Protein structure predictionProtein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).
Thermal energyThe term "thermal energy" is used loosely in various contexts in physics and engineering. It can refer to several different well-defined physical concepts. These include the internal energy or enthalpy of a body of matter and radiation; heat, defined as a type of energy transfer (as is thermodynamic work); and the characteristic energy of a degree of freedom, , in a system that is described in terms of its microscopic particulate constituents (where denotes temperature and denotes the Boltzmann constant).
Kinetic theory of gasesThe kinetic theory of gases is a simple, historically significant classical model of the thermodynamic behavior of gases, with which many principal concepts of thermodynamics were established. The model describes a gas as a large number of identical submicroscopic particles (atoms or molecules), all of which are in constant, rapid, random motion. Their size is assumed to be much smaller than the average distance between the particles. The particles undergo random elastic collisions between themselves and with the enclosing walls of the container.
Perpetual motionPerpetual motion is the motion of bodies that continues forever in an unperturbed system. A perpetual motion machine is a hypothetical machine that can do work infinitely without an external energy source. This kind of machine is impossible, as it would violate either the first or second law of thermodynamics, or both. These laws of thermodynamics apply regardless of the size of the system.
Trace (linear algebra)In linear algebra, the trace of a square matrix A, denoted tr(A), is defined to be the sum of elements on the main diagonal (from the upper left to the lower right) of A. The trace is only defined for a square matrix (n × n). It can be proven that the trace of a matrix is the sum of its (complex) eigenvalues (counted with multiplicities). It can also be proven that tr(AB) = tr(BA) for any two matrices A and B. This implies that similar matrices have the same trace.
Bounded complete posetIn the mathematical field of order theory, a partially ordered set is bounded complete if all of its subsets that have some upper bound also have a least upper bound. Such a partial order can also be called consistently or coherently complete (Visser 2004, p. 182), since any upper bound of a set can be interpreted as some consistent (non-contradictory) piece of information that extends all the information present in the set. Hence the presence of some upper bound in a way guarantees the consistency of a set.
Transition state theoryIn chemistry, transition state theory (TST) explains the reaction rates of elementary chemical reactions. The theory assumes a special type of chemical equilibrium (quasi-equilibrium) between reactants and activated transition state complexes. TST is used primarily to understand qualitatively how chemical reactions take place.
Partial differential equationIn mathematics, a partial differential equation (PDE) is an equation which computes a function between various partial derivatives of a multivariable function. The function is often thought of as an "unknown" to be solved for, similar to how x is thought of as an unknown number to be solved for in an algebraic equation like x2 − 3x + 2 = 0. However, it is usually impossible to write down explicit formulas for solutions of partial differential equations.
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.
Assertion (software development)In computer programming, specifically when using the imperative programming paradigm, an assertion is a predicate (a Boolean-valued function over the state space, usually expressed as a logical proposition using the variables of a program) connected to a point in the program, that always should evaluate to true at that point in code execution. Assertions can help a programmer read the code, help a compiler compile it, or help the program detect its own defects.
