Publications

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Preprints
  • Shape-Independent Fluidization in Epithelial Cell Monolayers
    Bera, P.K., Nguyen, A.Q., McCord, M., Bi, D., & Notbohm, J.
    arXiv (2026) arXiv
  • Cell-Cell Adhesion as a Double-Edged Sword in Tissue Fluidity
    Nguyen, A.Q., Bera, P.K., Notbohm, J., & Bi, D.
    arXiv (2026) arXiv
  • Cell jamming transition is regulated by mitochondrial pyruvate transport and endocytosis
    Bermudez, A., Latham, Z., Diaz, J., Yan, W., Chen, J., Bi, D., Goldstein, A.S., Hu, J.K., & Lin, N.Y.C.
    bioRxiv (2026) DOI
  • Tunable hyperuniformity in cellular structures
    Tang, Y., Li, X., & Bi, D.
    arXiv (2025) arXiv
Journal Publications
  • MultiCell: geometric learning in multicellular development
    Yang, H., Roy, G., Nguyen, A.Q., Bi, D., Stern, T., Buehler, M.J., & Guo, M.
    Nature Methods (2025) DOI
  • The Rheology of Living Tissues: From Cells to Organismal Mechanics
    Kayal, S., Nguyen, A.Q., & Bi, D.
    Annual Review of Condensed Matter Physics 17 (2025) DOI
  • Non-muscle Myosin IIA regulates anisotropic cell tension to maintain hexagonal packing of mouse lens meridional row cells
    Islam, S.T., Tang, Y., Boliver, H., Bi, D., & Fowler, V.M.
    Molecular Biology of the Cell (2025) DOI
  • Origin of yield stress and mechanical plasticity in model biological tissues
    Nguyen, A.Q., Huang, J., & Bi, D.
    Nature Communications 16:3260 (2025) DOI
  • Epithelial layer fluidization by curvature-induced unjamming
    De Marzio, M., Das, A., Fredberg, J.J., & Bi, D.
    Physical Review Letters 134:138402 (2025) DOI
  • Topology and Nuclear Size Determine Cell Packing on Growing Lung Spheroids
    Tang, W., Huang, J., Pegoraro, A.F., Zhang, J.H., Tang, Y., Kotton, D.N., et al.
    Physical Review X 15(1):011067 (2025) DOI
  • Mechanical imbalance between normal and transformed cells drives epithelial homeostasis through cell competition
    Gupta, P., Kayal, S., Tanimura, N., et al.
    eLife (2025) DOI
  • Regulation of chromatin modifications through coordination of nucleus size and epithelial cell morphology heterogeneity
    Bermudez, A., Latham, Z.D., Ma, A.J., et al.
    Communications Biology 8:269 (2025) DOI
  • A shape-driven reentrant jamming transition in confluent monolayers of synthetic cell-mimics
    Arora, P., Sadhukhan, S., Nandi, S.K., Bi, D., Sood, A.K., & Ganapathy, R.
    Nature Communications 15(1):5645 (2024) DOI
  • Cell Division and Motility Enable Hexatic Order in Biological Tissues
    Tang, Y., Chen, S., Bowick, M.J., & Bi, D.
    Physical Review Letters 132(21):218402 (2024) DOI
  • Ductile-to-brittle transition and yielding in soft amorphous materials: perspectives and open questions
    Divoux, T., et al.
    Soft Matter (2024) DOI
  • Matrix confinement modulates 3D spheroid sorting and burst-like collective migration
    Cai, G., Li, X., Lin, S.-S., Chen, S.J., Rodgers, N.C., Koning, K.M., Bi, D., & Liu, A.P.
    Acta Biomaterialia 179:192–206 (2024) DOI
  • Spatial confinement affects the heterogeneity and interactions between shoaling fish
    Kuntz, G., Huang, J., Rask, M., Lindgren-Ruby, A., Shinsato, J.Y., Bi, D., & Tabatabai, A.P.
    Scientific Reports 14(1):12296 (2024) DOI
  • Effect of non-linear strain stiffening in eDAH and unjamming
    Xie, X., Sauer, F., Grosser, S., et al.
