Related papers: Introduction to molecular dynamics simulations
We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms) and atomistic simulations of the Larson model of micelle…
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating 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)…
We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion…
The package performs molecular-dynamics-like agent-based simulations for models of aligning self-propelled particles in two dimensions such as e.g. the seminal Vicsek model or variants of it. In one class of the covered models, the…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
We present methods for exploratory studies of molecular dynamics using MATLAB. Such methods are not suitable for large scale applications, but they can be used for developement and testing of new types of interactions and other aspects of…
Owing to the advances in computational techniques and the increase in computational power, atomistic simulations of materials can simulate large systems with higher accuracy. Complex phenomena can be observed in such state-of-the-art…
We review recent results from computer simulation studies of polymer glasses, from chain dynamics around the glass transition temperature Tg to the mechanical behaviour below Tg. These results clearly show that modern computer simulations…
Incorporation of machine learning (ML) techniques into atomic-scale modeling has proven to be an extremely effective strategy to improve the accuracy and reduce the computational cost of simulations. It also entails conceptual and practical…
We present TTCF4LAMMPS, a toolkit for performing non-equilibrium molecular dynamics (NEMD) simulations to study fluid behaviour at low shear rates using the LAMMPS software. By combining direct NEMD simulations and the transient-time…
We explore how the fundamental problems in quantum molecular dynamics can be modelled using classical simulators (emulators) of quantum computers and the actual quantum hardware available to us today. The list of problems we tackle includes…
The ever-increasing quantity of multivariate process data is driving a need for skilled engineers to analyze, interpret, and build models from such data. Multivariate data analytics relies heavily on linear algebra, optimization, and…
We use molecular dynamics simulations to compute the Lyapunov spectra of many-particle systems resembling simple fluids in thermal equilibrium and in non-equilibrium stationary states. Here we review some of the most interesting results and…
With molecular dynamics simulations of a fluid mixture of classical particles interacting with pair-wise additive Weeks-Chandler-Andersen potentials, we consider the time series of particle displacements and thereby determine distributions…
The numerical simulation of a Poiseuille flow in a narrow channel using the molecular dynamics simulation (MDS) is performed. Poiseuille flow of liquid Argon in a carbon nanochannel is simulated by embedding the fluid particles in a uniform…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
This chapter presents a selection of theoretical and numerical tools suitable for the study of wave propagation in time-dependent media. The focus is on one-dimensional spring-mass chains whose properties are modulated in space and time in…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…