Conformation of an ideal bucky ball molecule by genetic algorithm and geometric constraint from pair distance data: genetic algorithm

  • Authors:

  • David M. Cherba;William Punch;Phil Duxbury;Simon Billinge;Pavol Juhas

  • Affiliations:

  • Michigan State University, East Lansing, MI;Michigan State University, East Lansing, MI;Michigan State University, East Lansing, MI;Michigan State University, East Lansing, MI;Michigan State University, East Lansing, MI

  • Venue:
  • GECCO '05 Proceedings of the 7th annual conference on Genetic and evolutionary computation
  • Year:
  • 2005

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Abstract

A genetic algorithm is proposed with real value variables, spatially based crossover operator, a small mutation, large scale mutation, vector sum local search and geometric only based objective function to generate candidate molecule conformations from atomic pair distance data. To better simulate experimental data only information from the pair distance data is used as constraints. Ideal Bucky ball with 60 atoms is used as the test case with both perfect pair distance data and Gaussian noise perturbed pair distance data. The GA generated result shows molecules close to ideal Bucky balls but with some defects. A description of the spatially based crossover operator is provided along with a local search based on vector summed error for each atom.