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From Thermodynamics of Computation
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Reference Materials > Reference group :
Artificial Biological Computation or
General Non-equilibrium Statistical Physics
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Showing below up to 117 results in range #1 to #117.
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- Manoj Gopalkrishnan A Cost / Speed / Reliability Trade-off in Erasing a Bit , (2015)
- Bernard Yurke, Andrew J. Turberfield, Allen P. Mills, Friedrich C. Simmel, Jennifer L. Neumann A DNA-fuelled molecular machine made of DNA Nature 406, 605-608 (2000)
- 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)
- Viviana Serreli, Chin Fa Lee, Euan R. Kay, David A. Leigh A molecular information ratchet Nature 445, 523-527 (2007)
- Dana Angluin, James Aspnes, David Eisenstat A simple population protocol for fast robust approximate majority Distributed Computing 21, 87-102 (2008)
- Udo Seifert, A. C. Barato An autonomous and reversible Maxwell's demon EPL 101, (2013)
- Vlatko Vedral An information-theoretic equality implying the Jarzynski relation Journal of Physics A: Mathematical and Theoretical 45, (2012)
- Tianqi Song, Sudhanshu Garg, Reem Mokhtar, Hieu Bui, John Reif Analog Computation by DNA Strand Displacement Circuits ACS Synthetic Biology 5, 898-912 (2016)
- Arkadiusz Chworos, Isil Severcan, Alexey Y. Koyfman, Patrick Weinkam, Emin Oroudjev, Helen G. Hansma, Luc Jaeger Building programmable jigsaw puzzles with RNA Science 306, 2068-2072 (2004)
- Koji Maruyama, Franco Nori, Vlatko Vedral Colloquium: The physics of Maxwell's demon and information Reviews of Modern Physics 81, 1-23 (2009)
- David Soloveichik, Matthew Cook, Erik Winfree, Jehoshua Bruck Computation with finite stochastic chemical reaction networks Natural Computing 7, 615-633 (2008)
- Robert Penchovsky, Ronald R. Breaker Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes Nature Biotechnology 23, 1424-1433 (2005)
- Bradley Hall, Jay R. Hesselberth, Andrew D. Ellington Computational selection of nucleic acid biosensors via a slip structure model Biosensors and Bioelectronics 22, 1939-1947 (2007)
- Jongmin Kim, Kristin S. White, Erik Winfree Construction of an in vitro bistable circuit from synthetic transcriptional switches Molecular Systems Biology 2, (2006)
- David Yu Zhang, Erik Winfree Control of DNA strand displacement kinetics using toehold exchange Journal of the American Chemical Society 131, 17303-17314 (2009)
- Johann Elbaz, Michal Moshe, Bella Shlyahovsky, Itamar Willner Cooperative multicomponent self-assembly of nucleic acid structures for the activation of DNAzyme cascades: A paradigm for DNA sensors and aptasensors Chemistry - A European Journal 15, 3411-3418 (2009)
- Jeffrey J. Tabor, Matthew Levy, Andrew D. Ellington Deoxyribozymes that recode sequence information Nucleic Acids Research 34, 2166-2172 (2006)
- 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 networks Natural Computing 13, 517-534 (2014)
- Arvind Murugan, David A. Huse, Stanislas Leibler Discriminatory proofreading regimes in nonequilibrium systems Physical Review X 4, (2014)
- David Yu Zhang, Georg Seelig Dynamic DNA nanotechnology using strand-displacement reactions Nature Chemistry 3, 103-113 (2011)
- Andre C. Barato, David Hartich, Udo Seifert Efficiency of cellular information processing New Journal of Physics 16, (2014)
- Vandana Sharma, Yoko Nomura, Yohei Yokobayashi Engineering complex riboswitch regulation by dual genetic selection Journal of the American Chemical Society 130, 16310-16315 (2008)
- 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)
- Niranjan Srinivas, James Parkin, Georg Seelig, Erik Winfree, David Soloveichik Enzyme-free nucleic acid dynamical systems Science 358, (2017)
- 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)
- Alexander Dobrinevski, Erwin Frey Extinction in neutrally stable stochastic Lotka-Volterra models Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 85, (2012)
- D. Abreu, Udo Seifert Extracting work from a single heat bath through feedback EPL 94, (2011)
- Francisco J. Cao, Luis Dinis, Juan M.R. Parrondo Feedback control in a collective flashing ratchet Physical Review Letters 93, (2004)
- 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)
- 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)
- Juewen Liu, Zehui Cao, Yi Lu Functional nucleic acid sensors Chemical Reviews 109, 1948-1998 (2009)
