Browse data: Reference Materials
From Thermodynamics of Computation
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- Shodhan Rao, Arjan van der Schaft, Bayu Jayawardhana A graph-theoretical approach for the analysis and model reduction of complex-balanced chemical reaction networks Journal of Mathematical Chemistry 51, 2401-2422 (2013)
- Thomas S. Shimizu, Yuhai Tu, Howard C. Berg A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli Molecular Systems Biology 6, (2010)
- Ganhui Lan, Sonja Schulmeister, Victor Sourjik, Yuhai Tu Adapt locally and act globally: Strategy to maintain high chemoreceptor sensitivity in complex environments Molecular Systems Biology 7, (2011)
- Hanna K.E. Landenmark, Duncan H. Forgan, Charles S. Cockell An estimate of the total DNA in the biosphere PLoS Biology 13, 1-10 (2015)
- Hong Qian, Sumit Roy An information theoretical analysis of kinase activated phosphorylation dephosphorylation cycle IEEE Transactions on Nanobioscience 11, 289-295 (2012)
- Jessica C. Flack, David C. Krakauer Challenges for complexity measures: A perspective from social dynamics and collective social computation Chaos 21, (2011)
- Monica Skoge, Sahin Naqvi, Yigal Meir, Ned S. Wingreen Chemical sensing by nonequilibrium cooperative receptors Physical Review Letters 110, (2013)
- Arjan van der Schaft, Shodhan Rao, Bayu Jayawardhana Complex and detailed balancing of chemical reaction networks revisited Journal of Mathematical Chemistry 53, 1445-1458 (2015)
- David C. Krakauer Darwinian demons, evolutionary complexity, and information maximization Chaos 21, (2011)
- Silke Neumann, Clinton H. Hansen, Ned S. Wingreen, Victor Sourjik Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis EMBO Journal 29, 3484-3495 (2010)
- Léo Granger, Holger Kantz Differential Landauer's principle EPL 101, (2013)
- Benjamin B. Machta Dissipation Bound for Thermodynamic Control Physical Review Letters 115, (2015)
- Peter M. van Bodegom, David Wolpert, Eric Libby, Jan Amend, Tori Hoehler, Chris Kempes Drivers of bacterial maintenance and minimal energy requirements Frontiers in Microbiology 8, (2017)
- Monica Skoge, Yigal Meir, Ned S. Wingreen Dynamics of cooperativity in chemical sensing among cell-surface receptors Physical Review Letters 107, (2011)
- Wiet Hendrik De Ronde, Filipe Tostevin, Pieter Rein ten Wolde Effect of feedback on the fidelity of information transmission of time-varying signals Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 82, (2010)
- Alexander M. Berezhkovskii, Attila Szabo Effect of ligand diffusion on occupancy fluctuations of cell-surface receptors Journal of Chemical Physics 139, (2013)
- Andre C. Barato, David Hartich, Udo Seifert Efficiency of cellular information processing New Journal of Physics 16, (2014)
- Christopher C. Govern, Pieter Rein ten Wolde Energy dissipation and noise correlations in biochemical sensing Physical Review Letters 113, (2014)
- Shou Wen Wang, Yueheng Lan, Lei Han Tang Energy dissipation in an adaptive molecular circuit Journal of Statistical Mechanics: Theory and Experiment 2015, (2015)
- Eric J. Chaisson Energy flows in low-entropy complex systems Entropy 17, 8007-8018 (2015)
- Martin Lindén, Pierre Sens, Rob Phillips Entropic tension in crowded membranes PLoS Computational Biology 8, (2012)
- J. Ricardo Arias-Gonzalez Entropy involved in fidelity of DNA replication PLoS ONE 7, (2012)
- Christopher Jarzynski Equalities and Inequalities: Irreversibility and the Second Law of Thermodynamics at the Nanoscale Annual Review of Condensed Matter Physics 2, 329-351 (2011)
- Matthew S. Dodd, Dominic Papineau, Tor Grenne, John F. Slack, Martin Rittner, Franco Pirajno, Jonathan O'Neil, Crispin T.S. Little Evidence for early life in Earth's oldest hydrothermal vent precipitates Nature 543, 60-64 (2017)
