The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics
暂无分享,去创建一个
[1] Erik Winfree,et al. Thermodynamic Analysis of Interacting Nucleic Acid Strands , 2007, SIAM Rev..
[2] M. Khammash,et al. Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks. , 2016, Cell systems.
[3] Ankit Gupta,et al. Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks. , 2014, Cell systems.
[4] Filipe Tostevin,et al. A stochastic model of Min oscillations in Escherichia coli and Min protein segregation during cell division , 2005, Physical biology.
[5] Pieter Rein Ten Wolde,et al. Optimal resource allocation in cellular sensing systems , 2014, Proceedings of the National Academy of Sciences.
[6] David Baker,et al. Accurate design of megadalton-scale two-component icosahedral protein complexes , 2016, Science.
[7] Lulu Qian,et al. Efficient Turing-Universal Computation with DNA Polymers , 2010, DNA.
[8] Erik Winfree,et al. Molecular robots guided by prescriptive landscapes , 2010, Nature.
[9] F. Crick. Central Dogma of Molecular Biology , 1970, Nature.
[10] John D. Norton. Waiting for Landauer , 2010 .
[11] Geoff S. Baldwin. Synthetic Biology — A Primer , 2012 .
[12] Olli Ikkala,et al. Switchable Static and Dynamic Self-Assembly of Magnetic Droplets on Superhydrophobic Surfaces , 2013, Science.
[13] Yuhai Tu,et al. The energy-speed-accuracy tradeoff in sensory adaptation , 2012, Nature Physics.
[14] Pablo Sartori,et al. Thermodynamics of Error Correction , 2015, 1504.06407.
[15] D. Y. Zhang,et al. Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.
[16] A. Turberfield,et al. Programmable energy landscapes for kinetic control of DNA strand displacement , 2014, Nature Communications.
[17] U. Seifert. Stochastic thermodynamics, fluctuation theorems and molecular machines , 2012, Reports on progress in physics. Physical Society.
[18] P. R. ten Wolde,et al. Biochemical Machines for the Interconversion of Mutual Information and Work. , 2017, Physical review letters.
[19] Richard A. Muscat,et al. A programmable molecular robot. , 2011, Nano letters.
[20] N. Seeman,et al. Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.
[21] David H. Mathews,et al. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure , 2009, Nucleic Acids Res..
[22] Sosuke Ito,et al. Maxwell's demon in biochemical signal transduction with feedback loop , 2014, Nature Communications.
[23] Massimiliano Esposito,et al. Second law and Landauer principle far from equilibrium , 2011, 1104.5165.
[24] David Baker,et al. Design of a hyperstable 60-subunit protein icosahedron , 2016, Nature.
[25] M. Saraste,et al. FEBS Lett , 2000 .
[26] Irving M. Klotz,et al. Symposia of the Society for Experimental Biology , 1952, The Yale Journal of Biology and Medicine.
[27] C. Jarzynski,et al. Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies , 2005, Nature.
[28] M. Radosavljevic,et al. Biological Physics: Energy, Information, Life , 2003 .
[29] Suriyanarayanan Vaikuntanathan,et al. Design principles for nonequilibrium self-assembly , 2015, Proceedings of the National Academy of Sciences.
[30] M. Bennett,et al. A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.
[31] Udo Seifert,et al. Thermodynamic uncertainty relation for biomolecular processes. , 2015, Physical review letters.
[32] C. Jarzynski. Equalities and Inequalities: Irreversibility and the Second Law of Thermodynamics at the Nanoscale , 2011 .
[33] D. Andrieux,et al. Nonequilibrium generation of information in copolymerization processes , 2008, Proceedings of the National Academy of Sciences.
[34] T. Ouldridge. Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble. , 2012, The Journal of chemical physics.
[35] Pieter Rein ten Wolde,et al. Thermodynamics of Computational Copying in Biochemical Systems , 2015, 1503.00909.
[36] T. Sagawa,et al. Thermodynamics of information , 2015, Nature Physics.
[37] Maclyn McCarty,et al. STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES , 1944, The Journal of experimental medicine.
[38] P. Yin,et al. A DNAzyme that walks processively and autonomously along a one-dimensional track. , 2005, Angewandte Chemie.
[40] T. L. Hill,et al. Free Energy Transduction and Biochemical Cycle Kinetics , 1988, Springer New York.
[41] P. Gaspard. Growth and Dissolution of Macromolecular Markov Chains , 2016, 1604.08011.
[42] Shawn M. Douglas,et al. Self-assembly of DNA into nanoscale three-dimensional shapes , 2009, Nature.
