|
Molecular Mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemistry), force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms. All-atomistic molecular mechanics methods have the following properties: * Each atom is simulated as one particle * Each particle is assigned a radius (typically the van der Waals radius), polarizability, and a constant net charge (generally derived from quantum calculations and/or experiment) * Bonded interactions are treated as ''springs'' with an equilibrium distance equal to the experimental or calculated bond length Variants on this theme are possible. For example, many simulations have historically used a ''united-atom'' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bond Stretching Energy
Bond or bonds may refer to: Common meanings * Bond (finance), a type of debt security * Bail bond, a commercial third-party guarantor of surety bonds in the United States * Chemical bond, the attraction of atoms, ions or molecules to form chemical compounds People * Bond (surname) * Bonds (surname) * Mr. Bond (musician), Austrian rapper Arts and entertainment * James Bond, a series of works about the eponymous fictional character * James Bond (literary character), a British secret agent in a series of novels and films * Bond (band), an Australian/British string quartet ** ''Bond: Video Clip Collection'', a video collection from the band * Bond (Canadian band), a Canadian rock band in the 1970s * The Bond (2007 book), ''The Bond'' (2007 book), an American autobiography written by The Three Doctors * ''The Bond'', a 1918 film by Charlie Chaplin supporting Liberty bonds * Bond International Casino, a former music venue in New York City Places Antarctica * Bond Glacier, at the he ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lennard-Jones Potential
The Lennard-Jones potential (also termed the LJ potential or 12-6 potential) is an intermolecular pair potential. Out of all the intermolecular potentials, the Lennard-Jones potential is probably the one that has been the most extensively studied. It is considered an archetype model for simple yet realistic intermolecular interactions. The Lennard-Jones potential models soft repulsive and attractive ( van der Waals) interactions. Hence, the Lennard-Jones potential describes electronically neutral atoms or molecules. It is named after John Lennard-Jones. The commonly used expression for the Lennard-Jones potential is V_\text(r) = 4\varepsilon \left \left(\frac\right)^ - \left(\frac\right)^6 \right, where r is the distance between two interacting particles, \varepsilon is the depth of the potential well (usually referred to as 'dispersion energy'), and \sigma is the distance at which the particle-particle potential energy V is zero (often referred to as 'size of the particle'). Th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Monte Carlo Method
Monte Carlo methods, or Monte Carlo experiments, are a broad class of computational algorithms that rely on repeated random sampling to obtain numerical results. The underlying concept is to use randomness to solve problems that might be deterministic in principle. They are often used in physical and mathematical problems and are most useful when it is difficult or impossible to use other approaches. Monte Carlo methods are mainly used in three problem classes: optimization, numerical integration, and generating draws from a probability distribution. In physics-related problems, Monte Carlo methods are useful for simulating systems with many coupled degrees of freedom, such as fluids, disordered materials, strongly coupled solids, and cellular structures (see cellular Potts model, interacting particle systems, McKean–Vlasov processes, kinetic models of gases). Other examples include modeling phenomena with significant uncertainty in inputs such as the calculation of ris ... [...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 '' Equatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Simulated Annealing
Simulated annealing (SA) is a probabilistic technique for approximating the global optimum of a given function. Specifically, it is a metaheuristic to approximate global optimization in a large search space for an optimization problem. It is often used when the search space is discrete (for example the traveling salesman problem, the boolean satisfiability problem, protein structure prediction, and job-shop scheduling). For problems where finding an approximate global optimum is more important than finding a precise local optimum in a fixed amount of time, simulated annealing may be preferable to exact algorithms such as gradient descent or branch and bound. The name of the algorithm comes from annealing in metallurgy, a technique involving heating and controlled cooling of a material to alter its physical properties. Both are attributes of the material that depend on their thermodynamic free energy. Heating and cooling the material affects both the temperature and the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gradient Descent
