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Metadynamics
Metadynamics (MTD; also abbreviated as METAD or MetaD) is a computer simulation method in computational physics, chemistry and biology. It is used to estimate the free energy and other state functions of a system, where ergodicity is hindered by the form of the system's energy landscape. It was first suggested by Alessandro Laio and Michele Parrinello in 2002 and is usually applied within molecular dynamics simulations. MTD closely resembles a number of recent methods such as adaptively biased molecular dynamics, adaptive reaction coordinate forces and local elevation umbrella sampling. More recently, both the original and well-tempered metadynamics were derived in the context of importance sampling and shown to be a special case of the adaptive biasing potential setting. MTD is related to the Wang–Landau sampling. Introduction The technique builds on a large number of related methods including (in a chronological order) the deflation, tunneling, tabu search, local elevation, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Wang And Landau Algorithm
The Wang and Landau algorithm, proposed by Fugao Wang and David P. Landau, is a Monte Carlo method designed to estimate the density of states of a system. The method performs a non-Markovian random walk to build the density of states by quickly visiting all the available energy spectrum. The Wang and Landau algorithm is an important method to obtain the density of states required to perform a multicanonical simulation. The Wang–Landau algorithm can be applied to any system which is characterized by a cost (or energy) function. For instance, it has been applied to the solution of numerical integrals and the folding of proteins. The Wang–Landau sampling is related to the metadynamics algorithm.Christoph Junghans, Danny Perez, and Thomas Vogel. "Molecular Dynamics in the Multicanonical Ensemble: Equivalence of Wang–Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics." Journal of Chemical Theory and Computation 10.5 (2014): 1843-1847. doibr>10.1021/ct5 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Michele Parrinello
Michele Parrinello (born 7 September 1945, Messina) is an Italian physicist particularly known for his work in molecular dynamics (the computer simulation of physical movements of atoms and molecules). Parrinello and Roberto Car were awarded the Dirac Medal and the Sidney Fernbach Award in 2009 for their continuing development of the Car–Parrinello method, first proposed in their seminal 1985 paper, "Unified Approach for Molecular Dynamics and Density-Functional Theory". They have continued to receive awards for this breakthrough, most recently the Dreyfus Prize in the Chemical SciencesLinda Wang (29 May 2017)Dreyfus Prize in the Chemical Sciences to Michele Parrinello ''Chemical & Engineering News''. Accessed August 2021. and the 2020 Benjamin Franklin Medal in Chemistry.The Franklin Institute (27 Jan 2020)Announcing the 2020 Franklin Institute Awards Laureates. ''PR Newswire''. Accessed August 2021. Parrinello also co-authored highly cited publications on "polymorphic trans ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Adaptive Biasing Force
Adaptation, in biology, is the process or trait by which organisms or population better match their environment Adaptation may also refer to: Arts * Adaptation (arts), a transfer of a work of art from one medium to another ** Film adaptation, a story from another work, adapted into a film ** Literary adaptation, a story from a literary source, adapted into another work ** ** Theatrical adaptation, a story from another work, adapted into a play * ''Adaptation'' (film), a 2002 film by Spike Jonze * "Adaptation" (''The Walking Dead''), a television episode *''Adaptation'', a 2012 novel by Malinda Lo Biology and medicine * Adaptation (eye), the eye's adjustment to light ** Chromatic adaptation, visual systems' adjustments to changes in illumination for preservation of colors ** Prism adaptation, sensory-motor adjustments after the visual field has been artificially shifted * Cellular adaptation, changes by cells/tissues in response to changed microenvironments * High-altitude a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Random-access Memory
Random-access memory (RAM; ) is a form of computer memory that can be read and changed in any order, typically used to store working Data (computing), data and machine code. A Random access, random-access memory device allows data items to be read (computer), read or written in almost the same amount of time irrespective of the physical location of data inside the memory, in contrast with other direct-access data storage media (such as hard disks, CD-RWs, DVD-RWs and the older Magnetic tape data storage, magnetic tapes and drum memory), where the time required to read and write data items varies significantly depending on their physical locations on the recording medium, due to mechanical limitations such as media rotation speeds and arm movement. RAM contains multiplexer, multiplexing and demultiplexing circuitry, to connect the data lines to the addressed storage for reading or writing the entry. Usually more than one bit of storage is accessed by the same address, and RAM ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Regular Grid
