Seminar

Engineering Research Seminar Series 30, 2011: (i) Dynamical Reaction Theory Based on Global Phase Space Structures (ii) Time Series Analysis using Wavelet toward Molecular Dynamics Simulation of Proteins

Prof. Mikito Toda, from Nara Women’s University, Japan


Date: 2011-08-16
Time: 12:00 to 13:30
Venue: Lecture Theatre 6-0-06


Abstract

(i) Dynamical Reaction Theory Based on Global Phase Space Structures

The speaker will give a review of the recent development of the reaction theory which is based on the dynamical view point. The theory relies on the concept of normally hyperbolic invariant manifolds (NHIMs),and has been developed by many researchers including our group. The dynamical reaction theory enables us to go beyond the conventional statistical reaction theory, and can be applied to reaction processes far from equilibrium.

(ii) Time Series Analysis using Wavelet toward Molecular Dynamics Simulation of Proteins

The speaker will give a talk on our recent study of time series analysis using wavelet and singular value decomposition (SVD) toward molecular dynamics simulation of proteins. The wavelet enables us to reveal transient non-stationary aspects, and SVD can be used to extract collective behavior involving many amino acids. We have applied the method to all-atom simulation of Adenylate Kinase (AK), and other proteins which play the role of enzymes. The method reveals some interesting aspects of dynamical behavior of proteins such as cracking, i.e., temporal deformation of secondary structures.

About the Speaker

Professor Mikito Toda obtained his PhD in Science at Kyoto University in 1986. After his PhD work on quantum chaos, he expanded his research area to dynamics of chemical reactions.  His current main research areas are (1) dynamical reaction theory, (2) time series analysis of the dynamics of proteins, (3) entanglement in quantum chaos and its application in quantum information. Prof. Toda has published more than 30 journal papers, including six in the prestigious physics journal - Physical Review Letters.  He was also co-editor of the special volume of Advances in Chemical Physics featuring dynamical reaction theory and its application to reaction processes in complex systems such as clusters and proteins.  He is a member of the Physical Society of Japan and Biophysical Society of Japan.