[43] Harry M. T. Choi,et al. Programming biomolecular self-assembly pathways , 2008, Nature.
[44] J. Sumner. THE ISOLATION AND CRYSTALLIZATION OF THE ENZYME UREASE PRELIMINARY PAPER , 1926 .
[45] Christopher Jarzynski,et al. Work and information processing in a solvable model of Maxwell’s demon , 2012, Proceedings of the National Academy of Sciences.
[46] E. Jaynes. Information Theory and Statistical Mechanics , 1957 .
[47] J. Collins,et al. Toehold Switches: De-Novo-Designed Regulators of Gene Expression , 2014, Cell.
[48] W. Ebeling. Stochastic Processes in Physics and Chemistry , 1995 .
[49] R. Rosenfeld. Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.
[50] D. Gillespie,et al. Deterministic limit of stochastic chemical kinetics. , 2009, The journal of physical chemistry. B.
[51] Teruo Fujii,et al. Predator-prey molecular ecosystems. , 2013, ACS nano.
[52] A. C. Barato,et al. Universal bound on the efficiency of molecular motors , 2016, 1609.08046.
[53] Antonio Celani,et al. Multiple-scale stochastic processes: Decimation, averaging and beyond , 2016, 1612.04999.
[54] S. Doniach. Biological Physics: Energy, Information, Life , 2003 .
[55] K. Dill,et al. The Protein-Folding Problem, 50 Years On , 2012, Science.
[56] Ruojie Sha,et al. A Bipedal DNA Brownian Motor with Coordinated Legs , 2009, Science.
[57] D. Tieleman,et al. The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.
[58] M. Perutz,et al. Structure of hemoglobin. , 1960, Brookhaven symposia in biology.
[59] E. M.,et al. Statistical Mechanics , 2021, Manual for Theoretical Chemistry.
[60] Jonathan Bath,et al. An autonomous molecular assembler for programmable chemical synthesis. , 2016, Nature chemistry.
[61] J. Ninio. Kinetic amplification of enzyme discrimination. , 1975, Biochimie.
[62] J. Doye,et al. Extracting bulk properties of self-assembling systems from small simulations , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.
[63] David J Schwab,et al. Energetic costs of cellular computation , 2012, Proceedings of the National Academy of Sciences.
[64] A. Turberfield,et al. Direct observation of stepwise movement of a synthetic molecular transporter. , 2011, Nature nanotechnology.
[65] M. Perutz,et al. Structure Of Hæemoglobin: A Three-Dimensional Fourier Synthesis of Reduced Human Haemoglobin at 5.5 Å Resolution , 1963, Nature.
[66] Richard A. Muscat,et al. DNA nanotechnology from the test tube to the cell. , 2015, Nature nanotechnology.
[67] F. Crick,et al. Molecular structure of nucleic acids , 2004, JAMA.
[68] A. Turberfield,et al. A free-running DNA motor powered by a nicking enzyme. , 2005, Angewandte Chemie.
[69] Berend Smit,et al. Understanding Molecular Simulation , 2001 .
[70] Iain G. Johnston,et al. Modelling the self-assembly of virus capsids , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.
[71] Chris Thachuk,et al. Logically and Physically Reversible Natural Computing: A Tutorial , 2013, RC.
[72] Luca Cardelli,et al. Programmable chemical controllers made from DNA. , 2013, Nature nanotechnology.
[73] J. Willard Gibbs,et al. The scientific papers of J. Willard Gibbs , 1907 .
[74] Georg Seelig,et al. Molecular circuits for dynamic noise filtering , 2016, Proceedings of the National Academy of Sciences.
[75] O. Avery,et al. STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES , 1944, The Journal of experimental medicine.
[76] Luca Cardelli,et al. Abstractions for DNA circuit design , 2011, Journal of The Royal Society Interface.
[77] Jeremy L. England,et al. Statistical physics of self-replication. , 2012, The Journal of chemical physics.
[78] Udo Seifert,et al. Universal bounds on current fluctuations. , 2015, Physical review. E.
[79] O. J. E. Maroney. The (absence of a) relationship between thermodynamic and logical reversibility , 2004 .
[80] D. Frenkel,et al. Numerical evidence for nucleated self-assembly of DNA brick structures. , 2014, Physical review letters.
[81] Hong Qian,et al. Phosphorylation energy hypothesis: open chemical systems and their biological functions. , 2007, Annual review of physical chemistry.
[82] Christopher Jarzynski,et al. Maxwell's refrigerator: an exactly solvable model. , 2013, Physical review letters.
