentrated alloys (RCCA) exhibit exceptional strength and thermal stability, yet their plastic deformation mechanisms under complex contact loading remain insufficiently understood. Here, the nanoindentation response of…

The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…

Machine learning (ML) methods provide advanced means for understanding inherent patterns within large and complex datasets. Here, we employ the principal component analysis (PCA) and the diffusion map (DM) techniques to evaluate the glass…

A stochastic approach to time-dependent density functional theory (TDDFT) is developed for computing the absorption cross section and the random phase approximation (RPA) correlation energy. The core idea of the approach involves…

We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic…

We propose a dynamical theory of low-temperature shear deformation in amorphous solids. Our analysis is based on molecular-dynamics simulations of a two-dimensional, two-component noncrystalline system. These numerical simulations reveal…

Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence,…

Spin relaxation and decoherence is at the heart of spintronics and spin-based quantum information science. Currently, theoretical approaches that can accurately predict spin relaxation of general solids including necessary scattering…

Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…

This is our current research perspective on models providing insight into statistical mechanics. It is necessarily personal, emphasizing our own interest in simulation as it developed from the National Laboratories' work to the worldwide…

The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds…

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…

Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…

We introduce a generalized machine learning framework to probabilistically parameterize upper-scale models in the form of nonlinear PDEs consistent with a continuum theory, based on coarse-grained atomistic simulation data of mechanical…

The accurate, reliable and efficient numerical approximation of multi-physics processes in heterogeneous porous media with varying media coefficients that include fluid flow and structure interactions is of fundamental importance in energy,…

Timed automata are the formal model for real-time systems. Extensions with discrete probabilistic branching have been considered in the literature and successfully applied. Probabilistic timed automata (PTA) do require all branching…

We introduce a simple model for implementing the concepts of quasi-energy and parametric resonances (PRs) in systems with the $\mathcal{PT}$ symmetry, i.e., a pair of coupled and mutually balanced gain and loss elements. The parametric (ac)…

We describe the development of a new object kinetic Monte Carlo code where the elementary defect objects are off-lattice atomistic configurations. Atomic-level transitions are used to transform and translate objects, to split objects and to…

Mixed-quantum-classical molecular dynamics simulation implies an effective measurement on the electronic states owing to continuously tracking the atomic forces.Based on this insight, we propose a quantum trajectory mean-field approach for…