Publications

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PUBLICATION YEAR

2024
2023

2025

Universal scaling in one-dimensional non-reciprocal matter. Liu S, Hanai R, Littlewood PB. [Preprint] arXiv; 2025. (PDF) https://doi.org/10.48550/arXiv.2503.14384

Temporal Contrastive Learning through implicit non-equilibrium memory. Falk MJ, Strupp AT, Scellier B, Murugan A. Nat Commun. 16(1): 2163. 2025. (PDF) https://doi.org/10.1038/s41467-025-57043-x

Spatially-structured inflammatory response in the presence of a uniform stimulus. Jerison ER, Romeo N, Quake SR. [Preprint] bioRxiv; 2025. (PDF) https://doi.org/10.1101/2025.01.28.635318

Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales. Russo CJ, Husain K, Murugan A. Annual Review of Biophysics. 54(Volume 54, 2025): 401–26. 2025. (PDF) https://doi.org/10.1146/annurev-biophys-081624-030543

Preserving predictive information under biologically plausible compression. Durian SCL, Bojanek K, Marre O, Palmer SE. [Preprint] bioRxiv; 2025. (PDF) https://doi.org/10.1101/2025.03.12.642864

Physical Considerations in Memory and Information Storage. Du M, Behera AK, Vaikuntanathan S. Annual Review of Physical Chemistry. 76(Volume 76, 2025): 471–95. 2025. (PDF) https://doi.org/10.1146/annurev-physchem-083122-010308

Phase Transitions in Nonreciprocal Driven-Dissipative Condensates. Belyansky R, Weis C, Hanai R, Littlewood PB, Clerk AA. [Preprint] arXiv; 2025. (PDF) https://doi.org/10.48550/arXiv.2502.05267

Non-Hermitian wave turbulence. Wit XM de, Galtier S, Fruchart M, Toschi F, Vitelli V. [Preprint] arXiv; 2025. (PDF) https://doi.org/10.48550/arXiv.2504.15403

Neuronal firing rate diversity lowers the dimension of population covariability. Tian GJ, Zhu O, Shirhatti V, Greenspon C, Downey JE, Freedman DJ, Doiron B. [Preprint] bioRxiv; 2025. (PDF) https://doi.org/10.1101/2024.08.30.610535

Microscopic Control of Cortical Flows in Polarized C. elegans Zygotes. White ED, Li Y, Kadzik R, Qiu Y, Dinner AR, Munro EM. [Preprint] bioRxiv; 2025. (PDF) https://doi.org/10.1101/2025.01.12.632635

Microbial functional guilds respond cohesively to rapidly fluctuating environments. Crocker K, Skwara A, Kannan R, Murugan A, Kuehn S. [Preprint] bioRxiv; 2025. (PDF) https://doi.org/10.1101/2025.01.30.635766

Learning via mechanosensitivity and activity in cytoskeletal networks. Banerjee DS, Falk MJ, Gardel ML, Walczak AM, Mora T, Vaikuntanathan S. [Preprint] arXiv; 2025. (PDF) https://doi.org/10.48550/arXiv.2504.15107

Interleaving asynchronous and synchronous activity in balanced cortical networks with short-term synaptic depression. Dunworth JB, Xu Y, Graupner M, Ermentrout B, Reyes AD, Doiron B. [Preprint] bioRxiv; 2025. (PDF) https://doi.org/10.1101/2025.03.13.643074

Inferring resource competition in microbial communities from time series. Chen X, Crocker K, Kuehn S, Walczak AM, Mora T. [Preprint] arXiv; 2025. (PDF) https://doi.org/10.48550/arXiv.2501.04520

Hardware Acceleration for HPS Algorithms in Two and Three Dimensions. Melia O, Fortunato D, Hoskins J, Willett R. [Preprint] arXiv; 2025. (PDF) https://doi.org/10.48550/arXiv.2503.17535

Gaussian fluctuations of nonreciprocal systems. Shmakov S. Phys Rev E. 111(3). 2025. (PDF) https://doi.org/10.1103/PhysRevE.111.034133

Field Theory of Birhythmicity. Shmakov S, Littlewood PB. [Preprint] arXiv; 2025. (PDF) https://doi.org/10.48550/arXiv.2501.14192

