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From Thermodynamics of Computation
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General Non-equilibrium Statistical Physics
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- Luigi P. Cordella, Pasquale Foggia, Carlo Sansone, Mario Vento A (sub)graph isomorphism algorithm for matching large graphs IEEE Transactions on Pattern Analysis and Machine Intelligence 26, 1367-1372 (2004)
- Manoj Gopalkrishnan A Cost / Speed / Reliability Trade-off in Erasing a Bit , (2015)
- Manoj Gopalkrishnan A cost/speed/reliability tradeoff to erasing 9252, 192-201 (2015)
- Bernard Gaveau, L. S. Schulman A general framework for non-equilibrium phenomena: The master equation and its formal consequences Physics Letters, Section A: General, Atomic and Solid State Physics 229, 347-353 (1997)
- 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)
- Viviana Serreli, Chin Fa Lee, Euan R. Kay, David A. Leigh A molecular information ratchet Nature 445, 523-527 (2007)
- N. Karmarkar A new polynomial-time algorithm for linear programming Combinatorica 4, 373-395 (1984)
- Daniel T. Gillespie A rigorous derivation of the chemical master equation Physica A: Statistical Mechanics and its Applications 188, 404-425 (1992)
- Michael B. Elowitz, Stanislas Leibier A synthetic oscillatory network of transcriptional regulators Nature 403, 335-338 (2000)
- 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)
- Udo Seifert, A. C. Barato An autonomous and reversible Maxwell's demon EPL 101, (2013)
- Sudhakar Jonnalagadda, Rajagopalan Srinivasan An efficient graph theory based method to identify every minimal reaction set in a metabolic network BMC Systems Biology 8, (2014)
- Donna G. Blackmond An examination of the role of autocatalytic cycles in the chemistry of proposed primordial reactions Angewandte Chemie - International Edition 48, 386-390 (2009)
- Hong Qian, Sumit Roy An information theoretical analysis of kinase activated phosphorylation dephosphorylation cycle IEEE Transactions on Nanobioscience 11, 289-295 (2012)
- Vlatko Vedral An information-theoretic equality implying the Jarzynski relation Journal of Physics A: Mathematical and Theoretical 45, (2012)
- Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter Stadler An intermediate level of abstraction for computational systems chemistry IEEE/ACM Transactions on Computational Biology and Bioinformatics 16, 510-523 (2019)
- James Aspnes, Eric Ruppert An introduction to population protocols Middleware for Network Eccentric and Mobile Applications , 97-120 (2009)
- Analog Versus Digital: Extrapolating from Electronics to Neurobiology ,
- Analog synthetic biology ,
- Christoph Kaleta, Florian Centler, Peter Dittrich Analyzing molecular reaction networks: From pathways to chemical organizations Molecular Biotechnology 34, 117-123 (2006)
- Allen P. Mills, Bernard Yurke, Philip M. Platzman Article for analog vector algebra computation BioSystems 52, 175-180 (1999)
- Hua Jiang, Marc D. Riedel, Keshab K. Parhi Asynchronous computation with molecular reactions Conference Record - Asilomar Conference on Signals, Systems and Computers , 493-497 (2011)
- Peter Reimann Brownian motors: Noisy transport far from equilibrium Physics Report 361, 57-265 (2002)
- Sayed Ahmad Salehi, Keshab K. Parhi, Marc D. Riedel Chemical Reaction Networks for Computing Polynomials ACS Synthetic Biology 6, 76-83 (2017)
- Chemical implementation of finite-state machines ,
- Chemical implementation of neural networks and Turing machines ,
- Jeremy Gunawardena Chemical reaction network theory for in-silico biologists Bauer Center for Genomics Research Harvard University Cambridge MA 138, 1-26 (2003)
