Publications

Vahin Pichairaj*, Jeffery Coulter*, and Taeyoon Kim^§, "How force generation and contraction of actin networks are governed by motor properties," in preparation

Jeffery Coulter and Taeyoon Kim^§, "A hybrid continuum-discrete model for multi-scale simulations of biological cells," in preparation

Serena P. Garcia, Étienne Pinard, Camille N. Plancke, Jing Li, Shashi K. Suman, Loan Bourdon, Christelle Gally, Taeyoon Kim, and François B. Robin^§, "Kinetic control of out-of-equilibrium dynamics in the RhoA signaling cascade shapes actomyosin contractility," bioRxiv

Donghyun Yim, Brandon Slater, and Taeyoon Kim^§, "Durotactic migration driven by anisotropic stiffening and mechanical feedback," bioRxiv

Md Foysal Rabbi, Donghyun Yim, Matthew Boyd, Sungmin Nam, Ovijit Chaudhuri, and Taeyoon Kim^§, "Mechanical checkpoint for cell division in three-dimensional microenvironments," under review — bioRxiv

Aashrith Saraswathibhatla, Md Foysal Rabbi, Sushama Varma, Vasudha Srivastava, Olga Ilina, Naomi Hassan Kahtan Alyafei, Louis Hodgson, Zev Gartner, Peter Friedl, Robert West, Taeyoon Kim^§, and Ovijit Chaudhuri^§, "Swirling motion of breast cancer cells radially aligns collagen fibers to enable collective invasion," in revision — bioRxiv

Shihang Ding*, Tsubasa S. Matsui*, Roland R. Kaunas, Taeyoon Kim^§, and Shinji Deguchi^§, "Dissecting molecular origins of the mechano-adaptive behaviors of actomyosin bundles," in revision — bioRxiv

Donghyun Yim, Laurel Patterson, Daniel Suter, Kyle Miller, and Taeyoon Kim^§, "Computational modeling of motor-driven extension of microtubule bundles in axons," npj Biological Physics and Mechanics (2026) 3: 13. DOI

Makito Miyazaki*^§, Fahmida Sultana Laboni*, and Taeyoon Kim^§, "Reconstitution of actomyosin networks in cell-sized liposomes dissects distinct mechanisms of membrane blebbing and symmetry breaking," Science Advances (2026) 12(31): eaed8818. DOI

June Hyung Kim, Weiwei Zhang, Anjali Iyer-Pascuzzi, Christopher J. Staiger^§, and Taeyoon Kim^§, "Agent-based computational modeling of the stochastic dynamic behavior of actin filaments recapitulates the homeostatic cortical array in plant epidermal cells," Cytoskeleton (2026) 83(6): 407–426. DOI

June Hyung Kim and Taeyoon Kim^§, "The mechanism of dynamic steady states in lamellipodia," PLOS Computational Biology (2025) 21(10): e1013572. DOI

Youngmin Jo*, Donghyun Yim*, Chan E Park, Insung Yong, Jongbeom Lee, Kwang Ho Ahn, Chanhee Yang, Jae-Byum Chang, Taek-Soo Kim, Jennifer H. Shin, Taeyoon Kim^§, and Pilnam Kim^§, "Reciprocal folding dynamics in cellular networks at the stroma-basement membrane interface," Acta Biomaterialia (2025) 201: 360–371. DOI

Md Foysal Rabbi, Gijsje H. Koenderink, Yuval Mulla, and Taeyoon Kim^§, "Fine-tuning of material properties by catch bonds," Acta Biomaterialia (2025) 201: 372–384. DOI

Brandon Slater, Alfredo Sciortino, Andreas R. Bausch, and Taeyoon Kim^§, "Cluster formation and phase separation driven by mobile myosin motors in the motility assay," Physical Review Research (2025) 7: 013312. DOI

Shihang Ding*, Pei-En Chou*, Shinji Deguchi^§, and Taeyoon Kim^§, "Impacts of structural properties of myosin II filaments on force generation," eLife (2025) 14: RP105236. DOI

Haiyan Li, Devon H. Harvey, Jiannong Dai, Steven P. Swingle, Anthony M. Compton, Chenna Kesavulu Sugali, Kamesh Dhamodaran, Jing Yao, Tsai-Yu Lin, Todd Sulcheck, Taeyoon Kim, Ross Ethier, and Weiming Mao^§, "Characterization, enrichment, and computational modeling of cross-linked actin networks in trabecular meshwork cells," Investigative Ophthalmology & Visual Science (2025) 66(2): 65. DOI

