Research

Cell-based integrated modeling & mechanics in 3D multicellular dynamics

Motivated in the boundary of non-living and living systems, I started research from studying solid mechanics and soft matter physics, and have explored biological phenomena from a mechanical viewpoint. Especially, attracted by self-organizing living systems, I have developed general frameworks of physical models for simulating 3D multicellular dynamics on scales of molecules and cells. Moreover, to reveal mechanisms in multicellular dynamics, I have combined my modeling frameworks with experiments of tissue cultures.

Biography

Honors

2016.10 - 2020.3: PRESTO Researcher, JST
2016.4 - 2017.3: Special Postdoctoral Researcher, RIKEN
2010.4 - 2013.3: Pre-Doctoral Fellow DC1, JSPS

Employments

2016.10 - current: PRESTO Researcher, JST
@ Laboratory of Developmental Systems (Dr. Mototsugu Eiraku), Kyoto University

2016.4 - 2017.3: Special Postdoctoral Researcher, RIKEN
2015.4 - 2016.3: Research Scientist, RIKEN
@ Laboratory for in vitro Histogenesis (Dr. Mototsugu Eiraku), RIKEN CDB

2013.4 - 2015.3: Research Scientist, RIKEN
@ Laboratory for Organogenesis and Neuroscience (Dr. Yoshiki Sasai), RIKEN CDB

2010.4 - 2013.3: Pre-Doctoral Fellow DC1, JSPS
@ Biomechanics Laboratory (Prof. Taiji Adachi), Kyoto University

Visiting

2018.4 - current: Visitng Researcher
@ Laboratory of Developmental Systems (Prof. Mototsugu Eiraku), Kyoto University

2018.4 - current: Visitng Researcher
@ Laboratory for Morphogenetic Signaling (Dr. Shigeo Hayashi), RIKEN BDR

2016.10 - 2016.11, 2017.6 - 2017.7: Visiting Research Associate Scholar
@ Laboratory of Prof. Stanislav Y. Shvartsman, Princeton University

Education

Ph.D. : Engineering, Kyoto University, Japan, 2013
@ Depertment of Micro Engineering, Kyoto University

M.S. : Engineering, Kyoto University, Japan, 2010
@ Depertment of Mechanical Engineering and Science, Kyoto University

B.S. : Mechanical Engineering, Kyoto University, Japan, 2008
@ School of Engineering Science, Faculty of Engineering, Kyoto University

Publication

*: Corresponding Author

Peer-Reviewed Original Papers

Satoru Okuda*, Nozomu Takata, Yuiko Hasegawa, Masako Kawada, Yasuhiro Inoue, Taiji Adachi, Yoshiki Sasai, Mototsugu Eiraku* "Strain-triggered mechanical feedback in self-organizing optic cup morphogenesis," Science Advances 4(11): eaau1354 (2018) DOI: 10.1126/sciadv.aau1354

Satoru Okuda*, Koichi Fuijimoto, "Mechanical instability leading epithelial cell delamination," (under review) arXiv:1810.01984

Satoru Okuda*, Katsuyuki Unoki, Mototsugu Eiraku, Ken-ichi Tsubota*, "Three-dimensional deformation mode of multicellular epithelial tube under tension and compression tests," Journal of Biomechanical Science and Engineering (accepted) DOI: 10.1299/jbse.17-00507

Satoru Okuda*, Takashi Miura, Yasuhiro Inoue, Taiji, Adachi, Mototsugu Eiraku, "Combining Turing and 3D vertex models reproduces autonomous multicellular morphogenesis with undulation, tubulation, and branching," Scientific Reports 8: 2386 (2018) DOI: 10.1038/s41598-018-20678-6

Atsushi Hashimoto, Atsuki Nagao, Satoru Okuda*, "Topological graph description of multicellular dynamics based on vertex model," Journal of Theoretical Biology 437: 187-201 (2018) DOI: 10.1016/j.jtbi.2017.10.023

