35. A model explaining environmental stiffness-dependent migration of fibroblasts with a focus on maturation of intracellular structures

Natsuki Saito, Tsubasa S. Matsui, Daiki Matsunaga, Kana Furukawa, Shinji Deguchi
bioRxiv, submitted

34. MagnetoChlamy: A magnetic micro-robot model driven by counter-rotating particles

Hideki Takayama, Shinji Deguchi, Joshua K. Hamilton, Daiki Matsunaga
submitted

33. Diffusion model predicts the geometry of actin cytoskeleton from cell morphology

Honghan Li, Shiyou Liu, Shinji Deguchi, Daiki Matsunaga
PLOS Computational Biology, volume 20(8), e1012312, 2024

32. Asymmetric response emerges between creation and disintegration of force-bearing subcellular structures as revealed by percolation analysis

Yuika Ueda, Daiki Matsunaga, Shinji Deguchi
Integrative Biology, volume 16, zyae012, 2024

31. Intracellular macromolecular crowding within individual stress fibers analyzed by fluorescence correlation spectroscopy

Aria Buenaventura, Takumi Saito, Taiga Kanao, Daiki Matsunaga, Tsubasa S. Matsui, Shinji Deguchi
Cellular and Molecular Bioengineering, volume 17, pp. 165-176, 2024

30. Asymmetric bistability of chiral particle orientation in viscous shear flows

Andreas Zöttl, Francesca Tesser, Daiki Matsunaga, Justine Laurent, Olivia Du Roure, Anke Lindner
Proceedings of the National Academy of Sciences of the United States of America, volume 120 (45), e2310939120, 2023

29. Long-term molecular turnover of actin stress fibers revealed by advection-reaction analysis in fluorescence recovery after photobleaching

Takumi Saito, Daiki Matsunaga, Shinji Deguchi
PLOS One, volume 17(11), e0276909, 2022

28. A statistical mechanics model for determining the length distribution of actin filaments under cellular tensional homeostasis

Yuika Ueda, Daiki Matsunaga, Shinji Deguchi
Scientific Reports, volume 12, 14466, 2022

27. Analysis of chemomechanical behavior of stress fibers by continuum mechanics-based FRAP

Takumi Saito, Daiki Matsunaga, Shinji Deguchi
Biophysical Journal, volume 121, pp. 2921-2930, 2022 (selected as Cover)

26. Field-controlling patterns of sheared ferrofluid droplets

Shunichi Ishida, Yaochen Yang, Fanlong Meng, Daiki Matsunaga
Physics of Fluids, volume 34, 063309, 2022

25. Particle segregation using crystal-like structure of capsules in wall-bounded shear flow

Shunichi Ishida, Ryota Matsumoto, Daiki Matsunaga, Yohsuke Imai
Physical Review Fluids, volume 7, 063601, 2022

24. Wrinkle force microscopy: a machine learning based approach to predict cell mechanics from images

Honghan Li, Daiki Matsunaga (co-first author), Tsubasa S. Matsui, Hiroki Aosaki,
Genki Kinoshita, Koki Inoue, Amin Doostmohammadi, Shinji Deguchi
Communications Biology, volume 5, 361, 2022

23. Determining the domain-level reaction-diffusion properties of an actin-binding protein transgelin-2 within cells

Takumi Saito, Daiki Matsunaga, Tsubasa S. Matsui, Kentaro Noi, Shinji Deguchi
Experimental Cell Research, volume 404, issue 1, 2021

22. Magnetic microswimmers exhibit Bose-Einstein-like condensation

Fanlong Meng, Daiki Matsunaga, Benoit Mahault, Ramin Golestanian
Physical Review Letters, volume 126, 078001, 2021

21. Rheology of a dilute ferrofluid droplet suspension in shear flow: viscosity and normal stress differences

Shunichi Ishida, Daiki Matsunaga (co-first author)
Physical Review Fluids, volume 5, 123603, 2020

20. Degenerate states, emergent dynamics and fluid mixing by magnetic rotors

Takuma Kawai, Daiki Matsunaga, Fanlong Meng, Julia M. Yeomans, Ramin Golestanian
Soft Matter, volume 16, pp. 6484-6492, 2020 (selected as Back cover)

