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Kinetic Scheme
In physics, chemistry and related fields, a kinetic scheme is a network of states and connections between them representing the scheme of a dynamical process. Usually a kinetic scheme represents a Markovian process, while for non-Markovian processes generalized kinetic schemes are used. Figure 1 shows an illustration of a kinetic scheme. A Markovian kinetic scheme Mathematical description A kinetic scheme is a network (a directed graph) of distinct states (although repetition of states may occur and this depends on the system), where each pair of states ''i'' and ''j'' are associated with directional rates, A_ (and A_). It is described with a master equation: a first-order differential equation for the probability \vec of a system to occupy each one its states at time ''t'' (element ''i'' represents state ''i''). Written in a matrix form, this states: \frac=\mathbf\vec, where \mathbf is the matrix of connections (rates) A_. In a Markovian kinetic scheme the connections are c ...
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Reduced Dimensions Form
In biophysics and related fields, reduced dimension forms (RDFs) are unique on-off mechanisms for random walks that generate two-state trajectories (see Fig. 1 for an example of a RDF and Fig. 2 for an example of a two-state trajectory). It has been shown that RDFs solve two-state trajectories, since only one RDF can be constructed from the data, where this property does not hold for on-off kinetic schemes, where many kinetic schemes can be constructed from a particular two-state trajectory (even from an ideal on-off trajectory). Two-state time trajectories are very common in measurements in chemistry, physics, and the biophysics of individual molecules (e.g. measurements of protein dynamics and DNA and RNA dynamics,
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Statistical Mechanics
In 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. Statistical mechanics arose out of the development of classical thermodynamics, a field for which it was successful in explaining macroscopic physical properties—such as temperature, pressure, and heat capacity—in terms of microscopic parameters that fluctuate about average values and are characterized by probability distributions. This established the fields of statistical thermodynamics and statistical physics. The founding of the field of statistical mechanics is generally credited to three physicists: *Ludwig Boltzmann, who developed the fundamental interpretation of entropy in terms of a collection of microstates *James Clerk Maxwell, who developed models of probability ...
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Theoretical Physics
Theoretical physics is a branch of physics that employs mathematical models and abstractions of physical objects and systems to rationalize, explain and predict natural phenomena. This is in contrast to experimental physics, which uses experimental tools to probe these phenomena. The advancement of science generally depends on the interplay between experimental studies and theory. In some cases, theoretical physics adheres to standards of mathematical rigour while giving little weight to experiments and observations.There is some debate as to whether or not theoretical physics uses mathematics to build intuition and illustrativeness to extract physical insight (especially when normal experience fails), rather than as a tool in formalizing theories. This links to the question of it using mathematics in a less formally rigorous, and more intuitive or heuristic way than, say, mathematical physics. For example, while developing special relativity, Albert Einstein was concer ...
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Physical Chemistry
Physical chemistry is the study of macroscopic and microscopic phenomena in chemical systems in terms of the principles, practices, and concepts of physics such as motion, energy, force, time, thermodynamics, quantum chemistry, statistical mechanics, analytical dynamics and chemical equilibria. Physical chemistry, in contrast to chemical physics, is predominantly (but not always) a supra-molecular science, as the majority of the principles on which it was founded relate to the bulk rather than the molecular or atomic structure alone (for example, chemical equilibrium and colloids). Some of the relationships that physical chemistry strives to resolve include the effects of: # Intermolecular forces that act upon the physical properties of materials ( plasticity, tensile strength, surface tension in liquids). # Reaction kinetics on the rate of a reaction. # The identity of ions and the electrical conductivity of materials. # Surface science and electrochemistry of cel ...
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Biophysics
Biophysics is an interdisciplinary science that applies approaches and methods traditionally used in physics to study biological phenomena. Biophysics covers all scales of biological organization, from molecular to organismic and populations. Biophysical research shares significant overlap with biochemistry, molecular biology, physical chemistry, physiology, nanotechnology, bioengineering, computational biology, biomechanics, developmental biology and systems biology. The term ''biophysics'' was originally introduced by Karl Pearson in 1892. Roland Glaser. Biophysics: An Introduction'. Springer; 23 April 2012. . The term ''biophysics'' is also regularly used in academia to indicate the study of the physical quantities (e.g. electric current, temperature, stress, entropy) in biological systems. Other biological sciences also perform research on the biophysical properties of living organisms including molecular biology, cell biology, chemical biology, and biochemistry. O ...
