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

A Simple and Efficient Algorithm for Nonlinear Model Predictive Control

We present PANOC, a new algorithm for solving optimal control problems arising in nonlinear model predictive control (NMPC). A usual approach to this type of problems is sequential quadratic programming (SQP), which requires the solution of a quadratic program at every iteration and, consequently, inner iterative procedures. As a result, when the problem is ill-conditioned or the prediction horizon is large, each outer iteration becomes computationally very expensive. We propose a line-search algorithm that combines forward-backward iterations (FB) and Newton-type steps over the recently introduced forward-backward envelope (FBE), a continuous, real-valued, exact merit function for the original problem. The curvature information of Newton-type methods enables asymptotic superlinear rates under mild assumptions at the limit point, and the proposed algorithm is based on very simple operations: access to first-order information of the cost and dynamics and low-cost direct linear algebra. No inner iterative procedure nor Hessian evaluation is required, making our approach computationally simpler than SQP methods. The low-memory requirements and simple implementation make our method particularly suited for embedded NMPC applications

Unconstrained Optimization with MINTOOLKIT for GNU Octave

The paper documents MINTOOLKIT for GNU Octave. MINTOOLKIT provides functions for minimization and numeric differentiation. The main algorithms are BFGS, LBFGS, and simulated annealing. Examples are given.minimization, optmization, software

Global convergence of the nonmonotone MBFGS method for nonconvex unconstrained minimization

AbstractIn this paper, we propose a new nonmonotone Armijo type line search and prove that the MBFGS method proposed by Li and Fukushima with this new line search converges globally for nonconvex minimization. Some numerical experiments show that this nonmonotone MBFGS method is efficient for the given test problems