Scott Weady*, Bryce Palmer*, Adam Lamson, Taeyoon Kim, Reza Farhadifar, and Michael J. Shelley^§, "Mechanics and morphology of proliferating cell collectives with self-inhibiting growth," Physical Review Letters (2024) 133(15): 158402. DOI

Kyohei Matsuda*, Wonyeong Jung*, Yusei Sato, Takuya Kobayashi, Masahiko Yamagishi, Taeyoon Kim^§, and Junichiro Yajima^§, "Myosin-induced F-actin fragmentation facilitates contraction of actin networks," Cytoskeleton (2024) 81(8): 339–355. DOI

Laura Pulido-Cifuentes, Ahmad Athamneh, Yuri Efremov, Arvind Raman, Taeyoon Kim, and Daniel Suter^§, "A modified motor-clutch model reveals that neuronal growth cones respond faster to soft substrates," Molecular Biology of the Cell (2024) 35(ar47): 1–12. DOI

Shihang Ding, Shinji Deguchi, and Taeyoon Kim^§, "Unraveling a key molecular player governing pulmonary alveolar development," American Journal of Respiratory Cell and Molecular Biology (2024) 70(4): 237–238. DOI (commentary)

Weiguo Fan, Kolade Adebowale, Lóránd Váncza, Yuan Li, Md Foysal Rabbi, Koshi Kunimoto, Dongning Chen, Gergely Mozes, David Kung-Chun Chiu, Yisi Li, Junyan Tao, Yi Wei, Nia Adeniji, Ryan L. Brunsing, Renumathy Dhanasekaran, Aatur Singhi, David Geller, Su Hao Lo, Louis Hodgson, Edgar G. Engleman, Gregory W. Charville, Vivek Charu, Satdarshan P. Monga, Taeyoon Kim, Rebecca G. Wells, Ovijit Chaudhuri, and Natalie J. Török^§, "Matrix viscoelasticity promotes liver cancer progression in the pre-cirrhotic liver," Nature (2024) 626: 635–642. DOI

Brandon Slater*, Wonyeong Jung*, and Taeyoon Kim^§, "Emergence of diverse patterns driven by molecular motors in the motility assay," Cytoskeleton (2024) 81(12): 902–912. DOI

Jing Li, Daniel Szymanski^§, and Taeyoon Kim^§, "Probing stress-regulated ordering of the plant cortical microtubule array via a computational approach," BMC Plant Biology (2023) 23: 308. DOI

Devin B. Mair, Ceylin Elmasli, June H. Kim, Amanda D. Barreto, Supeng Ding, Luo Gu, Seth H. Weinberg, Taeyoon Kim, Deok-Ho Kim^§, and Rong Li^§, "The Arp2/3 complex enhances cell migration on elastic substrates," Molecular Biology of the Cell (2023) 34(ar67): 1–10. DOI

Camelia G. Muresan*, Zachary G. Sun*, Vikrant Yadav, A. Pasha Tabatabai, Laura Lanier, June Hyung Kim, Taeyoon Kim, and Michael P. Murrell^§, "F-actin architecture determines constraints on myosin thick filament motion," Nature Communications (2022) 13: 7008. DOI

Hang Zhou, Wonyeong Jung, Tamanna Ishrat Farhana, Kazuya Fujimoto, Taeyoon Kim, and Ryuji Yokokawa^§, "Durability of aligned microtubules dependent on persistence length determines phase transition and pattern formation in collective motion," ACS Nano (2022) 16(9): 14765–14778. DOI

Yuval Mulla, Mario J. Avellaneda, Antoine Roland, Lucia Baldauf, Wonyeong Jung, Taeyoon Kim^§, Sander J. Tans^§, and Gijsje H. Koenderink^§, "Weak catch bonds make strong networks," Nature Materials (2022) 21: 1019–1023. DOI

Qilin Yu*, Jing Li*, Michael P. Murrell, and Taeyoon Kim^§, "Balance between force generation and relaxation leads to pulsed contraction of actomyosin networks," Biophysical Journal (2018) 115(10): 2003–2013. DOI

