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.
Coarse-grained modelingCoarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained (simplified) representation. Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water.
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.
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).
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).
Fluctuation theoremThe fluctuation theorem (FT), which originated from statistical mechanics, deals with the relative probability that the entropy of a system which is currently away from thermodynamic equilibrium (i.e., maximum entropy) will increase or decrease over a given amount of time. While the second law of thermodynamics predicts that the entropy of an isolated system should tend to increase until it reaches equilibrium, it became apparent after the discovery of statistical mechanics that the second law is only a statistical one, suggesting that there should always be some nonzero probability that the entropy of an isolated system might spontaneously decrease; the fluctuation theorem precisely quantifies this probability.
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.
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.
Stochastic differential equationA stochastic differential equation (SDE) is a differential equation in which one or more of the terms is a stochastic process, resulting in a solution which is also a stochastic process. SDEs have many applications throughout pure mathematics and are used to model various behaviours of stochastic models such as stock prices, random growth models or physical systems that are subjected to thermal fluctuations. SDEs have a random differential that is in the most basic case random white noise calculated as the derivative of a Brownian motion or more generally a semimartingale.
Implicit solvationImplicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes.
Supersymmetric theory of stochastic dynamicsSupersymmetric theory of stochastic dynamics or stochastics (STS) is an exact theory of stochastic (partial) differential equations (SDEs), the class of mathematical models with the widest applicability covering, in particular, all continuous time dynamical systems, with and without noise. The main utility of the theory from the physical point of view is a rigorous theoretical explanation of the ubiquitous spontaneous long-range dynamical behavior that manifests itself across disciplines via such phenomena as 1/f, flicker, and crackling noises and the power-law statistics, or Zipf's law, of instantonic processes like earthquakes and neuroavalanches.
Scheme (mathematics)In mathematics, a scheme is a mathematical structure that enlarges the notion of algebraic variety in several ways, such as taking account of multiplicities (the equations x = 0 and x2 = 0 define the same algebraic variety but different schemes) and allowing "varieties" defined over any commutative ring (for example, Fermat curves are defined over the integers). Scheme theory was introduced by Alexander Grothendieck in 1960 in his treatise "Éléments de géométrie algébrique"; one of its aims was developing the formalism needed to solve deep problems of algebraic geometry, such as the Weil conjectures (the last of which was proved by Pierre Deligne).
Hilbert schemeIn algebraic geometry, a branch of mathematics, a Hilbert scheme is a scheme that is the parameter space for the closed subschemes of some projective space (or a more general projective scheme), refining the Chow variety. The Hilbert scheme is a disjoint union of projective subschemes corresponding to Hilbert polynomials. The basic theory of Hilbert schemes was developed by . Hironaka's example shows that non-projective varieties need not have Hilbert schemes.
Group schemeIn mathematics, a group scheme is a type of object from algebraic geometry equipped with a composition law. Group schemes arise naturally as symmetries of schemes, and they generalize algebraic groups, in the sense that all algebraic groups have group scheme structure, but group schemes are not necessarily connected, smooth, or defined over a field. This extra generality allows one to study richer infinitesimal structures, and this can help one to understand and answer questions of arithmetic significance.
Cross-coupling reactionIn organic chemistry, a cross-coupling reaction is a reaction where two different fragments are joined. Cross-couplings are a subset of the more general coupling reactions. Often cross-coupling reactions require metal catalysts. One important reaction type is this: (R, R' = organic fragments, usually aryle; M = main group center such as Li or MgX; X = halide) These reactions are used to form carbon–carbon bonds but also carbon-heteroatom bonds. Cross-coupling reaction are a subset of coupling reactions.
Formal schemeIn mathematics, specifically in algebraic geometry, a formal scheme is a type of space which includes data about its surroundings. Unlike an ordinary scheme, a formal scheme includes infinitesimal data that, in effect, points in a direction off of the scheme. For this reason, formal schemes frequently appear in topics such as deformation theory. But the concept is also used to prove a theorem such as the theorem on formal functions, which is used to deduce theorems of interest for usual schemes.
Coupling reactionIn organic chemistry, a coupling reaction is a type of reaction in which two reactant molecules are bonded together. Such reactions often require the aid of a metal catalyst. In one important reaction type, a main group organometallic compound of the type R-M (where R = organic group, M = main group centre metal atom) reacts with an organic halide of the type R'-X with formation of a new carbon-carbon bond in the product R-R'. The most common type of coupling reaction is the cross coupling reaction. Richard F.
Hiyama couplingThe Hiyama coupling is a palladium-catalyzed cross-coupling reaction of organosilanes with organic halides used in organic chemistry to form carbon–carbon bonds (C-C bonds). This reaction was discovered in 1988 by Tamejiro Hiyama and Yasuo Hatanaka as a method to form carbon-carbon bonds synthetically with chemo- and regioselectivity. The Hiyama coupling has been applied to the synthesis of various natural products.
Kumada couplingIn organic chemistry, the Kumada coupling is a type of cross coupling reaction, useful for generating carbon–carbon bonds by the reaction of a Grignard reagent and an organic halide. The procedure uses transition metal catalysts, typically nickel or palladium, to couple a combination of two alkyl, aryl or vinyl groups. The groups of Robert Corriu and Makoto Kumada reported the reaction independently in 1972. The reaction is notable for being among the first reported catalytic cross-coupling methods.
Fiber product of schemesIn mathematics, specifically in algebraic geometry, the fiber product of schemes is a fundamental construction. It has many interpretations and special cases. For example, the fiber product describes how an algebraic variety over one field determines a variety over a bigger field, or the pullback of a family of varieties, or a fiber of a family of varieties. Base change is a closely related notion. The of schemes is a broad setting for algebraic geometry.
