Computational experience with the molecular distance geometry problem. (English) Zbl 1129.90389

Lavor, Carlile; Liberti, Leo; Maculan, Nelson

Pintér, János D. (ed.), Global optimization. Scientific and engineering case studies. New York, NY: Springer (ISBN 0-387-30408-8/hbk). Nonconvex Optimization and Its Applications 85, 213-225 (2006).

Summary: In this work we consider the molecular distance geometry problem, which can be defined as the determination of the three-dimensional structure of a molecule based on distances between some pairs of atoms. We address the problem as a nonconvex least-squares problem. We apply three global optimization algorithms (spatial branch-and-bound, variable neighbourhood search, multi level single linkage) to two sets of instances, one taken from the literature and the other new.
For the entire collection see [Zbl 1103.90011].

MSC:

90C90	Applications of mathematical programming
92E20	Classical flows, reactions, etc. in chemistry
90C57	Polyhedral combinatorics, branch-and-bound, branch-and-cut

Keywords:

molecular conformation; distance geometry; global optimization; spatial branch-and-bound; variable neighbourhood search; multi-level single linkage

Software:

SNOPT