Biophysical Modeling

Learning stochastic processes with intrinsic noise from cross-sectional biological data

S. Maddu, V. Chardès, and M. J. Shelley. Proceedings of the National Academy of Science of the USA, 122:e2420621122, Sep 2025. [DOI link] [preprint link]

Flat Elastic Disc Suspensions Are Indistinguishable from Solutions of Long Flexible Polymers within Planar Incompressible Flows

F. Hillebrand, R. J. Hill, M. Davoodi, S. J. Haward, A. Q. Shen, R. J. Poole, and S. Varchanis. Physical Review Letters, 135(2):024002, JUL 2025. [DOI link]

Nonlinear spontaneous flow instability in active nematics

I. Lavi, R. Alert, J. F. Joanny, and J. Casademunt. Physical Review Letters, 134:238301, JUN 2025. [DOI link] [preprint link]

Geometric Effects in Large Scale Intracellular Flows

O. Jain, B. Chakrabarti, R. Farhadifar, E. R. Gavis, M. J. Shelley, and S. Y. Shvartsman. PRX Life, 3(2):023007. MAY 2025. [DOI link] [preprint link]

Charge distribution and helicity tune the binding of septin's amphipathic helix domain to membranes

C. J. Edelmaier, S. J. Klawa, S. M. Mofidi, Q. Wang, S. Bhonge, E. J. D. Vogt, B. N. Curtis, W. Shi, S. M. Hanson, D. Klotsa, M. G. Forest, A. S. Gladfelter, R. Freeman, and E. Nazockdast. Biophysical Journal, 124(8):1298-1312. APR 2025. [DOI link] [preprint link]

Coarse-graining bacterial diffusion in disordered media to surface states

H. H. Mattingly. Proceedings of the National Academy of Science of the USA, 122:e2407313122, MAR 2025. [DOI link] [preprint link]

Self-propulsion, flocking and chiral active phases from particles spinning at intermediate Reynolds numbers

P. Chen, S. Weady, S. Atis, T. Matsuzawa, M. J. Shelley, and W. T. M. Irvine. Nature Physics, 21:146–154, JAN 2025. [DOI link] [preprint link]

Non-genetic adaptation by collective migration

L. Vo, F. Avgidis, H. H. Mattingly, K. Edmonds, I. Burgers, R. Balasubramanian, T. S. Shimizu, B. I. Kazmierczak, and T. Emonet. Proceedings of the National Academy of Science of the USA, 122:e2423774122, JAN 2025. [DOI link] [preprint link]

Geometric model for dynamics of motor-driven centrosomal asters

Y.-N. Young, V. G. Herrera, H. Z. Huan, R. Farhadifar, and M. J. Shelley. Physical Review Research, 7:013004, JAN 2025. [DOI link] [preprint link]

Ultrasensitivity without conformational spread: A mechanical origin for non-equilibrium cooperativity in the bacterial flagellar motor

H. H. Mattingly, and Y. Tu. [preprint link]

A fully adaptive, high-order, fast Poisson solver for complex two-dimensional geometries

D. Fortunato, D. B. Stein, and A. H. Barnett. [preprint link]

Correlations, mean-field limits, and transition to the concentrated regime in motile particle suspensions

B. Palmer, S. Weady, M. O'Brien, B. Burkhart, and M. J. Shelley. [preprint link]

Active hydrodynamic theory of euchromatin and heterochromatin

S. A. Rautu, A. Zidovska, D. Saintillan, and M. J. Shelley. [preprint link]

Stability of a passive viscous droplet in a confined active nematic liquid crystal

T. Dhar, M. J. Shelley, D. Saintillan. [preprint link]

Flow interactions and forward flight dynamics of tandem flapping wings

F. Fang, C. Mavroyiakoumou, L. Ristroph, and M. J. Shelley. [preprint link]

Inferring stochastic dynamics with growth from cross-sectional data

S. Zhang, S. Maddu, X. Qiu, and V. Chardès [preprint link]

Active liquid crystal theory explains the collective organization of microtubules in human mitotic spindles

C. P. Kelleher, S. Maddu, M. Basaran, T. Müller-Reichert, M. J. Shelley, and D. J. Needleman [preprint link]

The physical consequences of sperm gigantism

J. Imran Alsous, B. Chakrabarti, B. Palmer, M. J. Shelley [preprint link]

Traveling waves in a continuum model for schooling swimmers

A. U. Oza, E. Kanso, M. J. Shelley [preprint link]

Collective multicellular patterns arising from cadherin-linked cytoskeletal domains

