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From Thermodynamics of Computation
Author name | Source name | Year | Keyword | |
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An efficient 10GBASE-T ethernet LDPC decoder design with low error floors | Zhengya Zhang Venkat Anantharam Martin J. Wainwright Borivoje Nikolić | IEEE Journal of Solid-State Circuits | 2010 | Error floors Iterative decoder architecture Low-density parity-check (LDPC) code Message-passing decoding Post-processing |
Minimal energy requirements in communication | Rolf Landauer | Science | 1996 | |
Engineering aspects of enzymatic signal transduction: Photoreceptors in the retina | Peter B. Detwiler Sharad Ramanathan Anirvan Sengupta Boris I. Shraiman | Biophysical Journal | 2000 | |
Age-related alterations in the modular organization of structural cortical network by using cortical thickness from MRI | Zhang J. Chen Yong He Pedro Rosa-Neto Gaolang Gong Alan C. Evans | NeuroImage | 2011 | |
Cerebellar LTD and Pattern Recognition by Purkinje Cells | Volker Steuber Wolfgang Mittmann Freek E. Hoebeek R. Angus Silver Chris I. De Zeeuw Michael Häusser Erik De Schutter | Neuron | 2007 | MOLNEURO SYSBIO SYSNEURO |
Experimental test of the fluctuation theorem for a driven two-level system with time-dependent rates | S. Schuler T. Speck C. Tietz J. Wrachtrup Udo Seifert | Physical Review Letters | 2005 | |
Targeting olfaction | Peter Mombaerts | Current Opinion in Neurobiology | 1996 | |
Genetic networks: Small numbers of big molecules | Nina Fedoroff Walter Fontana | Science | 2002 | |
Does replication‐induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli? | Purnananda Guptasarma | BioEssays | 1995 | |
Diffusion of transcription factors can drastically enhance the noise in gene expression | Jeroen S. Van Zon Marco J. Morelli Sorin Tǎnase-Nicola Pieter Rein ten Wolde | Biophysical Journal | 2006 | |
Mutual information between input and output trajectories of biochemical networks | Filipe Tostevin Pieter Rein ten Wolde | Physical Review Letters | 2009 | |
Stochastic thermodynamics of chemical reaction networks | Tim Schmiedl Udo Seifert | Journal of Chemical Physics | 2007 | |
Thermodynamics of prediction | Susanne Still David A. Sivak Anthony J. Bell Gavin Crooks | Physical Review Letters | 2012 | |
The Stokes efficiency for molecular motors and its applications | Hongyun Wang G. Oster | Europhysics Letters | 2002 | |
Fifty years of the VSEPR model | R. J. Gillespie | Coordination Chemistry Reviews | 2008 | LCP model: Lone pairs Molecular geometry VSEPR model |
Asymmetric division of Drosophila male germline stem cell shows asymmetric histone distribution | Vuong Tran Cindy Lim Jing Xie Xin Chen | Science | 2012 | |
A stochastic-based FPGA controller for an induction motor drive with integrated neural network algorithms | Da Zhang Hui Li | IEEE Transactions on Industrial Electronics | 2008 | Antiwindup proportional-integral (PI) controller Field-programmable gate array (FPGA) Induction motor drive Motor drive control Neural network (NN) algorithms Stochastic theory Very high speed integrated circuit (VHSIC) hardware description language (VHDL) |
Principles underlying mammalian neocortical scaling | Mark A. Changizi | Biological Cybernetics | 2001 | |
Wiring economy and volume exclusion determine neuronal placement in the Drosophila brain | Marta Rivera-Alba Shiv N. Vitaladevuni Yuriy Mischenko Zhiyuan Lu Shin Ya Takemura Lou Scheffer Ian A. Meinertzhagen Dmitri B. Chklovskii Gonzalo G. De Polavieja | Current Biology | 2011 | |
Steady state thermodynamics | Y Oono Paniconi M 1998 | Theor. Phys. Suppl | 2006 | Fluctuation Nonequilibrium steady state Thermodynamics |
A fluctuation theorem for currents and non-linear response coefficients | David Andrieux Pierre Gaspard | Journal of Statistical Mechanics: Theory and Experiment | 2007 | Current fluctuations Exact results Stationary states (theory) |
Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics | Hao Ge Min Qian Hong Qian | Physics Reports | 2012 | Bistability Enzyme kinetics Fluctuating enzyme Gene regulatory network Kinetic proofreading Signaling network Zeroth-order ultrasensitivity |
Universal features in the energetics of symmetry breaking | É Roldán I. A. Martínez J. M.R. Parrondo D. Petrov | Nature Physics | 2014 | |
