A Class of Preconditioners for Large Indefinite Linear Systems, as by-product of Krylov subspace Methods: Part I

We propose a class of preconditioners, which are also tailored for symmetric linear systems from linear algebra and nonconvex optimization. Our preconditioners are specifically suited for large linear systems and may be obtained as by-product of Krylov subspace solvers. Each preconditioner in our class is identified by setting the values of a pair of parameters and a scaling matrix, which are user-dependent, and may be chosen according with the structure of the problem in hand. We provide theoretical properties for our preconditioners. In particular, we show that our preconditioners both shift some eigenvalues of the system matrix to controlled values, and they tend to reduce the modulus of most of the other eigenvalues. In a companion paper we study some structural properties of our class of preconditioners, and report the results on a significant numerical experience.preconditioners; large indefinite linear systems; large scale nonconvex optimization; Krylov subspace methods

A Class of Preconditioners for Large Indefinite Linear Systems, as by-product of Krylov subspace Methods: Part II

In this paper we consider the parameter dependent class of preconditioners M(a,d,D) defined in the companion paper The latter was constructed by using information from a Krylov subspace method, adopted to solve the large symmetric linear system Ax = b. We first estimate the condition number of the preconditioned matrix M(a,d,D). Then our preconditioners, which are independent of the choice of the Krylov subspace method adopted, proved to be effective also when solving sequences of slowly changing linear systems, in unconstrained optimization and linear algebra frameworks. A numerical experience is provided to give evidence of the performance of M(a,d,D).preconditioners; large indefinite linear systems; large scale nonconvex optimization; Krylov subspace methods

The LBFGS Quasi-Newtonian Method for Molecular Modeling Prion AGAAAAGA Amyloid Fibrils

Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein); theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method - an improved LBFGS Quasi-Newtonian mathematical optimization method - to produce 3D structures of Prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field

Updating constraint preconditioners for KKT systems in quadratic programming via low-rank corrections

This work focuses on the iterative solution of sequences of KKT linear systems arising in interior point methods applied to large convex quadratic programming problems. This task is the computational core of the interior point procedure and an efficient preconditioning strategy is crucial for the efficiency of the overall method. Constraint preconditioners are very effective in this context; nevertheless, their computation may be very expensive for large-scale problems, and resorting to approximations of them may be convenient. Here we propose a procedure for building inexact constraint preconditioners by updating a "seed" constraint preconditioner computed for a KKT matrix at a previous interior point iteration. These updates are obtained through low-rank corrections of the Schur complement of the (1,1) block of the seed preconditioner. The updated preconditioners are analyzed both theoretically and computationally. The results obtained show that our updating procedure, coupled with an adaptive strategy for determining whether to reinitialize or update the preconditioner, can enhance the performance of interior point methods on large problems.Comment: 22 page

Computational Potential Energy Minimization Studies on the Prion AGAAAAGA Amyloid Fibril Molecular Structures

X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, and dual polarization interferometry, etc are indeed very powerful tools to determine the 3D structures of proteins (including the membrane proteins), though they are time-consuming and costly. However, for some proteins, due to their unstable, noncrystalline and insoluble nature, these tools cannot work. Under this condition, mathematical and physical theoretical methods and computational approaches allow us to obtain a description of the protein 3D structure at a submicroscopic level. This Chapter presents some practical and useful mathematical optimization computational approaches to produce 3D structures of the Prion AGAAAAGA Amyloid Fibrils, from a potential energy minimization point of view. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements in order to produce a better structure. The computational methods presented in this Chapter can be also acted as a tool for the refinements.Comment: published in [Recent Advances in Crystallography, ISBN: 978-953-51-0754-5, Editor Jason B. Bendict, InTech Open Access Publisher, 19 Sept 2012, hardcover] Chapter 12, DOI: 10.5772/47733, pp.297-312: http://www.intechopen.com/books/recent-advances-in-crystallography/computational-potential-energy-minimization-studies-on-the-prion-agaaaaga-amyloid-fibril-molecular-

A class of preconditioners for large indefinite linear systems, as by-product of Krylov subspace methods: Part I

We propose a class of preconditioners, which are also tailored for symmetric linear systems from linear algebra and nonconvex optimization. Our preconditioners are specifically suited for large linear systems and may be obtained as by-product of Krylov subspace solvers. Each preconditioner in our class is identified by setting the values of a pair of parameters and a scaling matrix, which are user-dependent, and may be chosen according with the structure of the problem in hand. We provide theoretical properties for our preconditioners. In particular, we show that our preconditioners both shift some eigenvalues of the system matrix to controlled values, and they tend to reduce the modulus of most of the other eigenvalues. In a companion paper we study some structural properties of our class of preconditioners, and report the results on a significant numerical experience