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.
Force field (chemistry)In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.
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.
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.
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.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
Ergodic hypothesisIn physics and thermodynamics, the ergodic hypothesis says that, over long periods of time, the time spent by a system in some region of the phase space of microstates with the same energy is proportional to the volume of this region, i.e., that all accessible microstates are equiprobable over a long period of time. Liouville's theorem states that, for a Hamiltonian system, the local density of microstates following a particle path through phase space is constant as viewed by an observer moving with the ensemble (i.
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.
Ergodic theoryErgodic theory is a branch of mathematics that studies statistical properties of deterministic dynamical systems; it is the study of ergodicity. In this context, "statistical properties" refers to properties which are expressed through the behavior of time averages of various functions along trajectories of dynamical systems. The notion of deterministic dynamical systems assumes that the equations determining the dynamics do not contain any random perturbations, noise, etc.
ErgodicityIn mathematics, ergodicity expresses the idea that a point of a moving system, either a dynamical system or a stochastic process, will eventually visit all parts of the space that the system moves in, in a uniform and random sense. This implies that the average behavior of the system can be deduced from the trajectory of a "typical" point. Equivalently, a sufficiently large collection of random samples from a process can represent the average statistical properties of the entire process.
Ergodic processIn physics, statistics, econometrics and signal processing, a stochastic process is said to be in an ergodic regime if an observable's ensemble average equals the time average. In this regime, any collection of random samples from a process must represent the average statistical properties of the entire regime. Conversely, a process that is not in ergodic regime is said to be in non-ergodic regime. One can discuss the ergodicity of various statistics of a stochastic process.
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).
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.
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.
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).
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.
Stochastic simulationA stochastic simulation is a simulation of a system that has variables that can change stochastically (randomly) with individual probabilities. Realizations of these random variables are generated and inserted into a model of the system. Outputs of the model are recorded, and then the process is repeated with a new set of random values. These steps are repeated until a sufficient amount of data is gathered. In the end, the distribution of the outputs shows the most probable estimates as well as a frame of expectations regarding what ranges of values the variables are more or less likely to fall in.
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.
EvolutionismEvolutionism is a term used (often derogatorily) to denote the theory of evolution. Its exact meaning has changed over time as the study of evolution has progressed. In the 19th century, it was used to describe the belief that organisms deliberately improved themselves through progressive inherited change (orthogenesis). The teleological belief went on to include cultural evolution and social evolution. In the 1970s, the term "Neo-Evolutionism" was used to describe the idea that "human beings sought to preserve a familiar style of life unless change was forced on them by factors that were beyond their control.
