Molecular mechanicsMolecular 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 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.
Valence electronIn chemistry and physics, a valence electron is an electron in the outer shell associated with an atom, and that can participate in the formation of a chemical bond if the outer shell is not closed. In a single covalent bond, a shared pair forms with both atoms in the bond each contributing one valence electron. The presence of valence electrons can determine the element's chemical properties, such as its valence—whether it may bond with other elements and, if so, how readily and with how many.
Docking (molecular)In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction.
Dynamical billiardsA dynamical billiard is a dynamical system in which a particle alternates between free motion (typically as a straight line) and specular reflections from a boundary. When the particle hits the boundary it reflects from it without loss of speed (i.e. elastic collisions). Billiards are Hamiltonian idealizations of the game of billiards, but where the region contained by the boundary can have shapes other than rectangular and even be multidimensional.
Basis set (chemistry)In theoretical and computational chemistry, a basis set is a set of functions (called basis functions) that is used to represent the electronic wave function in the Hartree–Fock method or density-functional theory in order to turn the partial differential equations of the model into algebraic equations suitable for efficient implementation on a computer. The use of basis sets is equivalent to the use of an approximate resolution of the identity: the orbitals are expanded within the basis set as a linear combination of the basis functions , where the expansion coefficients are given by .
Ionization energyIn physics and chemistry, ionization energy (IE) (American English spelling), ionisation energy (British English spelling) is the minimum energy required to remove the most loosely bound electron of an isolated gaseous atom, positive ion, or molecule. The first ionization energy is quantitatively expressed as X(g) + energy ⟶ X+(g) + e− where X is any atom or molecule, X+ is the resultant ion when the original atom was stripped of a single electron, and e− is the removed electron.
Electron configurationIn atomic physics and quantum chemistry, the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals. For example, the electron configuration of the neon atom is 1s2 2s2 2p6, meaning that the 1s, 2s and 2p subshells are occupied by 2, 2 and 6 electrons respectively. Electronic configurations describe each electron as moving independently in an orbital, in an average field created by all other orbitals.
Measure-preserving dynamical systemIn mathematics, a measure-preserving dynamical system is an object of study in the abstract formulation of dynamical systems, and ergodic theory in particular. Measure-preserving systems obey the Poincaré recurrence theorem, and are a special case of conservative systems. They provide the formal, mathematical basis for a broad range of physical systems, and, in particular, many systems from classical mechanics (in particular, most non-dissipative systems) as well as systems in thermodynamic equilibrium.
Plane waveIn physics, a plane wave is a special case of wave or field: a physical quantity whose value, at any moment, is constant through any plane that is perpendicular to a fixed direction in space. For any position in space and any time , the value of such a field can be written as where is a unit-length vector, and is a function that gives the field's value as dependent on only two real parameters: the time , and the scalar-valued displacement of the point along the direction . The displacement is constant over each plane perpendicular to .
Tight bindingIn solid-state physics, the tight-binding model (or TB model) is an approach to the calculation of electronic band structure using an approximate set of wave functions based upon superposition of wave functions for isolated atoms located at each atomic site. The method is closely related to the LCAO method (linear combination of atomic orbitals method) used in chemistry. Tight-binding models are applied to a wide variety of solids.