Shoko Ito, Satoru Okuda, Masako Abe, Mari Fujimoto, Tetsuo Onuki, Tamako Nishimura, Masatoshi Takeichi*, "Induced cortical tension restores functional cell junctions to adhesion-defective carcinoma cells," Nature Communications 8(1):1834 (2017) DOI: 10.1038/s41467-017-01945-y

Satoru Okuda*, Katsuyuki Unoki, Mototsugu Eiraku, Ken-ichi Tsubota*, "Contractile actin belt and mesh structures provide the opposite dependence of epithelial stiffness on the spontaneous curvature of constituent cells," Development, Growth & Differentiation 59(5): 455-464 (2017) DOI: 10.1111/dgd.12373

Yasuhiro Inoue*, Tadashi Watanabe, Satoru Okuda, Taiji Adachi, "Mechanical role of the spatial patterns of contractile cells in invagination of growing epithelial tissue," Development, Growth & Differentiation 59(5): 444-454 (2017) DOI: 10.1111/dgd.12374

Satoru Okuda*, Mototsugu Eiraku, "Role of molecular turnover in dynamic deformation of a three-dimensional cellular membrane," Biomechanics and Modeling in Mechanobiology 16(5): 1805-1818 (2017) DOI: 10.1007/s10237-017-0920-8

Yuiko Hasegawa, Nozomu Takata, Satoru Okuda, Masako Kawada, Mototsugu Eiraku*, Yoshiki Sasai, "Emergence of dorsal-ventral polarity in ES cell-derived retinal tissue," Development 143 (21): 3895-3906 (2016) DOI: 10.1242/dev.134601

Satoru Okuda*, Yasuhiro Inoue, Mototsugu Eiraku, Taiji Adachi, Yoshiki Sasai, "Modeling cell apoptosis for simulating three-dimensional multicellular morphogenesis based on a reversible network reconnection framework," Biomechanics and Modeling in Mechanobiology 15(4): 805-816 (2016) DOI: 10.1007/s10237-015-0724-7

Satoru Okuda*, Yasuhiro Inoue*, Tadashi Watanabe, Taiji Adachi, "Coupling intercellular molecular signaling with multicellular deformation for simulating 3D tissue morphogenesis," Royal Society Interface Focus 5: 20140095 (2015) DOI: 10.1098/rsfs.2014.0095

Satoru Okuda*, Yasuhiro Inoue, Mototsugu Eiraku, Taiji Adachi, Yoshiki Sasai, "Vertex dynamics simulations of viscosity-dependent deformation during tissue morphogenesis," Biomechanics and Modeling in Mechanobiology 14(2), 413-425 (2015) DOI: 10.1007/s10237-014-0613-5

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi*, "Apical contractility in growing epithelium supports robust maintenance of smooth curvatures against cell-division-induced mechanical disturbance," Journal of Biomechanics 46(10): 1705-1713 (2013) DOI: 10.1016/j.jbiomech.2013.03.035

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi*, "Modeling cell proliferation for simulating three-dimensional tissue morphogenesis based on a reversible network reconnection framework," Biomechanics and Modeling in Mechanobiology 12(5): 987-996 (2013) DOI: 10.1007/s10237-012-0458-8

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi*, "Reversible network reconnection model for simulating large deformation during dynamic tissue morphogenesis," Biomechanics and Modeling in Mechanobiology 12(4): 627-644 (2013) DOI: 10.1007/s10237-012-0430-7

Satoru Okuda*, Takashi Uneyama, Yasuhiro Inoue, Yuichi Masubuchi, Masaki Hojo, "Soft-core interaction between entanglement segments for primitive chain network simulations," Journal of the Society of Rheology, Japan 40: 21-30 (2012) DOI: 10.1678/rheology.40.21

Mototsugu Eiraku, Nozomu Takata, Hiroki Ishibashi, Masako Kawada, Eriko Sakakura, Satoru Okuda, Kiyotoshi Sekiguchi, Taiji Adachi, Yoshiki Sasai*, "Self-organizing optic-cup morphogenesis in three-dimensional culture," Nature 472: 51-56 (2011) DOI: 10.1007/s10237-010-0250-6