- Koji Maruyama, Franco Nori, Vlatko Vedral Colloquium: The physics of Maxwell's demon and information Reviews of Modern Physics 81, 1-23 (2009)
- Combinatorial complexity of pathway analysis in metabolic networks. ,
- Anthony J. Genot, Jonathan Bath, Andrew J. Turberfield Combinatorial displacement of DNA strands: Application to matrix multiplication and weighted sums Angewandte Chemie - International Edition 52, 1189-1192 (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)
- Dana Angluin, James Aspnes, Zoë Diamadi, Michael J. Fischer, René Peralta Computation in networks of passively mobile finite-state sensors Distributed Computing 18, 235-253 (2006)
- David Soloveichik, Matthew Cook, Erik Winfree, Jehoshua Bruck Computation with finite stochastic chemical reaction networks Natural Computing 7, 615-633 (2008)
- Boyan Yordanov, Jongmin Kim, Rasmus L. Petersen, Angelina Shudy, Vishwesh V. Kulkarni, Andrew Phillips Computational design of nucleic acid feedback control circuits ACS Synthetic Biology 3, 600-616 (2014)
- Computers and Intractability: a guide to NP-completeness ,
- David Yu Zhang, Erik Winfree Control of DNA strand displacement kinetics using toehold exchange Journal of the American Chemical Society 131, 17303-17314 (2009)
- DNA COMPUTING ,
- David Soloveichik, Georg Seelig, Erik Winfree DNA as a universal substrate for chemical kinetics (Extended Abstract) Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 5347 LNCS, 57-69 (2009)
- Design and analysis of synthetic carbon fixation pathways. ,
- Jordan M. Horowitz, Juan M.R. Parrondo Designing optimal discrete-feedback thermodynamic engines New Journal of Physics 13, (2011)
- Ho Lin Chen, David Doty, David Soloveichik Deterministic Function Computation with Chemical Reaction Network Natural Computing 13, 517-534 (2014)
- Nathaniel Roquet, Timothy K. Lu Digital and analog gene circuits for biotechnology Biotechnology Journal 9, 597-608 (2014)
- Arvind Murugan, David A. Huse, Stanislas Leibler Discriminatory proofreading regimes in nonequilibrium systems Physical Review X 4, (2014)
- Maximilian Weitz, Jongmin Kim, Korbinian Kapsner, Erik Winfree, Elisa Franco, Friedrich C. Simmel Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator Nature Chemistry 6, 295-302 (2014)
- Purnananda Guptasarma Does replication‐induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli? BioEssays 17, 987-997 (1995)
- Ecology, the Ascendent Perspective ,
- Andre C. Barato, David Hartich, Udo Seifert Efficiency of cellular information processing New Journal of Physics 16, (2014)
- Elements of Information Theory 2nd Edition ,
- Energy balance for analysis of complex metabolic networks. ,
- Shou Wen Wang, Yueheng Lan, Lei Han Tang Energy dissipation in an adaptive molecular circuit Journal of Statistical Mechanics: Theory and Experiment 2015, (2015)
- Entropy Production of Brownian Macromolecules with Inertia ,
- 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)
- Massimiliano Esposito, Katja Lindenberg, Christian Van Den Broeck Entropy production as correlation between system and reservoir New Journal of Physics 12, (2010)
- Tim Schmiedl, Thomas Speck, Udo Seifert Entropy production for mechanically or chemically driven biomolecules Journal of Statistical Physics 128, 77-93 (2007)
- Georg Seelig, David Soloveichik, David Yu Zhang, Erik Winfree Enzyme-free nucleic acid logic circuits Science 314, 1585-1588 (2006)
- 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)
- John Earman, John D. Norton Exorcist XIV: The wrath of Maxwell's Demon. Part II. From Szilard to Landauer and beyond Studies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics 30, 1-40 (1999)
- 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)
- D. Abreu, Udo Seifert Extracting work from a single heat bath through feedback EPL 94, (2011)
