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Theoretical Biophysics Lab
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The lab explores molecular-level life phenomena through theory and simulation.
AboutAbout the lab
Decoding the molecular mechanisms of life through computation.
The Theoretical Biophysics Lab aims to understand the molecular mechanisms of fundamental life phenomena from a biophysical perspective.
Using theory, simulation, and single-molecule experiments, the lab studies the regulation of gene expression, the dynamic structure of chromosomes and chromatin, DNA replication and repair, and the workings of biomolecular machines.
The lab also uses methods from molecular evolution to explore the relationship between evolution at the level of form and behavior and evolution at the level of genes.
Key terms
- Molecular simulation
- A method of reproducing the motions of atoms and molecules on a computer to study how they function.
- Chromatin
- A structure in which DNA is wound around proteins; it forms the basis of chromosomes.
- Choanoflagellate
- A single-celled organism most closely related to animals. It offers clues to the origin of animal multicellularity.
NewsLab news
View More ↗ResearchResearch themes
Aiming to understand the molecular mechanisms of fundamental life phenomena from a biophysical perspective, the lab conducts molecular-level theoretical, simulation, and single-molecule experimental research, as well as research on molecular evolution.
*Illustrative imageMultiscale Molecular Simulation
The lab tackles genome structure and the regulation of gene expression, the operating principles of molecular motors, and the structural dynamics of proteins using multiscale molecular simulation.
*Illustrative imageSingle-Molecule Experiments and Simulation
The lab combines single-molecule experiments with molecular simulation to elucidate, at the level of molecular mechanisms, DNA replication, transcription, repair, and the formation of higher-order structures, which are fundamental processes of life.
*Illustrative imageInformation Analysis of Measurement Data
Using cutting-edge information science techniques, the lab develops methods for obtaining findings with high temporal and spatial resolution from measurement data of biomolecules, such as data obtained by high-speed atomic force microscopy.
*Illustrative imageMolecular Evolution and Animal Multicellularity
Using molecular phylogenetic inference, the lab analyzes the sequences of gene families and studies diversification through gene duplication and domain shuffling. By comparing the genomes of choanoflagellates, the protists most closely related to animals, it studies the evolution of animal multicellularity.
MembersFaculty
The members of the Theoretical Biophysics Lab are faculty members, postdoctoral researchers, doctoral and master's students, and undergraduates doing graduation research.As of 2026
- ProfessorShoji Takada
- Associate ProfessorTsuyoshi Terakawa
- Program-Specific LecturerGiovanni Brandani
- Assistant ProfessorNaoyuki Iwabe
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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: “Schematic of a single-tethered DNA curtain” Soyeong An, Youngseo Kim, and Ja Yil Lee / CC BY 4.0 (cropped)
- Multiscale Molecular Simulation: “Spindle Dynamics During the Mitotic Cell Cycle of HeLa Cells” Amina Aidarbek / CC BY 4.0 (cropped)
- Single-Molecule Experiments and Simulation: “Single YFP molecule superresolution microscopy” Andy Nestl / CC BY-SA 3.0 (cropped)
- Information Analysis of Measurement Data: “Cell membrane with proteins visualized by AFM” Nucturra / CC0 (cropped)
- Molecular Evolution and Animal Multicellularity: “Desmarella moniliformis” Sergey Karpov / CC BY-SA 3.0 (cropped)
- Related lab (Kawaguchi Lab): “Neurons (Purkinje cells)” Lennart Rikk / CC0 (cropped)
- Related lab (Molecular Biological Information Lab): “Mouse cone and rabbit rod nuclei” Irina Solovei, Moritz Kreysing, Christian Lanctôt, Süleyman Kösem, Leo Peichl, Thomas Cremer, Jochen Guck, Boris Joffe / CC BY 2.5 (cropped)
- Related lab (Kyoto University Institute for the Evolution of Human Behavior (Eishi Hirasaki) Lab): “Coquerel's sifaka lemur (Propithecus coquereli) terrestrial locomotion” Charles J. Sharp / CC BY-SA 3.0 (cropped)
- Related lab (Kyoto University Museum Lab): “Kyoto University Museum” J o / CC BY-SA 3.0 (cropped)
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