Satoru Okuda, Yasuhiro Inoue*, Yuichi Masubuchi, Takashi Uneyama, Masaki Hojo, "Wall boundary model for primitive chain network simulations," Journal of Chemical Physics 130: 214907-214913 (2009) DOI: 10.1063/1.3140941

Review Articles

Satoru Okuda*, Yasuhiro Inoue, Taiji Adachi, "Three-dimensional vertex model for simulating multicellular morphogenesis," Biophysics and Physicobiology 12: 13-20 (2015) DOI: 10.2142/biophysico.12.0_13

Satoru Okuda*, Yasuhiro Inoue, Taiji Adachi, "Mechanics-based simulations for understanding multicellular tissue morphogenesis," Seibutsu Butsuri 54(1): 31-34 (2014) DOI: 10.2142/biophys.54.031

Patents

Satoru Okuda, Mototsugu Eiraku, Kuwahara Atsushi,Region detecting method and region detecting device related to cell aggregate,Appeal/Trial number: WO 2017/09074 A1,25 Nov. 2016

奥田覚,永樂元次,桑原篤,細胞塊に関する領域検出方法及び領域検出装置,出願番号:特願2015-229706,25 Nov. 2015 (in Japan)

Book Chapters

奥田覚, 永楽元次, "眼杯オルガノイド×Computational Biologyーin vitroとin silicoの相補的アプローチ," 実験医学 35(16): 2683-2688 (2017) ISBN 978-4-7581-2500-0

奥田覚, 永楽元次, "器官をつくる―in vitro眼杯形成モデルと力学シミュレーションによる変形メカニズムの検証," 実験医学 33(3): 405-410 (2015) ISBN: 978-4-7581-0136-3

奥田覚, 井上康博, 安達泰治, "多細胞のダイナミクスに基づいた3次元組織形成シミュレーション," MOOK別冊「細胞の3次元組織化に不可欠な最先端材料技術―再生医療,その支援分野(細胞研究,創薬研究)への応用と発展のために」第4章4項2節,(編)田畑泰彦,(発)メディカルドゥ (2014) ISBN: 978-4-944157-71-6

Activity

*: Invited

Academic Pesentations

2018

Satoru Okuda, "Strain-Triggered Mechanical Feedback in Self-Organizing Optic Cup Morphogenesis," GfE-JSDB Meeting, Schloss Reisenburg, Germany, Oct. 12, 2018

*Satoru Okuda, "多細胞の三次元動態を1細胞から解析する汎用力学モデル:発生・代謝・疾患への応用," 金沢大学病理学I 第34回腫瘍病理セミナー, 金沢, Oct. 4, 2018

*Satoru Okuda, "In-vitro & in-silico combined approach to controling 3D multicellular dynamics," Workshop on Multi-Cellular Engineered Living Systems, Chicago, Aug. 3, 2018

*Satoru Okuda, Mototsugu Eiraku, "3D vertex modeling and computational simulations of multicellular dynamics," The 13th World Congress in Computational Mechanics, New York, Jul. 27, 2018

Satoru Okuda, "Predictive control of three-dimensional tissue morphogenesis based on complete modeling of single cell dynamics, " さきがけ「統合1細胞解析のための革新的技術基盤」研究領域第8回領域会議, Kanazawa, Jan. 17 – 19, 2018

*Satoru Okuda, "Strain-triggered mechanical feedback in self-organizing optic-cup morphogenesis," Joint annual meeting of JSDB 51st and JSCB 70th, Tokyo, Jun. 6, 2018

Satoru Okuda, "上皮組織における三次元多細胞動態の力学解析," Lab Seminar@東京大学大学院理学系研究科物理学専攻佐野研究室, Tokyo, Mar. 6, 2018

Satoru Okuda, "Mechanical analysis of three-dimensional multicellular morphogenesis," FY 2017 RIKEN SPDR & FPR Presentation of Research Results, Wako, Jan. 31, 2018 (Poster Award "Biology Prize")

Satoru Okuda, "Predictive control of three-dimensional tissue morphogenesis based on complete modeling of single cell dynamics, " さきがけ「統合1細胞解析のための革新的技術基盤」研究領域第7回領域会議, Kanazawa, Jan. 17 – 19, 2018

