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Biophysics Lab
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A lab that uses computers to theoretically investigate how biomolecules work.
AboutAbout the lab
Exploring the fundamental principles of life through molecular-level theory.
The Biophysics Group studies, theoretically and through computer simulation, the mechanisms by which the functions of biomolecules arise.
Focusing on proteins and nucleic acids, the lab calculates their motions and chemical reactions in living organisms using the supercomputers of the Center for Computational Sciences.
The lab works in collaboration with a biological experiment group, and also aims to extend its research to chemical synthesis, drug discovery, and medicine.
The lab is located in the Division of Life Sciences at the Center for Computational Sciences, and its members include students from the College of Physics and the Physics Degree Program.
Key terms
- QM/MM method
- A method that combines quantum mechanics and classical mechanics to calculate molecular reactions.
- Homochirality
- The state in which, of the two mirror-image forms of amino acids, life uses almost only the L-form.
- Prion
- An infectious agent made of protein, found in mammals. It converts the normal form of a protein into an abnormal form and causes it to aggregate.
NewsLab news
Research on chiral amplification of aminonitriles accepted for publication in PCCP
A doctoral student won the Best Poster Award at the CBI Society 2024 Annual Meeting
Joint research on SFX-QM/MM published in Nature Communications
ResearchResearch themes
Life is made of macromolecules (matter), yet it has advanced functions such as self-replication and consciousness (thought). The lab aims to theoretically clarify how the functions of these biomolecules arise, using computer simulations on supercomputers.
*Illustrative imageTheoretical Analysis of Reaction Mechanisms of Biological Enzymes
For important enzymatic reactions in living organisms, the lab uses the QM/MM method, which treats a system with a mixture of quantum mechanics and classical mechanics, to theoretically uncover how the reactions proceed.
*Illustrative imageThe Origin of Life and the Bias in Amino Acids
Amino acids come in mirror-image forms, L and D. Chemical synthesis produces them in equal amounts, yet life on Earth uses almost 100% L-form (homochirality). The lab theoretically investigates the origin of this bias.
*Illustrative imagePredicting the Three-Dimensional Structure of Abnormal Prions
Prions convert normal proteins into an abnormal form and cause them to aggregate, but neither their mechanism of infection nor their three-dimensional structure has been resolved. The lab builds models and uses computer simulations to get at the essence of the structure.
MembersFaculty
The members of the Biophysics Group are faculty members, researchers, administrative assistants, doctoral, master's, and undergraduate students, and international students.As of 2026
- ProfessorYasuteru Shigeta
- ProfessorMitsuo Shoji
- ProfessorKazuhisa Tani
- Associate ProfessorRyuhei Harada
- Assistant ProfessorHengphasatporn Kowit
- Assistant ProfessorLian Duan
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “Le Centre Datarmor, ambiance spatiale (Ifremer )” Gregory Rocher / CC BY 4.0 (cropped)
- Theoretical Analysis of Reaction Mechanisms of Biological Enzymes: “PURH-enzyme 1PKX” Ayacop / Public domain (cropped)
- The Origin of Life and the Bias in Amino Acids: “Discoveries from Asteroid Bennu- Media Briefing Graphics (SVS14772 - NASA Chiral Molecules V2)” NASA's Scientific Visualization Studio - NASA/Nicola Fox, Smithsonian Institution/Timothy McCoy, Natural History Museum, London/Sara Russell, NASA/GSFC/Daniel Glavin, NASA/GSFC/Jason Dworkin, NASA/GSFC/Rani Gran, eMITS/Dan Gallagher, Jacobs-JETS/Scott Eckley, Barrios Technology Ltd/Rachel Barry, ADNET Systems, Inc./Lonnie Shekhtman / Public domain (cropped)
- Predicting the Three-Dimensional Structure of Abnormal Prions: “Protein folding schematic” Tomixdf (talk) / Public domain (cropped)
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): “Institute of nuclear and particle physics 00048 REP SDR-65 (0666)” DimitrisSideridis / CC BY-SA 4.0 (cropped) - Related lab (プラズマ物理グループ（プラズマ研究センター）
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