X. Du, I. Lavi, M. J. Shelley [preprint link]

Cell clusters sense their global shape to drive collective migration

J. Térmens, I. Pi-Jaumà, I. Lavi, M. Matejčić, I. C. Fortunato, X. Trepat, J. Casademunt [preprint link]

Random matrix theory-guided sparse PCA for single-cell RNA-seq data

V. Chardès [preprint link]

The well: a large-scale collection of diverse physics simulations for machine learning

R. Ohana, M. McCabe, L. Meyer, R. Morel, F. J. Agocs, M. Beneitez, M. Berger, B. Burkhart, S. B. Dalziel, D. B. Fielding, D. Fortunato, J. A. Goldberg, K. Hirashima, Y.-F. Jiang, R. R. Kerswell, S. Maddu, J. Miller, P. Mukhopadhyay, S. S. Nixon, J. Shen, R. Watteaux, B. R.-S. Blancard, F. Rozet, L. H. Parker, M. Cranmer, and S. Ho. Advances in Neural Information Processing Systems, 37:44989-5037. DEC 2024. [DOI link]

Learning locally dominant force balances in active particle systems

D. Sturm, S. Maddu, and I. F. Sbalzarini. Proceedings of the Royal Society A, 480:20230532. DEC 2024. [DOI link]

Lab icebergs melt down and flip out

B. Johnson, Z. Zhang, A. Kim, and S. Weady. Physical Review Fluids, 9:110510, NOV 2024. [DOI link]

Spatiotemporal dynamics of nucleocytoplasmic transport

S. A. Rautu, A. Zidovska, and M. J. Shelley. Physical Review Research, 6(4):043022. OCT 2024. [DOI link] [preprint link]

Mechanics and Morphology of Proliferating Cell Collectives with Self-Inhibiting Growth

S. Weady, B. Palmer, A. Lamson, T. Kim, R. Farhadifar, and M. J. Shelley. Physical Review Letters, 133:158402, OCT 2024. [DOI link] [preprint link]

Mechanics of spindle orientation in human mitotic cells is determined by pulling forces on astral microtubules and clustering of cortical dynein

M. I. Anjur-Dietrich, V. G. Hererra, R. Farhadifar, H. Wu, H. Merta, S. Bahmanyar, M. J. Shelley, D. J. Needleman. Developmental Cell, 59:2429 – 2442.e4, SEP 2024. [DOI link]

OpenRAND: A performance portable, reproducible random number generation library for parallel computations

S. S. Khan, B. Palmer, C. Edelmaier, and H. M. Aktulga. SoftwareX, 27:101773, SEP 2024. [DOI link]

Computational tools for cellular scale biophysics

D. B. Stein and M. J. Shelley. Current Opinion in Cell Biology, 89:102379, AUG 2024. [DOI link]

Cytoplasmic stirring by active carpets

B. Chakrabarti, S. Y. Shvartsman, and M. J. Shelley. Proceedings of the National Academy of Science of the USA, 121:e2405114121, JUL 2024. [DOI link]

Yardangs sculpted by erosion of heterogeneous material

S. Boury, S. Weady, L. Ristroph. PNAS, 121:e2322411121, JUL 2024. [DOI link]

Variational bounds and nonlinear stability of an active nematic suspension

S. Weady. Journal of Fluid Mechanics, 988, JUN 2024. [DOI link]

Temperature compensation through kinetic regulation in biochemical oscillators

H. Fu, C. Fei, Q. Ouyang, and Y. Tu. Biophysics and Computational Biology, 12:e2401567121, MAY 2024. [DOI link]

Learning fast, accurate, and stable closures of a kinetic theory of an active fluid

S. Maddu, S. Weady, and M. J. Shelley. Journal of Computational Physics, 504:112869, MAY 2024. [DOI link]

Self-organized intracellular twisters

S. Dutta, R. Farhadifar, W. Lu, G. Kabacaoğlu, R. Blackwell, D. B. Stein, M. Lakonishok, V. I. Gelfand, S. Y. Shvartsman, and M. J. Shelley. Nature Physics, 20:666–674, JAN 2024. [DOI link]

Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak–Keller–Segel chemotaxis model