- Xiaohong Cheng, Xiangjun Liu, Tao Bing, Zehui Cao, Dihua Shangguan General peroxidase activity of G-quadruplex-hemin complexes and its application in ligand screening Biochemistry 48, 7817-7823 (2009)
- 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)
- Shawn K. Desai, Justin P. Gallivan Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation Journal of the American Chemical Society 126, 13247-13254 (2004)
- 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)
- Jordan M. Horowitz, Takahiro Sagawa, Juan M.R. Parrondo Imitating chemical motors with optimal information motors Physical Review Letters 111, (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)
- 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)
- Youhei Fujitani, Hiroyuki Suzuki Jarzynski equality modified in the linear feedback system Journal of the Physical Society of Japan 79, (2010)
- Pablo Sartori, Simone Pigolotti Kinetic versus energetic discrimination in biological copying Physical Review Letters 110, (2013)
- David Doty, Monir Hajiaghayi Leaderless deterministic chemical reaction networks Natural Computing 14, 213-223 (2015)
- Bella Shlyahovsky, Yang Li, Oleg Lioubashevski, Johann Elbaz, Itamar Willner Logic gates and antisense DNA devices operating on a translator nucleic acid scaffold ACS Nano 3, 1831-1843 (2009)
- 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)
- 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)
- Matthew R. Lakin, Darko Stefanovic, Andrew Phillips Modular verification of chemical reaction network encodings via serializability analysis Theoretical Computer Science 632, 21-42 (2016)
- Luca Cardelli Morphisms of reaction networks that couple structure to function BMC Systems Biology 8, (2014)
- Jordan M. Horowitz, Suriyanarayanan Vaikuntanathan Nonequilibrium detailed fluctuation theorem for repeated discrete feedback Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 82, (2010)
- 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)
- 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)
- 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)
- Yaakov Benenson, Tamar Paz-Elizur, Rivka Adar, Ehud Keinan, Zvi Llvneh, Ehud Shapiro Programmable and autonomous computing machine made of biomolecules Nature 414, 430-434 (2001)
- 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)
- Travis S. Bayer, Christina D. Smolke Programmable ligand-controlled riboregulators of eukaryotic gene expression Nature Biotechnology 23, 337-343 (2005)
- 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)
- 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)
- 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)
- 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)
- Takahiro Sagawa, Masahito Ueda Role of mutual information in entropy production under information exchanges New Journal of Physics 15, (2013)
- 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)
- Jordan M. Horowitz, Henrik Sandberg Second-law-like inequalities with information and their interpretations New Journal of Physics 16, (2014)
- Ravinderjit S. Braich, Nickolas Chelyapov, Cliff Johnson, Paul W.K. Rothemund, Leonard Adleman Solution of a 20-variable 3-SAT problem on a DNA computer Science 296, 499-502 (2002)
- 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)
- 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)
- Martin Bier, Francisco J. Cao Szilard-machine-like features in a processive motor protein Acta Physica Polonica B 43, 889-908 (2012)
- 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)
- M. B. Plenio, V. Vitelli The physics of forgetting: Landauer's erasure principle and information theory Contemporary Physics 42, 25-60 (2001)
- 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)
- 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)
- 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)
- 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)
- 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)
- Seth Lloyd Use of mutual information to decrease entropy: Implications for the second law of thermodynamics Physical Review A 39, 5378-5386 (1989)
- Seung Woo Shin, Chris Thachuk, Erik Winfree Verifying chemical reaction network implementations: A pathway decomposition approach Theoretical Computer Science 765, 67-96 (2019)
- Matthew R. Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips Visual DSD: A design and analysis tool for DNA strand displacement systems Bioinformatics 27, 3211-3213 (2011)