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Coarse-grained Modeling
Coarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained (simplified) representation. Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water. In these models, molecules are represented not by individual atoms, but by "pseudo-atoms" approximating groups of atoms, such as whole amino acid residue. By decreasing the degrees of freedom much longer simulation times can be studied at the expense of molecular detail. Coarse-grained models have found practical applications in molecular dynamics simulations. Another case of interest is the simplification of a given discrete-state system, as very often descriptions of the same system at different levels of detail are possible. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Complex System
A complex system is a system composed of many components which may interact with each other. Examples of complex systems are Earth's global climate, organisms, the human brain, infrastructure such as power grid, transportation or communication systems, complex software and electronic systems, social and economic organizations (like cities), an ecosystem, a living cell, and ultimately the entire universe. Complex systems are systems whose behavior is intrinsically difficult to model due to the dependencies, competitions, relationships, or other types of interactions between their parts or between a given system and its environment. Systems that are "complex" have distinct properties that arise from these relationships, such as nonlinearity, emergence, spontaneous order, adaptation, and feedback loops, among others. Because such systems appear in a wide variety of fields, the commonalities among them have become the topic of their independent area of research. In many cases, i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (a molecular mechanics approach), or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons (a quantum chemistry approach). Molecular mechanics Molecular mechanics is one aspect of molecular modelling, as it involves the use of classical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Granularity
Granularity (also called graininess), the condition of existing in granules or grains, refers to the extent to which a material or system is composed of distinguishable pieces. It can either refer to the extent to which a larger entity is subdivided, or the extent to which groups of smaller indistinguishable entities have joined together to become larger distinguishable entities. Precision and ambiguity Coarse-grained materials or systems have fewer, larger discrete components than fine-grained materials or systems. * A coarse-grained description of a system regards large subcomponents. * A fine-grained description regards smaller components of which the larger ones are composed. The concepts granularity, coarseness, and fineness are relative; and are used when comparing systems or descriptions of systems. An example of increasingly fine granularity: a list of nations in the United Nations, a list of all states/provinces in those nations, a list of all cities in those states, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acid Residue
Protein structure is the molecular geometry, three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a ''residue'' indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per chemical reaction, reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their Pro ... [...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 errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Michael Levitt
Michael Levitt, ( he, מיכאל לויט; born 9 May 1947) is a South African-born biophysicist and a professor of structural biology at Stanford University, a position he has held since 1987. Levitt received the 2013 Nobel Prize in Chemistry, together with Martin Karplus and Arieh Warshel, for "the development of multiscale models for complex chemical systems". In 2018, Levitt was a founding co-editor of the '' Annual Review of Biomedical Data Science''. Early life and education Michael Levitt was born in Pretoria, South Africa, to a Jewish family from Plungė, Lithuania; his father was from Lithuania and his mother from the Czech Republic. He attended Sunnyside Primary School and then Pretoria Boys High School between 1960 and 1962. The family moved to England when he was 15. Levitt spent 1963 studying applied mathematics at the University of Pretoria. He attended King's College London, graduating with a first-class honours degree in Physics in 1967. In 1967, he visited Is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Arieh Warshel
Arieh Warshel ( he, אריה ורשל; born November 20, 1940) is an Israeli-American biochemist and biophysicist. He is a pioneer in computational studies on functional properties of biological molecules, Distinguished Professor of Chemistry and Biochemistry, and holds the Dana and David Dornsife Chair in Chemistry at the University of Southern California. He received the 2013 Nobel Prize in Chemistry, together with Michael Levitt and Martin Karplus for "the development of multiscale models for complex chemical systems". Biography Warshel was born to a Jewish family in 1940 in kibbutz Sde Nahum, Mandatory Palestine. Warshel served in the Israeli Armored Corps. After serving the Israeli Army (final rank Captain), Warshel attended the Technion, Haifa, where he received his BSc degree in chemistry, ''summa cum laude'', in 1966. Subsequently, he earned both MSc and PhD degrees in Chemical Physics (in 1967 and 1969, respectively), with Shneior Lifson at Weizmann Institute o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiscale Modeling
Multiscale modeling or multiscale mathematics is the field of solving problems which have important features at multiple scales of time and/or space. Important problems include multiscale modeling of fluids, solids, polymers, proteins, nucleic acids as well as various physical and chemical phenomena (like adsorption, chemical reactions, diffusion). An example of such problems involve the Navier-Stokes equations for incompressible fluid flow. \begin \rho_0(\partial_t\mathbf+(\mathbf\cdot\nabla)\mathbf)=\nabla\cdot\tau, \\ \nabla\cdot\mathbf=0. \end In a wide-variety of applications, the stress tensor \tau is given as a linear function of the gradient \nabla u. Such a choice for \tau has been proven to be sufficient for describing the dynamics of a broad range of fluids. However, it’s use for more complex fluids such as polymers is dubious. In such a case, it may be necessary to use multiscale modeling to accurately model the system such that the stress tensor can be extracted ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Black Body
A black body or blackbody is an idealized physical body that absorbs all incident electromagnetic radiation, regardless of frequency or angle of incidence. The name "black body" is given because it absorbs all colors of light. A black body also emits black-body radiation. In contrast, a white body is one with a "rough surface that reflects all incident rays completely and uniformly in all directions." A black body in thermal equilibrium (that is, at a constant temperature) emits electromagnetic black-body radiation. The radiation is emitted according to Planck's law, meaning that it has a spectrum that is determined by the temperature alone (see figure at right), not by the body's shape or composition. An ideal black body in thermal equilibrium has two main properties: #It is an ideal emitter: at every frequency, it emits as much or more thermal radiative energy as any other body at the same temperature. #It is a diffuse emitter: measured per unit area perpendicular to th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Liouville Equation
:''For Liouville's equation in dynamical systems, see Liouville's theorem (Hamiltonian).'' : ''For Liouville's equation in quantum mechanics, see Von Neumann equation.'' : ''For Liouville's equation in Euclidean space, see Liouville–Bratu–Gelfand equation.'' In differential geometry, Liouville's equation, named after Joseph Liouville, is the nonlinear partial differential equation satisfied by the conformal factor of a metric on a surface of constant Gaussian curvature : :\Delta_0\log f = -K f^2, where is the flat Laplace operator :\Delta_0 = \frac +\frac = 4 \frac \frac. Liouville's equation appears in the study of isothermal coordinates in differential geometry: the independent variables are the coordinates, while can be described as the conformal factor with respect to the flat metric. Occasionally it is the square that is referred to as the conformal factor, instead of itself. Liouville's equation was also taken as an example by David Hilbert in the formulation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Information
Information is an abstract concept that refers to that which has the power to inform. At the most fundamental level information pertains to the interpretation of that which may be sensed. Any natural process that is not completely random, and any observable pattern in any medium can be said to convey some amount of information. Whereas digital signals and other data use discrete signs to convey information, other phenomena and artifacts such as analog signals, poems, pictures, music or other sounds, and currents convey information in a more continuous form. Information is not knowledge itself, but the meaning that may be derived from a representation through interpretation. Information is often processed iteratively: Data available at one step are processed into information to be interpreted and processed at the next step. For example, in written text each symbol or letter conveys information relevant to the word it is part of, each word conveys information rele ... [...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] |
