ThermodynamicsThermodynamics is a branch of physics that deals with heat, work, and temperature, and their relation to energy, entropy, and the physical properties of matter and radiation. The behavior of these quantities is governed by the four laws of thermodynamics which convey a quantitative description using measurable macroscopic physical quantities, but may be explained in terms of microscopic constituents by statistical mechanics.
Flow velocityIn continuum mechanics the flow velocity in fluid dynamics, also macroscopic velocity in statistical mechanics, or drift velocity in electromagnetism, is a vector field used to mathematically describe the motion of a continuum. The length of the flow velocity vector is the flow speed and is a scalar. It is also called velocity field; when evaluated along a line, it is called a velocity profile (as in, e.g., law of the wall).
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.
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.
Large eddy simulationLarge eddy simulation (LES) is a mathematical model for turbulence used in computational fluid dynamics. It was initially proposed in 1963 by Joseph Smagorinsky to simulate atmospheric air currents, and first explored by Deardorff (1970). LES is currently applied in a wide variety of engineering applications, including combustion, acoustics, and simulations of the atmospheric boundary layer. The simulation of turbulent flows by numerically solving the Navier–Stokes equations requires resolving a very wide range of time and length scales, all of which affect the flow field.
