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Sugita Lab
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A computational biophysics lab that reproduces the motions and functions of biomolecules inside a computer.
AboutAbout the lab
Understanding life through computation, from molecules to cells
The Sugita Lab studies the mechanisms of biological phenomena using theoretical and computational science that combines physics, chemistry, and information science.
Its goal is to clarify how proteins and nucleic acids move and function at scales from molecules to cells.
The lab develops new methods that combine theoretical chemistry, such as quantum chemistry and molecular dynamics, with information science approaches such as machine learning and Bayesian statistics.
The methods it develops are incorporated into the molecular dynamics software GENESIS, which is released as free software.
Key terms
- Molecular dynamics
- A method that reproduces the behavior of molecules on a computer by calculating the motions of atoms and molecules step by step using equations of motion
- Coarse-graining
- An approach that treats groups of several atoms as single particles, making it possible to simulate large systems over long timescales
- Liquid-liquid phase separation
- A phenomenon in which molecules in a cell separate into dense liquid droplets and the surrounding liquid, like oil and water
NewsLab news
A paper by Prof. Sugita and colleagues was published in The Journal of Physical Chemistry Letters
A paper by Prof. Sugita and colleagues was published in Journal of Computational Chemistry
Prof. Sugita and colleagues were jointly awarded the FY2025 RIKEN Eiho Award
A paper by Prof. Sugita and colleagues was published in Current Opinion in Structural Biology
Results from the research group were published in Proc. Natl. Acad. Sci. USA
ResearchResearch themes
The lab aims to clarify how many biomolecules interact inside the cell to give rise to cellular functions. Using efficient simulation methods and machine learning, it calculates the motions of biomolecules on state-of-the-art supercomputers.
*Illustrative imageMultiscale Molecular Dynamics
Atomistic molecular dynamics simulations are limited in the time and length scales they can cover. The lab overcomes this limit through faster computation, algorithms based on statistical mechanics, and multiscale molecular models such as coarse-graining, and it incorporates these methods into GENESIS, which it releases publicly.
*Illustrative imageAI and Machine Learning
The lab studies how to predict molecular motions with higher accuracy by combining machine learning with multiscale molecular dynamics and by assimilating experimental and simulation data. It is also starting research that uses simulation results as databases for machine learning.
*Illustrative imageBiomolecular Dynamics
Using molecular dynamics simulation as a "computational microscope," the lab investigates the motions and functions of membrane proteins, nucleic acids, glycans, molecular motors, and more. It also works on drug-protein binding and on quantum mechanical calculations of enzymatic reactions.
*Illustrative imageMolecular Crowding in the Cell
The inside of a cell is crowded with countless biomolecules. Using simulations of systems containing many proteins and nucleic acids, the lab investigates how this environment affects molecular structure and function, as well as the mechanisms of droplets formed by liquid-liquid phase separation.
MembersFaculty
Members of the Sugita Lab (The University of Tokyo) consist of faculty and master's students.As of 2026
- ProfessorYuji SugitaPublications ↗
- Assistant Professorウガルテ ラ トレ ディエゴ
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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: “Pleiades two row” NASA Ames Research Center / Public domain (cropped)
- Multiscale Molecular Dynamics: “RIKEN AICS” J o / CC BY-SA 3.0 (cropped)
- AI and Machine Learning: “Artificial Neural Network with Chip” mikemacmarketing / photo on flickr / CC BY 2.0 (cropped)
- Biomolecular Dynamics: “Myoglobin-1mba” Opabinia regalis / CC BY-SA 3.0 (cropped)
- Molecular Crowding in the Cell: “E coli at 10000x, original” Photo by Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU. / Public domain (cropped)
- Related lab (Okada Lab): “Multicolor fluorescence image of a living HeLa cell” 8x57is / CC BY-SA 4.0 (cropped)
- Related lab (Takeuchi Lab): “B72Textur” Minutemen / CC BY-SA 3.0 (cropped)
- Related lab (Nose Lab): “Drosophila larvae mariometzler” Mario Metzler / CC BY 2.5 (cropped)
- Related lab (Biological Nonequilibrium Physics Lab): “Nematic liquid crystal” Ingo Dierking / CC BY-SA 4.0 (cropped)
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