[83] K. Dill,et al. The protein folding problem. , 1993, Annual review of biophysics.
[84] Marta Kwiatkowska,et al. Modelling DNA origami self-assembly at the domain level. , 2015, The Journal of chemical physics.
[85] J. Keasling,et al. Synthetic and systems biology for microbial production of commodity chemicals , 2016, npj Systems Biology and Applications.
[86] J. Cardy. Scaling and Renormalization in Statistical Physics , 1996 .
[87] Yonggun Jun,et al. High-precision test of Landauer's principle in a feedback trap. , 2014, Physical review letters.
[88] N. Seeman,et al. Synthesis from DNA of a molecule with the connectivity of a cube , 1991, Nature.
[89] F. Crick,et al. Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.
[90] A. Turberfield,et al. DNA fuel for free-running nanomachines. , 2003, Physical review letters.
[91] Niles A. Pierce,et al. Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability , 2014, ACS nano.
[92] A. Turberfield,et al. Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. , 2008, Physical review letters.
[93] P. Schuster,et al. RNA folding at elementary step resolution. , 1999, RNA.
[94] Richard I. Kitney,et al. Synthetic Biology — A Primer , 2012 .
[95] James Ladyman,et al. The connection between logical and thermodynamic irreversibility , 2007 .
[96] E. Lutz,et al. Experimental verification of Landauer’s principle linking information and thermodynamics , 2012, Nature.
[97] P. Gräber,et al. Free Energy Transduction and Biochemical Cycle Kinetics. , 1990 .
[98] Isaac Meilijson,et al. Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model , 2011, PLoS Comput. Biol..
[99] T. Ouldridge,et al. Fundamental Costs in the Production and Destruction of Persistent Polymer Copies. , 2016, Physical review letters.
[100] T. Sulchek,et al. Enhanced stochastic fluctuations to measure steep adhesive energy landscapes , 2016, Proceedings of the National Academy of Sciences.
[101] David J. Schwab,et al. Landauer in the Age of Synthetic Biology: Energy Consumption and Information Processing in Biochemical Networks , 2015, bioRxiv.
[102] Amin Espah Borujeni,et al. Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism. , 2016, Journal of the American Chemical Society.
[103] C. J. Adkins. An introduction to thermal physics , 1987 .
[104] Masahito Ueda,et al. Minimal energy cost for thermodynamic information processing: measurement and information erasure. , 2008, Physical review letters.
[105] L. Christophorou. Science , 2018, Emerging Dynamics: Science, Energy, Society and Values.
[106] G. Seelig,et al. Enzyme-Free Nucleic Acid Logic Circuits , 2022 .
[107] Ho-Lin Chen,et al. Deterministic function computation with chemical reaction networks , 2012, Natural Computing.
[108] Charles H. Bennett,et al. The thermodynamics of computation—a review , 1982 .
[109] Noel A. Clark,et al. End-to-End Stacking and Liquid Crystal Condensation of 6– to 20–Base Pair DNA Duplexes , 2007, Science.
[110] J. Howard,et al. Mechanics of Motor Proteins and the Cytoskeleton , 2001 .
[111] Anne Condon,et al. Space and Energy Efficient Computation with DNA Strand Displacement Systems , 2012, DNA.
[112] J. Kendrew,et al. A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis , 1958, Nature.
[113] Stefan Hilbert,et al. Consistent thermostatistics forbids negative absolute temperatures , 2013, Nature Physics.
[114] Claude E. Shannon,et al. The mathematical theory of communication , 1950 .
[115] M. A. Cayless. Statistical Mechanics (2nd edn) , 1977 .
[116] S. Teichmann,et al. Principles of assembly reveal a periodic table of protein complexes , 2015, Science.
[117] Andre C. Barato,et al. Efficiency of cellular information processing , 2014, 1405.7241.
[118] J. SantaLucia,et al. The thermodynamics of DNA structural motifs. , 2004, Annual review of biophysics and biomolecular structure.
[119] G. J. Mulder. Ueber die Zusammensetzung einiger thierischen Substanzen , 1839 .
[120] Lauren K. Wolf,et al. Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison , 2006, Nucleic acids research.
[121] Arvind Murugan,et al. Undesired usage and the robust self-assembly of heterogeneous structures , 2015, Nature Communications.
[122] A. Turberfield,et al. Mechanism for a directional, processive, and reversible DNA motor. , 2009, Small.
[123] M. Tuckerman. Statistical Mechanics: Theory and Molecular Simulation , 2010 .
