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.
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.
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.
Frequency responseIn signal processing and electronics, the frequency response of a system is the quantitative measure of the magnitude and phase of the output as a function of input frequency. The frequency response is widely used in the design and analysis of systems, such as audio and control systems, where they simplify mathematical analysis by converting governing differential equations into algebraic equations.
Impulse responseIn signal processing and control theory, the impulse response, or impulse response function (IRF), of a dynamic system is its output when presented with a brief input signal, called an impulse (δ(t)). More generally, an impulse response is the reaction of any dynamic system in response to some external change. In both cases, the impulse response describes the reaction of the system as a function of time (or possibly as a function of some other independent variable that parameterizes the dynamic behavior of the system).
Force field (chemistry)In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
Transfer functionIn engineering, a transfer function (also known as system function or network function) of a system, sub-system, or component is a mathematical function that models the system's output for each possible input. They are widely used in electronic engineering tools like circuit simulators and control systems. In some simple cases, this function can be represented as two-dimensional graph of an independent scalar input versus the dependent scalar output, called a transfer curve or characteristic curve.
Classical antiquityClassical antiquity, also known as the classical era, classical period, classical age, or simply antiquity, is the period of cultural history between the 8th century BC and the 8th century AD centered on the Mediterranean Sea, comprising the interlocking civilizations of ancient Greece and ancient Rome known as the Greco-Roman world. It is the period in which both Greek and Roman societies flourished and wielded huge influence throughout much of Europe, North Africa, and West Asia.
Electron densityElectron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typically denoted as either or . The density is determined, through definition, by the normalised -electron wavefunction which itself depends upon variables ( spatial and spin coordinates). Conversely, the density determines the wave function modulo up to a phase factor, providing the formal foundation of density functional theory.
