Iterative methodIn computational mathematics, an iterative method is a mathematical procedure that uses an initial value to generate a sequence of improving approximate solutions for a class of problems, in which the n-th approximation is derived from the previous ones. A specific implementation with termination criteria for a given iterative method like gradient descent, hill climbing, Newton's method, or quasi-Newton methods like BFGS, is an algorithm of the iterative method.
Jacobi methodIn numerical linear algebra, the Jacobi method (a.k.a. the Jacobi iteration method) is an iterative algorithm for determining the solutions of a strictly diagonally dominant system of linear equations. Each diagonal element is solved for, and an approximate value is plugged in. The process is then iterated until it converges. This algorithm is a stripped-down version of the Jacobi transformation method of matrix diagonalization. The method is named after Carl Gustav Jacob Jacobi.
Quadratic formIn mathematics, a quadratic form is a polynomial with terms all of degree two ("form" is another name for a homogeneous polynomial). For example, is a quadratic form in the variables x and y. The coefficients usually belong to a fixed field K, such as the real or complex numbers, and one speaks of a quadratic form over K. If , and the quadratic form equals zero only when all variables are simultaneously zero, then it is a definite quadratic form; otherwise it is an isotropic quadratic form.
Definite quadratic formIn mathematics, a definite quadratic form is a quadratic form over some real vector space V that has the same sign (always positive or always negative) for every non-zero vector of V. According to that sign, the quadratic form is called positive-definite or negative-definite. A semidefinite (or semi-definite) quadratic form is defined in much the same way, except that "always positive" and "always negative" are replaced by "never negative" and "never positive", respectively.
Gradient descentIn mathematics, gradient descent (also often called steepest descent) is a iterative optimization algorithm for finding a local minimum of a differentiable function. The idea is to take repeated steps in the opposite direction of the gradient (or approximate gradient) of the function at the current point, because this is the direction of steepest descent. Conversely, stepping in the direction of the gradient will lead to a local maximum of that function; the procedure is then known as gradient ascent.
Conjugate gradient methodIn mathematics, the conjugate gradient method is an algorithm for the numerical solution of particular systems of linear equations, namely those whose matrix is positive-definite. The conjugate gradient method is often implemented as an iterative algorithm, applicable to sparse systems that are too large to be handled by a direct implementation or other direct methods such as the Cholesky decomposition. Large sparse systems often arise when numerically solving partial differential equations or optimization problems.
Orthogonal polynomialsIn mathematics, an orthogonal polynomial sequence is a family of polynomials such that any two different polynomials in the sequence are orthogonal to each other under some inner product. The most widely used orthogonal polynomials are the classical orthogonal polynomials, consisting of the Hermite polynomials, the Laguerre polynomials and the Jacobi polynomials. The Gegenbauer polynomials form the most important class of Jacobi polynomials; they include the Chebyshev polynomials, and the Legendre polynomials as special cases.
Isotropic quadratic formIn mathematics, a quadratic form over a field F is said to be isotropic if there is a non-zero vector on which the form evaluates to zero. Otherwise the quadratic form is anisotropic. More explicitly, if q is a quadratic form on a vector space V over F, then a non-zero vector v in V is said to be isotropic if q(v) = 0. A quadratic form is isotropic if and only if there exists a non-zero isotropic vector (or null vector) for that quadratic form. Suppose that (V, q) is quadratic space and W is a subspace of V.
Protein structureProtein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.
Classical orthogonal polynomialsIn mathematics, the classical orthogonal polynomials are the most widely used orthogonal polynomials: the Hermite polynomials, Laguerre polynomials, Jacobi polynomials (including as a special case the Gegenbauer polynomials, Chebyshev polynomials, and Legendre polynomials). They have many important applications in such areas as mathematical physics (in particular, the theory of random matrices), approximation theory, numerical analysis, and many others.
Successive over-relaxationIn numerical linear algebra, the method of successive over-relaxation (SOR) is a variant of the Gauss–Seidel method for solving a linear system of equations, resulting in faster convergence. A similar method can be used for any slowly converging iterative process. It was devised simultaneously by David M. Young Jr. and by Stanley P. Frankel in 1950 for the purpose of automatically solving linear systems on digital computers. Over-relaxation methods had been used before the work of Young and Frankel.
Protein tertiary structureProtein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.
Orthogonal matrixIn linear algebra, an orthogonal matrix, or orthonormal matrix, is a real square matrix whose columns and rows are orthonormal vectors. One way to express this is where QT is the transpose of Q and I is the identity matrix. This leads to the equivalent characterization: a matrix Q is orthogonal if its transpose is equal to its inverse: where Q−1 is the inverse of Q. An orthogonal matrix Q is necessarily invertible (with inverse Q−1 = QT), unitary (Q−1 = Q∗), where Q∗ is the Hermitian adjoint (conjugate transpose) of Q, and therefore normal (Q∗Q = QQ∗) over the real numbers.
Cholesky decompositionIn linear algebra, the Cholesky decomposition or Cholesky factorization (pronounced ʃəˈlɛski ) is a decomposition of a Hermitian, positive-definite matrix into the product of a lower triangular matrix and its conjugate transpose, which is useful for efficient numerical solutions, e.g., Monte Carlo simulations. It was discovered by André-Louis Cholesky for real matrices, and posthumously published in 1924. When it is applicable, the Cholesky decomposition is roughly twice as efficient as the LU decomposition for solving systems of linear equations.
Protein quaternary structureProtein quaternary structure is the fourth (and highest) classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also referred to as subunits). Protein quaternary structure describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits.
QR decompositionIn linear algebra, a QR decomposition, also known as a QR factorization or QU factorization, is a decomposition of a matrix A into a product A = QR of an orthonormal matrix Q and an upper triangular matrix R. QR decomposition is often used to solve the linear least squares problem and is the basis for a particular eigenvalue algorithm, the QR algorithm. Any real square matrix A may be decomposed as where Q is an orthogonal matrix (its columns are orthogonal unit vectors meaning ) and R is an upper triangular matrix (also called right triangular matrix).
Protein secondary structureProtein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.
LU decompositionIn numerical analysis and linear algebra, lower–upper (LU) decomposition or factorization factors a matrix as the product of a lower triangular matrix and an upper triangular matrix (see matrix decomposition). The product sometimes includes a permutation matrix as well. LU decomposition can be viewed as the matrix form of Gaussian elimination. Computers usually solve square systems of linear equations using LU decomposition, and it is also a key step when inverting a matrix or computing the determinant of a matrix.
Protein primary structureProtein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequencess.
Matrix splittingIn the mathematical discipline of numerical linear algebra, a matrix splitting is an expression which represents a given matrix as a sum or difference of matrices. Many iterative methods (for example, for systems of differential equations) depend upon the direct solution of matrix equations involving matrices more general than tridiagonal matrices. These matrix equations can often be solved directly and efficiently when written as a matrix splitting. The technique was devised by Richard S. Varga in 1960.
