Curriculum Vitae

General Research Interests

My research aims to develop theoretical and computational frameworks to understand biological processes at the cellular scale. I specialize in bridging statistical physics, continuum mechanics, and biological modeling to explain phenomena such as DNA loop extrusion, phase separation, and protein aggregation. Where analytical models are intractable, I apply molecular dynamics simulations to test and refine theoretical predictions.

Professional Experience

Education

Publications

First/Corresponding Author

• Active Loop Extrusion guides DNA-Protein Condensation
  R. Takaki, Yahor Savich, Jan Brugués, and Frank Jülicher.
  Physical Review Letters 134.12 (2025), p. 128401.
• Sequence complexity and monomer rigidity control the morphologies and aging dynamics of protein aggregates
  R. Takaki and Dave Thirumalai.
  Proceedings of the National Academy of Sciences 121.50 (2024), e2409973121.
• Theory of Rheology and Aging of Protein Condensates
  R. Takaki, Louise Jawerth, Marko Popović, and Frank Jülicher.
  PRX Life 1 (Aug. 2023), p. 013006.
• Information flow, gating, and energetics in dimeric molecular motors
  R. Takaki, Mauro L Mugnai, and D Thirumalai.
  Proceedings of the National Academy of Sciences 119.46 (2022), e2208083119.
• Theory and simulations of condensin mediated loop extrusion in DNA
  R. Takaki, Atreya Dey, Guang Shi, and Dave Thirumalai.
  Nature Communications 12.1 (2021), p. 5865.
• How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics
  R. Takaki, Mauro L Mugnai, Yonathan Goldtzvik, and D Thirumalai.
  Proceedings of the National Academy of Sciences 116.46 (2019), pp. 23091–23099.

Co-Author

• Structural changes in chromosomes driven by multiple condensin motors during mitosis
  Atreya Dey, Guang Shi, R. Takaki, and Dave Thirumalai.
  Cell Reports 42.4 (2023).

Under Review

• Fibers and Glasses are Competing Material States in FUS Protein Condensation
  Liru Feng, Iain Muntz, R. Takaki, Lionel Ndamba, Martine Ruer-Gruß, Frank Jülicher, and Louise Jawerth.
  Under review (2025).
• Fluctuation-Response Theory of Non-Equilibrium Complex Fluids
  R. Takaki and Frank Jülicher.
  arXiv preprint arXiv:2510.15559; Under review (2025).

Book Chapter

• Introduction to Stochastic Kinetic Models for Molecular Motors
  Mauro L. Mugnai, R. Takaki, and D. Thirumalai.
  Physics of Molecular and Cellular Processes. Springer International Publishing, 2022, pp. 117–146.

For a complete list of citations, please visit my Google Scholar profile.

Teaching Experience

Conferences / Presentations

Talks

• Physics of Life day (2023, Dresden, Germany)
• Soft matter seminar at Kyusyu university (2023, Fukuoka, Japan)
• APS March Meeting (2023, Las Vegas, USA)
• The Molecular Biology Society of Japan (Invited) (2022, Tokyo, Japan)
• iPoLS district meeting (2019, Rice university, USA)
• Nonlinear science research meeting (2015, Waseda university, Japan)

Posters

• Driven and active amorphous matter (2025, Göttingen, Germany)
• StatPhys29 (2025, Florence, Italy)
• Mechanics of Life II Workshop (2023, New York, USA)
• 7th Edwards Symposium (2023, Cambridge, UK)
• Annual Biophysical Society meeting (2020, San Diego, USA)
• GRC: Stochastic Physics in Biology (2019, Ventura, USA)

Fellowships / Grants

• Japan Society for the Promotion of Science: 6,278,000 (JPY)/year 2022-2024
• Shigeta Kyoiku Zaidan (Japan): 2,400,000 (JPY)/year 2017-2018

Awards

• Alexei Likhtman Poster Prize - 7th Edwards Symposium 2023, UK