Publications

Also see my Google Scholar page or CV.


Published

A. Kolchinsky, “Thermodynamic dissipation does not bound replicator growth and decay rates”, The Journal of Chemical Physics, 2024. (2024 JCP Emerging Investigators Special Collection) pdf link

R. Solé, C. P. Kempes, B. Corominas-Murtra, M. De Domenico, A. Kolchinsky, M. Lachmann, E. Libby, S. Saavedra, E., D. Wolpert, “Fundamental constraints to the logic of living systems”, Royal Society Interface, 2024. pdf link

P.M. Riechers, C. Gupta, A. Kolchinsky, M. Gu, “Thermodynamically ideal quantum state inputs to any device”, PRX Quantum, 2024. pdf link

A. Kolchinsky, “Partial information decomposition: redundancy as information bottleneck”, Entropy, 2024. pdf link

J. Piñero, R. Solé, A. Kolchinsky, “Optimization of nonequilibrium free energy harvesting illustrated on bacteriorhodopsin”, Physical Review Research, 2024. pdf link

A. Kolchinsky, N. Ohga, S. Ito, “Thermodynamic bound on spectral perturbations, with applications to oscillations and relaxation dynamics”, Physical Review Research, 2024. pdf link

D.R. Sowinski, J. Carroll-Nellenback, R.N. Markwick, J. Piñero, M. Gleiser, A. Kolchinsky, G. Ghoshal, A. Frank, “Semantic Information in a model of resource gathering agents”, PRX Life, 2023. pdf link

A. Kolchinsky, “Generalized Zurek’s bound on the cost of an individual classical or quantum computation”, Physical Review E, 2023. pdf link

M. Aguilera and A. Kolchinsky, “Quantifying higher-order entropy production in organized nonequilibrium states”, Proceedings of the ALIFE 2023, 2023. pdf link

N. Ohga, S. Ito, A. Kolchinsky, “Thermodynamic bound on the asymmetry of cross-correlations”, Physical Review Letters, 2023. (Editors’ Suggestion; Featured in Physics) pdf link

K. Yoshimura, A. Kolchinsky, A. Dechant, S. Ito, “Housekeeping and excess entropy production for general nonlinear dynamics”, Physical Review Research, 2023. pdf link

F.C. Sheldon, A. Kolchinsky, F. Caravelli, “Computational capacity of LRC, memristive, and hybrid reservoirs”, Physical Review E, 2022. pdf link

A. Kolchinsky, “A Novel Approach to the Partial Information Decomposition”, Entropy, 2022. pdf code link

A. Kolchinsky and D.H. Wolpert, “Dependence of integrated, instantaneous, and fluctuating entropy production on the initial state in quantum and classical processes”, Physical Review E, 2021. pdf link

A. Kolchinsky and D.H. Wolpert, “Work, entropy production, and thermodynamics of information under protocol constraints”, Physical Review X, 2021. pdf link

A. Kolchinsky and D.H. Wolpert, “Entropy production given constraints on the energy functions”, Physical Review E, 2021. pdf link

A. Kolchinsky and D.H. Wolpert, “Thermodynamic costs of Turing Machines”, Physical Review Research, 2020. pdf link

D.H. Wolpert and A. Kolchinsky, “The thermodynamics of computing with circuits”, New Journal of Physics, 2020. pdf link

A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying versus transformation”, Royal Society Interface, 2020. pdf link

A.M. Saxe, Y. Bansal, J. Dapello, M. Advani, A. Kolchinsky, B.D. Tracey, D.D. Cox, “On the information bottleneck theory of deep learning”, Journal of Statistical Mechanics, 2019. pdf code link

A. Kolchinsky, B.D. Tracey, D.H. Wolpert, “Nonlinear information bottleneck”, Entropy, 2019. (Entropy 2021 Best Paper Award) pdf link

A. Berdahl, C. Brelsford, C. De Bacco, M. Dumas, V. Ferdinand, J.A. Grochow, L. Hébert-Dufresne, Y. Kallus, C.P. Kempes, A. Kolchinsky, D. B. Larremore, E. Libby, E.A. Power, C.A. Stern, B.D.Tracey, “Dynamics of beneficial epidemics”, Scientific Reports, 2019. pdf link

E.A. Hobson, V. Ferdinand, A. Kolchinsky, J. Garland, “Rethinking animal social complexity measures with the help of complex systems concepts”, Animal Behaviour, 2019. pdf link

A. Kolchinsky, B.D. Tracey, S. Van Kuyk, “Caveats for information bottleneck in deterministic scenarios”, International Conf on Learning Representations (ICLR), 2019. pdf code link

