Computational Biophysics (B) Lab

AboutAbout the lab

Exploring how biomolecules work through physics and computation.

The Computational Biophysics Lab (B Lab) studies how biomolecules such as proteins function, using computational methods together with physics and chemistry.
Its goal is to reveal the structures and motions of biomolecular complexes, in which proteins and nucleic acids assemble together, and to understand how they work.
The lab combines experimental data from methods such as X-ray crystallography and cryo-electron microscopy with computer simulations.
The lab also studies how thermal energy flows through proteins and how energy is transferred in photosynthesis.

ResearchResearch themes

The lab aims to investigate the structures and motions of biomolecular complexes and to clarify how they work. Because malfunctions of these complexes lead to serious diseases, the lab believes that elucidating how they work is necessary for understanding diseases and developing treatments.

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Biomolecular Dynamics and Function↗

Using molecular dynamics simulations, the lab studies how proteins bind to other molecules and how they change shape. Recently, in collaboration with researchers at ITbM, it has also been studying proteins involved in the circadian clock.

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Structural Modeling That Incorporates Experimental Data↗

For molecules that are difficult to study by X-ray crystallography, the lab combines computation with low-resolution shape information obtained from methods such as cryo-electron microscopy and X-ray free-electron lasers. It develops methods to obtain atomic-level structural models, and also uses coarse-grained models.

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Thermal Energy Transfer in Proteins↗

Using condensed matter theory and molecular dynamics simulations, the lab investigates how thermal energy flows inside proteins and between proteins and solvent. With a program developed in the lab, it analyzes in detail the flow of heat and energy that accompanies molecular motion.

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Energy Conversion Mechanisms in Photosynthesis↗

The lab studies how the energy of pigment molecules that have absorbed light moves through proteins and reaches the reaction center. By analyzing electronic states and energy transfer pathways from information on the three-dimensional arrangement of pigments, it aims to understand from a physical perspective how photosynthesis works so efficiently.

VoicesStudent voices

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