A phylogenetic tree relates taxonomic units, based on their similarity over a set of characters. We propose a new genetic algorithm for the problem of building a phylogenetic tree under the parsimony criterion. This genetic algorithm makes use of an innovative optimized crossover strategy which is an extension of the path-relinking intensification technique originaly proposed … Read more
In this tutorial we discuss modeling issues in intensity modulated radiation therapy, contrasting the continuous model with the fully-discretized one and considering feasibility formulations versus optimization setups. We review briefly some mathematical optimization techniques for IMRT. These include global optimization, multi-objective optimization, linear and mixed integer programming and projection methods. Citationin: J.R. Palta and T.R. … Read more
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
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
Aperture-based inverse planning (ABIP) for intensity modulated radiation therapy (IMRT) treatment planning starts with external radiation fields (beams) that fully conform to the target(s) and then superimposes sub-fields called segments to achieve complex shaping of 3D dose distributions. The segments’ intensities are determined by solving a feasibility problem. The least-intensity feasible (LIF) solution, proposed and … Read more