Multivariate information transmission | William J. McGill | IRE Professional Group on Information Theory | 1954 | |
Patterns and mechanisms of Ancestral Histone protein inheritance in Budding yeast | Marta Radman-Livaja Kitty F. Verzijlbergen Assaf Weiner Tibor van Welsem Nir Friedman Oliver J. Rando Fred van Leeuwen | PLoS Biology | 2011 | |
Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements | Amar Nath Gupta Abhilash Vincent Krishna Neupane Hao Yu Feng Wang Michael T. Woodside | Nature Physics | 2011 | |
Histone H3 tail clipping regulates gene expression | Helena Santos-Rosa Antonis Kirmizis Christopher Nelson Till Bartke Nehme Saksouk Jacques Cote Tony Kouzarides | Nature Structural and Molecular Biology | 2009 | |
Application-level correctness and its impact on fault tolerance | Xuanhua Li Donald Yeung | Proceedings - International Symposium on High-Performance Computer Architecture | 2007 | |
Maxwell's demon assisted thermodynamic cycle in superconducting quantum circuits | H. T. Quan Y. D. Wang Yu Xi Liu C. P. Sun Franco Nori | Physical Review Letters | 2006 | |
Specific subtypes of cortical GABA interneurons contribute to the neurovascular coupling response to basal forebrain stimulation | Ara Kocharyan Priscilla Fernandes Xin Kang Tong Elvire Vaucher Edith Hamel | Journal of Cerebral Blood Flow and Metabolism | 2008 | Cerebral blood vessel Cholinergic lesion Cortical interneuron Hemodynamic response Inhibitory interneuron Microvessel |
Stochastic signal processing and transduction in chemotactic response of eukaryotic cells | Masahiro Ueda Tatsuo Shibata | Biophysical Journal | 2007 | |
Grid cells generate an analog error-correcting code for singularly precise neural computation | Sameet Sreenivasan Ila Fiete | Nature Neuroscience | 2011 | |
Cerebellar Golgi cells in the rat: Receptive fields and timing of responses to facial stimulation | Bart P. Vos Antonia Volny-Luraghi Erik De Schutter | European Journal of Neuroscience | 1999 | Cerebellum Inhibitory interneurons Mossy fibre Parallel fibre Somatosensory system Trigeminal stimulation |
Efficiency of autonomous soft nanomachines at maximum power | Udo Seifert | Physical Review Letters | 2011 | |
Feedback control in a collective flashing ratchet | Francisco J. Cao Luis Dinis Juan M.R. Parrondo | Physical Review Letters | 2004 | |
A new notation for quantum mechanics | P. A.M. Dirac | Mathematical Proceedings of the Cambridge Philosophical Society | 1939 | |
Systematic errors in free energy perturbation calculations due to a finite sample of configuration space: Sample-size hysteresis | Robert H. Wood Wolfgang C.F. Mühlbauer Peter T. Thompson | Journal of Physical Chemistry | 1991 | |
The chromatin code of fungal secondary metabolite gene clusters | Agnieszka Gacek Joseph Strauss | Applied Microbiology and Biotechnology | 2012 | Aspergillus Chromatin Histone modifications Secondary metabolism |
Classical and quantum limitations on energy consumption in computation | K. K. Likharev | International Journal of Theoretical Physics | 1982 | |
Delayed stochastic decoding of LDPC codes | Ali Naderi Shie Mannor Mohamad Sawan Warren J. Gross | IEEE Transactions on Signal Processing | 2011 | Delayed stochastic decoding iterative decoding low-density parity-check code stochastic decoding |
Relationship between subsistence and age at weaning in "preindustrial" societies | Daniel W. Sellen Diana B. Smay | Human Nature | 2001 | Agriculture Breastfeeding Childcare Comparative method Cross-cultural studies Cultural evolution Horticulture Hunter-gatherers Pastoralists Weanling's dilemma Women's work |
Extracting work from a single heat bath through feedback | D. Abreu Udo Seifert | EPL | 2011 | |
Calcium, the two-faced messenger of olfactory transduction and adaptation | Hugh R. Matthews Johannes Reisert | Current Opinion in Neurobiology | 2003 | |
Calcium signalling and regulation in olfactory neurons | Anna Menini | Current Opinion in Neurobiology | 1999 | |
Experimental Verification of a Modified Fluctuation-Dissipation Relation for a Micron-Sized Particle in a Nonequilibrium Steady State | J. R. Gomez-Solano A. Petrosyan S. Ciliberto R. Chetrite K. Gawȩdzki | Physical Review Letters | 2009 | |
