Laboratory

Computational Biophysics Research Team
RIKEN Center for Computational Science
(Team Principal: Yuji Sugita)

Research Field and Overview

This team performs molecular dynamics (MD) simulations to elucidate the structure, dynamics and function of biological macromolecules in various intracellular environments. Unlike dilute solutions, the cytoplasm is a crowded environment with huge number of proteins, nucleic acids and metabolites. Biological membranes also contain various lipid molecules, cholesterol and membrane proteins, and act as a platform for many biological phenomena. In order to understand biomolecular dynamics in such environments, we have developed multi-scale MD simulations using coarse-grained models, all-atom models, and QM/MM models. We have developed GENESIS software for multi-scale MD simulations with enhanced sampling methods, free energy calculations, and data-driven molecular dynamics. Large-scale simulations are performed using the Fugaku supercomputer and other systems to study molecular dynamics in the intracellular environments.

Job title and job description

Job title

Research Scientist: 1 person

Job description

Perform one or more of the following research duties

• (1)Development of multi-scale molecular models (coarse-grained molecules, all atoms, QM/MM) and calculation methods.
• (2)Introduce and upgrade the above models and computational methods into GENESIS, the software being developed by our team.
• (3)Applied calculations for biomolecular or material science systems using “Fugaku”.
• (4)Improve the efficiency of simulation research using machine learning.
  In addition to the execution of the above research and development tasks, the incumbent will also be responsible for various tasks in the assigned research team and the RIKEN Center for Computational Science, and also promoting our research not only within our research team, but also in collaboration with other research teams and researchers from domestic and international research institutes, universities, and companies.

Qualifications

Doctoral degree (or equivalent research ability and background) in the relevant research field

Work location

RIKEN Center for Computational Science, Integrated Innovation Building 7F
6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan

RIKEN may order the employee to change work locations, if necessary.
Potential sites of relocation: Any campus, branch, or office as ordered by RIKEN.

Conditions, Salary and Benefits

This post is an indefinite-term employment position. Mandatory retirement age for FY 2025 and FY 2026 is 62 years old.
Note: RIKEN has been increasing the mandatory retirement age by one year every two years from FY 2023.
There is a Special Temporary Employment Program that allows employees to be rehired and continue working until age 65.
As an exception, depending on screening results, the successful candidate may be initially employed on a fixed-term employment contract up to a maximum of 5 years with the possibility of being promoted to indefinite-term employment after a separate review process that will take place, as a general rule, at the end of the first 3 years of employment. Remuneration and work conditions for fixed-term employment are based on the same conditions as those for indefinite-term employment.

Full time. This position falls under the specialized duties discretionary work system; one working day will be calculated as 7 hours and 30 minutes.

In principle, the first two months of employment is considered a trial period.

Salary will be an annual salary based on experience, ability, and performance, and will consist of a base salary and a variable salary. The variable salary will be determined each fiscal year based on experience, ability, and performance. Discretionary work, commuting and housing allowances will be provided. Social insurance will be applied. Bonuses or retirement benefits will not be paid.

Approximate salary at the time of employment.
The monthly salary including discretionary work allowance at the time of employment will be 510,000 JPY or more.

RIKEN has implemented a telecommuting system that allows employees to work from home etc.

Days off include public holidays, New Year's holidays (Dec. 29 - Jan 3), and RIKEN Foundation Day.
Paid leave includes annual paid leave (up to 20 days depending on the month of employment), special paid leave (caring for a sick child, family nursing care, etc.), and work-life balance holidays (up to 7 days depending on the month of employment).
There are also additional leave systems such as maternity leave, childcare leave, and family nursing care leave.
Smoking is entirely prohibited on site.
These and other provisions are in accordance with RIKEN regulations.

Mandatory membership in the RIKEN Mutual Benefit Society (RIKEN Kyosaikai).

RIKEN may require changes of responsibilities, job category, and work place based on RIKEN regulations due to management decisions, budgetary situation, and organizational restructuring.

• *Eligible to apply for Grants-in-Aid for Scientific Research (Kakenhi).
• *RIKEN is actively undertaking initiatives to promote gender equality and diversity, and moving forward with the establishment of a diverse and vibrant research environment. If multiple candidates are found to have the same aptitude following a fair assessment, active efforts will be made to recruit female candidates.
• *The Kobe Campus has an on-site daycare, Po-I Kids Kobe. For details, please send an email to the General Administrative Section at kobe-kosei@riken.jp.

