Related papers: Interactive molecular dynamics
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of…
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
We describe an educational simulation of some effects within the gas of hard spheres. The focus of the presented simulation is on the comprehension of random character of the velocity of molecules in the gas and of the energy at fixed…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Real-life control tasks involve matters of various substances---rigid or soft bodies, liquid, gas---each with distinct physical behaviors. This poses challenges to traditional rigid-body physics engines. Particle-based simulators have been…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
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…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
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…
Kinetics of dislocations is studied by means of computer simulation during intensive plastic deformation. The dynamical effect in the form of soliton-like wave of sharply disrupted interparticle bonds is observed. Along with it, micropores…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…