Programmable energy landscapes for kinetic control of DNA strand displacement | Thomas E. Ouldridge Jonathan Bath Andrew J. Turberfield Robert R.F. Machinek Natalie E.C. Haley | Nature Communications | 2014 | |
Stochasticity of gene products from transcriptional pulsing | Srividya Iyer-Biswas F. Hayot C. Jayaprakash | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2009 | |
Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints | Anirikh Chakrabarti Ljubisa Miskovic Keng Cher Soh Vassily Hatzimanikatis | Biotechnology Journal | 2013 | Elasticity Mass action Saturation Stability Thermodynamics |
Chemical kinetics is turing universal | Marcelo O. Magnasco | Physical Review Letters | 1997 | |
Local potential connectivity in cat primary visual cortex | Armen Stepanyants Judith A. Hirsch Luis M. Martinez Zoltán F. Kisvárday Alex S. Ferecskó Dmitri B. Chklovskii | Cerebral Cortex | 2008 | Excitatory Inhibitory Interlaminar connectivity Morphology Neurogeometry |
Work fluctuations for a Brownian particle between two thermostats | Paolo Visco | Journal of Statistical Mechanics: Theory and Experiment | 2006 | Stochastic particle dynamics (theory) |
The Berry phase and the pump flux in stochastic chemical kinetics | N. A. Sinitsyn I. Nemenman | EPL | 2007 | |
Observable dependence of fluctuation-dissipation relations and effective temperatures | Suzanne Fielding Peter Sollich | Physical Review Letters | 2002 | |
Efficiency of cellular information processing | Andre C. Barato David Hartich Udo Seifert | New Journal of Physics | 2014 | cellular sensing nonequilibrium processes thermodynamics and information |
Fuzzy Memoization for Floating-Point Multimedia Applications | Carlos Alvarez Jesús Corbal Mateo Valero | IEEE Transactions on Computers | 2005 | Low-power design real-time and embedded systems special-purpose and application-based systems |
Methods for quantifying the informational structure of sensory and motor data | Max Lungarella Teresa Pegors Daniel Bulwinkle Olaf Sporns | Neuroinformatics | 2005 | Embodiment Information self-structuring Sensorimotor coordination |
What can spontaneous fluctuations of the blood oxygenationlevel-dependent signal tell us about psychiatric disorders? | Alex Fornito Edward T. Bullmore | Current Opinion in Psychiatry | 2010 | Connectivity Default mode Endogenous Networks Oscillations |
Global and regional brain metabolic scaling and its functional consequences | Jan Karbowski | BMC Biology | 2007 | |
Predictive information and explorative behavior of autonomous robots | N. Ay N. Bertschinger R. Der F. Güttler E. Olbrich | European Physical Journal B | 2008 | |
Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis | Aaron Fluitt Elsje Pienaar Hendrik Viljoen | Computational Biology and Chemistry | 2007 | Mistranslation frequencies Ribosome kinetics Translation tRNA availability |
Maxwell's demon and quantum-dot cellular automata | John Timler Craig S. Lent | Journal of Applied Physics | 2003 | |
Single-ensemble nonequilibrium path-sampling estimates of free energy differences | F. Marty Ytreberg Daniel M. Zuckerman | Journal of Chemical Physics | 2004 | |
Logic gates and antisense DNA devices operating on a translator nucleic acid scaffold | Bella Shlyahovsky Yang Li Oleg Lioubashevski Johann Elbaz Itamar Willner | ACS Nano | 2009 | Aptamer DNA DNAzyme Logic gate Nanomedicine Thrombin |
The synthesis of robust polynomial arithmetic with stochastic logic | Weikang Qian Marc D. Riedel | Proceedings - Design Automation Conference | 2008 | Polynomial arithmetic Probabilistic logic Stochastic logic |
Stoichiometric network theory for nonequilibrium biochemical systems | Hong Qian Daniel A. Beard Shou Dan Liang | European Journal of Biochemistry | 2003 | Biochemical network Chemical potential Flux Nonequilibrium thermodynamics Steady-state |
Sensory-Evoked Intrinsic Optical Signals in the Olfactory Bulb Are Coupled to Glutamate Release and Uptake | Hirac Gurden Naoshige Uchida Zachary F. Mainen | Neuron | 2006 | MOLNEURO SIGNALING SYSNEURO |
Effects of reservoir squeezing on quantum systems and work extraction | X. L. Huang Tao Wang X. X. Yi | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2012 | |
A quantitative estimation of the global translational activity in logarithmically growing yeast cells | Tobias von der Haar | BMC Systems Biology | 2008 | |
