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From Thermodynamics of Computation
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- A Gallavotti Cohen-Type Symmetry in the Large Deviation Functional for Stochastic Dynamics ,
- A Sampling of the Yeast Proteome ,
- Geoffrey B. West, James H. Brown, Brian J. Enquist A general model for ontogenetic growth Nature 413, 628-631 (2001)
- A general model for the origin of allometric scaling laws in biology ,
- Geoffrey B. West, James H. Brown, Brian J. Enquist A general model for the structure and allometry of plant vascular systems Nature 400, 664-667 (1999)
- Stefan Schuster, Ronny Schuster A generalization of Wegscheider's condition. Implications for properties of steady states and for quasi-steady-state approximation Journal of Mathematical Chemistry 3, 25-42 (1989)
- 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)
- M. Malek-Mansour, G. Nicolis A master equation description of local fluctuations Journal of Statistical Physics 13, 197-217 (1975)
- 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)
- Pankaj Mehta, Sidhartha Goyal, Ned S. Wingreen A quantitative comparison of sRNA-based and protein-based gene regulation Molecular Systems Biology 4, (2008)
- Tobias von der Haar A quantitative estimation of the global translational activity in logarithmically growing yeast cells BMC Systems Biology 2, (2008)
- Daniel T. Gillespie A rigorous derivation of the chemical master equation Physica A: Statistical Mechanics and its Applications 188, 404-425 (1992)
- A yeast protein similar to bacterial two-component regulators. ,
- Robert G. Endres, Ned S. Wingreen Accuracy of direct gradient sensing by cell-surface receptors Progress in Biophysics and Molecular Biology 100, 33-39 (2009)
- 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)
- W. H. Zurek Algorithmic randomness and physical entropy Physical Review A 40, 4731-4751 (1989)
- Amplification and adaptation in regulatory and sensory systems ,
- An amplified sensitivity arising from covalent modification in biological systems. ,
- David Shear An analog of the Boltzmann H-theorem (a Liapunov function) for systems of coupled chemical reactions Journal of Theoretical Biology 16, 212-228 (1967)
- Christopher A. Waudby, Glyn L. Devlin, Adriano Aguzzi, Michele Vendruscolo, Eugene M. Terentjev, Mark E. Welland, Christopher M. Dobson, Tuomas P.J. Knowles, Samuel I.A. Cohen An analytical solution to the kinetics of breakable filament assembly Science 326, 1533-1537 (2009)
- 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)
- Edward Fredkin An informational process based on reversible universal cellular automata Physica D: Nonlinear Phenomena 45, 254-270 (1990)
- Mark A. Danielson, Joseph J. Falke, Hans Peter Biemann, Daniel E. Koshland Attractant- and Disulfide-Induced Conformational Changes in the Ligand Binding Domain of the Chemotaxis Aspartate Receptor: A 19F NMR Study Biochemistry 33, 6100-6109 (1994)
- Gerald L. Hazelbauer, Joseph J. Falke, John S. Parkinson Bacterial chemoreceptors: high-performance signaling in networked arrays Trends in Biochemical Sciences 33, 9-19 (2008)
- Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer. ,
- Emmanuel Hermans Biochemical and pharmacological control of the multiplicity of coupling at G-protein-coupled receptors Pharmacology and Therapeutics 99, 25-44 (2003)
- Body size and metabolic rate. ,
- Anna Menini Calcium signalling and regulation in olfactory neurons Current Opinion in Neurobiology 9, 419-426 (1999)
- Hugh R. Matthews, Johannes Reisert Calcium, the two-faced messenger of olfactory transduction and adaptation Current Opinion in Neurobiology 13, 469-475 (2003)
- Mingshan Li, Gerald L. Hazelbauer Cellular stoichiometry of the components of the chemotaxis signaling complex Journal of Bacteriology 186, 3687-3694 (2004)
- Jessica C. Flack, David C. Krakauer Challenges for complexity measures: A perspective from social dynamics and collective social computation Chaos 21, (2011)
- Chemical implementation of finite-state machines ,
- Marcelo O. Magnasco Chemical kinetics is turing universal Physical Review Letters 78, 1190-1193 (1997)
- Jeremy Gunawardena Chemical reaction network theory for in-silico biologists Bauer Center for Genomics Research Harvard University Cambridge MA 138, 1-26 (2003)
- Monica Skoge, Sahin Naqvi, Yigal Meir, Ned S. Wingreen Chemical sensing by nonequilibrium cooperative receptors Physical Review Letters 110, (2013)
