相关论文: Volume Determination of Globular Proteins by Molec…
In this letter, by writing the volume as a function of coordinates of atoms, we present a new constant-pressure molecular dynamics method with parameters free. This method is specially appropriate for the finite system in which the periodic…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Classical molecular dynamics (MD) simulations will be able to reach sampling in the second timescale within five years, producing petabytes of simulation data at current force field accuracy. Notwithstanding this, MD will still be in the…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
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…
We report scaling results on the world's largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the atomic dynamics in structural…
Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…
Kinetics of dislocations is studied by means of computer simulation during intensive plastic deformation. The dynamical effect in the form of soliton-like wave of sharply disrupted interparticle bonds is observed. Along with it, micropores…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
Computer simulations of inhomogeneous soft matter systems often require accurate methods for computing the local pressure. We present a simple derivation, based on the virial relation, of two equivalent expressions for the local (atomistic)…
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 recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus,…
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to molecular dynamics, by replacing the…
We have carried out molecular dynamics simulations of the crystallization of hard spheres modelling colloidal systems that are studied in conventional and space-based experiments. We use microscopic probes to investigate the effects of…
This study determines the volume-fraction reduction of sheared fragile glass-forming liquids. We consider a group of hypothetical systems that consist of particles with anisotropic particle-size modulations yet have almost the same average…
Living cells actively regulate their volume in response to changes in the extra-cellular environment, such as osmolarity and chemo-attractant concentration. While the basic physical mechanisms of volume regulation are understood from the…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…