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SASAI Masaki


Theoretical Biological Physics


Our primary goal is to contribute to the research and education of an emerging interdisciplinary field, theoretical biological physics. Advances in quantitative biological physics have revealed that molecules and reactions in life systems are subjected to intense stochastic fluctuations. We study the roles of flexibly fluctuating dynamics in life phenomena by using computer simulations and statistical physical analyses.

Department of Applied Physics and Department of Computational Science and Engineering,
Nagoya University

Office:Room # 471, South, building#3 of School of Engineering
Phone +81-52-789-4763 / fax: +81-52-789-3719
Secretary: (Eiko Matsunami) +81-52-789-3718
matsunami[at]tbp.cse.nagoya-u.ac.jp

e-mail: sasai[at]nuap.nagoya-u.ac.jp
Please replace [at] with @

Education :
March 1980, Graduated from School of Science, Kyoto University
March 1985, Graduated from Department of Physics, Graduate School of Science, Kyoto University
May 1985, Received, Doctor of Science (Kyoto University)

Academic experience:
August 1985, Research Associate, Institute for Molecular Science (Okazaki)
April 1992, Associate Professor, Graduate School of Human Informatics, Nagoya University
April 1998, Professor, Graduate School of Human Informatics, Nagoya University
April 2006, Professor, Department of Computational Science and Engineering, Nagoya University

April 2017, Professor, Department of Applied Physics, Nagoya University

October 2003, Institute for Advanced Research Professor, Nagoya University
September 2008, KIAS scholar, Korea Institute for Advanced Study
April 2010, Affiliate Professor, Okazaki Institute for Integrative Bioscience

Publications




Projects

Protein folding and function
Proteins often express their function in timescale of milliseconds to seconds. In such macroscopic timescale, protein structure change should not follow a definite sequential pathway but should undergo stochastic movement characterized by diffusion on the energy landscape. Because energy landscape itself is subject to dynamical change upon reactions or binding, “dynamical energy landscape” should be a key concept to study protein functioning. We develop theoretical methods of dynamical energy landscape and apply those methods to enzymes, signal transduction, and molecular motors.

(1) Development of a consistent coarse-grained model of allosteric transitions
     T. P. Terada, T. Kimura and M. Sasai, J. Phys. Chem. B, 117, 12864-12877 (2013).

(2) Development of the Ising-like models of folding and allosteric transitions
    T. Inanami, T. P. Terada, and M. Sasai, Proc. Natl. Acad. Sci. USA, 111, 15969-15974 (2014).
    K. Itoh and M. Sasai, J. Chem. Phys., 134, 125102 (2011).
    K. Itoh and M. Sasai, Proc. Natl. Acad. Sci. USA, 107, 7775-7780 (2010).

    K. Itoh and M. Sasai, J. Chem. Phys., 130, 145104 (2009).

(3) Application of dynamical energy landscape method to myosin motors
    Q.-M. Nie, A. Togashi, T. N. Sasaki, M. Takano, M. Sasai, and T. P. Terada, PLoS Comp. Biol., 10, e1003552 (2014).
    M. Takano, T. P. Terada, and M. Sasai, Proc. Natl. Acad. Sci. USA, 107, 7769-7774 (2010).
   


Genome 3D structure and dynamics
Genome is not an abstract sequence of information but is a physical quantity confined in nucleus. Genome architecture and movement are studied by using computational approaches.
    K. Maeshima, S. Ide, K. Hibino, and M. Sasai, Curr. Opin. Genetics and Development. 37, 36-45 (2016).
    N. Tokuda, T. P. Terada, and M. Sasai, Biophys. J. 102, 296-304 (2012).


Stochastic cell biology
Noisy fluctuations are inevitable features of chemical reactions in cell, which should lead to cell-to-cell variation in a genetically identical population of cells. One of the important issues in modern cell biology is to understand how the molecular reaction network bearing such noisy fluctuations produces the orchestrated behavior for functioning.


(1) Noisy dynamics of gene switches is represented by
eddy current on the landscapes by using a mean-field description in a path-integral representation of switching dynamics
    K. Zhang, M. Sasai, and J. Wang, Proc. Natl. Acad. Sci. USA 110, 14930-14935 (2013).

 M. Sasai and P. G. Wolynes, Proc. Natl. Acad. Sci. USA, 100, 2374-2379 (2003).

(2) In eukaryotes, gene switches are regulated by various processes including chromatin structure change, histone modification, and DNA methylation. These epigenetic processes have hierarchically different timescales. We develop models to analyze the integrated systems behavior of epigenetic dynamics.
    S. S. Ashwin and M. Sasai, Scientific Reports 5 , 16746 (2015).
  M. Sasai, Y. Kawabata, K. Makishi, K. Itoh, and T. P. Terada, PLoS Comput. Biol. USA 9, e100338 (2013).

(3) Circadian rhythm arising from protein-protein interactions is studied by using KaiABC system as a model system.
    T. Nagai, T. P. Terada, and M. Sasai, Biophys. J. 98, 2469-2477 (2010).


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