Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
SimulationA simulation is the imitation of the operation of a real-world process or system over time. Simulations require the use of models; the model represents the key characteristics or behaviors of the selected system or process, whereas the simulation represents the evolution of the model over time. Often, computers are used to execute the simulation. Simulation is used in many contexts, such as simulation of technology for performance tuning or optimizing, safety engineering, testing, training, education, and video games.
Ensemble (mathematical physics)In physics, specifically statistical mechanics, an ensemble (also statistical ensemble) is an idealization consisting of a large number of virtual copies (sometimes infinitely many) of a system, considered all at once, each of which represents a possible state that the real system might be in. In other words, a statistical ensemble is a set of systems of particles used in statistical mechanics to describe a single system. The concept of an ensemble was introduced by J. Willard Gibbs in 1902.
Newtonian fluidA Newtonian fluid is a fluid in which the viscous stresses arising from its flow are at every point linearly correlated to the local strain rate — the rate of change of its deformation over time. Stresses are proportional to the rate of change of the fluid's velocity vector. A fluid is Newtonian only if the tensors that describe the viscous stress and the strain rate are related by a constant viscosity tensor that does not depend on the stress state and velocity of the flow.
Simulation video gameSimulation video games are a diverse super-category of video games, generally designed to closely simulate real world activities. A simulation game attempts to copy various activities from real life in the form of a game for various purposes such as training, analysis, prediction, or entertainment. Usually there are no strictly defined goals in the game, and the player is allowed to control a character or environment freely. Well-known examples are war games, business games, and role play simulation.
Symplectic integratorIn mathematics, a symplectic integrator (SI) is a numerical integration scheme for Hamiltonian systems. Symplectic integrators form the subclass of geometric integrators which, by definition, are canonical transformations. They are widely used in nonlinear dynamics, molecular dynamics, discrete element methods, accelerator physics, plasma physics, quantum physics, and celestial mechanics. Symplectic integrators are designed for the numerical solution of Hamilton's equations, which read where denotes the position coordinates, the momentum coordinates, and is the Hamiltonian.
Computer simulationComputer simulation is the process of mathematical modelling, performed on a computer, which is designed to predict the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be determined by comparing their results to the real-world outcomes they aim to predict. Computer simulations have become a useful tool for the mathematical modeling of many natural systems in physics (computational physics), astrophysics, climatology, chemistry, biology and manufacturing, as well as human systems in economics, psychology, social science, health care and engineering.
Fluid dynamicsIn physics, physical chemistry and engineering, fluid dynamics is a subdiscipline of fluid mechanics that describes the flow of fluids—liquids and gases. It has several subdisciplines, including aerodynamics (the study of air and other gases in motion) and hydrodynamics (the study of liquids in motion). Fluid dynamics has a wide range of applications, including calculating forces and moments on aircraft, determining the mass flow rate of petroleum through pipelines, predicting weather patterns, understanding nebulae in interstellar space and modelling fission weapon detonation.
Canonical ensembleIn statistical mechanics, a canonical ensemble is the statistical ensemble that represents the possible states of a mechanical system in thermal equilibrium with a heat bath at a fixed temperature. The system can exchange energy with the heat bath, so that the states of the system will differ in total energy. The principal thermodynamic variable of the canonical ensemble, determining the probability distribution of states, is the absolute temperature (symbol: T).
Verlet integrationVerlet integration (vɛʁˈlɛ) is a numerical method used to integrate Newton's equations of motion. It is frequently used to calculate trajectories of particles in molecular dynamics simulations and computer graphics. The algorithm was first used in 1791 by Jean Baptiste Delambre and has been rediscovered many times since then, most recently by Loup Verlet in the 1960s for use in molecular dynamics. It was also used by P. H. Cowell and A. C. C.
Non-Newtonian fluidA non-Newtonian fluid is a fluid that does not follow Newton's law of viscosity, that is, it has variable viscosity dependent on stress. In non-Newtonian fluids, viscosity can change when under force to either more liquid or more solid. Ketchup, for example, becomes runnier when shaken and is thus a non-Newtonian fluid. Many salt solutions and molten polymers are , as are many commonly found substances such as custard, toothpaste, starch suspensions, corn starch, paint, blood, melted butter, and shampoo.
Grand canonical ensembleIn statistical mechanics, the grand canonical ensemble (also known as the macrocanonical ensemble) is the statistical ensemble that is used to represent the possible states of a mechanical system of particles that are in thermodynamic equilibrium (thermal and chemical) with a reservoir. The system is said to be open in the sense that the system can exchange energy and particles with a reservoir, so that various possible states of the system can differ in both their total energy and total number of particles.
Numerical integrationIn analysis, numerical integration comprises a broad family of algorithms for calculating the numerical value of a definite integral, and by extension, the term is also sometimes used to describe the numerical solution of differential equations. This article focuses on calculation of definite integrals. The term numerical quadrature (often abbreviated to quadrature) is more or less a synonym for numerical integration, especially as applied to one-dimensional integrals.
Fluid mechanicsFluid mechanics is the branch of physics concerned with the mechanics of fluids (liquids, gases, and plasmas) and the forces on them. It has applications in a wide range of disciplines, including mechanical, aerospace, civil, chemical, and biomedical engineering, as well as geophysics, oceanography, meteorology, astrophysics, and biology. It can be divided into fluid statics, the study of fluids at rest; and fluid dynamics, the study of the effect of forces on fluid motion.
Classical mechanicsClassical mechanics is a physical theory describing the motion of macroscopic objects, from projectiles to parts of machinery and astronomical objects, such as spacecraft, planets, stars, and galaxies. For objects governed by classical mechanics, if the present state is known, it is possible to predict how it will move in the future (determinism), and how it has moved in the past (reversibility). The "classical" in "classical mechanics" does not refer classical antiquity, as it might in, say, classical architecture.
Training simulationIn business, training simulation is a virtual medium through which various types of skills can be acquired. Training simulations can be used in a variety of genres; however they are most commonly used in corporate situations to improve business awareness and management skills. They are also common in academic environments as an integrated part of a business or management course. The word simulation implies an imitation of a real-life process, usually via a computer or other technological device, in order to provide a lifelike experience.
Microcanonical ensembleIn statistical mechanics, the microcanonical ensemble is a statistical ensemble that represents the possible states of a mechanical system whose total energy is exactly specified. The system is assumed to be isolated in the sense that it cannot exchange energy or particles with its environment, so that (by conservation of energy) the energy of the system does not change with time. The primary macroscopic variables of the microcanonical ensemble are the total number of particles in the system (symbol: N), the system's volume (symbol: V), as well as the total energy in the system (symbol: E).
IntegralIn mathematics, an integral is the continuous analog of a sum, which is used to calculate areas, volumes, and their generalizations. Integration, the process of computing an integral, is one of the two fundamental operations of calculus, the other being differentiation. Integration started as a method to solve problems in mathematics and physics, such as finding the area under a curve, or determining displacement from velocity. Today integration is used in a wide variety of scientific fields.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
Cross-correlationIn signal processing, cross-correlation is a measure of similarity of two series as a function of the displacement of one relative to the other. This is also known as a sliding dot product or sliding inner-product. It is commonly used for searching a long signal for a shorter, known feature. It has applications in pattern recognition, single particle analysis, electron tomography, averaging, cryptanalysis, and neurophysiology. The cross-correlation is similar in nature to the convolution of two functions.
