Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils probed by hybrid local and global optimization searches

In recent years large-scale global optimization (GO) problems have drawn considerable attention. These problems have many applications, in particular in data mining and biochemistry. Numerical methods for GO are often very time consuming and could not be applied for high-dimensional non-convex and/or non-smooth optimization problems. The study of new algorithms which allow one to solve large-scale GO problem is very important. One technique is to use hybrid of global and local/global search algorithms. This paper presents two hybrid methods for solving the large-scale Lennard-Jones potential GO problem. The methods do not guarantee the calculation of a global solution; however results of numerical experiments show that they, as a rule, calculate a solution which is global one or close to it. One hybrid method is successfully applied to the construction of optimal atomic-resolution structures of prion (113-120) AGAAAAGA amyloid fibrils. Two successful structures constructed in this paper might be useful in furthering the goals of medicinal chemistry in this field