The Value of Information for Populations in Varying Environments | Olivier Rivoire Stanislas Leibler | Journal of Statistical Physics | 2011 | Branching processes Control Fitness Information Investment Population dynamics Regulation |
The berg-purcell limit revisited | Kazunari Kaizu Wiet De Ronde Joris Paijmans Koichi Takahashi Filipe Tostevin Pieter Rein ten Wolde | Biophysical Journal | 2014 | |
Stochastic thermodynamics of bipartite systems: Transfer entropy inequalities and a Maxwell's demon interpretation | D. Hartich A. C. Barato Udo Seifert | Journal of Statistical Mechanics: Theory and Experiment | 2014 | exact results |
The Effect of Phenobarbitone Anaesthesia on Blood Flow and Oxygen Consumption in the Rat Brain | Lorentz Nilsson Bo K. Siesjó | Acta Anaesthesiologica Scandinavica | 1975 | |
Effective temperature of red-blood-cell membrane fluctuations | Eyal Ben-Isaac Yongkeun Park Gabriel Popescu Frank L.H. Brown Nir S. Gov Yair Shokef | Physical Review Letters | 2011 | |
Measurement of stochastic entropy production | C. Tietz S. Schuler T. Speck J. Wrachtrup Udo Seifert | Physical Review Letters | 2006 | |
Heat generation required by information erasure | Kousuke Shizume | Physical Review E | 1995 | |
Dissipation-error tradeoff in proofreading | Charles H. Bennett | BioSystems | 1979 | |
New evidence for hominin carcass processing strategies at 1.5 Ma, Koobi Fora, Kenya | Briana L. Pobiner Michael J. Rogers Christopher M. Monahan John W.K. Harris | Journal of Human Evolution | 2008 | Bone modification Butchery Carnivory Cut mark Early Stone Age Oldowan Percussion mark |
Efficiency of molecular motors at maximum power | T. Schmiedl Udo Seifert | EPL | 2008 | |
Ueber die bewegende Kraft der Wärme und die Gesetze, welche sich daraus für die Wärmelehre selbst ableiten lassen | R. Clausius | Annalen der Physik | 1850 | |
The cell cycle switch computes approximate majority | Luca Cardelli Attila Csikász-Nagy | Scientific Reports | 2012 | |
A master equation description of local fluctuations | M. Malek-Mansour G. Nicolis | Journal of Statistical Physics | 1975 | Fluctuations master equations nonequilibrium thermodynamics nonlinear systems stochastic processes |
Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling switch | Hong Qian Timothy C. Reluga | Physical Review Letters | 2005 | |
Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality | Ioan Kosztin Bogdan Barz Lorant Janosi | Journal of Chemical Physics | 2006 | |
Modelling the development of cortical systems networks | Marcus Kaiser Claus C. Hilgetag | Neurocomputing | 2004 | Cortical connectivity Cortical systems development Network growth Optimal wiring |
Reaching optimal efficiencies using nanosized photoelectric devices | B. Rutten B. Cleuren Massimiliano Esposito | Physical Review B - Condensed Matter and Materials Physics | 2009 | |
Bidirectional single-electron counting and the fluctuation theorem | Y. Utsumi D. S. Golubev M. Marthaler K. Saito T. Fujisawa Gerd Schön | Physical Review B - Condensed Matter and Materials Physics | 2010 | |
Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensation | Hong Qian | Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics | 2002 | |
On rank vs. communication complexity | Noam Nisan Avi Wigderson | Combinatorica | 1995 | Mathematics Subject Classification (1991): 68Q05 68R05 05C50 |
Work and heat probability distribution of an optically driven Brownian particle: Theory and experiments | A. Imparato L. Peliti G. Pesce G. Rusciano A. Sasso | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2007 | |
Covariation of residues in the homeodomain sequence family | Neil D. Clarke | Protein Science | 1995 | covariation evolution homeodomains sequences structure‐function |
Engineering complex riboswitch regulation by dual genetic selection | Vandana Sharma Yoko Nomura Yohei Yokobayashi | Journal of the American Chemical Society | 2008 | |
Unifying three perspectives on information processing in stochastic thermodynamics | A. C. Barato Udo Seifert | Physical Review Letters | 2014 | |
Relationships between gene expression and brain wiring in the adult rodent brain | Leon French Paul Pavlidis | PLoS Computational Biology | 2011 | |
Off-equilibrium generalization of the fluctuation dissipation theorem for Ising spins and measurement of the linear response function | Eugenio Lippiello Federico Corberi Marco Zannetti | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2005 | |
