Publications

An up-to-date list is also on Google Scholar and in the CV.

All 78 papers

2026

  1. Coherent advantage in the computational expressivity of excitonic networks
    M. Du, C. Floyd, D. Jasrasaria, S. Vaikuntanathan
    arXiv (2026) arXiv Adaptable materials
  2. Diffusion models learn underlying trends in actomyosin networks and predict behavior at unseen filament turnover
    E. Rennert, A. K. Behera, Y. Qiu, S. Vaikuntanathan
    bioRxiv (2026) · submitted to Biophysical Journal bioRxiv Cytoskeletal dynamics Adaptable materials Generative AI + Stat mech
  3. In-context learning emerges in chemical reaction networks without attention
    C. Floyd†, H. M. Lopez Rios†, A. R. Dinner, S. Vaikuntanathan
    arXiv (2026) · under revision, Nature Communications · †equal contribution arXiv Adaptable materials Generative AI + Stat mech
  4. Local imperfect feedback control in nonequilibrium biophysical systems enabled by response constraints
    C. Floyd, A. R. Dinner, S. Vaikuntanathan
    Physical Review X, in press (2026) arXiv Cell states, decisions and control
  5. Fluctuation structure predicts genome-wide perturbation outcomes
    B. Kuznets-Speck, L. Schwartz, H. Sun, M. E. Melzer, N. Kumari, B. Haley, E. Prashnani, S. Vaikuntanathan, Y. Goyal
    Nature Biotechnology, in press (2026) bioRxiv Cell states, decisions and control
  6. Neuromodulation-inspired gated associative memory networks: Extended memory retrieval and emergent multistability
    D. Goto, H. M. Lopez Rios, M. Scholz, S. Vaikuntanathan
    Proc. Natl. Acad. Sci. USA, in press (2026) arXiv Chemical drivers of flexible computing in brains
  7. Hidden nonreciprocity as a stabilizing effective potential in active matter
    M. Du, A. Goychuk, S. Vaikuntanathan
    Phys. Rev. Research 8, 033330 (2026) Paper arXiv
  8. Learning to control non-equilibrium dynamics using local imperfect gradients
    C. Floyd, A. R. Dinner, S. Vaikuntanathan
    Newton 2, 100595 (2026) Paper arXiv Cell states, decisions and control
  9. Light-induced ordered pattern formation in 2D copper halide perovskites
    A. Ghosh†, J. L. Spellberg†, M. Du, Y. Dou, A. S. Thind, S. Qi, J. Rieger, C. Raab, S. Vaikuntanathan, R. F. Klie, L. Quan, S. B. King
    Nano Letters 26, 4189–4196 (2026) · †equal contribution Paper chemRxiv
  10. Unifying theories in high-dimensional biophysics: Approaches, challenges and opportunities
    M. Bauer, A. Goyal, S. Goyal, G. Reddy, S. Chakrabarti, M. M. Desai, W. Gilpin, J. Grilli, K. Husain, S. Jain, M. K. Jolly, K. Kawaguchi, A. Koseska, M. Lin, L. Narlikar, S. Pigolotti, A. Raju, K. Shrinivas, R. Siddharthan, G. J. Stephens, A. Tiffeau-Mayer, S. Vaikuntanathan
    npj Systems Biology and Applications 12, 43 (2026) Paper arXiv:2512.10111
  11. Non-equilibrium active noise enhances generative memory in diffusion models
    A. K. Behera, A. Lamtyugina, A. Nandy, D. Goto, D. Sanwal, C. Floyd, S. Vaikuntanathan
    Nature Communications, in press (2026) arXiv Research Square Generative AI + Stat mech
  12. Contractile to extensile transitions and mechanical adaptability enabled by activity in cytoskeletal structures
    A. Lamtyugina, D. S. Banerjee, Y. Qiu, S. Vaikuntanathan
    Biophysical Journal, in press (2026) Paper Cytoskeletal dynamics
  13. Learning via mechanosensitivity and activity in cytoskeletal networks
    D. S. Banerjee, M. J. Falk, M. L. Gardel, A. M. Walczak, T. Mora, S. Vaikuntanathan
    PRX Life 4, 013001 (2026) Paper arXiv Cytoskeletal dynamics Adaptable materials

