Continuous Optimization Methods for Structure Alignments

Structural Alignment is an important tool for fold identification of proteins, structural screening on ligand databases, pharmacophore identification and other applications. In the general case, the optimization problem of superimposing two structures is nonsmooth and nonconvex, so that most popular methods are heuristic and do not employ derivative information. Usually, these methods do not admit … Read more

Low Order-Value Optimization and Applications

Given r real functions F1 (x), . . . , Fr (x) and an integer p between 1 and r, the Low Order- Value Optimization problem (LOVO) consists of minimizing the sum of the functions that take the p smaller values. If (y1 , . . . , yr ) is a vector of data … Read more

Density-based Globally Convergent Trust-Region Methods for Self-Consistent Field Electronic Structure Calculations

A theory of globally convergent trust-region methods for self-consistent field electronic structure calculations that use the density matrices as variables is developed. The optimization is performed by means of sequential global minimizations of a quadratic model of the true energy. The global minimization of this quadratic model, subject to the idempotency of the density matrix … Read more