T. V. Phan, H. H. Mattingly, L. Vo, J. S. Marvin, L. L. Looger, and T. Emonet. Proceedings of the National Academy of Science of the USA, 121:e2309251121, JAN 2024. [DOI link]

Conformations, correlations, and instabilities of a flexible fiber in an active fluid

S. Weady, D. B. Stein, A. Zidovska, and M. J. Shelley. Physical Review Fluids, 9:013102, JAN 2024. [DOI link]

Dynamical arrest in active nematic turbulence

I. Lavi, R. Alert, J. F. Joanny, and J. Casademunt. [preprint link]

Chemotaxing E. coli do not count single molecules

H. H. Mattingly, K. Kamino, J. Ong, R. Kottou, T. Emonet, and B. B. Machta. [preprint link]

Dynamics of Flexible Filaments in Oscillatory Shear Flows

F. Bonacci, B. Chakrabarti, D. Saintillan, O. du Roure, and A. Lindner. Journal of Fluid Mechanics, 955:A35, JAN 2023. [DOI link]

Sculpting the Sphinx

S. Boury, S. Weady, and L. Ristroph. Physical Review Fluids, 8:110503, NOV 2023. [DOI link]

Collective Motion and Pattern Formation in Phase-Synchronizing Active Fluids

B. Chakrabarti, M.J. Shelley, and S. Fürthauer. Physical Review Letters, 130:128202, MAR 2023. [DOI link]

Stochastic force inference via density estimation

V. Chardès, S. Maddu, and M. J. Shelley. NeurIPS 2023 AI for Science Workshop, OCT 2023. [DOI link]

Modeling epithelial tissue and cell deformation dynamics using a viscoelastic slab sculpted by surface forces

X. Du, and M. J. Shelley. Physical Review Research, 5:023190, OCT 2023. [DOI link]

Chemomechanical model of sperm locomotion reveals two modes of swimming

C. Li and B. Chakrabarti, P. Castilla, A. Mahajan, and D. Saintillan. Physical Review Fluids, 8:113102, NOV 2023. [DOI link]

Adaptive weighting of Bayesian physics informed neural networks for multitask and multiscale forward and inverse problems

S. Perez, S. Maddu, I. F. Sbalzarini, and P. Poncet.Journal of Computational Physics, 21:1746–1758, OCT 2023. [DOI link]

Microtubules and intracellular transport — A microscopic perspective

A. Sahoo, R. Farhadifar, P. Cossio, and S. M. Hanson. Biophysical Journal, 122:124A„ FEB 2023. [DOI link]

A note about convected time derivatives for flows of complex fluids

H. A. Stone, M. J Shelley, and E. Boyko. Soft Matter, 19:5353–5359, JUL 2023. [DOI link]

Prebifurcation enhancement of imbibition-drainage hysteresis cycles

I. Lavi, L. Rose, and R. Planet, J. Casademunt, S. Santucci, and J. Ortín. Physical Review Fluids, 8:124002, DEC 2023. [DOI link]

The power of weak, transient interactions across biology: A paradigm of emergent behavior

P. A. Vasquez, B. Walker, K. Bloom, D. Kolbin, N. Caughman, R. Freeman, M. Lysy, C. Hult, K. A. Newhall, M. Papanikolas, C. Edelmaier, and M. G. Forest. Physica D, 454:133866, NOV 2023. [DOI link]

Laser ablation and fluid flows reveal the mechanism behind spindle and centrosome positioning

H.-Y. Wu, G. Kabacaoğlu, E. Nazockdast, H.-C. Chang, M. J. Shelley, and D. J. Needleman. Nature Physics, NOV 2023. [DOI link]

Interpretable neural architecture search and transfer learning for understanding CRISPR/Cas9 off-target enzymatic reactions

Z. Zhang, A. R. Lamson, M. J. Shelley, and O. Troyanskaya. Nature Computational Science, DEC 2023. [DOI link]

Dual mechanism of kinetochore microtubule detachment

W. Conway, G. Ha, and D. J. Needleman. [preprint link]

Quadrature by fundamental solutions: kernel-independent layer potential evaluation for large collections of simple objects

D. B. Stein, and A. H. Barnett. Advances in Computational Mathematics volume, 48:60, SEP 2022. [DOI link]

Studying Interstellar Turbulence Driving Scales Using the Bispectrum

M. J. O’Brien, B. Burkhart, and M. J. Shelley. Tha Astrophysical Journal, 930(2):149, MAY 2022. [DOI link] [preprint link]

