Related papers: Interactive molecular dynamics
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
Droplet motion over a surface with wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics. GROMACS and Visual Molecular Dynamics (VMD) were used for simulation and intermittent…
The Institute of Physics New Quantum Curriculum (quantumphysics.iop.org) consists of online texts and interactive simulations with accompanying activities for an introductory course in quantum mechanics starting from two-level systems.…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream…
Understanding what happens inside the rippling and dancing surface of a liquid remains one of the great challenges of fluid dynamics. Using molecular dynamics (MD) we can pick apart the interface structure and understand surface tension. In…
Complex (dusty) plasmas allow experimental studies of various physical processes occurring in classical liquids and solids by directly observing individual microparticles. A major problem is that the interaction between microparticles is…
Thermodynamics and dynamics of a classical two-dimensional system with dipole-like isotropic repulsive interactions are studied systematically using extensive molecular dynamics (MD) simulations supplemented by appropriate theoretical…
The chemical dynamics scene is the most important application of computer simulation. We show that electrons jump between potential holes of different depths (new molecular orbits, hybrid atomic orbits with different energies) under 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.…
We describe a simple numerical simulation, suitable for an undergraduate project (or graduate problem set), of the Brownian motion of a particle in a Hooke-law potential well. Understanding this physical situation is a practical necessity…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Particle suspensions are ubiquitous in our daily life, but are not well understood due to their complexity. During the last twenty years, various simulation methods have been developed in order to model these systems. Due to varying…
This article is an invitation. It is, first, an invitation to consider as a subject worthy of attention the wide range of situations where small discrete elements, either bubbles, droplets or solid particles, are embedded in turbulent…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
In this review we discuss the recent progress in the simulation of soft active matter systems and in particular the hydrodynamics of microswimmers using the method of multiparticle collision dynamics, which solves the hydrodynamic flows…