- Lawrence Wang, Jan P. Amend, John Doyle, Tori Hoehler, Chris Kempes Evolutionary tradeoffs in cellular composition across diverse bacteria ISME Journal 10, 2145-2157 (2016)
- Shoichi Toyabe, Takahiro Sagawa, Masahito Ueda, Eiro Muneyuki, Masaki Sano Experimental demonstration of information-to-energy conversion and validation of the generalized Jarzynski equality Nature Physics 6, 988-992 (2010)
- J. V. Koski, V. F. Maisi, T. Sagawa, J. P. Pekola Experimental observation of the role of mutual information in the nonequilibrium dynamics of a Maxwell demon Physical Review Letters 113, (2014)
- J Hong, B Lambson, S Dhuey, J Bokor Experimental verification of Landauer's principle in erasure of nanomagnetic memory bits arXiv preprint arXiv:1411.6730 , 1-20 (2014)
- Antoine Bérut, Artak Arakelyan, Artyom Petrosyan, Sergio Ciliberto, Raoul Dillenschneider, Eric Lutz Experimental verification of Landauer's principle linking information and thermodynamics Nature 483, 187-189 (2012)
- Brian Lambson, David Carlton, Jeffrey Bokor Exploring the thermodynamic limits of computation in integrated systems: Magnetic memory, nanomagnetic logic, and the landauer limit Physical Review Letters 107, (2011)
- W. H. De Ronde, F. Tostevin, P. R. Ten Wolde Feed-forward loops and diamond motifs lead to tunable transmission of information in the frequency domain Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 86, (2012)
- Giovanni Diana, G. Baris Bagci, Massimiliano Esposito Finite-time erasing of information stored in fermionic bits Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 87, (2013)
- Bernhard Altaner, Artur Wachtel, Jürgen Vollmer Fluctuating currents in stochastic thermodynamics. II. Energy conversion and nonequilibrium response in kinesin models Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 92, (2015)
- Takahiro Sagawa, Masahito Ueda Fluctuation theorem with information exchange: Role of correlations in stochastic thermodynamics Physical Review Letters 109, (2012)
- Thomas E. Ouldridge, Pieter Rein ten Wolde Fundamental Costs in the Production and Destruction of Persistent Polymer Copies Physical Review Letters 118, (2017)
- Christopher C. Govern, Pieter Rein ten Wolde Fundamental limits on sensing chemical concentrations with linear biochemical networks Physical Review Letters 109, (2012)
- H. H. Hasegawa, J. Ishikawa, K. Takara, D. J. Driebe Generalization of the second law for a nonequilibrium initial state Physics Letters, Section A: General, Atomic and Solid State Physics 374, 1001-1004 (2010)
- K. Takara, H. H. Hasegawa, D. J. Driebe Generalization of the second law for a transition between nonequilibrium states Physics Letters, Section A: General, Atomic and Solid State Physics 375, 88-92 (2010)
- James L. Friar, Terrance Goldman, Juan Pérez-Mercader Genome sizes and the benford distribution PLoS ONE 7, (2012)
- Riccardo Rao, David Lacoste, Massimiliano Esposito Glucans monomer-exchange dynamics as an open chemical network Journal of Chemical Physics 143, (2015)
- Yonggun Jun, Momčilo Gavrilov, John Bechhoefer High-precision test of Landauer's principle in a feedback trap Physical Review Letters 113, (2014)
- Alicia Dickenstein, Mercedes Pérez Millán How Far is Complex Balancing from Detailed Balancing? Bulletin of Mathematical Biology 73, 811-828 (2011)
- Gerardo Aquino, Robert G. Endres Increased accuracy of ligand sensing by receptor diffusion on cell surface Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 82, (2010)
- Mikhail Prokopenko, Itai Einav Information thermodynamics of near-equilibrium computation Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 91, (2015)
- A. C. Barato, D. Hartich, Udo Seifert Information-theoretic versus thermodynamic entropy production in autonomous sensory networks Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 87, (2013)