Dynamic coexistence driven by physiological transitions in microbial communities. Narla AV, Hwa T, Murugan A. Proceedings of the National Academy of Sciences. 122(16): e2405527122. 2025. (PDF) https://doi.org/10.1073/pnas.2405527122

Collective Microbial Effects Drive Toxin Bioremediation and Enable Rational Design. Yousef M, Lee KK, Tang J, Charisopoulos V, Willett R, Kuehn S. bioRxiv. : 2025.03.28.645802. 2025. (PMCID: PMC11974898) (PDF) https://doi.org/10.1101/2025.03.28.645802

Circuit-Based Understanding of Fine Spatial Scale Clustering of Orientation Tuning in Mouse Visual Cortex. Yu P, Yang Y, Gozel O, Oldenburg I, Dipoppa M, Rossi LF, Miller K, Adesnik H, Ji N, Doiron B. [Preprint] bioRxiv; 2025. (PDF) https://doi.org/10.1101/2025.02.11.637768

Characterizing nonlinear dynamics by contrastive cartography. Romeo N, Chi C, Dinner AR, Jerison ER. [Preprint] arXiv; 2025. (PDF) https://doi.org/10.48550/arXiv.2502.09628

Causal Spike Timing Dependent Plasticity Prevents Assembly Fusion in Recurrent Networks. Yang X, Doiron B. [Preprint] bioRxiv; 2025. (PDF) https://doi.org/10.1101/2025.01.14.633085

Bacterial motility patterns vary smoothly with spatial confinement and disorder. Zhang H, Wetherington MT, Ko H, FitzGerald CE, Luzzatto LV, Kovács IA, Munro EM, Nirody JA. [Preprint] bioRxiv; 2025. (PDF) https://doi.org/10.1101/2024.09.29.615714

Adaptive locomotion of active solids. Veenstra J, Scheibner C, Brandenbourger M, Binysh J, Souslov A, Vitelli V, Coulais C. Nature. 639(8056): 935–41. 2025. (PDF) https://doi.org/10.1038/s41586-025-08646-3

A minimal scenario for the origin of non-equilibrium order. Ravasio R, Husain K, Evans CG, Phillips R, Ribezzi M, Szostak JW, Murugan A. [Preprint] arXiv; 2025. (PDF) https://doi.org/10.48550/arXiv.2405.10911

2024

A correspondence between Hebbian unlearning and steady states generated by nonequilibrium dynamics. Behera AK, Du M, Jagadisan U, Sastry S, Rao M, Vaikuntanathan S. [Preprint] arXiv; 2024. (PDF) https://doi.org/10.48550/arXiv.2410.06269

Epistatic pathways in evolvable mechanical networks. Alqatari S, Nagel S. [Preprint] arXiv; 2024. (PDF)

Interpreting Neural Operators: How Nonlinear Waves Propagate in Nonreciprocal Solids. Colen J, Poncet A, Bartolo D, Vitelli V. Phys Rev Lett. 133(10): 107301. 2024. (PDF) https://doi.org/10.1103/PhysRevLett.133.107301

Between-area communication through the lens of within-area neuronal dynamics. Gozel O, Doiron B. Science Advances. 10(42): eadl6120. 2024. (PDF) https://doi.org/10.1126/sciadv.adl6120

Stimulus invariant aspects of the retinal code drive discriminability of natural scenes. Hoshal BD, Holmes CM, Bojanek K, Salisbury J, Berry MJ, Marre O, Palmer SE. [Preprint] bioRxiv; 2024. (PDF) https://doi.org/10.1101/2023.08.08.552526

The mechanics of correlated variability in segregated cortical excitatory subnetworks. Negrón A, Getz MP, Handy G, Doiron B. Proceedings of the National Academy of Sciences. 121(28): e2306800121. 2024. (PDF) https://doi.org/10.1073/pnas.2306800121

A dynamic scale-mixture model of motion in natural scenes. Salisbury JM, Palmer SE. [Preprint] bioRxiv; 2024. (PDF) https://doi.org/10.1101/2023.10.19.563101

Quantifying stimulus-relevant representational drift using cross-modality contrastive learning. Wang S, de Laittre EA, MacLean J, Palmer SE. [Preprint] arXiv; 2024. (PDF)

