|
Constraint (computational Chemistry)
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 c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry
Computational chemistry is a branch of chemistry that uses computer simulations to assist in solving chemical problems. It uses methods of theoretical chemistry incorporated into computer programs to calculate the structures and properties of molecules, groups of molecules, and solids. The importance of this subject stems from the fact that, with the exception of some relatively recent findings related to the hydrogen molecular ion (dihydrogen cation), achieving an accurate quantum mechanical depiction of chemical systems analytically, or in a closed form, is not feasible. The complexity inherent in the many-body problem exacerbates the challenge of providing detailed descriptions of quantum mechanical systems. While computational results normally complement information obtained by chemical experiments, it can occasionally predict unobserved chemical phenomena. Overview Computational chemistry differs from theoretical chemistry, which involves a mathematical description of chem ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biphenyl
Biphenyl (also known as diphenyl, phenylbenzene, 1,1′-biphenyl, lemonene or BP) is an organic compound that forms colorless crystals. Particularly in older literature, compounds containing the functional group consisting of biphenyl less one hydrogen (the site at which it is attached) may use the prefixes xenyl or diphenylyl. It has a distinctively pleasant smell. Biphenyl is an aromatic hydrocarbon with a molecular formula (C6H5)2. It is notable as a starting material for the production of polychlorinated biphenyls (PCBs), which were once widely used as dielectric fluids and heat transfer agents. Biphenyl is also an intermediate for the production of a host of other organic compounds such as emulsifiers, optical brighteners, crop protection products, and plastics. Biphenyl is insoluble in water, but soluble in typical organic solvents. The biphenyl molecule consists of two connected phenyl rings. Properties and occurrence Biphenyl is a solid at room temperature, wi ... [...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] |
Mechanics
Mechanics () is the area of physics concerned with the relationships between force, matter, and motion among physical objects. Forces applied to objects may result in displacements, which are changes of an object's position relative to its environment. Theoretical expositions of this branch of physics has its origins in Ancient Greece, for instance, in the writings of Aristotle and Archimedes (see History of classical mechanics and Timeline of classical mechanics). During the early modern period, scientists such as Galileo Galilei, Johannes Kepler, Christiaan Huygens, and Isaac Newton laid the foundation for what is now known as classical mechanics. As a branch of classical physics, mechanics deals with bodies that are either at rest or are moving with velocities significantly less than the speed of light. It can also be defined as the physical science that deals with the motion of and forces on bodies not in the quantum realm. History Antiquity The ancient Greek p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Eigenvalues
In linear algebra, an eigenvector ( ) or characteristic vector is a vector that has its direction unchanged (or reversed) by a given linear transformation. More precisely, an eigenvector \mathbf v of a linear transformation T is scaled by a constant factor \lambda when the linear transformation is applied to it: T\mathbf v=\lambda \mathbf v. The corresponding eigenvalue, characteristic value, or characteristic root is the multiplying factor \lambda (possibly a negative or complex number). Geometrically, vectors are multi-dimensional quantities with magnitude and direction, often pictured as arrows. A linear transformation rotates, stretches, or shears the vectors upon which it acts. A linear transformation's eigenvectors are those vectors that are only stretched or shrunk, with neither rotation nor shear. The corresponding eigenvalue is the factor by which an eigenvector is stretched or shrunk. If the eigenvalue is negative, the eigenvector's direction is reversed. The ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linear Convergence
In mathematical analysis, particularly numerical analysis, the rate of convergence and order of convergence of a sequence that converges to a limit are any of several characterizations of how quickly that sequence approaches its limit. These are broadly divided into rates and orders of convergence that describe how quickly a sequence further approaches its limit once it is already close to it, called asymptotic rates and orders of convergence, and those that describe how quickly sequences approach their limits from starting points that are not necessarily close to their limits, called non-asymptotic rates and orders of convergence. Asymptotic behavior is particularly useful for deciding when to stop a sequence of numerical computations, for instance once a target precision has been reached with an iterative root-finding algorithm, but pre-asymptotic behavior is often crucial for determining whether to begin a sequence of computations at all, since it may be impossible or imprac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Giovanni Ciccotti
