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Gillespie Algorithm
In probability theory, the Gillespie algorithm (or the Doob-Gillespie algorithm or ''Stochastic Simulation Algorithm'', the SSA) generates a statistically correct trajectory (possible solution) of a stochastic equation system for which the reaction rates are known. It was created by Joseph L. Doob and others (circa 1945), presented by Dan Gillespie in 1976, and popularized in 1977 in a paper where he uses it to simulate chemical or biochemical systems of reactions efficiently and accurately using limited computational power (see stochastic simulation). As computers have become faster, the algorithm has been used to simulate increasingly complex systems. The algorithm is particularly useful for simulating reactions within cells, where the number of reagents is low and keeping track of the position and behaviour of individual molecules is computationally feasible. Mathematically, it is a variant of a dynamic Monte Carlo method and similar to the kinetic Monte Carlo methods. It is used h ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Probability Theory
Probability theory is the branch of mathematics concerned with probability. Although there are several different probability interpretations, probability theory treats the concept in a rigorous mathematical manner by expressing it through a set of axioms. Typically these axioms formalise probability in terms of a probability space, which assigns a measure taking values between 0 and 1, termed the probability measure, to a set of outcomes called the sample space. Any specified subset of the sample space is called an event. Central subjects in probability theory include discrete and continuous random variables, probability distributions, and stochastic processes (which provide mathematical abstractions of non-deterministic or uncertain processes or measured quantities that may either be single occurrences or evolve over time in a random fashion). Although it is not possible to perfectly predict random events, much can be said about their behavior. Two major results in probability ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
William Feller
William "Vilim" Feller (July 7, 1906 – January 14, 1970), born Vilibald Srećko Feller, was a Croatian-American mathematician specializing in probability theory. Early life and education Feller was born in Zagreb to Ida Oemichen-Perc, a Croatian-Austrian Catholic, and Eugen Viktor Feller, son of a Polish-Jewish father (David Feller) and an Austrian mother (Elsa Holzer). Eugen Feller was a famous chemist and created ''Elsa fluid'' named after his mother. According to Gian-Carlo Rota, Eugen Feller's surname was a "Slavic tongue twister", which William changed at the age of twenty. This claim appears to be false. His forename, Vilibald, was chosen by his Catholic mother for the saint day of his birthday. Work Feller held a docent position at the University of Kiel beginning in 1928. Because he refused to sign a Nazi oath, he fled the Nazis and went to Copenhagen, Denmark in 1933. He also lectured in Sweden (Stockholm and Lund). As a refugee in Sweden, Feller reported being tro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry
Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials. Examples of such properties are structure (i.e., the expected positions of the constituent atoms), absolute and relative (interaction) energies, electronic charge density distributions, dipoles and higher multipole moments, vi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Kinetics
Chemical kinetics, also known as reaction kinetics, is the branch of physical chemistry that is concerned with understanding the rates of chemical reactions. It is to be contrasted with chemical thermodynamics, which deals with the direction in which a reaction occurs but in itself tells nothing about its rate. Chemical kinetics includes investigations of how experimental conditions influence the speed of a chemical reaction and yield information about the reaction's mechanism and transition states, as well as the construction of mathematical models that also can describe the characteristics of a chemical reaction. History In 1864, Peter Waage and Cato Guldberg pioneered the development of chemical kinetics by formulating the law of mass action, which states that the speed of a chemical reaction is proportional to the quantity of the reacting substances.C.M. Guldberg and P. Waage,"Studies Concerning Affinity" ''Forhandlinger i Videnskabs-Selskabet i Christiania'' (1864), 35P. W ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MATLAB
MATLAB (an abbreviation of "MATrix LABoratory") is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages. Although MATLAB is intended primarily for numeric computing, an optional toolbox uses the MuPAD symbolic engine allowing access to symbolic computing abilities. An additional package, Simulink, adds graphical multi-domain simulation and model-based design for dynamic and embedded systems. As of 2020, MATLAB has more than 4 million users worldwide. They come from various backgrounds of engineering, science, and economics. History Origins MATLAB was invented by mathematician and computer programmer Cleve Moler. The idea for MATLAB was based on his 1960s PhD thesis. Moler became a math professor at the University of New Mexico and starte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Example Calculation Illustrating The Gillespie Algorithm For Reversible Dimerising Molecules
Example may refer to: * '' exempli gratia'' (e.g.), usually read out in English as "for example" * .example, reserved as a domain name that may not be installed as a top-level domain of the Internet ** example.com, example.net, example.org, example.edu, second-level domain names reserved for use in documentation as examples * HMS ''Example'' (P165), an Archer-class patrol and training vessel of the Royal Navy Arts * ''The Example'', a 1634 play by James Shirley * ''The Example'' (comics), a 2009 graphic novel by Tom Taylor and Colin Wilson * Example (musician), the British dance musician Elliot John Gleave (born 1982) * ''Example'' (album), a 1995 album by American rock band For Squirrels See also * * Exemplar (other), a prototype or model which others can use to understand a topic better * Exemplum, medieval collections of short stories to be told in sermons * Eixample The Eixample (; ) is a district of Barcelona between the old city (Ciutat Vella) and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tau-leaping