D.H. Wolpert, A. Kolchinsky, J.A. Owen, “A space–time tradeoff for implementing a function with master equation dynamics”, Nature Communications, 2019. pdf link

A. Avena-Koenigsberger, X. Yan, A. Kolchinsky, M. van den Heuvel, P. Hagmann, O. Sporns, “A spectrum of routing strategies for brain networks”, PLoS Computational Biology, 2019. pdf link

J.A. Owen, A. Kolchinsky, D.H. Wolpert, “Number of hidden states needed to physically implement a given conditional distribution”, New Journal of Physics, 2019. (correction) pdf link

A. Kolchinsky and D.H. Wolpert, “Semantic information, autonomous agency, and nonequilibrium statistical physics”, Royal Society Interface Focus, 2018. pdf code link

A.M. Saxe, Y. Bansal, J. Dapello, M. Advani, A. Kolchinsky, B.D. Tracey, D.D. Cox, “On the information bottleneck theory of deep learning”, International Conf on Learning Representations (ICLR), 2018. pdf code link

A. Kolchinsky, N. Dhande, K. Park, Y.Y. Ahn, “The Minor Fall, the Major Lift: Inferring emotional valence of musical chords through lyrics”, Royal Society Open Science, 2017. pdf data code link

A. Kolchinsky, D.H. Wolpert, “Dependence of dissipation on the initial distribution over states”, Journal of Statistical Mechanics, 2017. pdf link

A. Kolchinsky, B.D. Tracey, “Estimating mixture entropy with pairwise distances”, Entropy, 2017. (correction) pdf code link

A. Kolchinsky, A.J. Gates, L.M. Rocha, “Modularity and the spread of perturbations in complex dynamical systems,” Physical Review E, 2015. pdf code link

A. Kolchinsky, A. Lourenço, H. Wu, L. Li, L.M. Rocha, “Extraction of pharmacokinetic evidence of drug-drug interactions from the literature,” PLOS One, 2015. pdf link

A. Kolchinsky, M.P. van den Heuvel, A. Griffa, P. Hagmann, L.M. Rocha, O. Sporns, J. Goñi, “Multi-scale integration and predictability in resting state brain activity,” Frontiers in Neuroinformatics, 2014. pdf link

A. Rossi, F.J. Parada, A. Kolchinsky, A. Puce, “Neural correlates of apparent motion perception of impoverished facial stimuli I: A comparison of ERP and ERSP activity,” NeuroImage, 2014. pdf link

A. Kolchinsky, A. Lourenço, L. Li, L.M. Rocha, “Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions,” Proc Pacific Symposium on Biocomputing, 2013. pdf link

A. Kolchinsky and L.M. Rocha, “Prediction and modularity in dynamical systems,” Proc of European Conf. on the Synthesis and Simulation of Living Systems (ECAL), 2011. pdf link

A. Kolchinsky, A. Abi-Haidar, J. Kaur, A.A. Hamed, L.M. Rocha, “Classification of protein-protein interaction full-text documents using text and citation network features,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010. pdf link


A. Kolchinsky, “The cost of sending a bit across a living cell”, Physics Magazine, 2023. link


Preprints

A. Kolchinsky, A. Dechant, K. Yoshimura, S. Ito, “Generalized free energy and excess entropy production for active systems”, arXiv:2412.08432, 2022. arxiv

K. R. Thomsen, A. Kolchinsky, S. Rasmussen, “Metabolism, information, and viability in a simulated physically-plausible protocell”, arXiv:2405.04654, 2024. arxiv

A. Kolchinsky, “Thermodynamics of Darwinian evolution in molecular replicators”, arXiv:2112.02809, 2024. arxiv

R. Nagayama, K. Yoshimura, A. Kolchinsky, S. Ito, “Geometric thermodynamics of reaction-diffusion systems: Thermodynamic trade-off relations and optimal transport for pattern formation”, arXiv:2311.16569 , 2023. arxiv

A. Kolchinsky, A. Dechant, K. Yoshimura, S. Ito, “Information geometry of excess and housekeeping entropy production”, arXiv:2206.14599, 2022. arxiv

C. Gokler, A. Kolchinsky, Z. Liu, I. Marvian , P. Shor, O. Shtanko, K. Thompson, D. Wolpert, S. Lloyd, “When is a bit worth much more than kTln 2?”, arXiv:1705.09598, 2017. arxiv

A. Kolchinsky, I. Marvian, C. Gokler, Z. Liu, P. Shor, O. Shtanko, K. Thompson, D. Wolpert, S. Lloyd, “Maximizing free energy gain”, arXiv:1705.00041, 2017. arxiv