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Langevin Dynamics
In physics, Langevin dynamics is an approach to the mathematical modeling of the dynamics of molecular systems. It was originally developed by French physicist Paul Langevin. The approach is characterized by the use of simplified models while accounting for omitted degrees of freedom by the use of stochastic differential equations. Langevin dynamics simulations are a kind of Monte Carlo simulation. Overview A real world molecular system is unlikely to be present in vacuum. Jostling of solvent or air molecules causes friction, and the occasional high velocity collision will perturb the system. Langevin dynamics attempts to extend molecular dynamics to allow for these effects. Also, Langevin dynamics allows temperature to be controlled like with a thermostat, thus approximating the canonical ensemble. Langevin dynamics mimics the viscous aspect of a solvent. It does not fully model an implicit solvent; specifically, the model does not account for the electrostatic screening and a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Physics
Physics is the natural science that studies matter, its fundamental constituents, its motion and behavior through space and time, and the related entities of energy and force. "Physical science is that department of knowledge which relates to the order of nature, or, in other words, to the regular succession of events." Physics is one of the most fundamental scientific disciplines, with its main goal being to understand how the universe behaves. "Physics is one of the most fundamental of the sciences. Scientists of all disciplines use the ideas of physics, including chemists who study the structure of molecules, paleontologists who try to reconstruct how dinosaurs walked, and climatologists who study how human activities affect the atmosphere and oceans. Physics is also the foundation of all engineering and technology. No engineer could design a flat-screen TV, an interplanetary spacecraft, or even a better mousetrap without first understanding the basic laws of physic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gaussian Process
In probability theory and statistics, a Gaussian process is a stochastic process (a collection of random variables indexed by time or space), such that every finite collection of those random variables has a multivariate normal distribution, i.e. every finite linear combination of them is normally distributed. The distribution of a Gaussian process is the joint distribution of all those (infinitely many) random variables, and as such, it is a distribution over functions with a continuous domain, e.g. time or space. The concept of Gaussian processes is named after Carl Friedrich Gauss because it is based on the notion of the Gaussian distribution (normal distribution). Gaussian processes can be seen as an infinite-dimensional generalization of multivariate normal distributions. Gaussian processes are useful in statistical modelling, benefiting from properties inherited from the normal distribution. For example, if a random process is modelled as a Gaussian process, the distribu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Classical Mechanics
Classical 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 earliest development of classical mechanics is often referred to as Newtonian mechanics. It consists of the physical concepts based on foundational works of Sir Isaac Newton, and the mathematical methods invented by Gottfried Wilhelm Leibniz, Joseph-Louis Lagrange, Leonhard Euler, and other contemporaries, in the 17th century to describe the motion of bodies under the influence of a system of forces. Later, more abstract methods were developed, leading to the reformulations of classical mechanics known as Lagrangian mechanics and Hamiltonian mechanics. These advance ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Klein–Kramers Equation
In physics and mathematics, the Klein–Kramers equation or sometimes referred as Kramers–Chandrasekhar equation is a partial differential equation that describes the probability density function of a Brownian particle in phase space . In one spatial dimension, is a function of three independent variables: the scalars , , and . In this case, the Klein–Kramers equation is : \frac + \frac \frac = \xi \frac \left( p \, f \right) + \frac \left( \frac \, f \right) + m\xi k_ T \, \frac where is the external potential, is the particle mass, is the friction (drag) coefficient, is the temperature, and is the Boltzmann constant. In spatial dimensions, the equation is : \frac + \frac \mathbf \cdot \nabla_ f = \xi \nabla_ \cdot \left( \mathbf \, f \right) + \nabla_ \cdot \left( \nabla V(\mathbf) \, f \right) + m \xi k_ T \, \nabla_^2 f Here \nabla_ and \nabla_ are the gradient operator with respect to and , and \nabla_^2 is the Laplacian with respect to . The fractional Klei ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stochastic Differential Equations
A 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 are used to model various phenomena such as stock prices or physical systems subject to thermal fluctuations. Typically, SDEs contain a variable which represents random white noise calculated as the derivative of Brownian motion or the Wiener process. However, other types of random behaviour are possible, such as jump processes. Random differential equations are conjugate to stochastic differential equations. Background Stochastic differential equations originated in the theory of Brownian motion, in the work of Albert Einstein and Smoluchowski. These early examples were linear stochastic differential equations, also called 'Langevin' equations after French physicist Langevin, describing the motion of a harmonic oscillator subject to a random force. The mathematical theory of stochas ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Implicit Solvation