In probability theory, tau-leaping, or τ-leaping, is an approximate method for the simulation of a stochastic system. It is based on the Gillespie algorithm, performing all reactions for an interval of length tau before updating the propensity functions. By updating the rates less often this sometimes allows for more efficient simulation and thus the consideration of larger systems. Many variants of the basic algorithm have been considered. Algorithm The algorithm is analogous to the Euler method In mathematics and computational science, the Euler method (also called forward Euler method) is a first-order numerical procedure for solving ordinary differential equations (ODEs) with a given initial value. It is the most basic explicit met ... for deterministic systems, but instead of making a fixed change x(t+\tau)=x(t)+\tau x'(t) the change is x(t+\tau)=x(t)+P(\tau x'(t)) where P(\tau x'(t)) is a Poisson distributed random variable with mean \tau x'(t). Given a state \ma ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rate Equation
In chemistry, the rate law or rate equation for a reaction is an equation that links the initial or forward reaction rate with the concentrations or pressures of the reactants and constant parameters (normally rate coefficients and partial reaction orders). For many reactions, the initial rate is given by a power law such as :v_0\; =\; k mathrmx mathrmy where and express the concentration of the species and usually in moles per liter (molarity, ). The exponents and are the partial ''orders of reaction'' for and and the ''overall'' reaction order is the sum of the exponents. These are often positive integers, but they may also be zero, fractional, or negative. The constant is the reaction rate constant or ''rate coefficient'' of the reaction. Its value may depend on conditions such as temperature, ionic strength, surface area of an adsorbent, or light irradiation. If the reaction goes to completion, the rate equation for the reaction rate v\; =\; k cex cey applies throug ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Maurice S
Maurice may refer to: People *Saint Maurice (died 287), Roman legionary and Christian martyr *Maurice (emperor) or Flavius Mauricius Tiberius Augustus (539–602), Byzantine emperor *Maurice (bishop of London) (died 1107), Lord Chancellor and Lord Keeper of England *Maurice of Carnoet (1117–1191), Breton abbot and saint * Maurice, Count of Oldenburg (fl. 1169–1211) *Maurice of Inchaffray (14th century), Scottish cleric who became a bishop *Maurice, Elector of Saxony (1521–1553), German Saxon nobleman *Maurice, Duke of Saxe-Lauenburg (1551–1612) *Maurice of Nassau, Prince of Orange (1567–1625), stadtholder of the Netherlands *Maurice, Landgrave of Hesse-Kassel or Maurice the Learned (1572–1632) *Maurice of Savoy (1593–1657), prince of Savoy and a cardinal *Maurice, Duke of Saxe-Zeitz (1619–1681) *Maurice of the Palatinate (1620–1652), Count Palatine of the Rhine *Maurice of the Netherlands (1843–1850), prince of Orange-Nassau *Maurice Chevalier (1888–1972), Fr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Manchester Mark 1
The Manchester Mark 1 was one of the earliest stored-program computers, developed at the Victoria University of Manchester, England from the Manchester Baby (operational in June 1948). Work began in August 1948, and the first version was operational by April 1949; a program written to search for Mersenne primes ran error-free for nine hours on the night of 16/17 June 1949. The machine's successful operation was widely reported in the British press, which used the phrase "electronic brain" in describing it to their readers. That description provoked a reaction from the head of the University of Manchester's Department of Neurosurgery, the start of a long-running debate as to whether an electronic computer could ever be truly creative. The Mark 1 was to provide a computing resource within the university, to allow researchers to gain experience in the practical use of computers, but it very quickly also became a prototype on which the design of Ferranti's commercial version could ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
David George Kendall
David George Kendall FRS (15 January 1918 – 23 October 2007) was an English statistician and mathematician, known for his work on probability, statistical shape analysis, ley lines and queueing theory. He spent most of his academic life in the University of Oxford (1946–1962) and the University of Cambridge (1962–1985). He worked with M. S. Bartlett during World War II, and visited Princeton University after the war. Life and career David George Kendall was born on 15 January 1918 in Ripon, West Riding of Yorkshire, and attended Ripon Grammar School before attending Queen's College, Oxford, graduating in 1939. He worked on rocketry during the World War II, before moving to Magdalen College, Oxford, in 1946. In 1962 he was appointed the first Professor of Mathematical Statistics in the Statistical Laboratory, University of Cambridge; in which post he remained until his retirement in 1985. He was elected to a professorial fellowship at Churchill College, and he wa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stochastic Process
In probability theory and related fields, a stochastic () or random process is a mathematical object usually defined as a family of random variables. Stochastic processes are widely used as mathematical models of systems and phenomena that appear to vary in a random manner. Examples include the growth of a bacterial population, an electrical current fluctuating due to thermal noise, or the movement of a gas molecule. Stochastic processes have applications in many disciplines such as biology, chemistry, ecology, neuroscience, physics, image processing, signal processing, control theory, information theory, computer science, cryptography and telecommunications. Furthermore, seemingly random changes in financial markets have motivated the extensive use of stochastic processes in finance. Applications and the study of phenomena have in turn inspired the proposal of new stochastic processes. Examples of such stochastic processes include the Wiener process or Brownian motion process, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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