A multiscale biophysical model gives quantized metachronal waves in a lattice of beating cilia

B. Chakrabarti, S. Fürthauer, and M. J. Shelley. Proceedings of the National Academy of Science of the USA, 119:e2113539119, JAN 2022. [DOI link]

How Cross-Link Numbers Shape the Large-Scale Physics of Cytoskeletal Materials

S. Fürthauer and M. J. Shelley. Annual Review of Condensed Matter Physics, 13:365– 384, MAR 2022. [DOI link]

Enhanced clamshell swimming with asymmetric beating at low Reynolds number

S. Hu, J. Zhang, and M. J. Shelley. Soft Matter, 18:3605-3612, APR 2022. [DOI link]

Incompressible active phases at an interface. Part 1. Formulation and axisymmetric odd flows

L. L. Jia, W. T. Irvine, and M. J. Shelley. Journal of Fluid Mechanics, 951:A36, NOV 2022. [DOI link]

The role of monolayer viscosity in Langmuir film hole closure dynamics

L. L. Jia, and M. J. Shelley. Journal of Fluid Mechanics, 948:A1, SEP 2022. [DOI link]

Parallel Discrete Convolutions on Adaptive Particle Representations of Images

J. Jonsson, B. L. Cheeseman, S. Maddu, K. Gonciarz and I. F. Sbalzarini. IEEE Transactions on Image Processing, 31:4197 – 4212, JUN 2022. [DOI link]

Controlling the shape and topology of two-component colloidal membranes

A. Khanra, L. L. Jia, N. P. Mitchell, A. Balchunas, R. A. Pelcovits, T. R. Powers, Z. Dogic, and P. Sharma. Proceedings of the National Academy of Science of the USA, 119:e2204453119, AUG 2022. [DOI link]

Independently paced Ca2+ oscillations in progenitor and differentiated cells in an ex vivo epithelial organ

A. A. Kim, A. Nguyen, X. Du, D. J. Montell, B. L. Pruitt, and L. E. O'Brien. Journal of Cell Science, 135:jcs260249, JUL 2022. [DOI link]

Stability selection enables robust learning of differential equations from limited noisy data

S. Maddu, B. L. Cheeseman, I. F. Sbalzarini, and C. L. Müller. Proceedings of the Royal Society A, 478:20210916, FEB 2022. [DOI link]

Inverse Dirichlet weighting enables reliable training of physics informed neural networks

S. Maddu, D. Sturm, and C. L. Müller, and I. F. Sbalzarini Machine Learning: Science and Technology, 3:15026, FEB 2022. [DOI link]

Euchromatin activity enhances segregation and compaction of heterochromatin in the cell nucleus

A. Mahajan, W. Yan, A. Zidovska, D. Saintillan, and M. J. Shelley. Physical Review X, 12:041033, DEC 2022. [DOI link]

Weakly nonlinear analysis of pattern formation in active suspensions

L. Ohm and M. J. Shelley. Journal of Fluid Mechanics, 942:A53, May 2022. [DOI link]

Hyperuniformity and phase enrichment in vortex and rotor assemblies

N. Oppenheimer, David B. Stein, M. Y. B. Zion, and M. J. Shelley. Nature Communications, 13:804, FEB 2022. [DOI link]

Understanding topological defects in fluidized dry active nematics

B. Palmer, S. Chen, P. Govan, W. Yan, and T. Gao. Soft Matter, 18:1013–1018, JAN 2022. [DOI link]

Fluid circulation driven by collectively organized metachronal waves in swimming T. aceiti nematodes

A. C. Quillen, A. Peshkov, B. Chakrabarti, N. Skerrett, S. McGaffigan, and R. Zapiach. Physical Review E, 106, DEC 2022. [DOI link]

Spectrally accurate solutions to inhomogeneous elliptic PDE in smooth geometries using function intension

D. B. Stein. Journal of Computational Physics, 470:111594, DEC 2022. [DOI link]

Thermodynamically consistent coarse-graining of polar active fluids

S. Weady, D. B. Stein, and M. J. Shelley. Physical Review Fluids, 7:063301, JUN 2022. [DOI link]

A fast Chebyshev method for the Bingham closure with application to active nematic suspension

