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Computational Biophysics

COMPUTATIONAL BIOPHYSICS RESEARCH TEAM

LEAD PI: YUJI SUGITA 

This project aims to perform molecular simulations using advanced methods such as enhanced sampling algorithms, free-energy calculations, and multi-scale simulations for understanding structure-dynamics-function relationships in biomacromolecules. Target systems will be determined after discussion between my team and the participants. 

In our group, there are several senior research scientists who are experts in at least one of the simulation techniques, who can mentor participants, depending on their specific research interests:

  • Membrane proteins and multi-scale simulations - Chigusa Kobayashi
  • QM/MM simulation for enzymatic reactions - Kiyoshi Yagi
  • Development of high-performance software and algorithm - Jaewoon Jung
  • Membrane proteins, multi-scale simulations, enhanced conformational sampling, and free-energy calculations - Yuji Sugita

Students participating in this project will: (i) contribute to application studies using GENESIS and our multi-scale simulation methods; (ii) provide substantial feedback to improve the software; and (iii) learn advanced simulation techniques.

Participating students and their U.S. mentors interested in continuing longer term collaborations with our group, are welcome to do so either by:

  1. using our methods and software, and we will keep in contact for sharing new methods and models. OR
  2. using our software as one of the platforms for developing (by themselves) new methods for their applications. 

Participants and their co-mentors can comply with RIKEN rules, in particular regarding network security, software licenses, and so on. The institute is very strict about this. Participants can attend group meeting (like other graduate students and scientists) and will hear unpublished information from the group. Unpublished information must be kept confidential until they are published. Discussion in the meetings is done using English, since we have many non-Japanese postdocs and scientists.

REQUIRED SKILLS

Students applying to this project are expected to have:

  1. Basic knowledge in physical chemistry and experiences in classical molecular dynamics and/or quantum chemistry are required. 
  2. Based on the basic skills, we can teach the participants advanced methods in molecular simulations. 

COMPUTATIONAL RESOURCES

US students and their mentors can use our resources, upon agreeing on the rules and regulations of Japanese Export Control and Act and compliance with the Foreign Exchange and Foreign Trade Act. US students will get access to: