Related papers: Interactive molecular dynamics
Exposing a molecule to intense light pulses may bring this molecule to a nonstationary quantum state, thus launching correlated dynamics of electronic and nuclear subsystems. Although much had been achieved in the understanding of…
Interactions between quantum particles, such as electrons, are the source of important effects, ranging from superconductivity, to the formation of molecular bonds, or the stability of elementary compounds at high-energies. In this article,…
Quantum chemical simulations can be greatly accelerated by constructing machine learning potentials, which is often done using active learning (AL). The usefulness of the constructed potentials is often limited by the high effort required…
The purpose of this work is to use active particles to study the effect of facilitation on supercooled liquids. To this end we investigate the behavior of a model supercooled liquid doped with intermittently active and intermittently slowed…
Machine learning encompasses a set of tools and algorithms which are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting…
Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration…
Discrete simulation methods are efficient tools to investigate the complex behaviors of complex fluids made of either dry granular materials or dilute suspensions. By contrast, materials made of soft and/or concentrated units (emulsions,…
Turbulent diffuse molecular clouds can exhibit complicated morphologies caused by the interactions among radiation, chemistry, fluids, and fields. We performed full 3D simulations for turbulent diffuse molecular interstellar media,…
The physics of glasses can be studied from many viewpoints, from material scientists interested in the development of new materials to statistical physicists inventing new theoretical tools to deal with disordered systems. In these lectures…
Multimodal simulations augment the presentation of abstract concepts facilitating theoretical models understanding and learning. Most simulations only engage two of our five senses: sight and hearing. If we employ additional sensory…
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…
Thermo-osmotic slip -- the flow induced by a thermal gradient along a surface -- is a well-known phenomenon, but curiously there is a lack of robust molecular-simulation techniques to predict its magnitude. Here, we compare three different…
The friction kernel (or memory function) $\gamma(t)$ characterizing single-molecule dynamics in strongly bound liquids exhibits two distinct relaxations with the longer time-scale relaxation associated with attractive intermolecular forces.…
The method of molecular dynamics is used to study behavior of a ultracold non-ideal ion-electron Be plasma in a uniform magnetic field. Our simulations yield an estimate for the rate of electron-ion collisions which is…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
We prove that for a combined system of classical and quantum particles, it is possible to write a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In…
This paper gives an overview of the particle transport theory essentials, the basics of particle-material interaction simulation, physical quantities needed to simulate particle transport and interactions in materials, Monte Carlo…
Classical topological concepts are applied to understand high performance computing simulations of molecules writhing in three dimensional space. These simulations produce peta-bytes of floating point data, to describe 3 dimensional changes…