Implicit 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. The implicit solvation model is justified in liquids, where the potential of mean force can be applied to approximate the averaged behavior of many highly dynamic solvent molecules. However, the interfaces and the interiors of biological membranes or proteins can also be considered as media with specific solvation or dielectric properties. These media are not necessarily uniform, since their proper ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 di ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hamiltonian Mechanics
Hamiltonian mechanics emerged in 1833 as a reformulation of Lagrangian mechanics. Introduced by Sir William Rowan Hamilton, Hamiltonian mechanics replaces (generalized) velocities \dot q^i used in Lagrangian mechanics with (generalized) ''momenta''. Both theories provide interpretations of classical mechanics and describe the same physical phenomena. Hamiltonian mechanics has a close relationship with geometry (notably, symplectic geometry and Poisson structures) and serves as a link between classical and quantum mechanics. Overview Phase space coordinates (p,q) and Hamiltonian H Let (M, \mathcal L) be a mechanical system with the configuration space M and the smooth Lagrangian \mathcal L. Select a standard coordinate system (\boldsymbol,\boldsymbol) on M. The quantities \textstyle p_i(\boldsymbol,\boldsymbol,t) ~\stackrel~ / are called ''momenta''. (Also ''generalized momenta'', ''conjugate momenta'', and ''canonical momenta''). For a time instant t, the Legendre transformat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Probability Distribution
In probability theory and statistics, a probability distribution is the mathematical function that gives the probabilities of occurrence of different possible outcomes for an experiment. It is a mathematical description of a random phenomenon in terms of its sample space and the probabilities of events (subsets of the sample space). For instance, if is used to denote the outcome of a coin toss ("the experiment"), then the probability distribution of would take the value 0.5 (1 in 2 or 1/2) for , and 0.5 for (assuming that the coin is fair). Examples of random phenomena include the weather conditions at some future date, the height of a randomly selected person, the fraction of male students in a school, the results of a survey to be conducted, etc. Introduction A probability distribution is a mathematical description of the probabilities of events, subsets of the sample space. The sample space, often denoted by \Omega, is the set of all possible outcomes of a rando ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fokker–Planck Equation
In statistical mechanics, the Fokker–Planck equation is a partial differential equation that describes the time evolution of the probability density function of the velocity of a particle under the influence of drag forces and random forces, as in Brownian motion. The equation can be generalized to other observables as well. It is named after Adriaan Fokker and Max Planck, who described it in 1914 and 1917. It is also known as the Kolmogorov forward equation, after Andrey Kolmogorov, who independently discovered it in 1931. When applied to particle position distributions, it is better known as the Smoluchowski equation (after Marian Smoluchowski), and in this context it is equivalent to the convection–diffusion equation. The case with zero diffusion is the continuity equation. The Fokker–Planck equation is obtained from the master equation through Kramers–Moyal expansion. The first consistent microscopic derivation of the Fokker–Planck equation in the sing ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Brownian Dynamics
Brownian dynamics (BD) can be used to describe the motion of molecules for example in molecular simulations or in reality. It is a simplified version of Langevin dynamics and corresponds to the limit where no average acceleration takes place. This approximation can also be described as 'overdamped' Langevin dynamics, or as Langevin dynamics without inertia. In Langevin dynamics, the equation of motion is :M\ddot = - \nabla U(X) - \gamma \dot + \sqrt R(t) where *\gamma is a friction coefficient, *U(X) is the particle interaction potential, *\nabla is the gradient operator such that - \nabla U(X) is the force calculated from the particle interaction potentials *the dot is a time derivative such that \dot is the velocity, and \ddot is the acceleration *T is the temperature *k_B is Boltzmann's constant *R(t) is a delta-correlated stationary Gaussian process with zero-mean, satisfying :\left\langle R(t) \right\rangle =0 :\left\langle R(t)R(t') \right\rangle = \delta(t-t'). In Br ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Brownian Motion
Brownian motion, or pedesis (from grc, πήδησις "leaping"), is the random motion of particles suspended in a medium (a liquid or a gas). This pattern of motion typically consists of random fluctuations in a particle's position inside a fluid sub-domain, followed by a relocation to another sub-domain. Each relocation is followed by more fluctuations within the new closed volume. This pattern describes a fluid at thermal equilibrium, defined by a given temperature. Within such a fluid, there exists no preferential direction of flow (as in transport phenomena). More specifically, the fluid's overall linear and angular momenta remain null over time. The kinetic energies of the molecular Brownian motions, together with those of molecular rotations and vibrations, sum up to the caloric component of a fluid's internal energy (the equipartition theorem). This motion is named after the botanist Robert Brown, who first described the phenomenon in 1827, while looking t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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