We perform theoretical analysis, molecular dynamics simulations, various experiments (e.g., single molecule fluorescence microscopy imaging) to understand life based on physical principles at the molecular level.

Biological phenomena

Our study target includes all the molecular biological phenomena.

Molecular level

Modern biological science has been developed maintaining a basic stance of understanding phenomena at the molecular level. There is little doubt that molecular level approaches offer the most direct understanding of biological phenomena from physical principles.

Concreteness

In textbooks of cellular molecular biology and biochemistry, there are complex and sophisticated schemes explaining the biological phenomena as if someone directly looks inside a cell. They are summarized in a series of beautiful figures. However, if you ask whether a randomly chosen simple process represented by an arrow in the schemes is realizable based on physical principles, the answer remains unknown in most cases. As such, these textbooks are treasure houses of biophysical study themes. We think that it is more fun to aim at a detailed understanding of individual phenomena, which brings attractive biophysical questions, rather than to simply accept an abstract or philosophical generalization. If you think twice, that arrow drawn in your textbook course might not be so simple as expected or might even be completely inconsistent with physics. Our work is guided by the belief that, in biophysics, reconsideration of these arrows based on physical principles deepens our understanding of biological phenomena.

Physical principles

In the textbooks, there are a lot of descriptions like "X proceeds using ATP hydrolysis energy." Indeed, it is correct in terms of energy balance that the endergonic reactions that absorb a smaller energy than that released upon ATP hydrolysis can proceeds using the ATP hydrolysis energy. However, the molecular mechanism of the conversion from ATP hydrolysis to mechanical energy is not trivial at all and sometimes seems miraculous. To understand biological phenomena based on physical principles is to understand the molecular mechanisms.

Emphasizing the physical basis does not necessarily mean pursuing novel physics. After all, our research targets are biological phenomena, and so we try to understand them as well as possible. A deep understanding of biology must be based on physical principles because all biological phenomena are no exception to the laws of physics. If well-known physical principles are sufficient to explain a phenomenon, as it should be usually the case, we do not need to bring up new physics. If not, we will face the task of discovering the new physical principle or concept required to understand the problem under study.

I entered the university while vaguely thinking that I would like to learn Mathematics and Physics. There, I enjoyed physics and chemistry, though mathematics was too difficult for me. I had a feeling of not being good at Biology because I was not able to overcome the image from high school that Biology is a purely memorization-based subject. Thus, I did not take any Biology classes as an undergraduate and master course student. I do not remember if I knew the concept of the "double helix" when I finished the master course. But eventually I became a faculty member of Bioscience, so one never knows what will happen.

Based on my experience, I would like to say that you can join our laboratory even if you do not have any biological knowledge. However, you should try to read through thick textbooks of molecular cellular biology after joining us. To make an extreme argument, I would say this laboratory is probably most suitable for people who have studied basic physics and chemistry and begun to think that biology seems to be interesting.

Graduate students

We are looking for graduate students to join our lab. The students are expected to design, perform, and accomplish their research independently as much as possible. Please contact us by e-mail if you are interested in and visit us. You should take the summer entrance examination of Division of Biology, Graduate School of Science, Kyoto University.

Postdoctoral researchers

We are looking for postdoctoral researchers to join our lab and engage in research about biomolecular simulations. Please contact us by e-mail if you are interested in.

Contact

Prof. Shoji Takada (takada at biophys.kyoto-u.ac.jp)