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Theoretical and Computational Molecular Science Saito Group

Location: Myoudaiji, South Laboratory Bldg. Room411
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Spatiotemporal Dynamics, Reactions, Functions

Theoretical Studies on Dynamics in Many-Body Molecular Systems

Many-body molecular systems, such as liquids and biomolecular systems, show dynamics over a wide range of spatiotemporal scales and yield various thermodynamic and dynamic properties. For example, in supercooled liquids, spatiotemporal non-uniform motions are found. The motions known as dynamic heterogeneity are now considered to be a crucial clue to understand supercooled liquids and glass transition. The heterogeneous dynamics also affect reaction dynamics. Furthermore, recent experimental and theoretical studies have demonstrated that reactions and conformational dynamics at single-molecule level are described by non-Poisson processes. In addition to these examples, it has been known that conformational changes with proper time scales are essential to protein functions. Thus, understanding of spatiotemporal heterogeneous dynamics in the many-body molecular systems is required for the elucidation of thermodynamics and dynamic properties, reactions, and functions. So far, we have studied the complicated dynamics in these systems using multidimensional spectroscopy and multi-time correlation functions. Now, we are theoretically and computationally investigating how reactions proceed and biological functions are generated in fluctuating environment and how conformational dynamics yield interesting thermodynamic properties and change toward glass transition.
 

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Scheme of enzymatic reaction. Reactions rapidly take place through ‘conformational excited states’ on a two-dimensional surface expressed by fast and slow variables.

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Schematic figure of water in terms of  low- (blue) and high- (red) density local structures. Thermodynamic and dynamic anomalies of water arise from the fluctuation between the local structures.

Selected Publications

  1. T. L. C. Jansen, S. Saito, J. Jeon, and M. Cho, "Theory of coherent two-dimensional vibrational spectroscopy," J. Chem. Phys. (Perspective) 150, 100901 (17 pages) (2019) (invited).
  2. K. Kim and S. Saito, “Multiple Length and Time Scales of Dynamic Heterogeneities in Model Glass-Forming Liquids: A Systematic Analysis of Multi-Point and Multi-Time Correlations,” J. Chem. Phys. (Special Topic: Glass Transition) 138, 12A506 (13 pages) (2013) (Invited).
  3. J. Ono, S. Takada, and S. Saito, “Couplings between Hierarchical Conformational Dynamics from Multi-Time Correlation Functions and Two-Dimensional Lifetime Spectra: Application to Adenylate Kinase,” J. Chem. Phys. (Special Topic: Multidimensional Spectroscopy) 142, 212404 (13 pages) (2015)(Invited).
  4. T. Mori and S. Saito, "Conformational excitation and non-equilibrium transition facilitate enzymatic reactions: Application to Pin1 peptidyl-prolyl isomerase," J. Phys. Chem. Lett. 10, 474-480 (2019).
  5. S. Saito and B. Bagchi, "Thermodynamic picture of vitrification of water through complex specific heat and entropy: A journey through "No Man's Land"," J. Chem. Phys. 150, 054502 (14 pages) (2019).