- Sonja J. Prohaska, David C. Krakauer, Peter Stadler Innovation in gene regulation: The case of chromatin computation Journal of Theoretical Biology 265, 27-44 (2010)
- Pablo Sartori, Simone Pigolotti Kinetic versus energetic discrimination in biological copying Physical Review Letters 110, (2013)
- Mark A. Lever, Karyn L. Rogers, Karen G. Lloyd, Jörg Overmann, Bernhard Schink, Rudolf K. Thauer, Tori M. Hoehler, Bo Barker Jørgensen Life under extreme energy limitation: A synthesis of laboratory- and field-based investigations FEMS Microbiology Reviews 39, 688-728 (2015)
- Thierry Mora, Ned S. Wingreen Limits of sensing temporal concentration changes by single cells Physical Review Letters 104, (2010)
- Joris Paijmans, Pieter Rein ten Wolde Lower bound on the precision of transcriptional regulation and why facilitated diffusion can reduce noise in gene expression Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 90, (2014)
- Sosuke Ito, Takahiro Sagawa Maxwell's demon in biochemical signal transduction with feedback loop Nature Communications 6, (2015)
- Gerardo Aquino, Luke Tweedy, Doris Heinrich, Robert G. Endres Memory improves precision of cell sensing in fluctuating environments Scientific Reports 4, (2014)
- Tori M. Hoehler, Bo Barker Jørgensen Microbial life under extreme energy limitation Nature Reviews Microbiology 11, 83-94 (2013)
- Pablo Sartori, Yuhai Tu Noise Filtering Strategies in Adaptive Biochemical Signaling Networks Journal of Statistical Physics 142, 1206-1217 (2011)
- Hao Ge, Hong Qian Nonequilibrium thermodynamic formalism of nonlinear chemical reaction systems with Waage-Guldberg's law of mass action Chemical Physics 472, 241-248 (2016)
- Thomas E Ouldridge, Christopher C Govern, Pieter Rein ten Wolde On the connection between computational and biochemical measurement Arxiv , 1-17 (2015)
- Prajwal Raj Kafle, Sanjib Sharma, Geraint F. Lewis, Joss Bland-Hawthorn On the shoulders of giants: Properties of the stellar halo and the milky way mass distribution Astrophysical Journal 794, (2014)
- Mikhail Prokopenko, Joseph T. Lizier, Don C. Price On thermodynamic interpretation of transfer entropy Entropy 15, 524-543 (2013)
- Nils B. Becker, Andrew Mugler, Pieter Rein ten Wolde Optimal Prediction by Cellular Signaling Networks Physical Review Letters 115, (2015)
- Thierry Mora Physical Limit to Concentration Sensing Amid Spurious Ligands Physical Review Letters 115, (2015)
- Rainer Feistel, Werner Ebeling Physics of Self-Organization and Evolution Physics of Self-Organization and Evolution , (2011)
- John C. Baez, Brendan Fong Quantum techniques for studying equilibrium in reaction networks Journal of Complex Networks 3, 22-34 (2015)
- Yuliya Pylayeva-Gupta, Elda Grabocka, Dafna Bar-Sagi RAS oncogenes: Weaving a tumorigenic web Nature Reviews Cancer 11, 761-774 (2011)
- Nils B. Becker, Pieter Rein ten Wolde Rare switching events in non-stationary systems Journal of Chemical Physics 136, (2012)
- C. Van Den Broeck, Massimiliano Esposito Second law and Landauer principle far from equilibrium EPL 95, (2011)
- Paul C.W. Davies, Elisabeth Rieper, Jack A. Tuszynski Self-organization and entropy reduction in a living cell BioSystems 111, 1-10 (2013)
- Aljaž Godec, Ralf Metzler Signal focusing through active transport Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 92, (2015)
- Sarah A. Cepeda-Humerez, Georg Rieckh, Gašper Tkačik Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation Physical Review Letters 115, (2015)
- Hao Ge, Min Qian, Hong Qian Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics Physics Reports 510, 87-118 (2012)
- D. Hartich, A. C. Barato, Udo Seifert Stochastic thermodynamics of bipartite systems: Transfer entropy inequalities and a Maxwell's demon interpretation Journal of Statistical Mechanics: Theory and Experiment 2014, (2014)