Vlad Costache*, Séréna P. Garcia*, Camille Plancke, Jing Li, Simon Begnaud, Shashi Kumar Suman, Anne-Cécile Reymann, Taeyoon Kim^§, and Francois B. Robin^§, "Rapid assembly of a polar network architecture drives efficient actomyosin contractility," Cell Reports (2022) 39(9): 110868. DOI

Vijay Rajagopal^§ and Taeyoon Kim^§ — Qilin Yu, "Role of actin filaments and cis binding in cadherin clustering and patterning," PLOS Computational Biology (2022) 18(7): e1010257. DOI

Brandon Slater*, Jing Li*, Dhiraj Indana*, Yihao Xie, Ovijit Chaudhuri^§, and Taeyoon Kim^§, "Transient mechanical interactions between cells and viscoelastic extracellular matrix," Soft Matter (2021) 17: 10274–10285. DOI

Vivek Gupta, Sungmin Nam, Donghyun Yim, Jaclyn Camuglia, Judy Martin, Erin N. Sanders, Lucy E. O'Brien, Adam C. Martin, Taeyoon Kim, and Ovijit Chaudhuri^§, "The nature of cell division forces in epithelial monolayers," Journal of Cell Biology (2021) 220(8): e202011106. DOI

Sungmin Nam, Yung-Hao Lin, Taeyoon Kim^§, and Ovijit Chaudhuri^§, "Cellular pushing forces during mitosis drive mitotic elongation in collagen gel," Advanced Science (2021) 8(4): 2000403. DOI

Wonyeong Jung*, Jing Li*, Ovijit Chaudhuri, and Taeyoon Kim^§, "Nonlinear elastic and inelastic properties of cells," Journal of Biomechanical Engineering (2020) 142(10): 100806. DOI

Katrina M. Wisdom, Dhiraj Indana, Pei-En Chou, Rajiv Desai, Taeyoon Kim^§, and Ovijit Chaudhuri^§, "Covalent cross-linking of basement membrane-like matrices physically restricts invasive protrusions in breast cancer cells," Matrix Biology (2020) 85–86: 94–111. DOI

Wonyeong Jung*, Luke Fillenwarth*, Atsushi Matsuda, Jing Li, Yasuhiro Inoue^§, and Taeyoon Kim^§, "Collective and contractile filament motions in the myosin motility assay," Soft Matter (2020) 16: 1548–1559. DOI

Wonyeong Jung, A. Pasha Tabatabai, Jacob Thomas, S. M. Ali Tabei, Michael Murrell, and Taeyoon Kim^§, "Dynamic motions of molecular motors in the actin cytoskeleton," Cytoskeleton (2019) 76(11-12): 517–531. DOI

Vikrant Yadav, Deb S. Banerjee, A. Pasha Tabatabai, David R. Kovar, Taeyoon Kim, Shiladitya Banerjee, and Michael Murrell^§, "Filament nucleation tunes mechanical memory in active polymer networks," Advanced Functional Materials (2019) 29: 1905243. DOI

Atsushi Matsuda*, Jing Li*, Peter Brumm, Taiji Adachi, Yasuhiro Inoue^§, and Taeyoon Kim^§, "Mobility of molecular motors regulates contractile behaviors of actin networks," Biophysical Journal (2019) 116: 2161–2171. DOI

Abdel-Rahman Hassan, Thomas Biel, and Taeyoon Kim^§, "Mechanical model for durotactic cell migration," ACS Biomaterials Science & Engineering (2019) 5(8): 3954–3963. DOI

Abdel-Rahman Hassan, Thomas Biel, David M. Umulis, and Taeyoon Kim^§, "Interplay between the persistent random walk and the contact inhibition of locomotion leads to collective cell behaviors," Bulletin of Mathematical Biology (2019) 81(8): 3301–3321. DOI

Jing Li, Taeyoon Kim, and Daniel B. Szymanski^§, "Multi-scale regulation of cell branching: Modeling morphogenesis," Developmental Biology (2019) 451(1): 40–52. DOI

Tamara C. Bidone*, Wonyeong Jung*, Daniel Maruri, Carlos Borau, Roger D. Kamm^§, and Taeyoon Kim^§, "Morphological transformation and force generation of active cytoskeletal networks," PLOS Computational Biology (2017) 13(1): e1005277. DOI

Jing Li*, Thomas Biel*, Pranith Lomada*, Qilin Yu, and Taeyoon Kim^§, "Buckling-induced F-actin fragmentation modulates the contraction of active cytoskeletal networks," Soft Matter (2017) 13: 3213–3220. DOI

