Molecular dynamicsMolecular 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.
JelliumJellium, also known as the uniform electron gas (UEG) or homogeneous electron gas (HEG), is a quantum mechanical model of interacting electrons in a solid where the positive charges (i.e. atomic nuclei) are assumed to be uniformly distributed in space; the electron density is a uniform quantity as well in space. This model allows one to focus on the effects in solids that occur due to the quantum nature of electrons and their mutual repulsive interactions (due to like charge) without explicit introduction of the atomic lattice and structure making up a real material.
Chirality (chemistry)In chemistry, a molecule or ion is called chiral (ˈkaɪrəl) if it cannot be superposed on its by any combination of rotations, translations, and some conformational changes. This geometric property is called chirality (kaɪˈrælɪti). The terms are derived from Ancient Greek χείρ (cheir) 'hand'; which is the canonical example of an object with this property. A chiral molecule or ion exists in two stereoisomers that are mirror images of each other, called enantiomers; they are often distinguished as either "right-handed" or "left-handed" by their absolute configuration or some other criterion.
Angular momentum couplingIn quantum mechanics, the procedure of constructing eigenstates of total angular momentum out of eigenstates of separate angular momenta is called angular momentum coupling. For instance, the orbit and spin of a single particle can interact through spin–orbit interaction, in which case the complete physical picture must include spin–orbit coupling. Or two charged particles, each with a well-defined angular momentum, may interact by Coulomb forces, in which case coupling of the two one-particle angular momenta to a total angular momentum is a useful step in the solution of the two-particle Schrödinger equation.
Potential energy surfaceA potential energy surface (PES) describes the energy of a system, especially a collection of atoms, in terms of certain parameters, normally the positions of the atoms. The surface might define the energy as a function of one or more coordinates; if there is only one coordinate, the surface is called a potential energy curve or . An example is the Morse/Long-range potential. It is helpful to use the analogy of a landscape: for a system with two degrees of freedom (e.g.
Ab initio quantum chemistry methodsAb initio quantum chemistry methods are computational chemistry methods based on quantum chemistry. The term ab initio was first used in quantum chemistry by Robert Parr and coworkers, including David Craig in a semiempirical study on the excited states of benzene. The background is described by Parr. Ab initio means "from first principles" or "from the beginning", implying that the only inputs into an ab initio calculation are physical constants.
Conway polyhedron notationIn geometry, Conway polyhedron notation, invented by John Horton Conway and promoted by George W. Hart, is used to describe polyhedra based on a seed polyhedron modified by various prefix operations. Conway and Hart extended the idea of using operators, like truncation as defined by Kepler, to build related polyhedra of the same symmetry. For example, tC represents a truncated cube, and taC, parsed as t(aC), is (topologically) a truncated cuboctahedron. The simplest operator dual swaps vertex and face elements; e.
Angular momentum operatorIn quantum mechanics, the angular momentum operator is one of several related operators analogous to classical angular momentum. The angular momentum operator plays a central role in the theory of atomic and molecular physics and other quantum problems involving rotational symmetry. Such an operator is applied to a mathematical representation of the physical state of a system and yields an angular momentum value if the state has a definite value for it.
Nuclear shell modelIn nuclear physics, atomic physics, and nuclear chemistry, the nuclear shell model is a model of the atomic nucleus which uses the Pauli exclusion principle to describe the structure of the nucleus in terms of energy levels. The first shell model was proposed by Dmitri Ivanenko (together with E. Gapon) in 1932. The model was developed in 1949 following independent work by several physicists, most notably Eugene Paul Wigner, Maria Goeppert Mayer, and J. Hans D. Jensen, who shared the 1963 Nobel Prize in Physics for their contributions.
Chemical potentialIn thermodynamics, the chemical potential of a species is the energy that can be absorbed or released due to a change of the particle number of the given species, e.g. in a chemical reaction or phase transition. The chemical potential of a species in a mixture is defined as the rate of change of free energy of a thermodynamic system with respect to the change in the number of atoms or molecules of the species that are added to the system.
