Experiences on memetic computation for locating transition states in biochemical applications

• Main Authors: Ellabaan, Mostafa Mostafa Hashim, Ong, Yew Soon
• Other Authors: School of Computer Engineering
• Format: Conference or Workshop Item
• Language: English
• Published: 2013
• Subjects: DRNTU::Engineering::Computer science and engineering
• Online Access: https://hdl.handle.net/10356/100754; http://hdl.handle.net/10220/16295
• Institution: Nanyang Technological University

Transition states constitute an essential component of the chemical reaction rate theory and are important for understanding the structural and mechanical properties of the systems, and how they react under different environmental conditions. The challenges behind the discovery of transition states however arise from the existence of a large number of rules and constraints as well as the computational complexity involved in energy calculations. In this paper, we present some recent successes of memetic computation and experiences for the discovery of first-order saddle points or transition states in biochemical systems. We show that the exploitation of a priori knowledge on the inherent structure of the problem in the form of memetic search operators led to enhanced search convergence and solution quality. This paper then concludes with a brief discussion on the potentials for the redefinition of memes not only as symbiosis of search operators but as building blocks for complex biochemical systems.