Simulated annealing : In mathematical global optimization computation, hybrid with local or global search, and practical applications in crystallography and molecular modelling of prion amyloid fibrils

Simulated annealing (SA) was inspired from annealing in metallurgy, a technique involving heating and controlled cooling of a material to increase the size of its crystals and reduce their defects, both are attributes of the material that depend on its thermodynamic free energy. In this Chapter, firstly we will study SA in details on its initial feasible solution choosing, initial temperature selecting, neighbourhood solution searching, efficient way of calculating for the difference of objective function values of two neighbourhood solutions, acceptance function (Metropolis function), temperature cooling, and the criteria of inner and outer loops’ stopping, etc. Then, hybrid pure SA with local (or global) search optimization methods allows us to be able to design several effective and efficient global search optimization methods. In order to keep the original sense of SA, we clarify our understandings of SA in crystallography and molecular modelling field through the studies of prion amyloid fibrils. © 2017 Nova Science Publishers, Inc