Advancing Theory for Kinetics and Dynamics of Complex, Many-Dimensional Systems

Series Editors Stuart A. Rice received his master's and doctorate from Harvard University and was a Junior Fellow at Harvard for two years before joining the faculty of The University of Chicago in 1957 where he remains a well-known theoretical chemist who also does experimental research and is currently the Frank P. Hixon Distinguished Service Professor Emeritus at The University of Chicago. Professor Rice has served the university in a wide variety of capacities during his forty-eight year tenure. He served as the director of the James Franck Institute (the university's center for physical chemistry and condensed matter physics) from 1961 to 1967, was Chairman of the Department of Chemistry from 1971 to 1976 and was Dean of the Physical Sciences Division from 1981 to 1995. In 1999 he received the National Medal of Science. In addition to his work at the University, he is currently on the Board of Governors at Argonne National Laboratory, managed by and affiliated with The University of Chicago, as well as Tel Aviv University. He has served as editor for Chemical Physics Letters, in addition to the series on Advances in Chemical Physics. He currently maintains a full research lab but has retired from teaching classes.  Aaron R. Dinner received his bachelor's degree and doctorate from Harvard University, after which he conducted postdoctoral research at the University of Oxford and the University of California, Berkely. He joined the faculty at the University of Chicago in 2003 and is the Principal Investigator of The Dinner Group, which develops and applies theoretical methods for relating cellular behavior to molecular properties. Volume Editors Tamiki Komatsuzaki is a professor at Hokkaido University in Japan and his research interests include complexity of protein landscape, conformation network and dynamics, developments of new methodologies and concepts to bridge molecules and life based on single molecule time series, information flow across hierarchies of time and space and its relation to biological functions, and adaptability, robustness and emergence in complex systems R. Stephen Berry is James Franck Distinguished Service Professor in the Department of Chemistry and the James Franck Institute at the University of Chicago. His research interests include structures, properties and dynamics of clusters and biopolymers. David M. Leitner is a Professor in the Departments of Theoretical and Biophysical Chemistry and Chemical Physics at the University of Nevada, Reno. His research interests include how energy flows within a molecule mediates the rate at which it reacts both in gas and condensed phases.

Preface xi

Non-Markovian Theory of Vibrational Energy Relaxation and its Applications to Biomolecular Systems 1
By Hiroshi Fujisaki, Yong Zhang, and John E. Straub

Protein Functional Motions: Basic Concepts and Computational Methodologies 35
By Sotaro Fuchigami, Hiroshi Fujisaki, Yasuhiro Matsunaga, and Akinori Kidera

Non-Brownian Phase Space Dynamics of Molecules, the Nature of Their Vibrational States, and Non-RRKM Kinetics 83
By David M. Leitner, Yasuhiro Matsunaga, Chun-Biu Li, Tamiki Komatsuzaki, Akira Shojiguchi, and Mikito Toda

Dynamical Reaction Theory Based on Geometric Structures in Phase Space 123
By Shinnosuke Kawai, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki, and Mikito Toda

Ergodic Problems for Real Complex Systems in Chemical Physics 171
By Tamiki Komatsuzaki, Akinori Baba, Shinnosuke Kawai, Mikito Toda, John E. Straub, and R. Stephen Berry

Author Index 221

Subject Index 247