In mathematics, gradient descent (also often called steepest descent) is a first-order iterative optimization algorithm for finding a local minimum of a differentiable function. The idea is to take repeated steps in the opposite direction of the gradient (or approximate gradient) of the function at the current point, because this is the direction of steepest descent. Conversely, stepping in the direction of the gradient will lead to a local maximum of that function; the procedure is then known as gradient ascent. Gradient descent is generally attributed to Augustin-Louis Cauchy, who first suggested it in 1847. Jacques Hadamard independently proposed a similar method in 1907. Its convergence properties for non-linear optimization problems were first studied by Haskell Curry in 1944, with the method becoming increasingly well-studied and used in the following decades. Description Gradient descent is based on the observation that if the multi-variable function F(\mathbf) is de ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Optimization (mathematics)
Mathematical optimization (alternatively spelled ''optimisation'') or mathematical programming is the selection of a best element, with regard to some criterion, from some set of available alternatives. It is generally divided into two subfields: discrete optimization and continuous optimization. Optimization problems of sorts arise in all quantitative disciplines from computer science and engineering to operations research and economics, and the development of solution methods has been of interest in mathematics for centuries. In the more general approach, an optimization problem consists of maximizing or minimizing a real function by systematically choosing input values from within an allowed set and computing the value of the function. The generalization of optimization theory and techniques to other formulations constitutes a large area of applied mathematics. More generally, optimization includes finding "best available" values of some objective function given a defi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ergodic Hypothesis
In physics and thermodynamics, the ergodic hypothesis says that, over long periods of time, the time spent by a system in some region of the phase space of microstates with the same energy is proportional to the volume of this region, i.e., that all accessible microstates are equiprobable over a long period of time. Liouville's theorem states that, for Hamiltonian systems, the local density of microstates following a particle path through phase space is constant as viewed by an observer moving with the ensemble (i.e., the convective time derivative is zero). Thus, if the microstates are uniformly distributed in phase space initially, they will remain so at all times. But Liouville's theorem does ''not'' imply that the ergodic hypothesis holds for all Hamiltonian systems. The ergodic hypothesis is often assumed in the statistical analysis of computational physics. The analyst would assume that the average of a process parameter over time and the average over the statist ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Force Field (chemistry)
In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both. Force fields are interatomic potentials and utilize the same concept as force fields in classical physics, with the difference that the force field parameters in chemistry describe the energy landscape, from which the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates. ''All-atom'' force fields provide parameters for every type of atom ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative erro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Norman L
Norman or Normans may refer to: Ethnic and cultural identity * The Normans, a people partly descended from Norse Vikings who settled in the territory of Normandy in France in the 10th and 11th centuries ** People or things connected with the Norman conquest of southern Italy in the 11th and 12th centuries ** Norman dynasty, a series of monarchs in England and Normandy ** Norman architecture, romanesque architecture in England and elsewhere ** Norman language, spoken in Normandy ** People or things connected with the French region of Normandy Arts and entertainment * ''Norman'' (film), a 2010 drama film * '' Norman: The Moderate Rise and Tragic Fall of a New York Fixer'', a 2016 film * ''Norman'' (TV series), a 1970 British sitcom starring Norman Wisdom * ''The Normans'' (TV series), a documentary * "Norman" (song), a 1962 song written by John D. Loudermilk and recorded by Sue Thompson * "Norman (He's a Rebel)", a song by Mo-dettes from '' The Story So Far'', 1980 Businesses ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fast Multipole Method
__NOTOC__ The fast multipole method (FMM) is a numerical technique that was developed to speed up the calculation of long-ranged forces in the ''n''-body problem. It does this by expanding the system Green's function using a multipole expansion, which allows one to group sources that lie close together and treat them as if they are a single source. The FMM has also been applied in accelerating the iterative solver in the method of moments (MOM) as applied to computational electromagnetics problems. The FMM was first introduced in this manner by Leslie Greengard and Vladimir Rokhlin Jr. and is based on the multipole expansion of the vector Helmholtz equation. By treating the interactions between far-away basis functions using the FMM, the corresponding matrix elements do not need to be explicitly stored, resulting in a significant reduction in required memory. If the FMM is then applied in a hierarchical manner, it can improve the complexity of matrix-vector products in an iterat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
