{Theoretical, Computational} Biophysics Researcher
 冨樫 祐一  研究者@{理論,計算}生物物理

Research Interests

Small Reaction Systems
- Effects of Fluctuations and Molecular Discreteness

In biochemical systems, there are lots of chemical species, but the total amount per cell is not large; i.e., some chemicals are rare (*). An extreme case is genome DNA; there are only 1 to a few copies in a cell. We investigate effects of finite-size fluctuations or discreteness in numbers of molecules for such rare species.
(*) Suppose that the cell volume is 1um3 (bacteria). If there are 10000 chemicals, 1000 molecules/cell each, with average molecular weight 10kDa, then the total concentration is 170g/L.

We ran a project "Spying Minority in Biological Phenomena" with experimentalists (2011-2016), and are still in collaboration. For further information, please see the project web-site.

Dynamical Properties of Molecular Machines

Biological cells utilize a variety of molecular machines (enzymes, motors, pumps and channels, etc.) for their activities. In these molecules, the function is often coupled with their motion (conformational changes). We study their dynamical properties by molecular dynamics simulations, using either or combination of all-atom and coarse-grained modeling, to understand their operation principles.

Modeling Molecular Machinery in the Cell

We are currently modeling systems consisting of molecular machines, as an expansion of reaction diffusion systems, taking into account features of the intracellular environment, e.g.:
- Excluded volume effects and congestion of molecules,
- Complex/complicated membrane structures,
- Active transport, which itself is driven by molecular machines.

Particularly, we are interested in the relationship between the structure and function of the chromatin strucure, a hybrid structure of DNA and proteins, in the cell nucleus.
Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University

Information Processing exploiting Fluctuations
- Application of Biological Mechanisms to Artificial Systems

In future:
Once we have described operation and design principles of a certain biological system in a theoretical or algorithmic way, it is highly expected that we can create an artificial device performing the same or similar function but made from different materials. Such a system may transcend the limitations of natural biomolecules.


Information about these publications is also available through

Acknowledgments: These research works were in part supported by Grants-in-Aid for Scientific Research (11CE2006, 15-11161, 20740243, 23115007, 16K05518, 16H01408, 18KK0388, 18H04720, 19H05424, 21K03487), Special Coordination Funds for Promoting Science and Technology (Yuragi Project), and Platform for Dynamic Approaches to Living System from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and Research Fellowships from the Japan Society for the Promotion of Science (15-11161, research abroad H17).
以上の研究は、文部科学省 科研費(特別推進研究(COE)・特別研究員奨励費・若手研究(B)・新学術領域研究・基盤研究(C)・国際共同研究強化(A))・科学技術振興調整費(先端融合領域イノベーション創出拠点の形成)・研究開発施設共用等促進費補助金(生命動態システム科学推進拠点事業)、並びに、日本学術振興会 特別研究員・海外特別研究員制度の支援を受けて行われました。

Ph.D., Professor
(冨樫 祐一, 立命館大学生命科学部生命情報学科, 教授)
Department of Bioinformatics, College of Life Sciences, Ritsumeikan University
1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
Tel. +81-77-561-4898 / Fax +81-50-3737-2462
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Also as:
Guest Professor, Applied Information Systems Research Division, Cyber Media Center, Osaka University
Senior Visiting Scientist, Laboratory for Cell Field Structure, RIKEN Center for Biosystems Dynamics Research (BDR)