- Dana Angluin, James Aspnes, David Eisenstat Fast computation by population protocols with a leader Distributed Computing 21, 183-199 (2008)
- Anders Dessmark, Andrzej Lingas, Andrzej Proskurowski Faster algorithms for subgraph isomorphism of k-Connected partial k-Trees Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 1136, 501-513 (1996)
- Fat synthesis in adipose tissue. An examination of stoichiometric constraints ,
- Francisco J. Cao, Luis Dinis, Juan M.R. Parrondo Feedback control in a collective flashing ratchet Physical Review Letters 93, (2004)
- R. J. Gillespie Fifty years of the VSEPR model Coordination Chemistry Reviews 252, 1315-1327 (2008)
- 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)
- Naoto Shiraishi, Takahiro Sagawa Fluctuation theorem for partially masked nonequilibrium dynamics Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 91, (2015)
- Takahiro Sagawa, Masahito Ueda Fluctuation theorem with information exchange: Role of correlations in stochastic thermodynamics Physical Review Letters 109, (2012)
- Kyung Hyuk Kim, Hong Qian Fluctuation theorems for a molecular refrigerator Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 75, (2007)
- Tameem Albash, Daniel A. Lidar, Milad Marvian, Paolo Zanardi Fluctuation theorems for quantum processes Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 88, (2013)
- R. J. Harris, G. M. Schütz Fluctuation theorems for stochastic dynamics Journal of Statistical Mechanics: Theory and Experiment , (2007)
- L. Onsager, S. MacHlup Fluctuations and irreversible processes Physical Review 91, 1505-1512 (1953)
- F. Horn, R. Jackson General mass action kinetics Archive for Rational Mechanics and Analysis 47, 81-116 (1972)
- 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)
- Takahiro Sagawa, Masahito Ueda Generalized Jarzynski equality under nonequilibrium feedback control Physical Review Letters 104, (2010)
- M. Ponmurugan Generalized detailed fluctuation theorem under nonequilibrium feedback control Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 82, (2010)
- Nina Fedoroff, Walter Fontana Genetic networks: Small numbers of big molecules Science 297, 1129-1131 (2002)
- Riccardo Rao, David Lacoste, Massimiliano Esposito Glucans monomer-exchange dynamics as an open chemical network Journal of Chemical Physics 143, (2015)
- Takahiro Sagawa Hamiltonian derivations of the generalized Jarzynski equalities under feedback control Journal of Physics: Conference Series 297, (2011)
- Jung Jun Park, Kang Hwan Kim, Takahiro Sagawa, Sang Wook Kim Heat engine driven by purely quantum information Physical Review Letters 111, (2013)
- Yonggun Jun, Momčilo Gavrilov, John Bechhoefer High-precision test of Landauer's principle in a feedback trap Physical Review Letters 113, (2014)
- Dvir Kafri, Sebastian Deffner Holevo's bound from a general quantum fluctuation theorem Physical Review A - Atomic, Molecular, and Optical Physics 86, (2012)
- Alice Bernamonti, Federico Galli, Robert C. Myers, Jonathan Oppenheim Holographic Second Laws of Black Hole Thermodynamics 2018, 70 (2018)
- Alicia Dickenstein, Mercedes Pérez Millán How Far is Complex Balancing from Detailed Balancing? Bulletin of Mathematical Biology 73, 811-828 (2011)
- Jordan M. Horowitz, Takahiro Sagawa, Juan M.R. Parrondo Imitating chemical motors with optimal information motors Physical Review Letters 111, (2013)
- Information Processing and the Second Law of Thermodynamics: An Inclusive, Hamiltonian Approach ,
- Takahiro Sagawa, Masahito Ueda Information Thermodynamics: Maxwell's Demon in Nonequilibrium Dynamics Nonequilibrium Statistical Physics of Small Systems: Fluctuation Relations and Beyond , 181-211 (2013)