[124] T. G. Martin,et al. Rapid Folding of DNA into Nanoscale Shapes at Constant Temperature , 2012, Science.
[125] J. Yeomans,et al. Statistical mechanics of phase transitions , 1992 .
[126] Joseph M. Schaeffer,et al. On the biophysics and kinetics of toehold-mediated DNA strand displacement , 2013, Nucleic acids research.
[127] E. Cino,et al. Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations , 2012, Journal of chemical theory and computation.
[128] M. Woodside,et al. Reconstructing folding energy landscape profiles from nonequilibrium pulling curves with an inverse Weierstrass integral transform. , 2014, Physical review letters.
[129] G. Crooks. Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[130] P. Rothemund. Folding DNA to create nanoscale shapes and patterns , 2006, Nature.
[131] E. Xie,et al. Direct visualization of transient thermal response of a DNA origami. , 2012, Journal of the American Chemical Society.
[132] J. Davies,et al. Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.
[133] Lorenzo Rovigatti,et al. Coarse-graining DNA for simulations of DNA nanotechnology. , 2013, Physical chemistry chemical physics : PCCP.
[134] F. J. Luque,et al. Theoretical methods for the simulation of nucleic acids. , 2003, Chemical Society reviews.
[135] Russell P. Goodman,et al. Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication , 2005, Science.
[136] Liam P. Shaw,et al. DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization , 2015, Nucleic acids research.
[137] Matt A. King,et al. Three-Dimensional Structures Self-Assembled from DNA Bricks , 2012 .
[138] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[139] A. Turberfield,et al. Guiding the folding pathway of DNA origami , 2015, Nature.
[140] Ludwig Boltzmann,et al. Lectures on Gas Theory , 1964 .
[141] Pieter Rein ten Wolde,et al. Energy dissipation and noise correlations in biochemical sensing. , 2014, Physical review letters.
[142] Mikuláš Teich,et al. A documentary history of biochemistry, 1770-1940 , 1991 .
[143] R. Landauer,et al. Irreversibility and heat generation in the computing process , 1961, IBM J. Res. Dev..
[144] S. Wereley,et al. soft matter , 2019, Science.
[145] Gabriela Koreisová,et al. Scientific Papers , 1997, Nature.
[146] Journal of Chemical Physics , 1932, Nature.
[147] Shirley Dex,et al. JR 旅客販売総合システム(マルス)における運用及び管理について , 1991 .
[148] G. Seelig,et al. Dynamic DNA nanotechnology using strand-displacement reactions. , 2011, Nature chemistry.
[149] Lulu Qian,et al. Programmable disorder in random DNA tilings. , 2017, Nature nanotechnology.
[150] F. Sciortino,et al. Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link , 2012, 1204.0985.
[151] U. Seifert. Stochastic thermodynamics of single enzymes and molecular motors , 2010, The European physical journal. E, Soft matter.
[152] Luvena L. Ong,et al. Three-Dimensional Structures Self-Assembled from DNA Bricks , 2012, Science.
[153] P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .
[154] Paul Freemont,et al. Synthetic biology – the state of play , 2012, FEBS letters.
[155] H. Fraenkel-conrat,et al. RECONSTITUTION OF ACTIVE TOBACCO MOSAIC VIRUS FROM ITS INACTIVE PROTEIN AND NUCLEIC ACID COMPONENTS. , 1955, Proceedings of the National Academy of Sciences of the United States of America.
[156] Jing Pan,et al. A synthetic DNA motor that transports nanoparticles along carbon nanotubes. , 2014, Nature nanotechnology.
[157] Sadi Carnot,et al. Reflections on the Motive Power of Fire: And Other Papers on the Second Law of Thermodynamics , 2005 .
[158] Erik Winfree,et al. Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands , 2015, DNA.
[159] Dexter Kozen,et al. New , 2020, MFPS.
[160] Y. Mukaigawa,et al. Large Deviations Estimates for Some Non-local Equations I. Fast Decaying Kernels and Explicit Bounds , 2022 .
[161] J. Hopfield. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. , 1974, Proceedings of the National Academy of Sciences of the United States of America.
[162] David Soloveichik,et al. Probability 1 Computation with Chemical Reaction Networks , 2014, DNA.
[163] U. Alon. An introduction to systems biology : design principles of biological circuits , 2019 .
[164] Udo Seifert. Entropy production along a stochastic trajectory and an integral fluctuation theorem. , 2005, Physical review letters.
[165] Lulu Qian,et al. Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .
[166] Joris Paijmans,et al. A thermodynamically consistent model of the post-translational Kai circadian clock , 2016, PLoS Comput. Biol..