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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] |
Molecule
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and ''molecule'' is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term ''molecule'' is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not consid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Simulation
A simulation is the imitation of the operation of a real-world process or system over time. Simulations require the use of Conceptual model, models; the model represents the key characteristics or behaviors of the selected system or process, whereas the simulation represents the evolution of the model over time. Often, computers are used to execute the computer simulation, simulation. Simulation is used in many contexts, such as simulation of technology for performance tuning or optimizing, safety engineering, testing, training, education, and video games. Simulation is also used with scientific modelling of natural systems or human systems to gain insight into their functioning, as in economics. Simulation can be used to show the eventual real effects of alternative conditions and courses of action. Simulation is also used when the real system cannot be engaged, because it may not be accessible, or it may be dangerous or unacceptable to engage, or it is being designed bu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 al ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Overdamped
Damping is an influence within or upon an oscillatory system that has the effect of reducing or preventing its oscillation. In physical systems, damping is produced by processes that dissipate the energy stored in the oscillation. Examples include viscous drag (a liquid's viscosity can hinder an oscillatory system, causing it to slow down; see viscous damping) in mechanical systems, resistance in electronic oscillators, and absorption and scattering of light in optical oscillators. Damping not based on energy loss can be important in other oscillating systems such as those that occur in biological systems and bikes (ex. Suspension (mechanics)). Not to be confused with friction, which is a dissipative force acting on a system. Friction can cause or be a factor of damping. The damping ratio is a dimensionless measure describing how oscillations in a system decay after a disturbance. Many systems exhibit oscillatory behavior when they are disturbed from their position of stat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Inertia
Inertia is the idea that an object will continue its current motion until some force causes its speed or direction to change. The term is properly understood as shorthand for "the principle of inertia" as described by Newton in his first law of motion. After some other definitions, Newton states in his first law of motion: The word "perseveres" is a direct translation from Newton's Latin. Other, less forceful terms such as "to continue" or "to remain" are commonly found in modern textbooks. The modern use follows from some changes in Newton's original mechanics (as stated in the ''Principia'') made by Euler, d'Alembert, and other Cartesians. The term inertia comes from the Latin word ''iners'', meaning idle, sluggish. The term inertia may also refer to the resistance of any physical object to a change in its velocity. This includes changes to the object's speed or direction of motion. An aspect of this property is the tendency of objects to keep moving in a straight li ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Friction Coefficient
Friction is the force resisting the relative motion of solid surfaces, fluid layers, and material elements sliding against each other. There are several types of friction: *Dry friction is a force that opposes the relative lateral motion of two solid surfaces in contact. Dry friction is subdivided into ''static friction'' ("stiction") between non-moving surfaces, and ''kinetic friction'' between moving surfaces. With the exception of atomic or molecular friction, dry friction generally arises from the interaction of surface features, known as asperities (see Figure 1). *Fluid friction describes the friction between layers of a viscous fluid that are moving relative to each other. *Lubricated friction is a case of fluid friction where a lubricant fluid separates two solid surfaces. *Skin friction is a component of drag, the force resisting the motion of a fluid across the surface of a body. *Internal friction is the force resisting motion between the elements making up a sol ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Boltzmann's Constant
The Boltzmann constant ( or ) is the proportionality factor that relates the average relative kinetic energy of particles in a gas with the thermodynamic temperature of the gas. It occurs in the definitions of the kelvin and the gas constant, and in Planck's law of black-body radiation and Boltzmann's entropy formula, and is used in calculating thermal noise in resistors. The Boltzmann constant has dimensions of energy divided by temperature, the same as entropy. It is named after the Austrian scientist Ludwig Boltzmann. As part of the 2019 redefinition of SI base units, the Boltzmann constant is one of the seven " defining constants" that have been given exact definitions. They are used in various combinations to define the seven SI base units. The Boltzmann constant is defined to be exactly . Roles of the Boltzmann constant Macroscopically, the ideal gas law states that, for an ideal gas, the product of pressure and volume is proportional to the product of amount of ... [...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 distribution ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Einstein Relation (kinetic Theory)
In physics (specifically, the kinetic theory of gases), the Einstein relation is a previously unexpected connection revealed independently by William Sutherland in 1904, Albert Einstein in 1905, and by Marian Smoluchowski in 1906 in their works on Brownian motion. The more general form of the equation is D = \mu \, k_\text T, where * is the diffusion coefficient; * is the "mobility", or the ratio of the particle's terminal drift velocity to an applied force, ; * is the Boltzmann constant; * is the absolute temperature. This equation is an early example of a fluctuation-dissipation relation. Two frequently used important special forms of the relation are: * Einstein–Smoluchowski equation, for diffusion of charged particles: D = \frac * Stokes–Einstein equation, for diffusion of spherical particles through a liquid with low Reynolds number: D = \frac Here * is the electrical charge of a particle; * is the electrical mobility of the charged particle; * is the dyna ... [...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 throu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Immersed Boundary Method
In computational fluid dynamics, the immersed boundary method originally referred to an approach developed by Charles Peskin in 1972 to simulate fluid-structure (fiber) interactions. Treating the coupling of the structure deformations and the fluid flow poses a number of challenging problems for numerical simulations (the elastic boundary changes the flow of the fluid and the fluid moves the elastic boundary simultaneously). In the immersed boundary method the fluid is represented in an Eulerian coordinate system and the structure is represented in Lagrangian coordinates. For Newtonian fluids governed by the Navier–Stokes equations, the fluid equations are : \rho \left(\frac + \cdot\nabla\right) = -\nabla p + \mu\, \Delta u(x,t) + f(x,t) and if the flow is incompressible, we have the further condition that : \nabla \cdot u = 0. \, The immersed structures are typically represented as a collection of one-dimensional fibers, denoted by \Gamma . Each fiber can be viewed as a ... [...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 advances, ma ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
