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Energy Drift
In computer simulations of mechanical systems, energy drift is the gradual change in the total energy of a closed system over time. According to the laws of mechanics, the energy should be a constant of motion and should not change. However, in simulations the energy might fluctuate on a short time scale and increase or decrease on a very long time scale due to numerical integration artifacts that arise with the use of a finite time step . This is somewhat similar to the flying ice cube problem, whereby numerical errors in handling equipartition of energy can change vibrational energy into translational energy. More specifically, the energy tends to increase exponentially; its increase can be understood intuitively because each step introduces a small perturbation to the true velocity , which (if uncorrelated with , which will be true for simple integration methods) results in a second-order increase in the energy E = \sum m \mathbf^2 = \sum m \mathbf_\text^2 + \sum m \, \delta ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computer Simulation
Computer simulation is the running of a mathematical model on a computer, the model being designed to represent the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be determined by comparing their results to the real-world outcomes they aim to predict. Computer simulations have become a useful tool for the mathematical modeling of many natural systems in physics (computational physics), astrophysics, climatology, chemistry, biology and manufacturing, as well as human systems in economics, psychology, social science, health care and engineering. Simulation of a system is represented as the running of the system's model. It can be used to explore and gain new insights into new technology and to estimate the performance of systems too complex for analytical solutions. Computer simulations are realized by running computer programs that can be either small, running almost instantly on small devices, or large-scale ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Constraint Algorithm
In computational chemistry, a constraint algorithm is a method for satisfying the Newtonian motion of a rigid body which consists of mass points. A restraint algorithm is used to ensure that the distance between mass points is maintained. The general steps involved are: (i) choose novel unconstrained coordinates (internal coordinates), (ii) introduce explicit constraint forces, (iii) minimize constraint forces implicitly by the technique of Lagrange multipliers or projection methods. Constraint algorithms are often applied to molecular dynamics simulations. Although such simulations are sometimes performed using internal coordinates that automatically satisfy the bond-length, bond-angle and torsion-angle constraints, simulations may also be performed using explicit or implicit constraint forces for these three constraints. However, explicit constraint forces give rise to inefficiency; more computational power is required to get a trajectory of a given length. Therefore, internal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), 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 dynamics (mechanics), dynamic "evolution" of the system. In the most common version, the trajectory, trajectories of atoms and molecules are determined by Numerical integration, numerically solving Newton's laws of motion, Newton's equations of motion for a system of interacting particles, where Force (physics), forces between the particles and their potential energy, potential energies are often calculated using interatomic potentials or molecular mechanics, molecular mechanical Force field (chemistry), 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 analyt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, Nuclear magnetic resonance spectroscopy of proteins, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert Biocuration, biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organizations (PDBe, PDBj, RCSB PDB, and BMRB). The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Canonical Ensemble
In statistical mechanics, a canonical ensemble is the statistical ensemble that represents the possible states of a mechanical system in thermal equilibrium with a heat bath at a fixed temperature. The system can exchange energy with the heat bath, so that the states of the system will differ in total energy. The principal thermodynamic variable of the canonical ensemble, determining the probability distribution of states, is the absolute temperature (symbol: ). The ensemble typically also depends on mechanical variables such as the number of particles in the system (symbol: ) and the system's volume (symbol: ), each of which influence the nature of the system's internal states. An ensemble with these three parameters, which are assumed constant for the ensemble to be considered canonical, is sometimes called the ensemble. The canonical ensemble assigns a probability to each distinct microstate given by the following exponential: :P = e^, where is the total energy of t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microcanonical Ensemble
In statistical mechanics, the microcanonical ensemble is a statistical ensemble that represents the possible states of a mechanical system whose total energy is exactly specified. The system is assumed to be isolated in the sense that it cannot exchange energy or particles with its environment, so that (by conservation of energy) the energy of the system does not change with time. The primary macroscopic variables of the microcanonical ensemble are the total number of particles in the system (symbol: ), the system's volume (symbol: ), as well as the total energy in the system (symbol: ). Each of these is assumed to be constant in the ensemble. For this reason, the microcanonical ensemble is sometimes called the ensemble. In simple terms, the microcanonical ensemble is defined by assigning an equal probability to every microstate whose energy falls within a range centered at . All other microstates are given a probability of zero. Since the probabilities must add up to 1, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thermodynamic Ensemble
