Related papers: Virtual Molecular Dynamics
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
We propose a simple microscopic model of molecular dynamics simulation to study orientational glass in three dimensions. We present simulation results for mixtures of mildly anisotropic particles and spherical impurities. We realize fcc…
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's…
Algorithmic approach is based on the assumption that any quantum evolution of many particle system can be simulated on a classical computer with the polynomial time and memory cost. Algorithms play the central role here but not the…
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral…
The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained…
An important task in the simulation of hard spheres and other hard particles is structure prediction via equilibration. Event-driven molecular dynamics is efficient because its Newtonian dynamics equilibrates fluctuations with the speed of…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matters in difference phases. Normally, the atomic dynamics are described by classical equations of motion…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
Classical algorithms for predicting the equilibrium geometry of strongly correlated molecules require expensive wave function methods that become impractical already for few-atom systems. In this work, we introduce a variational quantum…
A Molecular Dynamics (MD) parallel to the Control Volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood, J. Chem. Phys. 18, 817 (1950) over a finite cubic volume of molecular dimensions.…
The transport of ultra-cold atoms in magneto-optical potentials provides a clean setting in which to investigate the distinct predictions of classical versus quantum dynamics for a system with coupled degrees of freedom. In this system,…
As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs…
Endothelial cells are responsible for the formation of the capillary blood vessel network. We describe a system of endothelial cells by means of two-dimensional molecular dynamics simulations of point-like particles. Cells' motion is…
Molecular Dynamics method is based on solution of Newtonian differential equations of motion. A new very accurate and efficient time-reversible explicit integrator was derived on the basis of second order Tailor expansion of force. There is…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
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…