2025

  1. Interpretable thermodynamic score-based classification of relaxation excursions
    B. Kuznets-Speck, J. Jung, P. Pholraksa, A. Zhong, L. Schwartz, E. Prashnani, S. Vaikuntanathan, Y. Goyal
    bioRxiv (2025) · under review, Cell Systems bioRxiv
  2. Mapping the diverse topologies of protein–protein interaction fitness landscapes
    S. S. Lu†, M. J. Styles†, C. F. Gao†, A. Nandy, C. Basile, J. A. Pixley, S. Tao, A. R. Dinner, S. Vaikuntanathan*, B. C. Dickinson*
    bioRxiv (2025) · submitted · †equal contribution · *joint corresponding authors bioRxiv Deciphering the biophysical drivers of interactions
  3. Connection between Hebbian unlearning and steady states generated by nonequilibrium dynamics
    A. K. Behera, M. Du, U. K. Jagadisan, S. Sastry, M. Rao, S. Vaikuntanathan
    PRX Life (2025) Paper arXiv Generative AI + Stat mech
  4. Room-temperature charge localization in ion-coupled bilayer transistors
    M. Gao, H. Hong, S. Fan, T. Chowdhury, Z. Naqvi, J. Ge, C. Liang, Y. Han, N. P. Guisinger, Y. Qiu, D. H. Kim, S. Vaikuntanathan, C. Liu, J. Park
    Science 390, 356–360 (2025) Paper
  5. Limits on the computational expressivity of non-equilibrium biophysical processes
    C. Floyd, A. R. Dinner, A. Murugan, S. Vaikuntanathan
    Nature Communications 16, 7184 (2025) Paper Cell states, decisions and control
  6. Renormalized mechanics and stochastic thermodynamics of growing model protocells
    J. L. Shivers, M. Nguyen, A. R. Dinner, P. Vlahovska, S. Vaikuntanathan
    PRX Life (2025) arXiv
  7. Tailoring interactions between active nematic defects with reinforcement learning
    C. Floyd, A. R. Dinner, S. Vaikuntanathan
    Soft Matter 21, 4488–4497 (2025) Paper
  8. Physical considerations in memory and information storage
    M. Du, A. K. Behera, S. Vaikuntanathan
    Annual Review of Physical Chemistry 76 (2025) Adaptable materials
  9. A thermodynamic framework for nonequilibrium self-assembly and force–morphology tradeoffs in branched actin networks
    E. Rennert, S. Vaikuntanathan
    eLife 14, RP104513 (2025) Paper eLife Cytoskeletal dynamics
  10. Chemical waves in reaction-diffusion networks of small organic molecules
    A. Paikar, X. Li, L. Avram, B. S. Smith, I. Sütő, D. Horváth, E. Rennert, Y. Qiu, Á. Tóth, S. Vaikuntanathan, S. N. Semenov
    Chemical Science 16, 659–669 (2025) Paper
  11. Sequential pattern retrieval: New representations inspired by non-equilibrium physics and associative memory models
    M. Du, A. K. Behera, M. Rao, S. Vaikuntanathan
    ICLR 2025 Workshop on New Frontiers in Associative Memories (NFAM) (2025) OpenReview Generative AI + Stat mech

2024

  1. Learning dynamical behaviors in physical systems
    R. Mandal, R. Huang, M. Fruchart, P. G. Moerman, S. Vaikuntanathan, A. Murugan, V. Vitelli
    arXiv (2024) · under revision, Nature Physics arXiv Adaptable materials
  2. Active oscillatory associative memory
    M. Du, A. K. Behera, S. Vaikuntanathan
    J. Chem. Phys. 160, 055103 (2024) Paper Adaptable materials
  3. Pattern formation in odd viscoelastic fluids
    C. Floyd, A. R. Dinner, S. Vaikuntanathan
    Phys. Rev. Research 6, 033100 (2024) Paper
  4. Dissection and integration of bursty transcriptional dynamics for complex systems
    C. F. Gao, S. Vaikuntanathan*, S. J. Riesenfeld*
    Proc. Natl. Acad. Sci. USA 121, e2306901121 (2024) · *joint corresponding authors Paper

