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.
Quantum chemistryQuantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions to physical and chemical properties of molecules, materials, and solutions at the atomic level. These calculations include systematically applied approximations intended to make calculations computationally feasible while still capturing as much information about important contributions to the computed wave functions as well as to observable properties such as structures, spectra, and thermodynamic properties.
Schrödinger equationThe Schrödinger equation is a linear partial differential equation that governs the wave function of a quantum-mechanical system. Its discovery was a significant landmark in the development of quantum mechanics. The equation is named after Erwin Schrödinger, who postulated the equation in 1925 and published it in 1926, forming the basis for the work that resulted in his Nobel Prize in Physics in 1933. Conceptually, the Schrödinger equation is the quantum counterpart of Newton's second law in classical mechanics.
Molecular modellingMolecular 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.
WKB approximationIn mathematical physics, the WKB approximation or WKB method is a method for finding approximate solutions to linear differential equations with spatially varying coefficients. It is typically used for a semiclassical calculation in quantum mechanics in which the wavefunction is recast as an exponential function, semiclassically expanded, and then either the amplitude or the phase is taken to be changing slowly. The name is an initialism for Wentzel–Kramers–Brillouin. It is also known as the LG or Liouville–Green method.
Fast Fourier transformA fast Fourier transform (FFT) is an algorithm that computes the discrete Fourier transform (DFT) of a sequence, or its inverse (IDFT). Fourier analysis converts a signal from its original domain (often time or space) to a representation in the frequency domain and vice versa. The DFT is obtained by decomposing a sequence of values into components of different frequencies. This operation is useful in many fields, but computing it directly from the definition is often too slow to be practical.
Wave functionIn quantum physics, a wave function (or wavefunction), represented by the Greek letter Ψ, is a mathematical description of the quantum state of an isolated quantum system. In the Copenhagen interpretation of quantum mechanics, the wave function is a complex-valued probability amplitude; the probabilities for the possible results of the measurements made on a measured system can be derived from the wave function. The most common symbols for a wave function are the Greek letters ψ and Ψ (lower-case and capital psi, respectively).
Fourier transformIn physics and mathematics, the Fourier transform (FT) is a transform that converts a function into a form that describes the frequencies present in the original function. The output of the transform is a complex-valued function of frequency. The term Fourier transform refers to both this complex-valued function and the mathematical operation. When a distinction needs to be made the Fourier transform is sometimes called the frequency domain representation of the original function.
Phase-space formulationThe phase-space formulation of quantum mechanics places the position and momentum variables on equal footing in phase space. In contrast, the Schrödinger picture uses the position or momentum representations (see also position and momentum space). The two key features of the phase-space formulation are that the quantum state is described by a quasiprobability distribution (instead of a wave function, state vector, or density matrix) and operator multiplication is replaced by a star product.
Schrödinger pictureIn physics, the Schrödinger picture or Schrödinger representation is a formulation of quantum mechanics in which the state vectors evolve in time, but the operators (observables and others) are mostly constant with respect to time (an exception is the Hamiltonian which may change if the potential changes). This differs from the Heisenberg picture which keeps the states constant while the observables evolve in time, and from the interaction picture in which both the states and the observables evolve in time.
Molecular orbitalIn chemistry, a molecular orbital (ɒrbədl) is a mathematical function describing the location and wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of finding an electron in any specific region. The terms atomic orbital and molecular orbital were introduced by Robert S. Mulliken in 1932 to mean one-electron orbital wave functions. At an elementary level, they are used to describe the region of space in which a function has a significant amplitude.
Non-uniform discrete Fourier transformIn applied mathematics, the nonuniform discrete Fourier transform (NUDFT or NDFT) of a signal is a type of Fourier transform, related to a discrete Fourier transform or discrete-time Fourier transform, but in which the input signal is not sampled at equally spaced points or frequencies (or both). It is a generalization of the shifted DFT. It has important applications in signal processing, magnetic resonance imaging, and the numerical solution of partial differential equations.
Discrete Fourier transformIn mathematics, the discrete Fourier transform (DFT) converts a finite sequence of equally-spaced samples of a function into a same-length sequence of equally-spaced samples of the discrete-time Fourier transform (DTFT), which is a complex-valued function of frequency. The interval at which the DTFT is sampled is the reciprocal of the duration of the input sequence. An inverse DFT (IDFT) is a Fourier series, using the DTFT samples as coefficients of complex sinusoids at the corresponding DTFT frequencies.
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.
Electromagnetic fieldAn electromagnetic field (also EM field or EMF) is a classical (i.e. non-quantum) field produced by moving electric charges. It is the field described by classical electrodynamics (a classical field theory) and is the classical counterpart to the quantized electromagnetic field tensor in quantum electrodynamics (a quantum field theory). The electromagnetic field propagates at the speed of light (in fact, this field can be identified as light) and interacts with charges and currents.
Optical phase spaceIn quantum optics, an optical phase space is a phase space in which all quantum states of an optical system are described. Each point in the optical phase space corresponds to a unique state of an optical system. For any such system, a plot of the quadratures against each other, possibly as functions of time, is called a phase diagram. If the quadratures are functions of time then the optical phase diagram can show the evolution of a quantum optical system with time.
Hamiltonian mechanicsHamiltonian mechanics emerged in 1833 as a reformulation of Lagrangian mechanics. Introduced by Sir William Rowan Hamilton, Hamiltonian mechanics replaces (generalized) velocities used in Lagrangian mechanics with (generalized) momenta. Both theories provide interpretations of classical mechanics and describe the same physical phenomena. Hamiltonian mechanics has a close relationship with geometry (notably, symplectic geometry and Poisson structures) and serves as a link between classical and quantum mechanics.
Computational chemistryComputational chemistry is a branch of chemistry that uses computer simulation 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. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form.
Interaction pictureIn quantum mechanics, the interaction picture (also known as the interaction representation or Dirac picture after Paul Dirac) is an intermediate representation between the Schrödinger picture and the Heisenberg picture. Whereas in the other two pictures either the state vector or the operators carry time dependence, in the interaction picture both carry part of the time dependence of observables. The interaction picture is useful in dealing with changes to the wave functions and observables due to interactions.
Semi-empirical quantum chemistry methodSemi-empirical quantum chemistry methods are based on the Hartree–Fock formalism, but make many approximations and obtain some parameters from empirical data. They are very important in computational chemistry for treating large molecules where the full Hartree–Fock method without the approximations is too expensive. The use of empirical parameters appears to allow some inclusion of electron correlation effects into the methods. Within the framework of Hartree–Fock calculations, some pieces of information (such as two-electron integrals) are sometimes approximated or completely omitted.