    Soft Matter 20(9):1996–2007 (2024) DOI
  • Discontinuous shear thickening in biological tissue rheology
    Hertaeg, M.J., Fielding, S.M., & Bi, D.
    Physical Review X 14(1):011027 (2024) DOI
  • Network physics of attractive colloidal gels: Resilience, Rigidity, and Phase Diagram
    Nabizadeh, M., Nasirian, F., Li, X., et al.
    Proceedings of the National Academy of Sciences 121(3):e2316394121 (2024) DOI
  • Bridging the gap between collective motility and epithelial–mesenchymal transitions through the active finite voronoi model
    Huang, J., Levine, H., & Bi, D.
    Soft Matter (2023) DOI
  • A Mechanistic Model of the Organization of Cell Shapes in Epithelial Tissues
    Malakar, K., Rubenstein, R., Bi, D., & Chakraborty, B.
    Frontiers in Soft Matter (2023) DOI
  • Nature-inspired designs for disordered acoustic bandgap materials
    Li, X., & Bi, D.
    Soft Matter (2023) DOI
  • Discontinuous rigidity transition associated with shear jamming in granular simulations
    Babu, V., Vinutha, H.A., Bi, D., & Sastry, S.
    Soft Matter (2023) DOI
  • Constitutive model for the rheology of biological tissue
    Fielding, S., Cochran, J., Huang, J., Bi, D., & Marchetti, M.C.
    Physical Review E 108:L042602 (2023) DOI
  • Compressive stress drives adhesion-dependent unjamming transitions in breast cancer cell migration
    Cai, G., Nguyen, A., Bashirzadeh, Y., Lin, S.-S., Bi, D., & Liu, A.P.
    Frontiers in Cell and Developmental Biology 10:933042 (2022) DOI
  • Collective curvature sensing and fluidity in three-dimensional multicellular systems
    Tang, W., Das, A., Pegoraro, A.F., Han, Y.-L., Huang, J., et al.
    Nature Physics (2022) DOI
  • Rigid tumours contain soft cancer cells
    Fuhs, T., Wetzel, F., Fritsch, A.W., Li, X., et al.
    Nature Physics (2022) DOI
  • Stress-driven rigidity and non-linear elasticity in epithelial tissues
    Huang, J., Cochran, J., Fielding, S., Marchetti, M., & Bi, D.
    Physical Review Letters 128:178001 (2022) DOI
  • Controlled neighbor exchanges drive glassy behavior, intermittency and cell streaming in epithelial tissues
    Das, A., Sastry, S., & Bi, D.
    Physical Review X 11:041037 (2021) DOI
  • Configurational Fingerprints of Multicellular Living Systems
    Yang, H., Pegoraro, A.F., Han, Y.-L., Tang, W., Abeyaratne, R., Bi, D., & Guo, M.
    Proceedings of the National Academy of Sciences 118(44):e2109168118 (2021) DOI
  • Energetics of mesoscale cell turbulence in two-dimensional monolayers
    Lin, S.Z., Zhang, W.Y., Bi, D., Li, B., & Feng, X.Q.
    Communications Physics 4(1) (2021) DOI
  • The unjamming transition is distinct from the epithelial-to-mesenchymal transition
    Mitchel, J.A., Das, A., O'Sullivan, M., Stancil, I., DeCamp, S., et al.
    Nature Communications 11:5053 (2020) DOI
  • Unjamming and collective migration in MCF10A breast cancer cell lines
    Kim, J.-H., et al.
    Biochemical and Biophysical Research Communications 521(3) (2020) DOI
  • Collective migration of non-cancerous, well-differentiated human airway epithelial cells by ionizing radiation
    O'Sullivan, M.J., Mitchel, J.A., Das, A., et al.
    Frontiers in Cell and Developmental Biology 8 (2020) DOI
  • Mechanical Heterogeneity in Tissues Promotes Rigidity and Controls Cellular Invasion
    Li, X., Das, A., & Bi, D.
    Physical Review Letters 123:058101 (2019) DOI
  • Multicellular rosettes drive fluid-solid transition in epithelial tissues
    Yan, L., & Bi, D.
    Physical Review X 9:011029 (2019) DOI
  • Epithelial Wound Healing Coordinates Distinct F-actin Architectures to Conserve Work and Balance Power
    Ajeti, V., Tabatabai, A., Fleszar, A., et al.