A regular grid is a tessellation of ''n''-dimensional Euclidean space by congruent parallelotopes (e.g. bricks). Its opposite is irregular grid. Grids of this type appear on graph paper and may be used in finite element analysis, finite volume methods, finite difference methods, and in general for discretization of parameter spaces. Since the derivatives of field variables can be conveniently expressed as finite differences, structured grids mainly appear in finite difference methods. Unstructured grids offer more flexibility than structured grids and hence are very useful in finite element and finite volume methods. Each cell in the grid can be addressed by index (i, j) in two dimensions or (i, j, k) in three dimensions, and each vertex has coordinates (i\cdot dx, j\cdot dy) in 2D or (i\cdot dx, j\cdot dy, k\cdot dz) in 3D for some real numbers ''dx'', ''dy'', and ''dz'' representing the grid spacing. Related grids A Cartesian grid is a special case where the elements are uni ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Kernel Density Estimation
In statistics, kernel density estimation (KDE) is the application of kernel smoothing for probability density estimation, i.e., a non-parametric method to estimate the probability density function of a random variable based on ''kernels'' as weights. KDE answers a fundamental data smoothing problem where inferences about the population are made, based on a finite data sample. In some fields such as signal processing and econometrics it is also termed the Parzen–Rosenblatt window method, after Emanuel Parzen and Murray Rosenblatt, who are usually credited with independently creating it in its current form. One of the famous applications of kernel density estimation is in estimating the class-conditional marginal densities of data when using a naive Bayes classifier, which can improve its prediction accuracy. Definition Let (''x''1, ''x''2, ..., ''xn'') be independent and identically distributed samples drawn from some univariate distribution with an unknown density ''ƒ'' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Infinite Swapping
Infinite may refer to: Mathematics *Infinite set, a set that is not a finite set *Infinity, an abstract concept describing something without any limit Music * Infinite (group), a South Korean boy band *''Infinite'' (EP), debut EP of American musician Haywyre, released in 2012 * ''Infinite'' (Eminem album), the debut album of American rapper Eminem, released in 1996 :* ''Infinite'' (Eminem song), the debut song of American rapper Eminem, released in 1996 * ''Infinite'' (Stratovarius album), a studio album by power metal band Stratovarius, released in 2000 * ''The Infinite'' (album), by trumpeter Dave Douglas, released in 2002 *" Infinite...", a 2004 single by Japanese singer Beni Arashiro *Infinite (Notaker song), a 2016 single by American electronic producer Notaker *Infinite (rapper), a Canadian rapper * ''Infinite'' (Sam Concepcion album), the second studio album by Filipino singer Sam Concepcion * ''Infinite'' (Deep Purple album), the twentieth studio album by Deep Purple *"I ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metropolis–Hastings Algorithm
In statistics and statistical physics, the Metropolis–Hastings algorithm is a Markov chain Monte Carlo (MCMC) method for obtaining a sequence of random samples from a probability distribution from which direct sampling is difficult. This sequence can be used to approximate the distribution (e.g. to generate a histogram) or to compute an integral (e.g. an expected value). Metropolis–Hastings and other MCMC algorithms are generally used for sampling from multi-dimensional distributions, especially when the number of dimensions is high. For single-dimensional distributions, there are usually other methods (e.g. adaptive rejection sampling) that can directly return independent samples from the distribution, and these are free from the problem of autocorrelated samples that is inherent in MCMC methods. History The algorithm was named after Nicholas Metropolis and W.K. Hastings. Metropolis was the first author to appear on the list of authors of the 1953 article ''Equation of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Parallel Tempering
Parallel tempering in physics and statistics, is a computer simulation method typically used to find the lowest free energy state of a system of many interacting particles at low temperature. That is, the one expected to be observed in reality. It addresses the problem that at high temperature one may have a stable state different from low temperature, whereas simulations at low temperature may become "stuck" in a metastable state. It does this by using the fact that the high temperature simulation may visit states typical of both stable and metastable low temperature states. More specifically, parallel tempering (also known as replica exchange MCMC sampling), is a simulation method aimed at improving the dynamic properties of Monte Carlo method simulations of physical systems, and of Markov chain Monte Carlo (MCMC) sampling methods more generally. The replica exchange method was originally devised by Swendsen and Wang then extended by Geyer and later developed, among othe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
