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Showing below up to 123 results in range #1 to #123.
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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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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. ,
- 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)
- 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 ,
- 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)
- J. Ricardo Arias-Gonzalez Entropy involved in fidelity of DNA replication PLoS ONE 7, (2012)
- 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)
- 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 ,
- 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)
- 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)
- 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)
- 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)
- Alicia Dickenstein, Mercedes Pérez Millán How Far is Complex Balancing from Detailed Balancing? Bulletin of Mathematical Biology 73, 811-828 (2011)
- 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)
- 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 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)
- 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)
- Michael Zuker, Patrick Stiegler Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucleic Acids Research 9, 133-148 (1981)
- 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 ,
- John C. Baez, Brendan Fong Quantum techniques for studying equilibrium in reaction networks Journal of Complex Networks 3, 22-34 (2015)
- 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)
- 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)
- Robust stochastic chemical reaction networks and bounded tau-leaping. ,
- 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)
- 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 Stochastic thermodynamics under coarse graining Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 85, (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)
- TRANSACTIONS ON COMPUTATIONAL SYSTEMS BIOLOGY XII ,
- The Activated Complex in Chemical Reactions ,
- 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. ,
- 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)
- Daniel A. Beard, Eric Babson, Edward Curtis, Hong Qian Thermodynamic constraints for biochemical networks Journal of Theoretical Biology 228, 327-333 (2004)
- Thomas E. Ouldridge, Christopher C. Govern, Pieter Rein ten Wolde Thermodynamics of Computational Copying in Biochemical Systems Physical Review X 7, (2017)
- Philipp Strasberg, Gernot Schaller, Tobias Brandes, Massimiliano Esposito Thermodynamics of a physical model implementing a Maxwell demon Physical Review Letters 110, (2013)
- 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)
- Jordan M. Horowitz, Massimiliano Esposito Thermodynamics with continuous information flow Physical Review X 4, (2014)
- 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 ,
- Pier Luigi Gentili Untangling Complex Systems: A Grand Challenge for Science , (2018)
- M. Born, R. Oppenheimer Zur Quantentheorie der Molekeln Annalen der Physik 389, 457-484 (1927)