Related papers: Molecular Dynamics Analysis of Biomolecular System…
Selected results of a classical simulation of N bodies in strong interaction are presented. The static properties of such classical systems are qualitatively similar to the known properties of atomic nuclei. The simulations of collisions…
Understanding the binding dynamics of liquid molecules is of fundamental importance in physical and life sciences. However, nanoscale fast dynamics pose great challenges for experimental characterization. Conventionally, the binding…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
While experimental advancements continue to expand the capabilities to control and probe non-equilibrium quantum matter at an unprecedented level, the numerical simulation of the dynamics of correlated quantum systems remains a pivotal…
The past few years have seen dramatic improvements in the scope and realism of star cluster simulations. Accurate treatments of stellar evolution, coupled with robust descriptions of all phases of binary evolution, have been incorporated…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
To provide a practitioner's introduction to the study of the nuclear pasta, this article presents a brief review of the evolution of the methods used to study nucleon dynamics. This is followed with a more complete description of the…
A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the…
A recently developed method of nanoclusters growth in a pulsed plasma is studied by means of molecular dynamics. A model that allows one to consider high-energy charged particles in classical molecular dynamics is suggested, and applied for…
Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms,…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator.…
Nanoscale biosystems are widely used in numerous medical applications. The approaches for structure and function of the nanomachines that are available in the cell (natural nanomachines) are discussed. Molecular simulation studies have been…
This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as…
Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…
We compare two recently proposed methods for the characterization of phase transitions in small systems. The usefulness of these techniques is evaluated for the case of structural transition in alanine-based peptides.
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
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 present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…