2023

  1. Elucidating the role of filament turnover in cortical flow using simulations and representation learning
    Y. Qiu, E. D. White, E. M. Munro, S. Vaikuntanathan*, A. R. Dinner*
    arXiv (2023) · under revision, Proc. Natl. Acad. Sci. USA · *joint corresponding authors arXiv Cytoskeletal dynamics
  2. Enhanced associative memory, classification, and learning with active dynamics
    A. K. Behera, M. Rao, S. Sastry, S. Vaikuntanathan
    Physical Review X 13, 041043 (2023) Paper Adaptable materials Generative AI + Stat mech
  3. Cluster-spin-glass magnetic behavior and morphology in the coordination polymer alloys Fey Co1−y BTT
    A. Ritchhart, Z. Chen, A. Behera, I. Jeon, K. Chapman, S. Vaikuntanathan, J. Anderson
    J. Am. Chem. Soc. 145 (2023) Paper
  4. Giant gateable osmotic power generation from a Goldilocks two-dimensional membrane
    B. Cheng, Y. Zhong, Y. Qiu, S. Vaikuntanathan, J. Park
    J. Am. Chem. Soc. 145, 2952–2960 (2023) Paper
  5. A unified model for the dynamics of ATP-independent ultrafast contraction
    C. Floyd, A. T. Molines, X. Lei, J. E. Honts, F. Chang, M. W. Elting*, S. Vaikuntanathan*, A. R. Dinner*, M. S. Bhamla*
    Proc. Natl. Acad. Sci. USA 120, e2217737120 (2023) · *joint corresponding authors Paper Cytoskeletal dynamics
  6. Simulating structured fluids with tensorial viscoelasticity
    C. Floyd, S. Vaikuntanathan*, A. R. Dinner*
    J. Chem. Phys. 158, 054906 (2023) · *joint corresponding authors Paper
  7. Direct synthesis and chemical vapor deposition of 2D carbide and nitride MXenes
    D. Wang, C. Zhou, A. S. Filatov, W. Cho, F. Lagunas, M. Wang, S. Vaikuntanathan, C. Liu, R. F. Klie, D. V. Talapin
    Science 379, 1009–1015 (2023) Paper

2022

  1. Thermodynamic control of activity patterns in cytoskeletal networks
    A. Lamtyugina, Y. Qiu, E. Fodor, A. R. Dinner, S. Vaikuntanathan
    Phys. Rev. Lett. 129, 128002 (2022) Paper Cytoskeletal dynamics
  2. From predicting to learning dissipation from pair correlations of active liquids
    G. Rassolov, L. Tociu, E. Fodor, S. Vaikuntanathan
    J. Chem. Phys. 157, 054901 (2022) Paper
  3. Mean-field theory for the structure of strongly interacting active liquids
    L. Tociu, G. Rassolov, E. Fodor, S. Vaikuntanathan
    J. Chem. Phys. 157, 014902 (2022) Paper

2021

  1. A strong nonequilibrium bound for sorting of cross-linkers on growing biopolymers
    Y. Qiu, M. Nguyen, G. M. Hocky, A. R. Dinner, S. Vaikuntanathan
    Proc. Natl. Acad. Sci. USA 118, e2102881118 (2021) Paper Cytoskeletal dynamics
  2. Mechanism for the generation of robust circadian oscillations through ultrasensitivity and differential binding affinity
    A. K. Behera, C. del Junco, S. Vaikuntanathan
    J. Phys. Chem. B 125, 11179– 11187 (2021) Paper
  3. Energy rectification in active gyroscopic networks under time-periodic modulations
    Z. Liao, S. Vaikuntanathan
    Phys. Rev. E 104, 014601 (2021) Paper
  4. Fluctuating hydrodynamics of chiral active fluids
    M. Han, M. Fruchart, C. Scheibner, S. Vaikuntanathan, J. J. de Pablo, V. Vitelli
    Nature Physics 17, 1260–1269 (2021) Paper
  5. Organization and self-assembly away from equilibrium: Toward thermodynamic design principles
    M. Nguyen, Y. Qiu, S. Vaikuntanathan
    Annual Review of Condensed Matter Physics 12 (2021) Paper