- F. J. Cao, M. Feito, H. Touchette Information and flux in a feedback controlled Brownian ratchet Physica A: Statistical Mechanics and its Applications 388, 113-119 (2009)
- Sebastian Deffner, Christopher Jarzynski Information processing and the second law of thermodynamics: An inclusive, Hamiltonian approach Physical Review X 3, (2014)
- O Maroney Information processing and thermodynamic entropy The Stanford Encyclopedia of Philosophy , - (2009)
- Sosuke Ito, Takahiro Sagawa Information thermodynamics on causal networks Physical Review Letters 111, (2013)
- Marc Mézard, Andrea Montanari Information, Physics, and Computation Information, Physics, and Computation 9780198570837, 1-584 (2009)
- Ken Funo, Yu Watanabe, Masahito Ueda Integral quantum fluctuation theorems under measurement and feedback control Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 88, (2013)
- Martin Depken, Stephan W. Grill, Juan M.R. Parrondo Intermittent Transcription Dynamics for the Rapid Production of Long Transcripts of High Fidelity Cell Reports 5, 521-530 (2013)
- Rolf Landauer Irreversibility and Heat Generation in the Computing Process 5, 183-191 (1961)
- Youhei Fujitani, Hiroyuki Suzuki Jarzynski equality modified in the linear feedback system Journal of the Physical Society of Japan 79, (2010)
- Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity ,
- 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 ,
- Anne Condon, Alan Hu, Ján Maňuch, Chris Thachuk Less haste, less waste: On recycling and its limits in strand displacement systems Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 6937 LNCS, 84-99 (2011)
- Max Horn SAT and the minimum cut problem in directed hypergraphs ,
- Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter Stadler Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete Journal of Systems Chemistry 3, (2012)
- Henrik Sandberg, Jean Charles Delvenne, Nigel J. Newton, Sanjoy K. Mitter Maximum work extraction and implementation costs for nonequilibrium Maxwell's demons Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 90, (2014)
- H. T. Quan, Y. D. Wang, Yu Xi Liu, C. P. Sun, Franco Nori Maxwell's demon assisted thermodynamic cycle in superconducting quantum circuits Physical Review Letters 97, (2006)
- Sosuke Ito, Takahiro Sagawa Maxwell's demon in biochemical signal transduction with feedback loop Nature Communications 6, (2015)
- Dibyendu Mandal, H. T. Quan, Christopher Jarzynski Maxwell's refrigerator: An exactly solvable model Physical Review Letters 111, (2013)
- Raoul Dillenschneider, Eric Lutz Memory erasure in small systems Physical Review Letters 102, (2009)
- Microscopic analysis of Clausius-Duhem processes ,
- Takahiro Sagawa, Masahito Ueda Minimal energy cost for thermodynamic information processing: Measurement and information erasure Physical Review Letters 102, (2009)
- Suriyanarayanan Vaikuntanathan, Christopher Jarzynski Modeling Maxwell's demon with a microcanonical Szilard engine Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 83, (2011)
- F. Horn Necessary and sufficient conditions for complex balancing in chemical kinetics Archive for Rational Mechanics and Analysis 49, 172-186 (1972)
- Lulu Qian, Erik Winfree, Jehoshua Bruck Neural network computation with DNA strand displacement cascades Nature 475, 368-372 (2011)
- Nonequilibrium Thermodynamics of Feedback Control ,
- Jordan M. Horowitz, Suriyanarayanan Vaikuntanathan Nonequilibrium detailed fluctuation theorem for repeated discrete feedback Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 82, (2010)
- Nonequilibrium generation of information in copolymerization processes. ,