Giovanni Ciccotti (born 19 December 1943, in Rome Italy) is an Italian physicist. Ciccotti held the position of Professor of the Structure of Matter at the University of Rome La Sapienza until 2013. He is the author of more than a hundred articles on molecular dynamics and statistical mechanics In physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. Sometimes called statistical physics or statistical thermodynamics, its applicati .... He worked with J.P. Ryckaert on new methods for molecular dynamics on constrained systems. See also SHAKE algorithm. He has edited several books on molecular dynamics and statistical mechanics developments, including: # "Molecular Dynamics Simulation of Statistical Mechanical Systems", E. Fermi 1985 Summer School. G. Ciccotti and W. G. Hoover Eds. North Holland, Amsterdam, 1986. # "Simulation of Liquids and Solids. Molecular Dynamics a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quadratic Convergence
In mathematical analysis, particularly numerical analysis, the rate of convergence and order of convergence of a sequence that converges to a limit are any of several characterizations of how quickly that sequence approaches its limit. These are broadly divided into rates and orders of convergence that describe how quickly a sequence further approaches its limit once it is already close to it, called asymptotic rates and orders of convergence, and those that describe how quickly sequences approach their limits from starting points that are not necessarily close to their limits, called non-asymptotic rates and orders of convergence. Asymptotic behavior is particularly useful for deciding when to stop a sequence of numerical computations, for instance once a target precision has been reached with an iterative root-finding algorithm, but pre-asymptotic behavior is often crucial for determining whether to begin a sequence of computations at all, since it may be impossible or imprac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LU Decomposition
In numerical analysis and linear algebra, lower–upper (LU) decomposition or factorization factors a matrix as the product of a lower triangular matrix and an upper triangular matrix (see matrix multiplication and matrix decomposition). The product sometimes includes a permutation matrix as well. LU decomposition can be viewed as the matrix form of Gaussian elimination. Computers usually solve square systems of linear equations using LU decomposition, and it is also a key step when inverting a matrix or computing the determinant of a matrix. It is also sometimes referred to as LR decomposition (factors into left and right triangular matrices). The LU decomposition was introduced by the Polish astronomer Tadeusz Banachiewicz in 1938, who first wrote product equation LU=A=h^Tg (The last form in his alternate yet equivalent matrix notation appears as g\times h. ) Definitions Let ''A'' be a square matrix. An LU factorization refers to expression of ''A'' into product of two facto ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecule
A molecule is a group of two or more atoms that are held together by Force, attractive forces known as chemical bonds; depending on context, the term may or may not include ions that 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 (molecule), 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Velocity Verlet
Verlet integration () is a numerical method used to integrate Newton's equations of motion. It is frequently used to calculate trajectories of particles in molecular dynamics simulations and computer graphics. The algorithm was first used in 1791 by Jean Baptiste Delambre and has been rediscovered many times since then, most recently by Loup Verlet in the 1960s for use in molecular dynamics. It was also used by P. H. Cowell and A. C. C. Crommelin in 1909 to compute the orbit of Halley's Comet, and by Carl Størmer in 1907 to study the trajectories of electrical particles in a magnetic field (hence it is also called Størmer's method). The Verlet integrator provides good numerical stability, as well as other properties that are important in physical systems such as time reversibility and preservation of the symplectic form on phase space, at no significant additional computational cost over the simple Euler method. Basic Størmer–Verlet For a second-order differential eq ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metabolic reactions, DNA replication, Cell signaling, responding to stimuli, providing Cytoskeleton, structure to cells and Fibrous protein, organisms, and Intracellular transport, transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the Nucleic acid sequence, nucleotide sequence of their genes, and which usually results in protein folding into a specific Protein structure, 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called pep ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