Dissipation and lag in irreversible processes | S. Vaikuntanathan C. Jarzynski | EPL | 2009 | |
The minimal work cost of information processing | Philippe Faist Frédéric Dupuis Jonathan Oppenheim Renato Renner | Nature Communications | 2015 | |
Information thermodynamics on causal networks | Sosuke Ito Takahiro Sagawa | Physical Review Letters | 2013 | |
Dietary constraints on encephalization in primates | Jennifer L. Fish Charles A. Lockwood | American Journal of Physical Anthropology | 2003 | Brain size Comparative methods Expensive tissue hypothesis Independent contrasts |
Receptive fields and functional architecture in the retina | Vijay Balasubramanian Peter Sterling | Journal of Physiology | 2009 | |
Unattainability of Carnot efficiency in the Brownian heat engine | Tsuyoshi Hondou Ken Sekimoto | Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics | 2000 | |
Relative entropy: Free energy associated with equilibrium fluctuations and nonequilibrium deviations | Hong Qian | Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics | 2001 | |
Nitric oxide and adenosine mediate vasodilation during functional activation in cerebellar cortex | J. Li C. Iadecola | Neuropharmacology | 1994 | GABA Parallel fibers adenosine cerebellar blood flow glutamate nitric oxide nitro-l-arginine vasodilation |
Thermodynamic reversibility in feedback processes | Jordan M. Horowitz Juan M.R. Parrondo | EPL | 2011 | |
Two subtypes of non-pyramidal cells in rat hippocampal formation identified by intracellular recording and HRP injection | Yasuo Kawaguchi Kiyoshi Hama | Brain Research | 1987 | Dentate gyrus Fast spiking cell GABAergic neuron Hippocampus Intracellular injection of HRP Non-pyramidal cell Slice preparation |
Maxwell's refrigerator: An exactly solvable model | Dibyendu Mandal H. T. Quan Christopher Jarzynski | Physical Review Letters | 2013 | |
Exploiting correlation in stochastic circuit design | Armin Alaghi John P. Hayes | 2013 IEEE 31st International Conference on Computer Design, ICCD 2013 | 2013 | Stochastic computing low-power design signal correlation stochastic circuit design |
Compendium of the Foundations of Classical Statistical Physics | Jos Uffink | Philosophy of Physics | 2007 | |
Optimized free energies from bidirectional single-molecule force spectroscopy | David D.L. Minh Artur B. Adib | Physical Review Letters | 2008 | |
Kinetics of reversible diffusion influenced reactions: The self-consistent relaxation time approximation | Irina V. Gopich Attila Szabo | Journal of Chemical Physics | 2002 | |
Maximum likelihood and the single receptor | Robert G. Endres Ned S. Wingreen | Physical Review Letters | 2009 | |
Thermodynamics of genuine nonequilibrium states under feedback control | David Abreu Udo Seifert | Physical Review Letters | 2012 | |
Digital genetics: Unravelling the genetic basis of evolution | Christoph Adami | Nature Reviews Genetics | 2006 | |
ERSA: Error resilient system architecture for probabilistic applications | Hyungmin Cho Larkhoon Leem Subhasish Mitra | IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems | 2012 | Error resilience hardware errors probabilistic applications reliability robust systems |
Fluctuation theorem for transport in mesoscopic systems | David Andrieux Pierre Gaspard | Journal of Statistical Mechanics: Theory and Experiment | 2006 | Current fluctuations Exact results Stationary states (theory) |
Fluctuation theorems for quantum processes | Tameem Albash Daniel A. Lidar Milad Marvian Paolo Zanardi | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2013 | |
An update on the nonequilibrium linear response | M. Baiesi C. Maes | New Journal of Physics | 2013 | |
Fluctuation theorem for a single enzym or molecular motor | Udo Seifert | Europhysics Letters | 2005 | |
On a hypothetical generational relationship between HCN and constituents of the reductive citric acid cycle | Albert Eschenmoser | Chemistry and Biodiversity | 2007 | |
Perfect and near-perfect adaptation in a model of bacterial chemotaxis | Bernardo A. Mello Yuhai Tu | Biophysical Journal | 2003 | |
Non-equilibrium work relations | Jorge Kurchan | Journal of Statistical Mechanics: Theory and Experiment | 2007 | Current fluctuations Stochastic particle dynamics (theory) Transport processes/heat transfer (theory) |