19. Complex viscosity of dilute capsule suspensions: a numerical study

Daiki Matsunaga, Yohsuke Imai
Journal of Biomechanical Science and Engineering, 20-00102, 2020

18. Image based cellular contractile force evaluation with small-world network inspired CNN: SW-UNet

Honghan Li, Daiki Matsunaga, Tsubasa S. Matsui, Hiroki Aosaki, Shinji Deguchi
Biochemical and Biophysical Research Communications, volume 530, issue 3, pp. 527-532, 2020

17. Diffusion and collective motion of rotlets in 2D space

Daiki Matsunaga, Takumi Chodo, Takuma Kawai
Chinese Physics B (Special issue "Active Matter Physics"), volume 29, No. 6, 064705, 2020

16. Multi-well plate cell contraction assay detects negatively correlated cellular responses to pharmacological inhibitors in contractility and migration

Foncham J. Nehwa, Tsubasa S. Matsui, Honghan Li, Daiki Matsunaga,
Yoshiyuki Sakaguchi, Shinji Deguchi
Biochemical and Biophysical Research Communications, volume 521, issue 2, pp. 527-532, 2020

15. Shear viscosity of bimodal capsule suspensions in simple shear flow

Hiroki Ito, Daiki Matsunaga, Yohsuke Imai
Physical Review Fluids, volume 4, 113601, 2019

14. Controlling collective rotational patterns of magnetic rotors

Daiki Matsunaga, Joshua K. Hamilton, Fanlong Meng, Nick Bukin, Elizabeth L. Martin,
Feodor Y. Ogrin, Julia M. Yeomans, Ramin Golestanian
Nature Communications, volume 10, 4696, 2019
(Press release: Osaka University News)

13. Tunable self-healing of magnetically propelling colloidal carpets

Helena Massana-Cid, Fanlong Meng, Daiki Matsunaga, Ramin Golestanian, Pietro Tierno
Nature Communications, volume 10, 2444, 2019

12. Magnetically-actuated articial cilium: A simple theoretical model

Fanlong Meng, Daiki Matsunaga, Julia M. Yeomans, Ramin Golestanian
Soft Matter, volume 15, pp. 3964-3871, 2019 (selected as Inside back cover)

11. Far-field theory for trajectories of magnetic ellipsoids in rectangular and circular channels

Daiki Matsunaga, Andreas Zöttl, Fanlong Meng, Ramin Golestanian, Julia M. Yeomans
IMA Journal of Applied Mathematics, volume 83, issue 4, pp. 767-782, 2018

10. Clustering of magnetic swimmers in a Poiseuille flow

Fanlong Meng, Daiki Matsunaga, Ramin Golestanian
Physical Review Letters, volume 120, 188101, 2018

9. Focusing and sorting of ellipsoidal magnetic particles in microchannels

Daiki Matsunaga, Fanlong Meng, Andreas Zöttl, Ramin Golestanian, Julia M. Yeomans
Physical Review Letters, volume 119, 198002, 2017
(Editors' suggestion: highlighted in APS Physics Synopsis, Oxford Physics News)

8. Reorientation of a single red blood cell during sedimentation

Daiki Matsunaga, Yohsuke Imai, Christian Wagner, Takuji Ishikawa
Journal of Fluid Mechanics, volume 806, pp. 102-128, 2016

7. A numerical model of a red blood cell infected by Plasmodium falciparum malaria: coupling cell mechanics with ligand-receptor interactions

Shunichi Ishida, Yohsuke Imai, Yuki Ichikawa, Stephanie Nix, Daiki Matsunaga, Toshihiro Omori, Takuji Ishikawa
Science and Technology of Advanced Materials, volume 17, No. 1, pp. 454-461, 2016

6. Deformation of a micro torque swimmer

Takuji Ishikawa, Tomoyuki Tanaka, Yohsuke Imai, Toshihiro Omori, Daiki Matsunaga
Proceedings of the Royal Society of London A, volume 472, issue 2185, 2016

5. Rheology of a dense suspension of spherical capsules under simple shear flow

Daiki Matsunaga, Yohsuke Imai, Takami Yamaguchi, Takuji Ishikawa
Journal of Fluid Mechanics, volume 786, pp. 110-127, 2016

4. Shape matters: Near-field fluid mechanics dominates collective motions of ellipsoidal squirmers

Kohei Kyoya, Daiki Matsunaga, Yohsuke Imai, Toshihiro Omori, Takuji Ishikawa
Physical Review E, volume 92 (6), 063027, 2015

