相关论文: Averaging Molecular Dynamics simulations to study …
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Deformation heterogeneities within microstructures of polycrystalline shape memory alloys (SMAs) during superelastic stressing are studied using both experiments and simulations. In situ X-ray diffraction, specifically the far-field high…
Anharmonic inter-atomic potential x to power of n, n>1, has been used in molecular dynamics (MD) simulations of stress dynamics of FCC oriented crystal. The model of the chain of masses and springs is found as a convenient and accurate…
The weighted ensemble (WE) simulation strategy provides unbiased sampling of non-equilibrium processes, such as molecular folding or binding, but the extraction of rate constants relies on characterizing steady state behavior.…
Principal component analysis (PCA) represents a standard approach to identify collective variables $\{x_i\}\!=\!\boldsymbol{x}$, which can be used to construct the free energy landscape $\Delta G(\boldsymbol{x})$ of a molecular system.…
Atomic-scale phase-field modeling formulates the probability densities of atomic vibrations as Gaussian distributions and derives a free energy functional using variational Gaussian theory and interatomic potentials. This framework permits…
Three-dimensional discrete dislocation dynamics simulations are used to study strain-controlled plastic deformation of face-centered cubic aluminium single crystals. After describing the rate and size dependence of the average stress-strain…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
In this work, we present a method for simulating the large-scale deformation and crumpling of thin, elastoplastic sheets. Motivated by the physical behavior of thin sheets during crumpling, two different formulations of the governing…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
Fracture involves interaction across large and small length scales. With the application of enough stress or strain to a brittle material, atomistic scale bonds will break, leading to fracture of the macroscopic specimen. From the…
Processes slow compared to atomic vibrations pose significant challenges in atomistic simulations, particularly for phenomena such as diffusive relaxations and phase transitions, where repeated crossings and the shear number of thermally…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
Point defects in solid-state materials are now routinely simulated using large supercell structures, requiring efficient quantum mechanical solutions. Data-driven and machine learning (ML) models trained on computational data can enable…
The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…
Molecular dynamics (MD) simulations of successive collision cascades within the same simulation domain were performed using two different inter-atomic potentials (IAP) in tungsten, one EAM based and the other a `quantum accurate' machine…
Recrystallization is a phenomenon in which a plastically deformed polycrystalline microstructure with a high dislocation density transforms into another that has low dislocation density. This evolution is driven by the stored energy in…
Large-scale molecular dynamics simulations of shear deformation under constant pressures of amorphous silicon, PT from low-density-amorphous (LDA) to high-density-amorphous (HDA) Si, and formation of shear bands (SBs) are performed using…
The dynamics of inertial particles in turbulence is modelled and investigated by means of direct numerical simulation of an axisymmetrically expanding homogeneous turbulent strained flow. This flow can mimic the dynamics of particles close…