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.
Statistical mechanicsIn physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. It does not assume or postulate any natural laws, but explains the macroscopic behavior of nature from the behavior of such ensembles. Sometimes called statistical physics or statistical thermodynamics, its applications include many problems in the fields of physics, biology, chemistry, and neuroscience.
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.
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.
Quantum statistical mechanicsQuantum statistical mechanics is statistical mechanics applied to quantum mechanical systems. In quantum mechanics a statistical ensemble (probability distribution over possible quantum states) is described by a density operator S, which is a non-negative, self-adjoint, trace-class operator of trace 1 on the Hilbert space H describing the quantum system. This can be shown under various mathematical formalisms for quantum mechanics. One such formalism is provided by quantum logic.
Microstate (statistical mechanics)In statistical mechanics, a microstate is a specific configuration of a system that describes the precise positions and momenta of all the individual particles or components that make up the system. Each microstate has a certain probability of occurring during the course of the system's thermal fluctuations. In contrast, the macrostate of a system refers to its macroscopic properties, such as its temperature, pressure, volume and density.
Partition function (statistical mechanics)In physics, a partition function describes the statistical properties of a system in thermodynamic equilibrium. Partition functions are functions of the thermodynamic state variables, such as the temperature and volume. Most of the aggregate thermodynamic variables of the system, such as the total energy, free energy, entropy, and pressure, can be expressed in terms of the partition function or its derivatives. The partition function is dimensionless.
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.
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.
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).
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.
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.
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
Excess chemical potentialIn thermodynamics, the excess chemical potential is defined as the difference between the chemical potential of a given species and that of an ideal gas under the same conditions (in particular, at the same pressure, temperature, and composition). The chemical potential of a particle species is therefore given by an ideal part and an excess part. Chemical potential of a pure fluid can be estimated by the Widom insertion method.
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.
Python syntax and semanticsThe syntax of the Python programming language is the set of rules that defines how a Python program will be written and interpreted (by both the runtime system and by human readers). The Python language has many similarities to Perl, C, and Java. However, there are some definite differences between the languages. It supports multiple programming paradigms, including structured, object-oriented programming, and functional programming, and boasts a dynamic type system and automatic memory management.
Periodic boundary conditionsPeriodic boundary conditions (PBCs) are a set of boundary conditions which are often chosen for approximating a large (infinite) system by using a small part called a unit cell. PBCs are often used in computer simulations and mathematical models. The topology of two-dimensional PBC is equal to that of a world map of some video games; the geometry of the unit cell satisfies perfect two-dimensional tiling, and when an object passes through one side of the unit cell, it re-appears on the opposite side with the same velocity.
History of PythonPython (programming language) The programming language Python was conceived in the late 1980s, and its implementation was started in December 1989 by Guido van Rossum at CWI in the Netherlands as a successor to ABC capable of exception handling and interfacing with the Amoeba operating system. Van Rossum is Python's principal author, and his continuing central role in deciding the direction of Python is reflected in the title given to him by the Python community, Benevolent Dictator for Life (BDFL).
Interatomic potentialInteratomic potentials are mathematical functions to calculate the potential energy of a system of atoms with given positions in space. Interatomic potentials are widely used as the physical basis of molecular mechanics and molecular dynamics simulations in computational chemistry, computational physics and computational materials science to explain and predict materials properties.