S. Weady, M. J. Shelley, and D. B. Stein. Journal of Computational Physics, 457:110937, May 2022. [DOI link]

Toward the cellularscale simulation of motor-driven cytoskeletal assemblies

W. Yan, S. Ansari, A. Lamson, M. A. Glaser, R. Blackwell, M. D. Betterton, and M. J. Shelley. eLife, 11:e74160, MAY 2022. [DOI link]

Hydrodynamic instabilities of activity-balanced binary suspensions

B. Palmer, W. Yan, and T. Gao. Physical Review Fluids, 7:063101, JUN 2022. [DOI link]

Force-Induced Formation of Twisted Chiral Ribbons

A. Balchunas and L. L. Jia, M. J. Zakhary, J. Robaszewski, T. Gibaud, Z. Dogic, R. A. Pelcovits, and T. R. Powers. Force-Induced Formation of Twisted Chiral Ribbons. Physical Review Letters, 125:018002, June 2021. [DOI link]

Motile dislocations knead odd crystals into whorls

E. S. Bililign, F. B. Usabiaga, Y. A. Ganan, A. Poncet, V. Soni, S. Magkiriadou, M. J. Shelley, D. Bartolo, and W. T. M. Irvine. Nature Physics, DEC 2021. [DOI link]

Metallic microswimmers driven up the wall by gravity

Q. Brosseau, F. B. Usabiaga, E. Lushi, Y. Wu, L. Ristroph, M. D. Ward, M. J. Shelley, and J. Zhang. Soft Matter, 17:6597–6602, Jun 2021. [DOI link]

Signatures of elastoviscous buckling in the dilute rheology of stiff polymers

B. Chakrabarti, Y. Liu, O. du Roure, A. Lindner, and D. Saintillan. Journal of Fluid Mechanics, page a12, JUL 2021. [DOI link]

A hydraulic instability drives the cell death decision in the nematode germline

N. T. Chartier, A. Mukherje, J. Pfanzelter, S. Fürthauer, B. T. Larson, A. W. Fritsch, R. Amini, M. Kreysing, F. Jülicher, and S. W. Grill. Nature Physics, 17:920–925, MAY 2021. [DOI link]

Tissue fluidity mediated by adherens junction dynamics promotes planar cell polarity-driven ommatidial rotation

N. Founounou, R. Farhadifar, G. M. Collu, U. Weber, M. J. Shelley, and M. Mlodzik. Nature Communications, 12:6974, NOV 2021. [DOI link]

A design framework for actively crosslinked filament networks

S. Fürthauer, D. J. Needleman, and M. J. Shelley. New Journal of Physics, 23:013012, JAN 2021. [DOI link]

Lévy Walks and Path Chaos in the Dispersal of Elongated Structures Moving across Cellular Flows

S.-Y. Hu, J.-J. Chu, M. J. Shelley, and J. Zhang. Physical Review Letters, 127:074503, AUG 2021. [DOI link]

A stable and accurate scheme for solving the Stefan problem coupled with natural convection using the Immersed Boundary Smooth Extension method

J. M. Huang, M. J. Shelley, and D. B. Stein. Journal of Computational Physics, 432:110162, May 2021. [DOI link]

Axisymmetric membranes with edges under external force: buckling, minimal surfaces, and tethers

L. L. Jia, S. Pei, R. A. Pelcovits, and T. R. Powers. Soft Matter 17:7268-7286. JUL 2021. [DOI link]

Comparison of explicit and mean-field models of cytoskeletal filaments with crosslinking motors

A. Lamson, J. M. Moore, F. Fang, M. A. Glaser, M. J. Shelley, and M. D. Betterton. The European Physical Journal E, 44:44, Mar 2021. [DOI link]

Microtubule reorganization during female meiosis in C. elegans

I. Lantzsch and S. Fürthauer. eLife, 10:e58903, JUN 2021. [DOI link]

Swirling instability of the microtubule cytoskeleton

D. B. Stein, G. D. Canio, E. Lauga, M. J. Shelley, and R. E. Goldstein. Physical Review Letters, 126:028103, JAN 2021. [DOI link]

Kernel aggregated fast multipole method

W. Yan and R. Blackwell. Advances in Computational Mathematics volume, 47:69, SEP 2021. [DOI link]

The many behaviors of deformable active droplets

Y. N. Young, M. J. Shelley, and D. B. Stein. Mathematical Biosciences and Engineering, 18:2849–2881, MAR 2021. [DOI link]