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It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
The Minkowski operators (addition and substraction of sets in vectorial spaces) has been extensively used for Computer Graphics and Image Processing to represent complex shapes. Here we propose to apply those mathematical concepts to extend…
In this review article, we first briefly introduce the transport theory and quantum molecular dynamics model applied in the study of the heavy ion collisions from low to intermediate energies. The developments of improved quantum molecular…
Magnetic fields are widely observed in the Universe in virtually all astrophysical objects, from individual stars to entire galaxies, even in the intergalactic medium, but their specific generation has long been debated. Due to the…
In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which…
Inertial microfluidic devices (IMDs) offer low-cost, high-throughput alternative techniques for many traditional particle- (or cell-) manipulation tasks, but simulating them requires being able to predict particle migration, and thus…
Predictive modeling of the phonon/thermal transport properties of materials is vital to rational design for a diverse spectrum of engineering applications. Classical Molecular Dynamics (MD) simulations serve as a tool to simulate the time…
Dynamic Mode Decomposition (DMD) is a data-driven technique to identify a low dimensional linear time invariant dynamics underlying high-dimensional data. For systems in which such underlying low-dimensional dynamics is time-varying, a…
Non-radiative decay in photoexcited molecular systems is driven by nuclear motion toward conical intersections (CIs), where electronic states become degenerate and nonadiabatic transitions occur. Identifying the nuclear degrees of freedom…
We demonstrate the application of the Dynamic Mode Decomposition (DMD) for the diagnostic analysis of the nonlinear dynamics of a magnetized plasma in resistive magnetohydrodynamics. The DMD method is an ideal spatio-temporal matrix…
The Improved Quantum Molecular Dynamics (ImQMD) model incorporated with the statistical decay model is used to investigate the intermediate energy nucleon-induced reactions. In our last work, the description on light complex particle…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
We introduce Gradient Particle Magnetohydrodynamics (GPM), a new Lagrangian method for magnetohydrodynamics based on gradients corrected for the locally disordered particle distribution. The development of a numerical code for MHD…
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…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
The discovery and study of new material systems rely on molecular simulations that often come with significant computational expense. We propose MDDM, a Molecular Dynamics Diffusion Model, which is capable of predicting a valid output…