Publications

Publications List (from 2017)

• I. Neri and S. Pigolotti, "Amendable decisions in living systems", biorXiv preprint (2025).
• M. Klann, S. Miura, S. Lee, S. Vianello, R. Ross, M. Watanabe, E. Gairin, Y. Liang, H. W. Hutto, B. M. McCluskey, M. Herrera, L. Solnica-Krezel, L. Besseau, S. Pigolotti, D. M. Parichy, M. Kinoshita, V. Laudet, "Cell-cell communication as underlying principle governing color pattern formation in fishes", biorXiv preprint (2025).
• P. Zhou, R. S. Kasai, W. Fujita, T. A. Tsunoyama, H. Ueda, S. Pigolotti, T. K. Fujiwara, A. Kusumi, "Single-molecule detection of transient dimerization of opioid receptors 2: Heterodimer blockage reduces morphine tolerance", bioRxiv preprint, accepted for publication in Nature Communications (2025).
• P. Zhou, T. A. Tsunoyama, R. S. Kasai, K. M. Hirosawa, Z. Kalay, A. Aladag, T. K. Fujiwara, S. Pigolotti, A. Kusumi, "Single-molecule detection of transient dimerization of opioid receptors 1: Homodimers’ effect on signaling and internalization", biorXiv preprint, accepted for publication in Nature Communications (2025).
• S. Cure, F. Pflug, S. Pigolotti, "Fast and exact stochastic simulations of epidemics on static and temporal networks", PLoS Comput Biol 21(9): e1013490 (2025).
• S. Pigolotti, S. Roldán-Vargas, "Inspection paradox and jump detection in glassy systems", arXiv/2407.19873 , Phys. Rev. E 112, 035415 (2025).
• R. J. H. Ross, G. D. Masucci, C. Yen Lin, T. L. Iglesias, S. Reiter, S. Pigolotti, "Hyperdisordered cell packing on a growing surface", Phys. Rev. X 15, 021064 (2025).
• S. Cure, F. Pflug, S. Pigolotti, "Exponential rate of epidemic spreading on complex networks", Phys. Rev. E 111, 044311 (2025).
• T. Takahashi, H. Aoyanagi, S. Pigolotti, S. Toyabe, "Blocking uncertain mispriming errors of PCR", Biophys. Jour. 123(20), 3558-3568 (2024).
• Q. Lu, S. Pigolotti, "Target search in the CRISPR/Cas9 system: Facilitated diffusion with target cues", New Journal of Physics 26, 043007 (2024).
• É. Roldán, I. Neri, R. Chetrite, S. Gupta, S. Pigolotti, F. Jülicher, K. Sekimoto, "Martingales for physicists: A treatise on stochastic thermodynamics and beyond", arXiv:2210.09983, Advances in Physics 72(1–2), 1–258 (2024). 
• F. Pflug, D. Bhat, S. Pigolotti, "Genome replication in asynchronously growing microbial populations", arXiv:2308:12664, PLOS Computational Biology 20(1), e1011753 (2024).
• S. Liang, S. Pigolotti, "Thermodynamic bounds on time-reversal asymmetry", arXiv:2308.14497, Phys. Rev. E (letter) 108, L062101 (2023).
• D. Chiuchiù, S. Mondal, S. Pigolotti, "Pareto optimal front of kinetic proofreading", arXiv/2208.09381 , New Journal of Physics 25, 043007 (2023).
• H. Aoyanagi, S. Pigolotti, S. Ono. S. Toyabe, "Error-suppression mechanism of PCR by blocker strands", bioRxiv preprint , Biophys. Jour. 122(7), 1334-1341 (2023).
• P.V. Martín, A. Koldaeva, S. Pigolotti, "Coalescent dynamics of planktonic communities", Phys. Rev. E 106, 044408, arXiv/2204.04609, (2022).
• D. Bhat, S. Hauf, C. Plessy, Y. Yokobayashi, S. Pigolotti, "Speed variations of bacterial replisomes", Elife11:e75884 (2022).
• H. Tsai, D.W. Carlson, A. Koldaeva, S. Pigolotti, A.Q. Shen, "Optimization and Fabrication of Multi-Level Microchannels for Long-Term Imaging of Bacterial Growth and Expansion", Micromachines 13(4), 576 (2022).
• A. Koldaeva, H. Tsai, A.Q. Shen, S. Pigolotti, "Population genetics in microchannels", Proc. Natl. Acad. Sci. 119 (12) e2120821119 (2022).
• L. Peliti, S. Pigolotti, "Stochastic Thermodynamics: An Introduction". Princeton University Press, (2021)
• Q. Lu, D. Bhat, D. Stepanenko, S. Pigolotti, "Search and localization dynamics of the CRISPR/Cas9 system", Phys. Rev. Lett. 127, 208102, arXiv/2103.10667 , Featured in Physics, (2021).
• J.M. Miotto, S. Pigolotti, A.V. Chechkin, S. Roldán-Vargas, "Length scales in Brownian yet non-Gaussian dynamics", Phys. Rev. X 11, 031002 , arXiv/1991.07761, (2021).
• S. Pigolotti, "Generalized Euler-Lotka equation for correlated cell divisions" , Phys. Rev. E (Letter) 103, L060402 (Editors' Suggestion), arXiv/2101.02403 (2021).
•  Y. Kinjo, N. Lo, P. V. Martín, G. Tokuda, S. Pigolotti, T. Bourguignon, "Enhanced Mutation Rate, Relaxed Selection, and the “Domino Effect” are associated with Gene Loss in Blattabacterium, A Cockroach Endosymbiont", Molecular Biology and Evolution, msab159, (2021).
• X. Yang, M. Heinemann, J. Howard, G. Huber, S. Iyer-Biswas, G. Le Treut, M. Lynch, K. L. Montooth, D. J. Needleman, S. Pigolotti, J. Rodenfels, P. Ronceray, S. Shankar, I. Tavassoly, S. Thutupalli, D. V. Titov, J. Wang, and P. J. Foster, "Physical bioenergetics: Energy fluxes, budgets, and constraints in cells". Proc. Natl. Acad. Sci. (Perspective), 118 (26) (2021).
• S. Pigolotti, D.Chiuchiù, P.V. Martín, D. Bhat, "Modeling the COVID-19 epidemic in Okinawa", 