Towards understanding neural collapse in supervised contrastive learning with the information bottleneck method. Wang S, Palmer SE. [Preprint] arXiv; 2024. (PDF)

Functional regimes define the response of the soil microbiome to environmental change. Lee KK, Liu S, Crocker K, Huggins DR, Tikhonov M, Mani M, Kuehn S. [Preprint] bioRxiv; 2024. (PDF) https://doi.org/10.1101/2024.03.15.584851

Odd Viscosity Suppresses Intermittency in Direct Turbulent Cascades. Chen S, De Wit XM, Fruchart M, Toschi F, Vitelli V. Phys Rev Lett. 133(14): 144002. 2024. (PDF) https://doi.org/10.1103/PhysRevLett.133.144002

Perceptual Resolution of Ambiguity: Can Tuned, Divisive Normalization Account for both Interocular Similarity Grouping and Difference Enhancement. Peiso JR, Palmer SE, Shevell SK. [Preprint]. 2024. (PDF) https://doi.org/10.1101/2024.04.01.587646

Pattern formation by turbulent cascades. de Wit XM, Fruchart M, Khain T, Toschi F, Vitelli V. Nature. 627(8004): 515–21. 2024. (PDF) https://doi.org/10.1038/s41586-024-07074-z

Odd elasticity and topological waves in active surfaces. Fossati M, Scheibner C, Fruchart M, Vitelli V. Phys Rev E. 109(2): 024608. 2024. (PDF) https://doi.org/10.1103/PhysRevE.109.024608

Sociohydrodynamics: data-driven modelling of social behavior. Seara DS, Colen J, Fruchart M, Avni Y, Martin D, Vitelli V. [Preprint] arXiv; 2024. (PDF)

Spiking at the edge: Excitability at interfaces in reaction–diffusion systems. Scheibner C, Ori H, Cohen AE, Vitelli V. Proceedings of the National Academy of Sciences. 121(3): e2307996120. 2024. (PDF) https://doi.org/10.1073/pnas.2307996120

Dynamic coexistence driven by physiological transitions in microbial communities. Narla AV, Hwa T, Murugan A. [Preprint] arXiv; 2024. (PDF)

Machine learning interpretable models of cell mechanics from protein images. Schmitt MS, Colen J, Sala S, Devany J, Seetharaman S, Caillier A, Gardel ML, Oakes PW, Vitelli V. Cell. 187(2): 481-494.e24. 2024. (PDF) https://doi.org/10.1016/j.cell.2023.11.041

2023

Contrastive learning through non-equilibrium memory. Falk M, Strupp A, Scellier B, Murugan A. [Preprint] arXiv; 2023. (PDF)

Closed ecosystems extract energy through self-organized nutrient cycles. Goyal A, Flamholz AI, Petroff AP, Murugan A. Proceedings of the National Academy of Sciences. 120(52): e2309387120. 2023. (PDF) https://doi.org/10.1073/pnas.2309387120

Learning a conserved mechanism for early neuroectoderm morphogenesis. Lefebvre M, Colen J, Claussen N, Brauns F, Raich M, Mitchell N, Fruchart M, Vitelli V, Streichan SJ. [Preprint] bioRxiv; 2023. (PDF) https://doi.org/10.1101/2023.12.22.573058

Statistical prediction of microbial metabolic traits from genomes. Li Z, Selim A, Kuehn S. PLOS Computational Biology. 19(12): e1011705. 2023. (PDF) https://doi.org/10.1371/journal.pcbi.1011705

Global patterns in gene content of soil microbiomes emerge from microbial interactions. Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. [Preprint] bioRxiv; 2023. (PDF) https://doi.org/10.1101/2023.05.31.542950

Elucidating the Role of Filament Turnover in Cortical Flow using Simulations and Representation Learning. Qiu Y, White ED, Munro EM, Vaikuntanathan S, Dinner AR. [Preprint] arXiv; 2023. (PDF)

Kinematics and coordination of moth flies walking on smooth and rough surfaces. Brandt EE, Manyama MR, Nirody JA. Annals of the New York Academy of Sciences. n/a(n/a). (PDF) https://doi.org/10.1111/nyas.15176