- Howard C. Berg, Douglas A. Brown Chemotaxis in Escherichia coli analysed by three-dimensional tracking Nature 239, 500-504 (1972)
- Huan Xiang Zhou, Attila Szabo Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard-sphere liquid Journal of Chemical Physics 95, 5948-5952 (1991)
- 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 Soloveichik, Matthew Cook, Erik Winfree, Jehoshua Bruck Computation with finite stochastic chemical reaction networks Natural Computing 7, 615-633 (2008)
- T. A.J. Duke, N. Le Novère, D. Bray Conformational spread in a ring of proteins: A stochastic approach to allostery Journal of Molecular Biology 308, 541-553 (2001)
- Edward Fredkin, Tommaso Toffoli Conservative logic International Journal of Theoretical Physics 21, 219-253 (1982)
- William Bialek, Sima Setayeshgar Cooperativity, sensitivity, and noise in biochemical signaling Physical Review Letters 100, (2008)
- E. R. Weibel, W. Stäubli, H. R. Gnägi, F. A. Hess Correlated morphometric and biochemical studies on the liver cell. I. Morphometric model, stereologic methods, and normal morphometric data for rat liver. The Journal of cell biology 42, 68-91 (1969)
- Crowding Effects on Diffusion in Solutions and Cells ,
- David C. Krakauer Darwinian demons, evolutionary complexity, and information maximization Chaos 21, (2011)
- Wenzhe Ma, Ala Trusina, Hana El-Samad, Wendell A. Lim, Chao Tang Defining Network Topologies that Can Achieve Biochemical Adaptation Cell 138, 760-773 (2009)
- Sonja J. Prohaska, Christian V. Forst, David C. Krakauer, Peter Stadler Defining genes: A computational framework Theory in Biosciences 128, 165-170 (2009)
- Markus Kollmann, Linda Løvdok, Kilian Bartholomé, Jens Timmer, Victor Sourjik Design principles of a bacterial signalling network Nature 438, 504-507 (2005)
- 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)
- Jeroen S. Van Zon, Marco J. Morelli, Sorin Tǎnase-Nicola, Pieter Rein ten Wolde Diffusion of transcription factors can drastically enhance the noise in gene expression Biophysical Journal 91, 4350-4367 (2006)
- Benjamin B. Machta Dissipation Bound for Thermodynamic Control Physical Review Letters 115, (2015)
- Rolf Landauer Dissipation and noise immunity in computation and communication Nature 335, 779-784 (1988)
- Charles H. Bennett Dissipation-error tradeoff in proofreading BioSystems 11, 85-91 (1979)
- 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)
- Early metazoan life: divergence, environment and ecology ,
- 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)
- Thomas M. Cover, Joy A. Thomas Elements of Information Theory Elements of Information Theory , 1-748 (2005)
- Elements of Information Theory 2nd Edition ,
- Michael A. Savageau, Rolf R. Freter Energy Cost of Proofreading to Increase Fidelity of Transfer Ribonucleic Acid Aminoacylation Biochemistry 18, 3486-3493 (1979)
- S. B. Laughlin Energy as a constraint on the coding and processing of sensory information Current Opinion in Neurobiology 11, 475-480 (2001)
- Energy balance for analysis of complex metabolic networks. ,
- 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)
- Energy limitation as a selective pressure on the evolution of sensory systems ,
- Andrea Parmeggiani, Frank Jülicher, Armand Ajdari, Jacques Prost Energy transduction of isothermal ratchets: Generic aspects and specific examples close to and far from equilibrium Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 60, 2127-2140 (1999)
- Peter B. Detwiler, Sharad Ramanathan, Anirvan Sengupta, Boris I. Shraiman Engineering aspects of enzymatic signal transduction: Photoreceptors in the retina Biophysical Journal 79, 2801-2817 (2000)
- 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)
- Udo Seifert Entropy production along a stochastic trajectory and an integral fluctuation theorem Physical Review Letters 95, (2005)
- Gavin Crooks Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 60, 2721-2726 (1999)
- Tim Schmiedl, Thomas Speck, Udo Seifert Entropy production for mechanically or chemically driven biomolecules Journal of Statistical Physics 128, 77-93 (2007)
- 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)
- Eukaryotic organisms in Proterozoic oceans ,
- 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)
- P. H. Von Hippel, O. G. Berg Facilitated target location in biological systems Journal of Biological Chemistry 264, 675-678 (1989)
- 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)
