Since 2025, Yuji Sugita has started a research laboratory in the Department of Physics, Faculty of Science & Graduate School of Science, The University of Tokyo, and has taught courses on “Biophysics” and related subjects. Yuji Sugita has conducted intensive lectures at other universities and has participated in the GENESIS Users’ Group, where we discuss the application of molecular dynamics using the GENESIS software.
In 2026, Yuji Sugita will be teaching the First-Year Seminar (S Semester: Komaba Campus to 1st-year students) and Biophysics (A Semester: Hongo Campus to 3rd-year students). Lecture materials will be provided via UTokyo Slack or UTOL.
Fourth-year students in the Department of Physics, Faculty of Science, The University of Tokyo, conduct either “Special Experiments” or “Theoretical Seminars” in the Department of Physics laboratories. During S Semester (April–July) and A Semester (October–January), students are assigned to different laboratories. The Sugita Lab is responsible for the “Theoretical Seminar” on “Computational Biophysics”. Students who wish to confirm the details of laboratory activities should contact the faculty members directly.
Computational biophysics is a field situated at the intersection of physics, chemistry, computer science, and life sciences. Therefore, a foundation of knowledge across multiple research fields is required before beginning actual research. Through group readings of textbooks and papers, as well as computer exercises conducted in this theoretical seminar, we will build the foundation necessary to conduct cutting-edge research in computational biophysics. In the computer lab sessions, we will conduct molecular dynamics exercises using GENESIS tutorials and machine learning exercises. We will also introduce Linux and visualization tools (such as VMD).
To date, Yuji Sugita has conducted intensive courses on molecular dynamics simulations at numerous universities in Japan. In 2026, Yuji Sugita will lead an intensive course on “Biophysics” at the Graduate School of Gakushuin University.
GENESIS is molecular dynamics software developed primarily by RIKEN and is used for a wide range of applications, from life sciences and drug discovery to materials science and material development. As it is free software licensed under the LGPL v3, it can be freely used not only by academia, such as universities and research institutions, but also by private companies and other organizations. The GENESIS Users’ Group aims to provide a forum where developers and users can discuss directly, with the goal of promoting goal-oriented development of GENESIS features and expanding the user base and usage. Meetings are held approximately three times a year, both online and in person.