2017

*Satoru Okuda, "In-silico & in-vitro modeling of multicellular dynamics in development and disease," Seminar at EMBL Barcelona, Dec. 14 – 15, 2017

*Satoru Okuda, "Versatile Model for Computational Simulation of Three-Dimensional Multicellular Dynamics," XXVI Congress of the International Society of Biomechanics 2017, Brisbane, Jul. 23 – 27, 2017 (For the award lecture of Yamaguchi Medal)

*Satoru Okuda, "Mechanics in collective Cell Migration as Maintaining an epithelial Sheet Structure: 3D Vertex Model Approach," The 69th Annual Meeting of the Japan Society for Cell Biology, Sendai, Jun. 13 – 15, 2017

Satoru Okuda, "Predictive control of three-dimensional tissue morphogenesis based on complete modeling of single cell dynamics," さきがけ「統合1細胞解析のための革新的技術基盤」研究領域第6回領域会議, Okayama, Jun. 1 – 3, 2017

Satoru Okuda, "1細胞動態に基づく立体組織構築の力学モデリングと応用," 新学術領域「脳構築における発生時計と場の連携」第1回領域班会議, Numazu, Jan. 27 – 28, 2017

Satoru Okuda, "Predictive control of three-dimensional tissue morphogenesis based on complete modeling of single cell dynamics," さきがけ「統合1細胞解析のための革新的技術基盤」研究領域第5回領域会議, Hamamatsu, Jan. 23 – 25, 2017

Satoru Okuda, Mototsugu Eiraku, “Versatile three-dimensional vertex model for analyzing multicellular morphogenesis,” JSME 29th Bioengineering Conference, 2A11, Nagoya, Jan. 19 – 20, 2017

2016

*Satoru Okuda, Mototsugu Eiraku, "Mechanical regulatory mechanism of 3D multicellular dynamics during optic-cup morphogenesis," The 39th Annual Meeting of the Molecular biology Society of Japan, Yokohama, Nov. 30 - Dec. 2, 2016

Satoru Okuda, Mototsugu Eiraku, "Mechanical regulatory mechanism of 3D multicellular dynamics during epithelial invagination," The 54th Annual Meeting of the Biophysical Society of Japan, 1Pos281, Tsukuba, Nov. 25 - 27, 2016 (Poster)

Satoru Okuda, "4Dイメージベースモデリングによる多細胞力学動態の推定と予測," 4D細胞計測若手の会2016, Shizuoka, Aug. 31 – Sep. 1, 2016 (Best Presentation Award)

Satoru Okuda, "三次元組織形成における1細胞力学動態の統合モデル化と多細胞らしさの探索," Lab Seminar@東京大学大学院理学系研究科物理学専攻佐野研究室, Tokyo, Jun. 23, 2016

*Satoru Okuda, "三次元多細胞ダイナミクスの力学シミュレーション," 第57回HMMCセミナー(北海道大学電子科学研究所附属社会創造数学研究センター), Hokkaido, May 27, 2016

Satoru Okuda, "in vitro/in silico の立体組織構築," The 2nd RIKEN Quantitative and Developmental Biology Joint Workshop, Kobe, Apr. 19, 2016

Satoru Okuda, Yasuhiro Inoue, Taiji Adachi, Mototsugu Eiraku, “Modeling cell apoptosis for simulating three-dimensional multicellular morphogenesis,” JSME 28th Bioengineering Conference, 1D16, Tokyo, Jan. 9 – 10, 2016

2015

Satoru Okuda, "多細胞のダイナミクスを解析するvertex modelの概要と有用性," 第一回数理モデル研究会(新学術領域研究 植物発生ロジックの多元的開拓), Osaka, Sep. 14, 2015

Satoru Okuda, Yasuhiro Inoue, Taiji Adachi, Yoshiki Sasai, Mototsugu Eiraku, "Versatile modeling of three-dimensional multicellular morphogenesis: application to apically-convex invagination during optic-cup formation," The 26th CDB meeting: Mechanistic Perspectives of Multicellular Organization, S4-1, Kobe, Japan, Sep. 8 - 9, 2015

*Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Taiji Adachi, Yoshiki Sasai, "Vertex dynamics simulations of viscosity-dependent deformation during 3D multicellular morphogenesis," S8-1, 15th International Congress of Biorheology and 8th International Conference on Clinical Hemorheology Seoul, Korea, May. 24–28, 2015

Satoru Okuda, "多細胞の立体組織形成ダイナミクスを理解するための力学シミュレーション," 第1021回生物科学セミナー(東京大学大学院理学系研究科生物科学専攻), Tokyo, Jan. 28, 2015

2014

*Satoru Okuda, "立体組織形成における多細胞ダイナミクスの力学シミュレーション," 第4回イノバイオ研究会セミナー(イノバイオ研究会), Tokyo, Dec. 10, 2014

Satoru Okuda, Yoshiki Sasai ,"Vertex Model for Simulating Mechanics-Based Multicellular Dynamics in 3D," The 62nd NIBB Conference "Force in Development" P23, NIBB, Japan 17 - 19, Nov. 2014 (Short Talk Selected from Posters)

Satoru Okuda, Yoshiki Sasai, "多細胞の形態形成ダイナミクスを理解するための力学シミュレーション", 戦略的研究展開事業「多階層をつなぐ 4D 細胞計測の次世代化による動態理解と操作」第 1回 「4D細胞計測 若手の会」, O13, Shizuoka, Oct. 6 – 7, 2014

Satoru Okuda, Yoshiki Sasai, "Computational simulation for exploring biomechanics in 3D multicellular morphogenesis," CDB Retreat 2014, RT1-2 and P53-A, Unitopia Sasayama, Sep. 29 - 30, 2014 (Gold Poster Award)

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, "Vertex model for revealing mechanics in multicellular morphogenesis," The 52th Annual Meeting of the Biophysical Society of Japan, 2PT137, Sapporo, Sep. 25 – 27, 2014 (Poster)

*Satoru Okuda, Yoshiki Sasai, "Vertex model for simulating multicellular dynamics during developmental morphogenesis", Joint Meeting of the 1st Africa International Biotechnology & Biomedical Conference and the 8th International Workshop on Approaches to Single-Cell Analysis WS3-1 Safari Park Hotel Nairobi Kenya Sep. 10 - 12, 2014

*Satoru Okuda, Yoshiki Sasai, "Coupling activator-inhibitor system with growth-induced multicellular morphodynamics in 3D", Joint Annual Meeting of the Japanese Society for Mathematical Biology and the Society for Mathematical Biology Osaka International Convention Center Osaka Japan Jul.28 - Aug. 1, 2014

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Taiji Adachi, and Yoshiki Sasai, "Vertex dynamics simulation of multicellular morphodynamics with visco-elastic-plastic large deformation," The 7th World Congress of Biomechanics, W284, Hynes Convention Center, Boston,US, 6 - 11, July, 2014 (Poster)

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Taiji Adachi, and Yoshiki Sasai, "Vertex dynamics model for simulating multicellular tissue deformation during developmental morphogenesis," International Symposium of Mechanobiology 2014, S17-3, Okayama University, Okayama, Japan, 20 - 23, May, 2014

2013

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Taiji Adachi, and Yoshiki Sasai, "Three-dimensional vertex model for biomechanical simulations of multicellular dynamics during tissue morphogenesis," The 1st Labex INFORM workshop: Quantitative Biology Signaling, Poster 20, p. 62, Institut des Etudes Scientifiques de Cargèse, Corsica France, 21 - 26, Oct., 2013 (Poster)

*Satoru Okuda, Yasuhiro Inoue , Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, "三次元的な組織の形態形成における多細胞ダイナミクスの力学シミュレーション," The 77th Annual Meeting of the Botanical Society of Japan, 1aSI04, p. 93, Hokkaido University, Hokkaido, Sep.13 - 15, 2013

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, “Reversible network reconnection simulation of effects of apical contractility on curvature of growing epithelia," Mechanical Engineering Congress, 2013 Japan, S021011, Okayama University, Okayama, Sep. 8 - 11, 2013

*Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, "三次元バーテックスモデルによる組織形態形成の多細胞ダイナミクスシミュレーション," 熊本シンポジウム2013-神経発生を多角的に討論する会-, 熊本大学発生医学研究所, グリーンピア南阿蘇, Kumamoto, Jun.25 - 26, 2013

Yoshiki Sasai, Satoru Okuda, "組織変形の力学動態:計測とシミュレーションの統合に向けて," 4D細胞計測キックオフミーティング, Saitama, Apr. 23, 2013

*Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, "多細胞間の力学的相互作用に基づく三次元組織形成シミュレーション," 生命情報科学若手の会 第4回研究会, Aichi, Mar.1-3, 2013

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, "組織の形態形成過程における多細胞ダイナミクスの力学シミュレーション," 第3回 Vivid Workshop ―細胞機能と分子活性の多次元蛍光生体イメージング―, Ishikawa, Feb. 2013

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, "三次元バーテックスモデルに基づく多細胞組織形成過程の力学シミュレーション," 名古屋大学大学院医学系研究科細胞生物学分野にてセミナー, Nagoya, Feb. 2013

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, "多細胞組織の形態形成ダイナミクスシミュレーション," 5拠点ミーティング, PD3, Hyogom, Feb. 2013

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, “Modeling cell proliferation for simulating tissue morphogenesis using reversible network reconnection model," JSME 25th Bioengineering Conference, Japan, 2F16, Osaka, Jan. 2013

2012

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, "Computational Biomechanics in Complicated Deformation during Dynamic Tissue Morphogenesis," 平成24年度京都大学再生医科学研究所若手発表会, YO-2, YP-9, Kyoto, Dec. 2012 (Best Presentation Award)

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, and Taiji Adachi, "Large deformation of multicellular tissues during morphogenesis using reversible network reconnection model," Exciting Biologies: Forces in Biology, Dublin, Irland, Oct. 2012

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, “Simulation of large deformation during tissue morphogenesis using reversible network reconnection model," The 50th Annual Meeting of the Biophysical Society of Japan, 1PT219, Aichi, Sep. 2012

*Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, “Reversible network reconnection model for simulating large deformations of multicellular tissues during morphogenesis," Japan Society for Mathematical Biology Annual Meeting 2012, Okayama, Sep. 10 – 12, 2012

*Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, and Taiji Adachi, "Computational model for large deformations of multiple-cell aggregate during tissue morphogenesis," 10th World Congress of Computational Mechanics, 16818, Sao Paulo, Brazil, Jul. 8 – 13, 2012

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, and Taiji Adachi, "Three-dimensional vertex model for morphogenesis of multiple-cell tissue with physical and topological consistency," CDB Symposium 2012: Quantitative Developmental Biology, P61, Kobe, Japan, Mar. 2012 (Poster)

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, and Taiji Adachi, "Three-dimensional vertex model for simulating large deformation of cell aggregates during tissue morphogenesis," International Symposium on Cellular Mechanobiology, PP-18, Kyoto, Japan, Mar. 2012 (Poster)

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, “Modeling cell division and growth in morphogenetic dynamics of tissue development," JSME 24th Bioengineering Conference, Japan, 8C43, Osaka, Jan. 2012

2011

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, “Computational biomechanics for large deformations of multiple-cell aggregates during tissue morphogenesis," 京都大学再生医科学研究所「再生医学・再生医療の先端融合的共同研究拠点」平成23年度学術講演会, 25, Kyoto, Dec. 2011 (Poster)

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, Taiji Adachi, “Mathematical insight into modeling morphological development of sheet-like multicellular tissue," Mechanica Engineering Congress, 2011 Japan, J025021, Tokyo, Sep. 2011

Satoru Okuda, Yasuhiro Inoue, Mototsugu Eiraku, Yoshiki Sasai, and Taiji Adachi, "Physical and geometrical improvements of three-dimensional vertex model for simulating morphogenetic dynamics of multicellular tissue in development," Exciting biology series: Biology at the interface, P44, Kobe, Japan, Sep. 2011 (Poster)