- Pierre Gaspard Fluctuation theorem for nonequilibrium reactions Journal of Chemical Physics 120, 8898-8905 (2004)
- Takahiro Sagawa, Masahito Ueda Fluctuation theorem with information exchange: Role of correlations in stochastic thermodynamics Physical Review Letters 109, (2012)
- R. J. Harris, G. M. Schütz Fluctuation theorems for stochastic dynamics Journal of Statistical Mechanics: Theory and Experiment , (2007)
- Rosalind J. Allen, Chantal Valeriani, Pieter Rein ten Wolde Forward flux sampling for rare event simulations Journal of Physics Condensed Matter 21, (2009)
- Thomas E. Ouldridge, Pieter Rein ten Wolde Fundamental Costs in the Production and Destruction of Persistent Polymer Copies Physical Review Letters 118, (2017)
- G. Schreiber, G. Haran, H. X. Zhou Fundamental aspects of protein - Protein association kinetics Chemical Reviews 109, 839-860 (2009)
- 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)
- O. J.E. Maroney Generalizing Landauer's principle Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 79, (2009)
- 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)
- Growth, metabolic partitioning, and the size of microorganisms ,
- Kousuke Shizume Heat generation required by information erasure Physical Review E 52, 3495-3499 (1995)
- 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)
- Sebastian E. Ahnert, Andrei Zinovyev, Thomas M.A. Fink How much non-coding DNA do eukaryotes require? Journal of Theoretical Biology 252, 587-592 (2008)
- 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)
- Information theory, evolution, and the origin of life ,
- Mikhail Prokopenko, Itai Einav Information thermodynamics of near-equilibrium computation Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 91, (2015)
- Hugo Touchette, Seth Lloyd Information-theoretic approach to the study of control systems Physica A: Statistical Mechanics and its Applications 331, 140-172 (2004)
- Information-theoretic lower bound on energy cost of stochastic computation ,
- 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)
- Inhibition of the olfactory cyclic nucleotide gated ion channel by intracellular calcium. ,
- 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)
- J. Boeckh, K. E. Kaissling, D. Schneider Insect olfactory receptors. Cold Spring Harbor symposia on quantitative biology 30, 263-280 (1965)
- Tommaso Toffoli, Norman H. Margolus Invertible cellular automata: A review Physica D: Nonlinear Phenomena 45, 229-253 (1990)
- Rolf Landauer Irreversibility and Heat Generation in the Computing Process 5, 183-191 (1961)
- Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity ,
- Jacques Ninio Kinetic amplification of enzyme discrimination Biochimie 57, 587-595 (1975)
- Pablo Sartori, Simone Pigolotti Kinetic versus energetic discrimination in biological copying Physical Review Letters 110, (2013)
- Kinetics and thermodynamics of amyloid formation from direct measurements of fluctuations in fibril mass ,
- Kinetics of protein-protein association explained by Brownian dynamics computer simulation. ,
- Irina V. Gopich, Attila Szabo Kinetics of reversible diffusion influenced reactions: The self-consistent relaxation time approximation Journal of Chemical Physics 117, 507-517 (2002)
- Edward H. Feng, Gavin Crooks Length of time's arrow Physical Review Letters 101, (2008)
- 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)
- Light adaptation in retinal rods of the rabbit and two other nonprimate mammals. ,
- Thierry Mora, Ned S. Wingreen Limits of sensing temporal concentration changes by single cells Physical Review Letters 104, (2010)
- Logical Reversibility of Computation ,
- 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)
- R. J. Ellis Macromolecular crowding: An important but neglected aspect of the intracellular environment Current Opinion in Structural Biology 11, 114-119 (2001)
- L. Chang, M. Karin Mammalian MAP kinase signalling cascades Nature 410, 37-40 (2001)
- Robert G. Endres, Ned S. Wingreen Maximum likelihood and the single receptor Physical Review Letters 103, (2009)
- Maxwell's demon and the entropy cost of information ,
- 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)
- Metabolically efficient information processing. ,
- Tori M. Hoehler, Bo Barker Jørgensen Microbial life under extreme energy limitation Nature Reviews Microbiology 11, 83-94 (2013)