Application and required documents

Application documents

All the application documents should be prepared in English. (Only letters of recommendation may be either in English or in Japanese)

• 1.CV or CV
  • *Email address is required.
  • *Application Number [25-1453] should be clearly written at top-right in the margin.
  • *Format is free. Or the format attached is available.
• 2.Research and development achievements (list of publications, list of patents, list of presentations etc. including ResearcherID or Google Scholar ID, if available)
• 3.Lists of external funds received, awards received, and other achievements including contribution to society through activities in scientific societies, joint research projects, technology transfers, and the like.
• 4.Outlines of your research and development projects to date (3 pages, A4 size)
• 5.Your future research and development plans and perspectives if you are accepted for the position (3 pages in A4 size in total)
• 6.One set of copies of your major papers (maximum number: 5, For open access papers, links are also acceptable.)
• 7.Consent form for handling personal information based on GDPR/UK GDPR
  If you are a resident of the European Economic Area (EEA) or the UK, you are required to sign and submit the document, “Consent form for handling personal information based on Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC (General Data Protection Regulation) and the United Kingdom General Data Protection Regulation.”
  • *For residents of the EEA, you will find detailed information about the General Data Protection Regulation (GDPR) on the following website:
    Data protection | European Commission
  • *For residents of the UK, you will find detailed information about Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data (United Kingdom General Data Protection Regulation) on the following website:
    The UK GDPR | Information Commissioner’s Office
• 8.Letters of recommendation from two persons who can evaluate your work
  • *One letter should be written by the applicant’s current supervisor. If this is difficult to provide, letters of recommendation written by third parties may be accepted. However, any letters of recommendation should be written by persons do not belong to Computational Biophysics Research Team.
  • *Both letters of recommendation should not come from the same institution.

How to apply

• -Combine the above documents (items 1 to 7), except the letters of recommendation, into a single PDF file and upload the file to the following link:
  25-1453 Applications for R-CCS Computational Biophysics Research Team.
• -The file name of the PDF should contain the job ad number " 25-1453, R-CCS Computational Biophysics Research Team" and the applicant's name.
• -After uploading the PDF file, please email us (r-ccs-recruit@ml.riken.jp) know the file name of the uploaded file. When you send us an email, please write your name, job ad. number and the name of the position that you are applying for.
• -Please make the email subject line: "[applicant’s name] 25-1453 R-CCS Computational Biophysics Research Team application documents"

About letters of recommendation

• - Letters of recommendation must be directly uploaded from the referees to the website mentioned above with the file name "[applicant’s name] letter of recommendation for Computational Biophysics Research Team Application”. Please tell the referees to email us (r-ccs-recruit@ml.riken.jp) that they have uploaded the PDF file and to specify the applicant's name, referee's name and contact information in the body of the email.
  There is no set format for the letters of recommendation, but they must meet the following conditions: they must be addressed to the President of RIKEN, Makoto Gonokami, and include the date of issue. Please specify the referee’s contact information (Name, affiliation, job title, phone number, and email address).

If a confirmation email is not received within 7 days after submission, please contact: r-ccs-recruit@ml.riken.jp

Note: All the submitted documents will not be returned.

Deadline

Noon, November 20, 2025 (Japan time)

Handling Personal Data

Submitted documents are strictly protected under the RIKEN Personal Information Protection Regulations and will be used only for the purpose of applicant screening at RIKEN. Personal information will not be disclosed, transferred or loaned to a third party under any circumstances without just cause.

Selection process

After application documents are screened, only the successful candidates will be asked to have an interview. There will be the final interview with RIKEN executives as part of the hiring process. We will notify all applicants regardless of acceptance or rejection.

Notification of hiring decision

The notification of hiring decision (conditional offer of employment) regarding this selection shall be carried out through the presentation of Statement of Working Conditions or a Conditional Offer of Employment issued by RIKEN.

Start of Employment

RIKEN expects that the successful candidate will be able to take up this position at the earliest opportunity after April 1, 2026.
Other conditions at the time of appointment will be negotiable.

Contact Information

For inquiries on research conducted by the Team, please contact the Team Principal by email below.
Dr. Yuji Sugita
Computational Biophysics Research Team of RIKEN Center for Computational Science (R-CCS)
Email: sugita@riken.jp

Note: No inquiries on the selection process and results will be answered.