2020

  1. Tuning shape and internal structure of protein droplets via biopolymer filaments
    D. R. Scheff, K. L. Weirich, K. Dasbiswas, A. Patel, S. Vaikuntanathan, M. L. Gardel
    Soft Matter 16, 5659–5668 (2020) Paper
  2. Dissipation controls transport and phase transitions in active fluids: Mobility, diffusion and biased ensembles
    E. Fodor, T. Nemoto, S. Vaikuntanathan
    New J. Phys. 22, 013052 (2020) Paper
  3. Robust oscillations in multi-cyclic models of biochemical clocks
    C. del Junco, S. Vaikuntanathan
    J. Chem. Phys. 152, 055101 (2020) · Featured Article; JCP Scilight; Emerging Investigators special issue Paper
  4. Nucleation and shape dynamics of model nematic tactoids around adhesive colloids
    N. B. Ludwig, K. L. Weirich, E. Aster, T. A. Witten, M. L. Gardel, K. Dasbiswas, S. Vaikuntanathan
    J. Chem. Phys. 152, 084901 (2020) Paper
  5. Rectification of energy and motion in non-equilibrium parity violating metamaterials
    Z. Liao, W. T. M. Irvine, S. Vaikuntanathan
    Physical Review X 10, 021036 (2020) Paper
  6. High chemical affinity increases the robustness of biochemical oscillations
    C. del Junco, S. Vaikuntanathan
    Phys. Rev. E 101, 012410 (2020) Paper

2019

  1. A mechanism for anomalous transport in chiral active liquids
    Z. Liao, M. Han, M. Fruchart, V. Vitelli, S. Vaikuntanathan
    J. Chem. Phys. 151, 194108 (2019) · Editor’s Pick; Emerging Investigators special issue Paper
  2. Nanocrystals in molten salts and ionic liquids: Experimental observation of ionic correlations extending beyond the Debye length
    V. Kamysbayev†, V. Srivastava†, N. B. Ludwig†, O. J. Borkiewicz, H. Zhang, J. Ilavsky, B. Lee, K. W. Chapman, S. Vaikuntanathan, D. V. Talapin
    ACS Nano 13, 5760–5770 (2019) · †equal contribution Paper
  3. Self-organizing motors divide active liquid droplets
    K. L. Weirich, K. Dasbiswas, T. A. Witten, S. Vaikuntanathan, M. L. Gardel
    Proc. Natl. Acad. Sci. USA 116, 11125–11130 (2019) Paper
  4. How dissipation constrains fluctuations in nonequilibrium liquids: Diffusion, structure, and biased interactions
    L. Tociu, E. Fodor, T. Nemoto, S. Vaikuntanathan
    Physical Review X 9, 041026 (2019) Paper
  5. Topological waves in fluids with odd viscosity
    A. Souslov, K. Dasbiswas, M. Fruchart, S. Vaikuntanathan, V. Vitelli
    Phys. Rev. Lett. 122, 128001 (2019) Paper
  6. Interface height fluctuations and surface tension of driven liquids with time-dependent dynamics
    C. del Junco, S. Vaikuntanathan
    J. Chem. Phys. 150, 094708 (2019) · Editor’s Pick; AIP Scilight Paper

2018

  1. Describing screening in dense ionic fluids with a charge-frustrated Ising model
    N. B. Ludwig, K. Dasbiswas, D. V. Talapin, S. Vaikuntanathan
    J. Chem. Phys. 149, 164505 (2018) · JCP Editors’ Choice 2018
  2. Topological localization in out-of-equilibrium dissipative systems
    K. Dasbiswas, K. K. Mandadapu, S. Vaikuntanathan
    Proc. Natl. Acad. Sci. USA 115, E9031–E9040 (2018) Paper
  3. Energy dissipation and fluctuations in a driven liquid
    C. del Junco, L. Tociu, S. Vaikuntanathan
    Proc. Natl. Acad. Sci. USA 115, 3569–3574 (2018) Paper

