  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 Paper, firstly
we will study SA in details on its practical implementation. 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 modeling field through the studies of prion
amyloid fibrils.