2010

Satoru Okuda, Yasuhiro Inoue, Masaki Hojo, Yuichi Masubuchi, Takashi Uneyama, "Simulation of Entangled Polymer Chain in Solid-Liquid Interface," 九州大学応用力学研究所研究集会報告21ME-S5ナノ複合材料等次世代複合材料の創製及び評価, Fukuoka, Jan. 2010

Satoru Okuda, Yasuhiro Inoue, Yuichi Masubuchi, Takashi Uneyama, Masaki Hojo, "Chain diffusivity of molten polymer confined between solid walls in primitive chain network simulations," The 57th Rheology Symposium, Japan, 1B06, Niigata, Oct. 2010

2009

Satoru Okuda, Yasuhiro Inoue, Yuichi Masubuchi, Takashi Uneyama, Masaki Hojo, ”Primitive chain network simulations: confinement effect of slit width between solid walls on entanglement of chains in polymer melt," JSME 22th Computational Mechanics Conference, 1037, Ishikawa, Oct. 2009

Satoru Okuda, Yasuhiro Inoue, Yuichi Masubuchi, Takashi Uneyama, Masaki Hojo, "Development of wall boundary model for primitive chain network simulations," The 81st Annual Meeting of The Society of Rheology, PO69, Madison, Wisconsin, USA, Oct. 2009 (Poster)

Satoru Okuda, Yasuhiro Inoue, Masaki Hojo, Yuichi Masubuchi, Takashi Uneyama, "Investigation of confinement effect of micro slit channels to molten polymer using primitive chain network model," The 14th Molecular dynamics Symposium, Society of Materials Science, Japan, O7, Ehime, May. 2009

Satoru Okuda, Yasuhiro Inoue, Yuichi Masubuchi, Takashi Uneyama, Masaki Hojo, "Investigation of the dynamics simulation of molten polymer confined between walls using primitive chain network model," The 36th Annual Meeting of the society of Rheology, Japan, P11, Kyoto, May. 2009 (Poster)

2008

Satoru Okuda, Yasuhiro Inoue,Masaki Hojo, Yuichi Masubuchi, "Proposal of a wall boundary condition for Primitive Chain Network simulations," JSME 21th Computational Mechanics Conference, 223, Okinawa, Nov. 2011

Satoru Okuda, Yasuhiro Inoue, Masaki Hojo, Yuichi Masubuchi, "Primitive chain network simulations of molten polymer confined between solid walls," The 56th Rheology Symposium, Japan, 1D07, Niigata, Oct. 2008

Satoru Okuda, Yasuhiro Inoue, Masaki Hojo, Yuichi Masubuchi, "A wall boundary condition for primitive chain network simulations", Meso-scale dynamics on interface 2008, Poster-18, Tokyo, Japan, Mar. 2008 (Poster)

Satoru Okuda, Yasuhiro Inoue, Masaki Hojo, Yuichi Masubuchi, "Primitive chain network simulation of confined polymer dynamics between walls," Rheology and Dynamics of Entangled Polymers, Kyoto, Japan, Mar. 2008 (Poster)

Public Presentations

Satoru Okuda, "実験・物理・コンピュータシミュレーションを組み合わせた組織形成の研究," 平成26年度「高校生のための発生生物学実習講座」, Kobe, Dec. 25 – 26, 2014

Awards

Satoru Okuda, Young Scientist Award for Presentation at Joint annual meeting of JSDB 51st and JSCB 70th, Jun. 6 (2018)

Satoru Okuda, Poster Award "Biology Prize" at FY 2017 RIKEN SPDR & FPR Presentation of Research Results, Jan. 31 (2018)

Satoru Okuda, Yamaguchi Medal from Asian-Pacific Association for Biomechanics, Jul. 27 (2017)

奥田覚, 日本機械学会奨励賞(研究), Apr. 20 (2017)

奥田覚, 第3回 4D細胞計測プロジェクト 若手の会 プレセンテーション賞, Aug. 31 (2016)