- Takahiro Sagawa, Masahito Ueda Minimal energy cost for thermodynamic information processing: Measurement and information erasure Physical Review Letters 102, (2009)
- Rolf Landauer Minimal energy requirements in communication Science 272, 1914-1918 (1996)
- Modeling the chemotactic response of Escherichia coli to time-varying stimuli ,
- Hans Bremer, Patrick P Dennis Modulation of Chemical Composition and Other Parameters of the Cell by Growth Rate Escherichia coli and Salmonella: cellular and molecular biology 2, 1527-1542 (1987)
- Filipe Tostevin, Pieter Rein ten Wolde Mutual information between input and output trajectories of biochemical networks Physical Review Letters 102, (2009)
- F. Horn Necessary and sufficient conditions for complex balancing in chemical kinetics Archive for Rational Mechanics and Analysis 49, 172-186 (1972)
- Pablo Sartori, Yuhai Tu Noise Filtering Strategies in Adaptive Biochemical Signaling Networks Journal of Statistical Physics 142, 1206-1217 (2011)
- Noisy signal amplification in ultrasensitive signal transduction ,
- Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems ,
- C. Jarzynski Nonequilibrium equality for free energy differences Physical Review Letters 78, 2690-2693 (1997)
- Nonequilibrium generation of information in copolymerization processes. ,
- 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)
- Hong Qian, Timothy C. Reluga Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling switch Physical Review Letters 94, (2005)
- Charles H. Bennett Notes on Landauer's principle, reversible computation, and Maxwell's Demon Studies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics 34, 501-510 (2003)
- Eric R. Pianka On r- and K-Selection The American Naturalist 104, 592-597 (1970)
- Thomas E Ouldridge, Christopher C Govern, Pieter Rein ten Wolde On the connection between computational and biochemical measurement Arxiv , 1-17 (2015)
- On the decrease of entropy in a thermodynamic system by the intervention of intelligent beings ,
- Jacque Monod, Jeffries Wyman, Jean Pierre Changeux On the nature of allosteric transitions: A plausible model Journal of Molecular Biology 12, 88-118 (1965)
- 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)
- Luke E. Ulrich, Eugene V. Koonin, Igor B. Zhulin One-component systems dominate signal transduction in prokaryotes Trends in Microbiology 13, 52-56 (2005)
- Open Markov Processes and Open Reaction Networks ,
- Nils B. Becker, Andrew Mugler, Pieter Rein ten Wolde Optimal Prediction by Cellular Signaling Networks Physical Review Letters 115, (2015)
- Optimal resource allocation in cellular sensing systems ,
- Erez Dekel, Uri Alon Optimality and evolutionary tuning of the expression level of a protein Nature 436, 588-592 (2005)
- Osmotic Stress Signaling and Osmoadaptation in Yeasts ,
- Bernardo A. Mello, Yuhai Tu Perfect and near-perfect adaptation in a model of bacterial chemotaxis Biophysical Journal 84, 2943-2956 (2003)
- Phosphorylation Energy Hypothesis: Open Chemical Systems and Their Biological Functions ,
- Sven Zimmermann, Karin Moelling Phosphorylation and regulation of Raf by Akt (protein kinase B) Science 286, 1741-1744 (1999)
- Thierry Mora Physical Limit to Concentration Sensing Amid Spurious Ligands Physical Review Letters 115, (2015)
- Ady Vaknin, Howard C. Berg Physical Responses of Bacterial Chemoreceptors Journal of Molecular Biology 366, 1416-1423 (2007)
- Physical limits on cellular sensing of spatial gradients. ,
- Rainer Feistel, Werner Ebeling Physics of Self-Organization and Evolution Physics of Self-Organization and Evolution , (2011)
- H. C. Berg, E. M. Purcell Physics of chemoreception Biophysical Journal 20, 193-219 (1977)
- Precise adaptation in bacterial chemotaxis through "assistance neighborhoods" ,
- Predicting temporal fluctuations in an intracellular signalling pathway. ,
- Prediction and Dissipation in Biochemical Sensing ,
- Probing kinase and phosphatase activities of two-component systems in vivo with concentration-dependent phosphorylation profiling ,
- Thomas Gregor, David W. Tank, Eric F. Wieschaus, William Bialek Probing the Limits to Positional Information Cell 130, 153-164 (2007)
- Proliferation of amyloid- 42 aggregates occurs through a secondary nucleation mechanism ,
- Protein accumulation in the endoplasmic reticulum as a non-equilibrium phase transition ,
- Kai Wang, Wouter Jan Rappel, Rex Kerr, Herbert Levine Quantifying noise levels of intercellular signals Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 75, (2007)