- Massimiliano Esposito Stochastic thermodynamics under coarse graining Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 85, (2012)
- Udo Seifert Stochastic thermodynamics, fluctuation theorems and molecular machines Reports on Progress in Physics 75, (2012)
- Guy Shinar, Martin Feinberg Structural sources of robustness in biochemical reaction networks Science 327, 1389-1391 (2010)
- Xuan Yi, Jintao Liu, James R. Faeder, Peter Setlow Synergism between different germinant receptors in the germination of Bacillus subtilis spores Journal of Bacteriology 193, 4664-4671 (2011)
- Kazunari Kaizu, Wiet De Ronde, Joris Paijmans, Koichi Takahashi, Filipe Tostevin, Pieter Rein ten Wolde The berg-purcell limit revisited Biophysical Journal 106, 976-985 (2014)
- Nick Lane, William Martin The energetics of genome complexity Nature 467, 929-934 (2010)
- Olivia P. Judson The energy expansions of evolution Nature Ecology and Evolution 1, (2017)
- Ganhui Lan, Pablo Sartori, Silke Neumann, Victor Sourjik, Yuhai Tu The energy-speed-accuracy trade-off in sensory adaptation Nature Physics 8, 422-428 (2012)
- David H. Wolpert The free energy requirements of biological organisms; implications for evolution Entropy 18, (2016)
- Petter Hammar, Prune Leroy, Anel Mahmutovic, Erik G. Marklund, Otto G. Berg, Johan Elf The lac repressor displays facilitated diffusion in living cells Science 336, 1595-1598 (2012)
- Brendan A. Bicknell, Peter Dayan, Geoffrey J. Goodhill The limits of chemosensation vary across dimensions Nature Communications 6, (2015)
- Philippe Faist, Frédéric Dupuis, Jonathan Oppenheim, Renato Renner The minimal work cost of information processing Nature Communications 6, (2015)
- Lídia Del Rio, Johan Åberg, Renato Renner, Oscar Dahlsten, Vlatko Vedral The thermodynamic meaning of negative entropy Nature 474, 61-63 (2011)
- Pablo Sartori, Léo Granger, Chiu Fan Lee, Jordan M. Horowitz Thermodynamic Costs of Information Processing in Sensory Adaptation PLoS Computational Biology 10, (2014)
- Andre C. Barato, Udo Seifert Thermodynamic Uncertainty Relation for Biomolecular Processes Physical Review Letters 114, (2015)
- Philipp Strasberg, Gernot Schaller, Tobias Brandes, Massimiliano Esposito Thermodynamics of a physical model implementing a Maxwell demon Physical Review Letters 110, (2013)
- Juan M.R. Parrondo, Jordan M. Horowitz, Takahiro Sagawa Thermodynamics of information Nature Physics 11, 131-139 (2015)
- Susanne Still, David A. Sivak, Anthony J. Bell, Gavin Crooks Thermodynamics of prediction Physical Review Letters 109, (2012)
- Alex H. Lang, Charles K. Fisher, Thierry Mora, Pankaj Mehta Thermodynamics of statistical inference by cells Physical Review Letters 113, (2014)
- Jordan M. Horowitz, Massimiliano Esposito Thermodynamics with continuous information flow Physical Review X 4, (2014)
- Massimiliano Esposito, Christian Van Den Broeck Three faces of the second law. I. Master equation formulation Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 82, (2010)
- Anirikh Chakrabarti, Ljubisa Miskovic, Keng Cher Soh, Vassily Hatzimanikatis Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints Biotechnology Journal 8, 1043-1057 (2013)
- Mikhail Prokopenko, Joseph T. Lizier Transfer entropy and transient limits of computation Scientific Reports 4, (2014)
- J. L. Friar, T. Goldman, J. Pérez-Mercader Ubiquity of Benford's law and emergence of the reciprocal distribution Physics Letters, Section A: General, Atomic and Solid State Physics 380, 1895-1899 (2016)
- É Roldán, I. A. Martínez, J. M.R. Parrondo, D. Petrov Universal features in the energetics of symmetry breaking Nature Physics 10, 457-461 (2014)
- Giovanna de Palo, Robert G. Endres Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells PLoS Computational Biology 9, (2013)