Related papers: Introduction to molecular dynamics simulations
Dynamical maps describe general transformations of the state of a physical system, and their iteration can be interpreted as generating a discrete time evolution. Prime examples include classical nonlinear systems undergoing transitions to…
CP2K is a versatile open-source software package for simulations across a wide range of atomistic systems, from isolated molecules in the gas phase to low-dimensional functional materials and interfaces, as well as highly symmetric…
We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for…
It was recently shown that the real part of the frequency-dependent fluidity for several glass-forming liquids of different chemistry conforms to the prediction of the random barrier model (RBM) devised for ac electrical conduction in…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
A template-based generic programming approach was presented in a previous paper that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
We introduce a new quantity to probe the glass transition. This quantity is a linear generalized compressibility which depends solely on the positions of the particles. We have performed a molecular dynamics simulation on a glass forming…
Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting…
We review achievements made in recent years in the field of numerical modeling of ultra-relativistic projectiles propagation in oriented crystals, radiation emission and related phenomena. This topic is highly relevant to the problem of…
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 provide Python tools enabling numerical simulation and analysis of the propagation dynamics of ultrashort laser pulses in nonlinear waveguides. The modeling approach is based on the widely used generalized nonlinear Schr\"odinger…
KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations. The program can handle simulations of the diffusion and reaction of millions of particles in one, two, or three dimensions, and is designed to be easily…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
In this paper I present a first attempt for a possible description of fluids dynamics by mean of a cellular automata technique. With the use of simple and elementary rules, based on random behaviour either, the model permits to obtain the…
Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding meaningful low-dimensional structures hidden in their high-dimensional observations. Such practice is needed in atomistic simulations of complex…
We push the boundaries of electronic structure-based \textit{ab-initio} molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise barely reachable with classical force-field methods or novel neural network and machine…
We map molecular dynamics simulations of fluid-fluid interfaces onto mesoscale continuum theories for partially miscible fluids. Unlike most previous work, we examine not only the interface order parameter and density profiles, but also the…