- 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)
- Receptor clustering as a cellular mechanism to control sensitivity. ,
- Wouter Jan Rappel, Herbert Levine Receptor noise and directional sensing in eukaryotic chemotaxis Physical Review Letters 100, (2008)
- Receptor sensitivity in bacterial chemotaxis ,
- Hong Qian Reducing Intrinsic Biochemical Noise in Cells and Its Thermodynamic Limit Journal of Molecular Biology 362, 387-392 (2006)
- Regulation of cell size in the yeast Saccharomyces cerevisiae. ,
- Robust perfect adaptation in bacterial chemotaxis through integral feedback control ,
- U. Alon, M. G. Surette, N. Barkai, S. Leibler Robustness in bacterial chemotaxis Nature 397, 168-171 (1999)
- N. Barkai, S. Leibler Robustness in simple biochemical networks Nature 387, 913-917 (1997)
- Thorsten Erdmann, Martin Howard, Pieter Rein ten Wolde Role of spatial averaging in the precision of gene expression patterns Physical Review Letters 103, (2009)
- 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)
- J. E.M. Hornos, D. Schultz, G. C.P. Innocentini, J. Wang, A. M. Walczak, J. N. Onuchic, P. G. Wolynes Self-regulating gene: An exact solution Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 72, (2005)
- Shifts in metabolic scaling, production, and efficiency across major evolutionary transitions of life ,
- Aljaž Godec, Ralf Metzler Signal focusing through active transport Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 92, (2015)
- F. Rieke, D. A. Baylor Single-photon detection by rod cells of the retina Reviews of Modern Physics 70, 1027-1036 (1998)
- Spatial partitioning improves the reliability of biochemical signaling ,
- Specificity in Two-Component Signal Transduction Pathways ,
- Spontaneous evolution of modularity and network motifs ,
- Stability and Complex Balancing in Mass-Action Systems with Three Short Complexes ,
- Statistical mechanics of isomerization dynamics in liquids and the transition state approximation ,
- Paolo Visco, Rosalind J. Allen, Martin R. Evans Statistical physics of a model binary genetic switch with linear feedback Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 79, (2009)
- Stochastic Processes in Physics and Chemistry ,
- Sarah A. Cepeda-Humerez, Georg Rieckh, Gašper Tkačik Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation Physical Review Letters 115, (2015)
- Stochastic gene expression in a single cell. ,
- Masahiro Ueda, Tatsuo Shibata Stochastic signal processing and transduction in chemotactic response of eukaryotic cells Biophysical Journal 93, 11-20 (2007)
- 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)
- Srividya Iyer-Biswas, F. Hayot, C. Jayaprakash Stochasticity of gene products from transcriptional pulsing Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 79, (2009)
- Hong Qian, Daniel A. Beard, Shou Dan Liang Stoichiometric network theory for nonequilibrium biochemical systems European Journal of Biochemistry 270, 415-421 (2003)
- Guy Shinar, Martin Feinberg Structural sources of robustness in biochemical reaction networks Science 327, 1389-1391 (2010)
- Eduardo D. Sontag Structure and stability of certain chemical networks and applications to the kinetic proofreading model of T-cell receptor signal transduction IEEE Transactions on Automatic Control 46, 1028-1047 (2001)
- Johan Paulsson Summing up the noise in gene networks Nature 427, 415-418 (2004)
- 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)
- System wide analyses have underestimated protein abundances and the importance of transcription in mammals ,
- O. J.E. Maroney The (absence of a) relationship between thermodynamic and logical reversibility Studies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics 36, 355-374 (2005)
- The Gibbs paradox ,
- The Rotary Motor of Bacterial Flagella ,
- 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)
- The bioenergetic costs of a gene ,
- James Ladyman, Stuart Presnell, Anthony J. Short, Berry Groisman The connection between logical and thermodynamic irreversibility Studies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics 38, 58-79 (2007)
- 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)
- The energy relay: a proofreading scheme based on dynamic cooperativity and lacking all characteristic symptoms of kinetic proofreading in DNA replication and protein synthesis. ,
- 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)
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