- M. Bonaldi, L. Conti, P. De Gregorio, L. Rondoni, G. Vedovato, A. Vinante, M. Bignotto, M. Cerdonio, P. Falferi, N. Liguori, S. Longo, R. Mezzena, A. Ortolan, G. A. Prodi, F. Salemi, L. Taffarello, S. Vitale, J. P. Zendri Nonequilibrium steady-state fluctuations in actively cooled resonators Physical Review Letters 103, (2009)
- 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)
- Albert Eschenmoser On a hypothetical generational relationship between HCN and constituents of the reductive citric acid cycle Chemistry and Biodiversity 4, 554-573 (2007)
- A. Mielke, M. A. Peletier, D. R.M. Renger On the Relation between Gradient Flows and the Large-Deviation Principle, with Applications to Markov Chains and Diffusion Potential Analysis 41, 1293-1327 (2014)
- J. Hoppenau, A. Engel On the energetics of information exchange EPL 105, (2014)
- Hiroyuki Suzuki, Youhei Fujitani One-dimensional shift of a brownian particle under the feedback control Journal of the Physical Society of Japan 78, (2009)
- Michael Zuker, Patrick Stiegler Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucleic Acids Research 9, 133-148 (1981)
- Patrick R. Zulkowski, Michael R. Deweese Optimal finite-time erasure of a classical bit Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 89, (2014)
- Jordan M. Horowitz, Juan M.R. Parrondo Optimizing non-ergodic feedback engines Acta Physica Polonica B 44, 803-814 (2013)
- Rainer Feistel, Werner Ebeling Physics of Self-Organization and Evolution Physics of Self-Organization and Evolution , (2011)
- Predator-prey molecular ecosystems. ,
- Programmability of Chemical Reaction Networks ,
- Yuan Jyue Chen, Neil Dalchau, Niranjan Srinivas, Andrew Phillips, Luca Cardelli, David Soloveichik, Georg Seelig Programmable chemical controllers made from DNA Nature Nanotechnology 8, 755-762 (2013)
- Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach ,
- Thomas E. Ouldridge, Jonathan Bath, Andrew J. Turberfield, Robert R.F. Machinek, Natalie E.C. Haley Programmable energy landscapes for kinetic control of DNA strand displacement Nature Communications 5, (2014)
- Peng Yin, Rizal F. Hariadi, Sudheer Sahu, Harry M.T. Choi, Ha Park Sung, Thomas H. LaBean, John H. Reif Programming DNA tube circumferences Science 321, 824-826 (2008)
- Peng Yin, Harry M.T. Choi, Colby R. Calvert, Niles A. Pierce Programming biomolecular self-assembly pathways Nature 451, 318-322 (2008)
- Proliferation of amyloid- 42 aggregates occurs through a secondary nucleation mechanism ,
- Protein accumulation in the endoplasmic reticulum as a non-equilibrium phase transition ,
- Yohei Morikuni, Hal Tasaki Quantum Jarzynski-Sagawa-Ueda Relations Journal of Statistical Physics 143, 1-10 (2011)
- Wojciech Hubert Zurek Quantum discord and Maxwell’s demons Physical Review A - Atomic, Molecular, and Optical Physics 67, 6 (2003)
- Sang Wook Kim, Takahiro Sagawa, Simone De Liberato, Masahito Ueda Quantum szilard engine Physical Review Letters 106, (2011)
- John C. Baez, Brendan Fong Quantum techniques for studying equilibrium in reaction networks Journal of Complex Networks 3, 22-34 (2015)
- Andre C. Barato, David Hartich, Udo Seifert Rate of Mutual Information Between Coarse-Grained Non-Markovian Variables Journal of Statistical Physics 153, 460-478 (2013)
- Rate-independent Computation in Continuous Chemical Reaction Networks ,
- Anne Condon, Bonnie Kirkpatrick, Ján Maňuch Reachability bounds for chemical reaction networks and strand displacement systems Natural Computing 13, 499-516 (2014)
- Benjamin J. Lopez, Nathan J. Kuwada, Erin M. Craig, Brian R. Long, Heiner Linke Realization of a feedback controlled flashing ratchet Physical Review Letters 101, (2008)
- Reciprocal relations in irreversible processes. I. ,
- Richard M. Karp Reducibility among combinatorial problems 50 Years of Integer Programming 1958-2008: From the Early Years to the State-of-the-Art , 219-241 (2010)