Structural isomerIn chemistry, a structural isomer (or constitutional isomer in the IUPAC nomenclature) of a compound is another compound whose molecule has the same number of atoms of each element, but with logically distinct bonds between them. The term metamer was formerly used for the same concept. For example, butanol , methyl propyl ether , and diethyl ether have the same molecular formula but are three distinct structural isomers. The concept applies also to polyatomic ions with the same total charge.
Cis–trans isomerismCis–trans isomerism, also known as geometric isomerism or configurational isomerism, is a term used in chemistry that concerns the spatial arrangement of atoms within molecules. The prefixes "cis" and "trans" are from Latin: "this side of" and "the other side of", respectively. In the context of chemistry, cis indicates that the functional groups (substituents) are on the same side of some plane, while trans conveys that they are on opposing (transverse) sides.
Density functional theoryDensity-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases. Using this theory, the properties of a many-electron system can be determined by using functionals, i.e. functions of another function. In the case of DFT, these are functionals of the spatially dependent electron density.
IsomerIn chemistry, isomers are molecules or polyatomic ions with identical molecular formula – that is, same number of atoms of each element – but distinct arrangements of atoms in space. Isomerism refers to the existence or possibility of isomers. Isomers do not necessarily share similar chemical or physical properties. Two main forms of isomerism are structural or constitutional isomerism, in which bonds between the atoms differ; and stereoisomerism or spatial isomerism, in which the bonds are the same but the relative positions of the atoms differ.
Penrose tilingA Penrose tiling is an example of an aperiodic tiling. Here, a tiling is a covering of the plane by non-overlapping polygons or other shapes, and a tiling is aperiodic if it does not contain arbitrarily large periodic regions or patches. However, despite their lack of translational symmetry, Penrose tilings may have both reflection symmetry and fivefold rotational symmetry. Penrose tilings are named after mathematician and physicist Roger Penrose, who investigated them in the 1970s.
Genetic algorithmIn computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA). Genetic algorithms are commonly used to generate high-quality solutions to optimization and search problems by relying on biologically inspired operators such as mutation, crossover and selection. Some examples of GA applications include optimizing decision trees for better performance, solving sudoku puzzles, hyperparameter optimization, causal inference, etc.
Ant colony optimization algorithmsIn computer science and operations research, the ant colony optimization algorithm (ACO) is a probabilistic technique for solving computational problems which can be reduced to finding good paths through graphs. Artificial ants stand for multi-agent methods inspired by the behavior of real ants. The pheromone-based communication of biological ants is often the predominant paradigm used. Combinations of artificial ants and local search algorithms have become a method of choice for numerous optimization tasks involving some sort of graph, e.
Angular momentumIn physics, angular momentum (sometimes called moment of momentum or rotational momentum) is the rotational analog of linear momentum. It is an important physical quantity because it is a conserved quantity – the total angular momentum of a closed system remains constant. Angular momentum has both a direction and a magnitude, and both are conserved. Bicycles and motorcycles, flying discs, rifled bullets, and gyroscopes owe their useful properties to conservation of angular momentum.
Bohr modelIn atomic physics, the Bohr model or Rutherford–Bohr model of the atom, presented by Niels Bohr and Ernest Rutherford in 1913, consists of a small, dense nucleus surrounded by orbiting electrons. It is analogous to the structure of the Solar System, but with attraction provided by electrostatic force rather than gravity, and with the electron energies quantized (assuming only discrete values).
Swarm intelligenceSwarm intelligence (SI) is the collective behavior of decentralized, self-organized systems, natural or artificial. The concept is employed in work on artificial intelligence. The expression was introduced by Gerardo Beni and Jing Wang in 1989, in the context of cellular robotic systems. SI systems consist typically of a population of simple agents or boids interacting locally with one another and with their environment. The inspiration often comes from nature, especially biological systems.