    Nature Physics 15:696–705 (2019) DOI
  • Dynamic instability and migration modes of collective cells in channels
    Lin, S.Z., Bi, D., Li, B., & Feng, X.Q.
    Journal of the Royal Society Interface 16(156):20190258 (2019) DOI
  • Biological tissue-inspired tunable photonic fluid
    Li, X., Das, A., & Bi, D.
    Proceedings of the National Academy of Sciences 115(26):6650–6655 (2018) DOI
  • Flocking Transition in Confluent Tissues
    Giavazzi, F., Paoluzzi, M., Macchi, M., Bi, D., et al.
    Soft Matter 14:3471–3477 (2018) DOI
  • Hydrodynamics of shape-driven rigidity transitions in motile tissues
    Czajkowski, M., Bi, D., Manning, L., & Marchetti, M.
    Soft Matter 14:5628–5642 (2018) DOI
  • Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing
    Staddon, M.F., Bi, D., Murrell, M.P., & Banerjee, S.
    PLOS Computational Biology 14(10):e1006502 (2018) DOI
  • Geometrical constraints during epithelial jamming
    Atia, L., Bi, D., et al.
    Nature Physics 14:613–620 (2018) DOI
  • Correlating Cell Shape and Cellular Stress in Motile Confluent Tissues
    Yang, X., Bi, D., Czajkowski, M., Merkel, M., Manning, M.L., & Marchetti, M.C.
    Proceedings of the National Academy of Sciences 114(48):12663–12668 (2017) DOI
Prior to Northeastern
  • Motility-driven glass and jamming transitions in biological tissues
    Bi, D., Yang, X., Marchetti, M.C., & Manning, M.L.
    Physical Review X 6:021011 (2016) DOI
  • Shear-induced rigidity of frictional particles: Analysis of emergent order in stress space
    Sarkar, S., Bi, D., Zhang, J., Ren, J., Behringer, R.P., & Chakraborty, B.
    Physical Review E 93:042901 (2016) DOI
  • A density-independent rigidity transition in biological tissues
    Bi, D., Lopez, J.H., Schwarz, J.M., & Manning, M.L.
    Nature Physics 11:1074–1079 (2015) DOI
  • Unjamming and cell shape in the asthmatic airway epithelium
    Park, J.-A., Kim, J.H., Bi, D., et al.
    Nature Materials 14:1040–1048 (2015) DOI
  • The Statistical Physics of Athermal Materials
    Bi, D., Henkes, S., Daniels, K., & Chakraborty, B.
    Annual Review of Condensed Matter Physics 6:63–83 (2015) DOI
  • Energy barriers and cell migration in densely packed tissues
    Bi, D., Lopez, J.H., Schwarz, J.M., & Manning, M.L.
    Soft Matter 10:1885–1890 (2014) DOI
  • Statistical Properties of Granular Materials near Jamming
    Behringer, R.P., Bi, D., Chakraborty, B., Clark, A., Dijksman, J., Ren, J., & Zhang, J.
    Journal of Statistical Mechanics: Theory and Experiment P06004 (2014) DOI
  • Origin of Rigidity in Dry Granular Solids
    Sarkar, S., Bi, D., Zhang, J., Behringer, R.P., & Chakraborty, B.
    Physical Review Letters 111:068301 (2013) DOI
  • Fluctuations in Shear-Jammed States: A Statistical Ensemble Approach
    Bi, D., Zhang, J., Behringer, R.P., & Chakraborty, B.
    Europhysics Letters 102:34002 (2013) DOI
  • Jamming by shear
    Bi, D., Zhang, J., Chakraborty, B., & Behringer, R.P.
    Nature 480:355–358 (2011) DOI
  • Rheology of granular materials: dynamics in a stress landscape
    Bi, D., & Chakraborty, B.
    Philosophical Transactions of the Royal Society A 367(1909):5073–5090 (2009) DOI
  • Why Do Granular Materials Stiffen with Shear Rate? Test of Novel Stress-Based Statistics
    Behringer, R.P., Bi, D., Henkes, S., & Chakraborty, B.
    Physical Review Letters 103:268301 (2008) DOI