- Leonard Mlodinow, Todd A. Brun Relation between the psychological and thermodynamic arrows of time Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 89, (2014)
- Hong Qian Relative entropy: Free energy associated with equilibrium fluctuations and nonequilibrium deviations Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 63, (2001)
- Robust stochastic chemical reaction networks and bounded tau-leaping. ,
- Takahiro Sagawa, Masahito Ueda Role of mutual information in entropy production under information exchanges New Journal of Physics 15, (2013)
- Scaling up digital circuit computation with DNA strand displacement cascades. ,
- C. Van Den Broeck, Massimiliano Esposito Second law and Landauer principle far from equilibrium EPL 95, (2011)
- Kurt Jacobs Second law of thermodynamics and quantum feedback control: Maxwell’s demon with weak measurements Physical Review A - Atomic, Molecular, and Optical Physics 80, (2009)
- Christian Maes, Hal Tasaki Second law of thermodynamics for macroscopic mechanics coupled to thermodynamic degrees of freedom Letters in Mathematical Physics 79, 251-261 (2007)
- Takahiro Sagawa, Masahito Ueda Second law of thermodynamics with discrete quantum feedback control AIP Conference Proceedings 1110, 21-24 (2009)
- Jordan M. Horowitz, Henrik Sandberg Second-law-like inequalities with information and their interpretations New Journal of Physics 16, (2014)
- Stability and Complex Balancing in Mass-Action Systems with Three Short Complexes ,
- Stably computable predicates are semilinear ,
- Stochastic Simulation of Chemical Kinetics ,
- Hao Ge, Min Qian, Hong Qian Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics Physics Reports 510, 87-118 (2012)
- Massimiliano Esposito, Gernot Schaller Stochastic thermodynamics for Maxwell demon feedbacks EPL 99, (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)
- Andre C. Barato, Udo Seifert Stochastic thermodynamics with information reservoirs Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 90, (2014)
- Udo Seifert Stochastic thermodynamics, fluctuation theorems and molecular machines Reports on Progress in Physics 75, (2012)
- Hong Qian, Daniel A. Beard, Shou Dan Liang Stoichiometric network theory for nonequilibrium biochemical systems European Journal of Biochemistry 270, 415-421 (2003)
- Luca Cardelli Strand algebras for DNA computing Natural Computing 10, 407-428 (2011)
- 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)
- Synchronizing genetic relaxation oscillators by intercell signaling ,
- Ramiz Daniel, Jacob R. Rubens, Rahul Sarpeshkar, Timothy K. Lu Synthetic analog computation in living cells Nature 497, 619-623 (2013)
- Herbert M. Sauro, Kyung Kim Synthetic biology: It's an analog world Nature 497, 572-573 (2013)
- Jongmin Kim, Erik Winfree Synthetic in vitro transcriptional oscillators Molecular Systems Biology 7, (2011)
- Martin Bier, Francisco J. Cao Szilard-machine-like features in a processive motor protein Acta Physica Polonica B 43, 889-908 (2012)
- TRANSACTIONS ON COMPUTATIONAL SYSTEMS BIOLOGY XII ,
- The Activated Complex in Chemical Reactions ,
- Juan M.R. Parrondo The Szilard engine revisited: Entropy, macroscopic randomness, and symmetry breaking phase transitions Chaos 11, 725-733 (2001)
- Luca Cardelli, Attila Csikász-Nagy The cell cycle switch computes approximate majority Scientific Reports 2, (2012)
- The energy relay: a proofreading scheme based on dynamic cooperativity and lacking all characteristic symptoms of kinetic proofreading in DNA replication and protein synthesis. ,
- M. B. Plenio, V. Vitelli The physics of forgetting: Landauer's erasure principle and information theory Contemporary Physics 42, 25-60 (2001)