  working manuscript

  (2020).
• S. Pigolotti, M.H. Jensen, Y. Zhan, G. Tiana, "Bifractal nature of chromosome contact maps", Physical Review Research 2, 043078 (2020).
• P.V. Martín, Virginia Domínguez-García, Miguel A Muñoz, "Intermittent percolation and the scale-free distribution of vegetation clusters", New Journal of Physics Vol. 22 (2020).
• P.V Martín, A. Bucek, T. Bourguignon, S. Pigolotti, "Ocean currents promote rare species diversity in protists", Science Advances 6(29), eaaz9037 (2020).
• T. Bourguignon, Y. Kinjo, P. Villa-Martin, N.V. Coleman, Q. Tang, D.A. Arab, Z. Wang, G. Tokuda, Y. Hongoh, M. Ohkuma, S. Ho, S. Pigolotti, N. Lo, "Increased Mutation Rate is Linked to Genome Reduction in Prokaryotes", Current Biology D-20-00217 (2020). 
• J. Bechoefer, S. Ciliberto, S. Pigolotti, É. Roldán, "Stochastic Thermodynamics: Experiments and Theory" (editorial), J. Stat. Mech. 064001 (2020)
• D.M. Busiello, S. Pigolotti, "Hyperaccurate currents in stochastic thermodynamics", Phys. Rev. E (Rapid Communication)100, 060102, arXiv/1908.00738 (2019).
• D. Chiuchiù, J. Ferrare, S. Pigolotti, "Assembly of heteropolymers via a continuous reaction coordinate", Phys. Rev. E 100, 062502, arXiv:1905.05490 (2019).
• D. Chiuchiù, Y. Tu, S. Pigolotti, "Error-speed correlations in biopolymer synthesis", Phys. Rev. Lett. 123, 038101, arXiv:1905.12869 (2019).
• I. Neri, É. Roldán, S. Pigolotti, F. Jülicher, "Integral fluctuation relations for entropy production at stopping times", J. Stat. Mech. 104006J, arXiv:1903.08115 (2019).
• P.V. Martín, M.A. Muñoz, S. Pigolotti, "Bet-hedging strategies in expanding populations", Plos. Comp. Biol. 15(4), e100652, BioRxiv preprint (2019).
• A.C. Barato, É. Roldán, I.A. Martínez, S. Pigolotti, "Arcsine laws in stochastic thermodynamics", Phys. Rev. Lett. 121, 090601, arXiv/1712.00795 (2018).
• N. Azaña Schednler-Meyer, S. Pigolotti, P. Mariani, "Evolution of complex asexual reproductive strategies in jellyfish", American Naturalist 192(1), 72-80 (2018). 
• D. Chiuchiù, S. Pigolotti, "Mapping of uncertainty relations between continuous and discrete time", Phys. Rev. E 97, 032110 , preprint arXiv:1711.00615 (2018).
• M. Cencini, S. Pigolotti, "Energetic funnel facilitates facilitated diffusion", Nucleic Acid Research 46(2), 558-567 (2018).
• S. Pigolotti, M. Cencini, D. Molina, M.A. Muñoz, "Stochastic spatial models in ecology: a statistical physics approach", J. Stat. Phys. 1-30, preprint arXiv:1708.03475 (2017).
• S. Pigolotti, I. Neri, É. Roldán, F. Jülicher, "Generic Properties of Stochastic Entropy Production". Phys. Rev. Lett. 119, 140604 (2017).

Older publications: see the Google Scholar page.