A randomized global optimization method for protein-protein docking

In this paper we report results on the problem of docking two large proteins by means of a two-phase monotonic basin hopping method. Given an appropriate force field which is used to measure the interaction energy between two biomolecules which are considered as rigid bodies, we used a randomized global optimization methods based upon the … Read more

New global optima for Morse clusters at $\rho=8$

We recently discovered 5 new putative globally optimum configurations for Morse clusters at $\rho=8$. This report contains some algorithmic details as well as the structures determined with our method. CitationTechnical Report DSI 3-2003, Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze, Firenze, 2003.ArticleDownload View PDF

Efficient Algorithms for Large Scale Global Optimization: Lennard-Jones clusters

A standard stochastic global optimization method is applied to the challenging problem of finding the minimum energy conformation of cluster of identical atoms interacting through the Lennard-Jones potential. The method proposed is based on the use of a two-phase local search procedure which is capable of significantly enlarge the basin of attraction of the global … Read more

The Sample Average Approximation Method for Stochastic Programs with Integer Recourse

This paper develops a solution strategy for two-stage stochastic programs with integer recourse. The proposed methodology relies on approximating the underlying stochastic program via sampling, and solving the approximate problem via a specialized optimization algorithm. We show that the proposed scheme will produce an optimal solution to the true problem with probability approaching one exponentially … Read more

Adaptive Simulated Annealing (ASA)

Adaptive Simulated Annealing (ASA) is a C-language code developed to statistically find the best global fit of a nonlinear constrained non-convex cost-function over a D-dimensional space. Citation%A L. Ingber %R Global optimization C-code %I Caltech Alumni Association %C Pasadena, CA %T Adaptive Simulated Annealing (ASA) %D 1993 %K 200701 %L Ingber:1993:CODE-ASA %O URL http://www.ingber.com/#ASA-CODEArticleDownload View … Read more