3. Deformation of a spherical capsule under oscillating shear flow

Daiki Matsunaga, Yohsuke Imai, Takami Yamaguchi, Takuji Ishikawa
Journal of Fluid Mechanics, volume 762, pp. 288-301, 2015

2. Lateral migration of a spherical capsule near a plane wall in Stokes flow

Stephanie Nix, Yohsuke Imai, Daiki Matsunaga, Takami Yamaguchi, Takuji Ishikawa
Physical Review E, volume 90 (4), 043009, 2014

1. A full GPU implementation of a numerical method for simulating capsule suspensions

Daiki Matsunaga, Yohsuke Imai, Toshihiro Omori, Takuji Ishikawa, Takami Yamaguchi
Journal of Biomechanical Science and Engineering, 14-00039, 2014

2. Long-Term Fluorescence Recovery After Photobleaching (FRAP)

Takumi Saito, Daiki Matsunaga, Shinji Deguchi
Mechanobiology --- Methods and Protocols
Methods in Molecular Biology 2600
Springer Protocols, 2023

1. A Numerical Analysis of Rheology of Capsule Suspsneions Using a GPU-Accelerated Boundary Element Method

Yohsuke Imai, Daiki Matsunaga
Frontiers in Computational Fluid-Structure Interaction and Flow Simulation
Modeling and Simulation in Science, Engineering and Technology
Springer Nature Switzerland, 2018

Associate Professor: Jun 2021 - now

@ Graduate school of Engineering Science, Osaka University, Japan
working with Prof. Shinji Deguchi

Assistant Professor: Aug 2018 - Jun 2021

@ Graduate school of Engineering Science, Osaka University, Japan
worked with Prof. Shinji Deguchi

Review Editor, Editorial Board: Feb 2018 - now

frontiers in Physiology | Red Blood Cell Physiology

Postdoctoral Research Assistant: Apr 2016 - Jul 2018

@ Rudolf Peierls Centre for Theoretical Physics, University of Oxford, UK
worked with Prof. Julia M. Yeomans and Prof. Ramin Golestanian

Research Fellowship for Young Scientists (DC2): Apr 2014 - Mar 2016

Japan Society for the Promotion of Science

PhD/Engineering: Apr 2013 - Mar 2016

@ Department of Bioengineering and Robotics, Tohoku University, Japan
BFSL (Biological Flow Studies Laboratory)
Supervisor: Prof. Takuji Ishikawa

Visiting PhD student: Oct 2014 - Jun 2015

@ Experimental Physics, Saarland University, Germany
Supervisor: Prof. Christian Wagner

Master/Engineering: Apr 2011 - Mar 2013

@ Department of Bioengineering and Robotics, Tohoku University, Japan
PFSL (Physiological Flow Studies Laboratory)
Supervisor: Prof. Takami Yamaguchi

TUSAP21 (Short studying program): Mar 2008

@ The University of Sydney, Australia

Bachelor/Engineering: Apr 2007 - Mar 2011

@ Department of Mechanical and Aerospace Engineering, Tohoku University, Japan
PFSL (Physiological Flow Studies Laboratory)
Supervisor: Prof. Takami Yamaguchi

Hometown: Kanazawa, Ishikawa prefecture

Kanazawa University High School

1. Yamaguchi Medal: Nov 2019

@ AP Biomech 2019 (Asian-Pacific Association for Biomechanics), Taiwan

2. JSME Young Engineers Award: Mar 2018

@ JSME (The Japanese Society of Mechanical Engineers), Tokyo

3. Presidential Prize for Excellence: Mar 2016

@ Graduation ceremony, Tohoku University

4. Best Poster Award: Jun 2014

@ DynaCaps2014, Compiègne, France

5. Poster Award (2nd place): Mar 2014

@ Advances in Computational Fluid-Structure Interaction and Flow Simulation, Tokyo, Japan

6. Oral Presentation Award: Mar 2013

@ 6th East Asian Pacific Student Workshop on Nano-Biomedical Engineering, Singapore

7. JSME Fellow Award for Outstanding Young Engineers: Jan 2012

@ 22nd JSME Conference on Frontiers in Bioengineering, Tsu, Japan