2017

  1. Driven optical matter: Dynamics of electrodynamically coupled nanoparticles in an optical ring vortex
    P. Figliozzi, N. Sule, Z. Yan, Y. Bao, S. Burov, S. K. Gray, S. A. Rice, S. Vaikuntanathan, N. F. Scherer
    Phys. Rev. E 95, 022604 (2017) Paper
  2. Liquid behavior of cross-linked actin bundles
    K. L. Weirich, S. Banerjee, K. Dasbiswas, T. A. Witten, S. Vaikuntanathan, M. L. Gardel
    Proc. Natl. Acad. Sci. USA 114, 2131–2136 (2017) Paper Cytoskeletal dynamics
  3. On the role of nonspherical cavities in short length-scale density fluctuations in water
    G. C. Sosso, S. Caravati, G. Rotskoff, S. Vaikuntanathan, A. Hassanali
    J. Phys. Chem. A 121, 370–380 (2017)
  4. Topologically protected modes in non-equilibrium stochastic systems
    A. Murugan, S. Vaikuntanathan
    Nature Communications 8, 13881 (2017) Paper
  5. Stable colloids in molten inorganic salts
    H. Zhang, K. Dasbiswas, N. B. Ludwig, G. Han, B. Lee, S. Vaikuntanathan, D. V. Talapin
    Nature 542, 328–331 (2017) · Commentary in C&EN

2016

  1. Design principles for nonequilibrium self-assembly
    M. Nguyen, S. Vaikuntanathan
    Proc. Natl. Acad. Sci. USA 113, 14231–14236 (2016) · Commentary in Nature Materials arXiv Commentary
  2. Biological implications of dynamical phases in non-equilibrium networks
    A. Murugan, S. Vaikuntanathan
    J. Stat. Phys. 162, 1183–1202 (2016)
  3. Pre-transition effects mediate forces of assembly between transmembrane proteins
    S. Katira†, K. K. Mandadapu†, S. Vaikuntanathan†, B. Smit, D. Chandler
    eLife 5, e13150 (2016) · †equal contribution Paper
  4. Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation
    S. Vaikuntanathan*, G. M. Rotskoff, A. Hudson, P. L. Geissler
    Proc. Natl. Acad. Sci. USA 113, E2224–E2230 (2016) · Commentary in PNAS · *joint corresponding authors Paper Commentary

2014

  1. Efficiency and large deviations in time-asymmetric stochastic heat engines
    T. R. Gingrich, G. M. Rotskoff, S. Vaikuntanathan, P. L. Geissler
    New J. Phys. 16, 102003 (2014) · NJP Highlight of 2014
  2. Heterogeneity-induced large deviations in activity and (in some cases) entropy production
    T. R. Gingrich, S. Vaikuntanathan, P. L. Geissler
    Phys. Rev. E 90, 042123 (2014)
  3. Dynamic phase transitions in simple driven kinetic networks
    S. Vaikuntanathan, T. R. Gingrich, P. L. Geissler
    Phys. Rev. E 89, 062108 (2014)
  4. Putting water on a lattice: The importance of long wavelength density fluctuations in theories of hydrophobic and interfacial phenomena
    S. Vaikuntanathan, P. L. Geissler
    Phys. Rev. Lett. 112, 020603 (2014) · Commentary in PNAS Commentary

2012

  1. Adsorption of solutes at liquid–vapor interfaces: Insights from lattice gas models
    S. Vaikuntanathan, P. R. Shaffer, P. L. Geissler
    Faraday Discuss. 160, 63–74 (2012)

2011

  1. Modeling Maxwell’s demon with a microcanonical Szilard engine
    S. Vaikuntanathan, C. Jarzynski
    Phys. Rev. E 83, 061120 (2011)
  2. Escorted free energy simulations
    S. Vaikuntanathan, C. Jarzynski
    J. Chem. Phys. 134, 054107 (2011)
  3. Density-dependent analysis of nonequilibrium paths improves free energy estimates II. A Feynman–Kac formalism
    D. D. L. Minh, S. Vaikuntanathan
    J. Chem. Phys. 134, 034117 (2011)

2010

  1. Nonequilibrium detailed fluctuation theorem for repeated discrete feedback
    J. M. Horowitz, S. Vaikuntanathan
    Phys. Rev. E 82, 061120 (2010)

2009

  1. Dissipation and lag in irreversible processes
    S. Vaikuntanathan, C. Jarzynski
    EPL 87, 60005 (2009)

2008

  1. Escorted free energy simulations: Improving convergence by reducing dissipation
    S. Vaikuntanathan, C. Jarzynski
    Phys. Rev. Lett. 100, 190601 (2008)