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.
Coupled clusterCoupled cluster (CC) is a numerical technique used for describing many-body systems. Its most common use is as one of several post-Hartree–Fock ab initio quantum chemistry methods in the field of computational chemistry, but it is also used in nuclear physics. Coupled cluster essentially takes the basic Hartree–Fock molecular orbital method and constructs multi-electron wavefunctions using the exponential cluster operator to account for electron correlation. Some of the most accurate calculations for small to medium-sized molecules use this method.
Q (software)Q is a computer software package for molecular dynamics (MD) simulation (current release: Q6). Unlike other MD codes, it has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations. These calculations are based on the methods: empirical valence bond (EVB), free energy perturbation (FEP), and linear interaction energy (LIE), as well as, more recently, also path integral calculations using the bisection quantum classical path (BQCP) approach.
Coupling (computer programming)In software engineering, coupling is the degree of interdependence between software modules; a measure of how closely connected two routines or modules are; the strength of the relationships between modules. Coupling is usually contrasted with cohesion. Low coupling often correlates with high cohesion, and vice versa. Low coupling is often thought to be a sign of a well-structured computer system and a good design, and when combined with high cohesion, supports the general goals of high readability and maintainability.
Wave function collapseIn quantum mechanics, wave function collapse occurs when a wave function—initially in a superposition of several eigenstates—reduces to a single eigenstate due to interaction with the external world. This interaction is called an observation, and is the essence of a measurement in quantum mechanics, which connects the wave function with classical observables such as position and momentum. Collapse is one of the two processes by which quantum systems evolve in time; the other is the continuous evolution governed by the Schrödinger equation.
MultiprocessingMultiprocessing is the use of two or more central processing units (CPUs) within a single computer system. The term also refers to the ability of a system to support more than one processor or the ability to allocate tasks between them. There are many variations on this basic theme, and the definition of multiprocessing can vary with context, mostly as a function of how CPUs are defined (multiple cores on one die, multiple dies in one package, multiple packages in one system unit, etc.).
Periodic functionA periodic function or cyclic function is a function that repeats its values at regular intervals. For example, the trigonometric functions, which repeat at intervals of radians, are periodic functions. Periodic functions are used throughout science to describe oscillations, waves, and other phenomena that exhibit periodicity. Any function that is not periodic is called aperiodic. A function f is said to be periodic if, for some nonzero constant P, it is the case that for all values of x in the domain.
Single instruction, multiple threadsSingle instruction, multiple threads (SIMT) is an execution model used in parallel computing where single instruction, multiple data (SIMD) is combined with multithreading. It is different from SPMD in that all instructions in all "threads" are executed in lock-step. The SIMT execution model has been implemented on several GPUs and is relevant for general-purpose computing on graphics processing units (GPGPU), e.g. some supercomputers combine CPUs with GPUs. The processors, say a number p of them, seem to execute many more than p tasks.
Computational anatomyComputational anatomy is an interdisciplinary field of biology focused on quantitative investigation and modelling of anatomical shapes variability. It involves the development and application of mathematical, statistical and data-analytical methods for modelling and simulation of biological structures. The field is broadly defined and includes foundations in anatomy, applied mathematics and pure mathematics, machine learning, computational mechanics, computational science, biological imaging, neuroscience, physics, probability, and statistics; it also has strong connections with fluid mechanics and geometric mechanics.
Sine waveA sine wave, sinusoidal wave, or sinusoid is a mathematical curve defined in terms of the sine trigonometric function, of which it is the graph. It is a type of continuous wave and also a smooth periodic function. It occurs often in mathematics, as well as in physics, engineering, signal processing and many other fields. Its most basic form as a function of time (t) is: where: A, amplitude, the peak deviation of the function from zero. f, ordinary frequency, the number of oscillations (cycles) that occur each second of time.