Ian Linsmeier, Shiladitya Banerjee, Patrick Oakes, Wonyeong Jung, Taeyoon Kim, and Michael P. Murrell^§, "Disordered actomyosin networks are sufficient to produce cooperative and telescopic contractility," Nature Communications (2016) 7: 12615. DOI

Michael Mak, Muhammad Zaman^§, Roger D. Kamm^§, and Taeyoon Kim^§, "Interplay of active processes modulates tension and drives phase transition in self-renewing, motor-driven cytoskeletal networks," Nature Communications (2016) 7: 10323. DOI

Wonyeong Jung, Michael P. Murrell, and Taeyoon Kim^§, "F-actin fragmentation induces distinct mechanisms of stress relaxation in the actin cytoskeleton," ACS Macro Letters (2016) 5(6): 641–645. DOI

Michael Mak, Taeyoon Kim, Muhammad Zaman^§, and Roger D. Kamm^§, "Multiscale mechanobiology: Computational models for integrating molecules to multicellular systems," Integrative Biology (2015) 7(10): 1093–1108. DOI

Wonyeong Jung, Michael P. Murrell, and Taeyoon Kim^§, "F-actin cross-linking enhances the stability of force generation in disordered actomyosin networks," Computational Particle Mechanics (2015) 2(4): 317–327. DOI

Tamara C. Bidone, Taeyoon Kim, Marco A. Deriu, Umberto Morbiducci, and Roger D. Kamm^§, "Multiscale impact of nucleotides and cations on the conformational equilibrium, elasticity and rheology of actin filaments and crosslinked networks," Biomechanics and Modeling in Mechanobiology (2015) 14(5): 1143–1155. DOI

Taeyoon Kim^§, "Determinants of contractile forces generated in disorganized actomyosin bundles," Biomechanics and Modeling in Mechanobiology (2015) 14(2): 345–355. DOI

Taeyoon Kim, Margaret L. Gardel^§, and Ed Munro^§, "Determinants of fluidlike behavior and effective viscosity in cross-linked actin networks," Biophysical Journal (2014) 106(3): 526–534. DOI

Carlos Borau*, Taeyoon Kim*, Tamara C. Bidone, José Manuel García-Aznar, and Roger D. Kamm^§, "Dynamic mechanisms of cell rigidity sensing: Insights from a computational model of actomyosin networks," PLOS One (2012) 7(11): e49174. DOI

Taeyoon Kim, Wonmuk Hwang, and Roger D. Kamm^§, "Dynamic role of cross-linking proteins in actin rheology," Biophysical Journal (2011) 101(7): 1597–1603. DOI

Hyungsuk Lee, Benjamin Pelz, Jorge M. Ferrer, Taeyoon Kim, Matthew J. Lang, and Roger D. Kamm^§, "Cytoskeletal deformation at high strains and the role of cross-link unfolding or unbinding," Cellular and Molecular Bioengineering (2009) 2(1): 28–38. DOI

Taeyoon Kim, Wonmuk Hwang, Hyungsuk Lee, and Roger D. Kamm^§, "Computational analysis of viscoelastic properties of crosslinked actin networks," PLOS Computational Biology (2009) 5(7): e1000439. DOI

Taeyoon Kim, Wonmuk Hwang, and Roger D. Kamm^§, "Computational analysis of a cross-linked actin-like network," Experimental Mechanics (2009) 49(1): 91–104. DOI

Taeyoon Kim, Wonmuk Hwang, and Roger D. Kamm^§, "Computational investigation of dynamic properties of actin networks with crosslinking proteins," ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology (2010) Houston, TX, NEMB2010-13156, 343–344. DOI

Jing Li*, Wonyeong Jung*, Sungmin Nam, Ovijit Chaudhuri, and Taeyoon Kim^§, "Roles of interactions between cells and extracellular matrices for cell migration and matrix remodeling," in Multi-Scale Extracellular Matrix Mechanics and Mechanobiology (2019), Springer. Link

Roger D. Kamm^§, Taeyoon Kim, and Wonmuk Hwang, "Ch. 13: Analysis of the models for cytoskeletal rheology," in Tributes to Yuan-Cheng Fung on His 90th Birthday: Biomechanics: From Molecules to Man (2009), World Scientific. Link