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Graph Theory
In mathematics, graph theory is the study of '' graphs'', which are mathematical structures used to model pairwise relations between objects. A graph in this context is made up of '' vertices'' (also called ''nodes'' or ''points'') which are connected by ''edges'' (also called ''links'' or ''lines''). A distinction is made between undirected graphs, where edges link two vertices symmetrically, and directed graphs, where edges link two vertices asymmetrically. Graphs are one of the principal objects of study in discrete mathematics. Definitions Definitions in graph theory vary. The following are some of the more basic ways of defining graphs and related mathematical structures. Graph In one restricted but very common sense of the term, a graph is an ordered pair G=(V,E) comprising: * V, a set of vertices (also called nodes or points); * E \subseteq \, a set of edges (also called links or lines), which are unordered pairs of vertices (that is, an edge is associated with t ...
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Detailed Balance
The principle of detailed balance can be used in kinetic systems which are decomposed into elementary processes (collisions, or steps, or elementary reactions). It states that at equilibrium, each elementary process is in equilibrium with its reverse process. History The principle of detailed balance was explicitly introduced for collisions by Ludwig Boltzmann. In 1872, he proved his H-theorem using this principle.Boltzmann, L. (1964), Lectures on gas theory, Berkeley, CA, USA: U. of California Press. The arguments in favor of this property are founded upon microscopic reversibility. Tolman, R. C. (1938). ''The Principles of Statistical Mechanics''. Oxford University Press, London, UK. Five years before Boltzmann, James Clerk Maxwell used the principle of detailed balance for gas kinetics with the reference to the principle of sufficient reason. He compared the idea of detailed balance with other types of balancing (like cyclic balance) and found that "Now it is impossible ...
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Master Equation
In physics, chemistry and related fields, master equations are used to describe the time evolution of a system that can be modelled as being in a probabilistic combination of states at any given time and the switching between states is determined by a transition rate matrix. The equations are a set of differential equations – over time – of the probabilities that the system occupies each of the different states. Introduction A master equation is a phenomenological set of first-order differential equations describing the time evolution of (usually) the probability of a system to occupy each one of a discrete set of states with regard to a continuous time variable ''t''. The most familiar form of a master equation is a matrix form: : \frac=\mathbf\vec, where \vec is a column vector (where element ''i'' represents state ''i''), and \mathbf is the matrix of connections. The way connections among states are made determines the dimension of the problem; it is either *a d ...
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Continuous-time Markov Process
A continuous-time Markov chain (CTMC) is a continuous stochastic process in which, for each state, the process will change state according to an exponential random variable and then move to a different state as specified by the probabilities of a stochastic matrix. An equivalent formulation describes the process as changing state according to the least value of a set of exponential random variables, one for each possible state it can move to, with the parameters determined by the current state. An example of a CTMC with three states \ is as follows: the process makes a transition after the amount of time specified by the holding time—an exponential random variable E_i, where ''i'' is its current state. Each random variable is independent and such that E_0\sim \text(6), E_1\sim \text(12) and E_2\sim \text(18). When a transition is to be made, the process moves according to the jump chain, a discrete-time Markov chain with stochastic matrix: :\begin 0 & \frac & \frac \\ \frac & ...
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Markov Process
A Markov chain or Markov process is a stochastic model describing a sequence of possible events in which the probability of each event depends only on the state attained in the previous event. Informally, this may be thought of as, "What happens next depends only on the state of affairs ''now''." A countably infinite sequence, in which the chain moves state at discrete time steps, gives a discrete-time Markov chain (DTMC). A continuous-time process is called a continuous-time Markov chain (CTMC). It is named after the Russian mathematician Andrey Markov. Markov chains have many applications as statistical models of real-world processes, such as studying cruise control systems in motor vehicles, queues or lines of customers arriving at an airport, currency exchange rates and animal population dynamics. Markov processes are the basis for general stochastic simulation methods known as Markov chain Monte Carlo, which are used for simulating sampling from complex probability ...
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Fokker Planck Equation
Fokker was a Dutch aircraft manufacturer named after its founder, Anthony Fokker. The company operated under several different names. It was founded in 1912 in Berlin, Germany, and became famous for its fighter aircraft in World War I. In 1919 the company moved its operations to the Netherlands. During its most successful period in the 1920s and 1930s, it dominated the civil aviation market. Fokker went into bankruptcy in 1996, and its operations were sold to competitors. History Fokker in Germany At age 20, while studying in Germany, Anthony Fokker built his initial aircraft, the ''Spin'' (Spider)—the first Dutch-built plane to fly in his home country. Taking advantage of better opportunities in Germany, he moved to Berlin, where in 1912, he founded his first company, Fokker Aeroplanbau, later moving to the Görries suburb just southwest of Schwerin (at ), where the current company was founded, as Fokker Aviatik GmbH, on 12 February 1912. World War I Fokker capitalized on ...
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