- Thomas G. Kurtz The relationship between stochastic and deterministic models for chemical reactions The Journal of Chemical Physics 57, 2976-2978 (1972)
- Charles H. Bennett The thermodynamics of computation-a review International Journal of Theoretical Physics 21, 905-940 (1982)
- Paul G. Mezey The topology of energy hypersurfaces III. The fundamental group of reaction mechanisms on potential energy hypersurfaces Theoretica Chimica Acta 67, 43-61 (1985)
- Pablo Sartori, Léo Granger, Chiu Fan Lee, Jordan M. Horowitz Thermodynamic Costs of Information Processing in Sensory Adaptation PLoS Computational Biology 10, (2014)
- Takahiro Sagawa Thermodynamic and logical reversibilities revisited Journal of Statistical Mechanics: Theory and Experiment 2014, (2014)
- Daniel A. Beard, Eric Babson, Edward Curtis, Hong Qian Thermodynamic constraints for biochemical networks Journal of Theoretical Biology 228, 327-333 (2004)
- Armen E. Allahverdyan, Dominik Janzing, Guenter Mahler Thermodynamic efficiency of information and heat flow Journal of Statistical Mechanics: Theory and Experiment 2009, (2009)
- Ken Funo, Yu Watanabe, Masahito Ueda Thermodynamic work gain from entanglement Physical Review A - Atomic, Molecular, and Optical Physics 88, (2013)
- Herbert B. Callen, H. L. Scott Thermodynamics and an Introduction to Thermostatistics, 2nd ed. American Journal of Physics 66, 164-167 (1998)
- Thomas E. Ouldridge, Christopher C. Govern, Pieter Rein ten Wolde Thermodynamics of Computational Copying in Biochemical Systems Physical Review X 7, (2017)
- Thermodynamics of Information Processing in Small Systems ,
- Philipp Strasberg, Gernot Schaller, Tobias Brandes, Massimiliano Esposito Thermodynamics of a physical model implementing a Maxwell demon Physical Review Letters 110, (2013)
- F. J. Cao, M. Feito Thermodynamics of feedback controlled systems Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 79, (2009)
- David Abreu, Udo Seifert Thermodynamics of genuine nonequilibrium states under feedback control Physical Review Letters 108, (2012)
- Juan M.R. Parrondo, Jordan M. Horowitz, Takahiro Sagawa Thermodynamics of information Nature Physics 11, 131-139 (2015)
- Eric Smith Thermodynamics of natural selection I: Energy flow and the limits on organization Journal of Theoretical Biology 252, 185-197 (2008)
- Eric Smith Thermodynamics of natural selection II: Chemical Carnot cycles Journal of Theoretical Biology 252, 198-212 (2008)
- Eric Smith Thermodynamics of natural selection III: Landauer’s principle in computation and chemistry Journal of Theoretical Biology 252, 213-220 (2008)
- Susanne Still, David A. Sivak, Anthony J. Bell, Gavin Crooks Thermodynamics of prediction Physical Review Letters 109, (2012)
- 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 formulation2 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)
- Towards programming languages for genetic engineering of living cells. ,
- Two approaches for metabolic pathway analysis? ,
- Two-Domain DNA Strand Displacement ,
- L. Szilard Uber die Entropieverminderung in einem thermodynamischen System bei Eingriffen intelligenter Wesen Zeitschrift für Physik 53, 840-856 (1929)
- A. C. Barato, Udo Seifert Unifying three perspectives on information processing in stochastic thermodynamics Physical Review Letters 112, (2014)
- 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)
- Pier Luigi Gentili Untangling Complex Systems: A Grand Challenge for Science , (2018)
- Seth Lloyd Use of mutual information to decrease entropy: Implications for the second law of thermodynamics Physical Review A 39, 5378-5386 (1989)
- Work and information processing in a solvable model of Maxwell's demon ,
- M. Born, R. Oppenheimer Zur Quantentheorie der Molekeln Annalen der Physik 389, 457-484 (1927)