Satoru Okuda, CDB Retreat Gold Award for poster presentation, Sep. 3 (2014)

奥田覚, 京都大学再生医科学研究所若手発表会優秀賞, Dec. 19 (2012)

Grants

Source: JSPS Grant-in-Aid for Scientific Research B
Number: 17KT0021
Title: Constructive understanding of embryogenesis via single cell genomics and mechanics (translation)
Principal Investigator: Prof. Takashi Kondo (Kyoto University)
Co-Investigator: Satoru Okuda
Period: 2017.4 –2020.3

Source: JSPS Grant-in-Aid for Scientific Research B
Number: 17H02939
Title: Basic mechanism of collective migration of epithelial cells during morphogenesis
Principal Investigator: Prof. Katsuhiko Sato (Hokkaido University)
Co-Investigator: Satoru Okuda, Daiki Umetsu (Tohoku University)
Period: 2017.4 –2020.3

Source: JST PRESTO
Number: JPMJPR16F3
Title: Predictive control of three-dimensional tissue morphogenesis based on complete modeling of single cell dynamics
Principal Investigator: Satoru Okuda
Period: 2016.10 –2020.3

Source: RIKEN Grant-in-Aid for Special Postdoctoral Researcher
Number: -
Title: Mechanical analysis of multicellular dynamics during three-dimensional tissue morphogenesis
Principal Investigator: Satoru Okuda
Period: 2016.4 –2019.3

Source: JSPS Grant-in-Aid for Challenging Exploratory Research
Number: 15K14534
Title: Stress field estimation in three-dimensional optic-cup by image-based modeling
Principal Investigator: Satoru Okuda
Co-Investigator: Atsushi Hashimoto
Period: 2015.4 –2016.3

Source: Research Grant of Sasakawa Foundation
Number: 27-413
Title: Computational simulation of cell polarization during epithelial formation (translation)
Principal Investigator: Satoru Okuda
Period: 2015.4 –2016.3

Source: JSPS Grant-in-Aid for Research Activity Start-up
Number: 25889070
Title: Stress analysis of three-dimensional multicellular dynamics during organogenesis
Principal Investigator: Satoru Okuda
Period: 2013.4 –2015.3

Source: JSPS Grant-in-Aid for Pre-Doctoral Fellow DC1
Number: 10J01270
Title: Mechanical analysis of entanglement structure in molten polymer liquid (translation)
Principal Investigator: Satoru Okuda
Period: 2010.4 –2013.3

Etcetra

Executive committee member
The JSME 30th Bioengineering Conference
Date: December 14 - 15, 2017
Venue: Kyoto University, Japan
Home page: https://www.jsme.or.jp/conference/bioconf17-2/

Logo design
Institute for Frontier Life and Medical Sciences, Kyoto University

Principal organizer
The 26th CDB Meeting "Mechanistic Perspectives of Multicellular Organization"
Date: September 8 - 9, 2015
Venue: RIKEN Center for Developmental Biology (CDB), Japan
Principal Organizers: Mototsugu Eiraku & Satoru Okuda
Home page: http://www.cdb.riken.jp/mechanistic2015/
Report: http://www.cdb.riken.jp/news/2015/events/1105_8887.html

Poster design
The 26th CDB Meeting "Mechanistic Perspectives of Multicellular Organization"

Membership

The Japan Society of Mechanical Engineers

Japanese Society of Developmental Biologists

The Biophysical Society of Japan

The Society of Rheology, Japan

Laboratory for in-vitro Histogenesis, RIKEN CDB (Dr. Mototsugu Eiraku)

Biomechanics Laboratory, Kyoto University (Prof. Taiji Adachi)

Mechanics of Adaptive Materials and Structures Laboratory (Prof. Masaki Hojo)

Special Postdoctoral Researcher, RIKEN

Integrated Single Cell Analysis, JST PRESTO

Prof. Masakazu Akiyama @ Hokkaido University

Dr. Fu-Lai Wen @ RIKEN

Paraview (visualization software)

TeXclip (online equation converter from TeX to EPS)

GSL (numerical library for c & c++ programming)

Mersenne Twister (random number generator)