In physics, specifically statistical mechanics, an ensemble (also statistical ensemble) is an idealization consisting of a large number of virtual copies (sometimes infinitely many) of a system, considered all at once, each of which represents a possible state that the real system might be in. In other words, a statistical ensemble is a set of systems of particles used in statistical mechanics to describe a single system. The concept of an ensemble was introduced by J. Willard Gibbs in 1902. A thermodynamic ensemble is a specific variety of statistical ensemble that, among other properties, is in statistical equilibrium (defined below), and is used to derive the properties of thermodynamic systems from the laws of classical or quantum mechanics. Physical considerations The ensemble formalises the notion that an experimenter repeating an experiment again and again under the same macroscopic conditions, but unable to control the microscopic details, may expect to observe a ran ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Particle Mesh Ewald
Ewald summation, named after Paul Peter Ewald, is a method for computing long-range interactions (e.g. electrostatic interactions) in periodic systems. It was first developed as the method for calculating the electrostatic energies of ionic crystals, and is now commonly used for calculating long-range interactions in computational chemistry. Ewald summation is a special case of the Poisson summation formula, replacing the summation of interaction energies in real space with an equivalent summation in Fourier space. In this method, the long-range interaction is divided into two parts: a short-range contribution, and a long-range contribution which does not have a singularity. The short-range contribution is calculated in real space, whereas the long-range contribution is calculated using a Fourier transform. The advantage of this method is the rapid convergence of the energy compared with that of a direct summation. This means that the method has high accuracy and reasonable spee ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electrostatic
Electrostatics is a branch of physics that studies slow-moving or stationary electric charges. Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word (), meaning 'amber', was thus the root of the word ''electricity''. Electrostatic phenomena arise from the forces that electric charges exert on each other. Such forces are described by Coulomb's law. There are many examples of electrostatic phenomena, from those as simple as the attraction of plastic wrap to one's hand after it is removed from a package, to the apparently spontaneous explosion of grain silos, the damage of electronic components during manufacturing, and photocopier and laser printer operation. The electrostatic model accurately predicts electrical phenomena in "classical" cases where the velocities are low and the system is macroscopic so no quantum effects are involved. It also plays a role in quantum mechanics, where addition ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Function (mathematics)
In mathematics, a function from a set (mathematics), set to a set assigns to each element of exactly one element of .; the words ''map'', ''mapping'', ''transformation'', ''correspondence'', and ''operator'' are sometimes used synonymously. The set is called the Domain of a function, domain of the function and the set is called the codomain of the function. Functions were originally the idealization of how a varying quantity depends on another quantity. For example, the position of a planet is a ''function'' of time. History of the function concept, Historically, the concept was elaborated with the infinitesimal calculus at the end of the 17th century, and, until the 19th century, the functions that were considered were differentiable function, differentiable (that is, they had a high degree of regularity). The concept of a function was formalized at the end of the 19th century in terms of set theory, and this greatly increased the possible applications of the concept. A f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Femtosecond
A femtosecond is a unit of time in the International System of Units (SI) equal to 10 or of a second; that is, one quadrillionth, or one millionth of one billionth, of a second. A femtosecond is to a second, as a second is to approximately 31.69 million years. For context, a ray of light travels approximately 0.3 μm (micrometers) in 1 femtosecond, a distance comparable to the diameter of a virus.Compared with overview in: The first to make femtosecond measurements was the Egyptian Nobel Laureate Ahmed Zewail, for which he was awarded the Nobel Prize in Chemistry in 1999. Professor Zewail used lasers to measure the movement of particles at the femtosecond scale, thereby allowing chemical reactions to be observed for the first time. The word ''femtosecond'' is formed by the SI prefix ''femto'' and the SI unit ''second''. Its symbol is fs. A femtosecond is equal to 1000 attoseconds, or 1/1000 picosecond. Because the next higher SI unit is 1000 times larger, times of 10� ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrogen
Hydrogen is a chemical element; it has chemical symbol, symbol H and atomic number 1. It is the lightest and abundance of the chemical elements, most abundant chemical element in the universe, constituting about 75% of all baryon, normal matter. Under standard conditions, hydrogen is a gas of diatomic molecules with the chemical formula, formula , called dihydrogen, or sometimes hydrogen gas, molecular hydrogen, or simply hydrogen. Dihydrogen is colorless, odorless, non-toxic, and highly combustible. Stars, including the Sun, mainly consist of hydrogen in a plasma state, while on Earth, hydrogen is found as the gas (dihydrogen) and in molecular forms, such as in water and organic compounds. The most common isotope of hydrogen (H) consists of one proton, one electron, and no neutrons. Hydrogen gas was first produced artificially in the 17th century by the reaction of acids with metals. Henry Cavendish, in 1766–1781, identified hydrogen gas as a distinct substance and discovere ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
