Solving molecular distance geometry problems by global optimization algorithms

In this paper we consider global optimization algorithms based on multiple local searches for the Molecular Distance Geometry Problem (MDGP). Three distinct approaches (Multistart, Monotonic Basin Hopping, Population Basin Hopping) are presented and for each of them a computational analysis is performed. The results are also compared with those of two other approaches in the … Read more

Efficiently packing unequal disks in a circle: a computational approach which exploits the continuous and combinatorial structure of the problem

Placing $N$ non-overlapping circles in a smallest container is a well known, widely studied problem that can be easily formulated as a mathematical programming model. Solving this problem is notoriously extremely hard. Recently a public contest has been held for finding putative optimal solutions to a special case in circle packing. The contest saw the … Read more

Disk Packing in a Square: A New Global Optimization Approach

We present a new computational approach to the problem of placing $n$ identical non overlapping disks in the unit square in such a way that their radius is maximized. The problem has been studied in a large number of papers, both from a theoretical and from a computational point of view. In this paper we … Read more

New results for molecular formation under pairwise potential minimization

We establish new lower bounds on the distance between two points of a minimum energy configuration of $N$ points in $\mathbb{R}^3$ interacting according to a pairwise potential function. For the Lennard-Jones case, this bound is 0.67985 (and 0.7633 in the planar case). A similar argument yields an estimate for the minimal distance in Morse clusters, … Read more

Packing circles in a square: new putative optima obtained via global optimization

The problem of finding the optimal placement of $N$ identical, non overlapping, circles with maximum radius in the unit square is a well known challenge both in classical geometry and in optimization. A database of putative optima is currently maintained at \url{www.packomania.com}. Recently, through clever use of an extremely simple global optimization method, we succeeded … Read more

A Population Based Approach for Hard Global Optimization Problems Based on Dissimilarity Measures

When dealing with extremely hard global optimization problems, i.e. problems with a large number of variables and a huge number of local optima, heuristic procedures are the only possible choice. In this situation, lacking any possibility of guaranteeing global optimality for most problem instances, it is quite difficult to establish rules for discriminating among different … Read more

Local optima smoothing for global optimization

It is widely believed that in order to solve large scale global optimization problems an appropriate mixture of local approximation and global exploration is necessary. Local approximation, if first order information on the objective function is available, is efficiently performed by means of local optimization methods. Unfortunately, global exploration, in absence of some kind of … Read more

The global optimization of Morse clusters by potential energy transformations

The Morse potential is a simple model pair potential that has a single parameter $\rho$ which determines the width of the potential well and allows a wide variety of materials to be modelled. Morse clusters provide a particularly tough test system for global optimization algorithms, and one that is highly relevant to methods that are … Read more

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. Citation Technical Report DSI 3-2003, Dipartimento di Sistemi e Informatica, Universit√† degli Studi di Firenze, Firenze, 2003. Article Download View New global optima for Morse clusters … Read more