Stochastic thermodynamics of single enzymes and molecular motors | Udo Seifert | European Physical Journal E | 2011 | |
Exorcist XIV: The wrath of Maxwell's Demon. Part II. From Szilard to Landauer and beyond | John Earman John D. Norton | Studies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics | 1999 | |
Thermodynamic universality of quantum Carnot engines | Bartłomiej Gardas Sebastian Deffner | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2015 | |
Nonequilibrium work fluctuations for oscillators in non-Markovian baths | Trieu Mai Abhishek Dhar | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2007 | |
Experimental study of the fluctuation theorem in a nonequilibrium steady state | G. M. Wang J. C. Reid D. M. Carberry D. R.M. Williams E. M. Sevick Denis J. Evans | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2005 | |
Realization of a feedback controlled flashing ratchet | Benjamin J. Lopez Nathan J. Kuwada Erin M. Craig Brian R. Long Heiner Linke | Physical Review Letters | 2008 | |
Nonequilibrium fluctuations and mechanochemical couplings of a molecular motor | A. W.C. Lau D. Lacoste K. Mallick | Physical Review Letters | 2007 | |
Mapping out-of-equilibrium into equilibrium in one-dimensional transport models | Julien Tailleur Jorge Kurchan Vivien Lecomte | Journal of Physics A: Mathematical and Theoretical | 2008 | |
Efficient turing-universal computation with DNA polymers | Lulu Qian David Soloveichik Erik Winfree | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | 2011 | |
Physical Responses of Bacterial Chemoreceptors | Ady Vaknin Howard C. Berg | Journal of Molecular Biology | 2007 | chemotaxis fluorescence polarization fluorescence resonance energy transfer membrane proteins receptors |
Imitating chemical motors with optimal information motors | Jordan M. Horowitz Takahiro Sagawa Juan M.R. Parrondo | Physical Review Letters | 2013 | |
An autonomous and reversible Maxwell's demon | Udo Seifert A. C. Barato | EPL | 2013 | |
The statistical neuroanatomy of frontal networks in the macaque | Bruno B. Averbeck Moonsang Seo | PLoS Computational Biology | 2008 | |
Motor-Driven Dynamics in Actin-Myosin Networks | Loïc Le Goff François Amblard Eric M. Furst | Physical Review Letters | 2002 | |
Heat conduction in a three dimensional anharmonic crystal | Keiji Saito Abhishek Dhar | Physical Review Letters | 2010 | |
Exploring the thermodynamic limits of computation in integrated systems: Magnetic memory, nanomagnetic logic, and the landauer limit | Brian Lambson David Carlton Jeffrey Bokor | Physical Review Letters | 2011 | |
Thermodynamics of feedback controlled systems | F. J. Cao M. Feito | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2009 | |
Covalent modifications of histones during mitosis and meiosis | Dazhong Xu Jingxiang Bai Qing Duan Max Costa Wei Dai | Cell Cycle | 2009 | Cell cycle Covalent modifications Histone Meiosis Mitosis |
Deterministic function computation with chemical reaction networks | Ho Lin Chen David Doty David Soloveichik | Natural Computing | 2014 | Distributed computing Molecular programming Population protocols Semilinear functions Stochastic chemical kinetics |
Alternative splicing in the nervous system: An emerging source of diversity and regulation | Christopher J. Lee Kris Irizarry | Biological Psychiatry | 2003 | Alternative splicing Genomics Receptors mRNA |
Length of time's arrow | Edward H. Feng Gavin Crooks | Physical Review Letters | 2008 | |
Entropy production in full phase space for continuous stochastic dynamics | Richard E. Spinney Ian J. Ford | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2012 | |
Experimental test of the Gallavotti-Cohen fluctuation theorem in turbulent flows | S. Ciliberto N. Garnier S. Hernandez C. Lacpatia J. F. Pinton G. Ruiz Chavarria | Physica A: Statistical Mechanics and its Applications | 2004 | Fluctuation theorem Statistical mechanics Turbulence |
Deterministic Function Computation with Chemical Reaction Network | Ho Lin Chen David Doty David Soloveichik | Natural Computing | 2014 | Distributed computing Molecular programming Population protocols Semilinear functions Stochastic chemical kinetics |
An introduction to population protocols | James Aspnes Eric Ruppert | Middleware for Network Eccentric and Mobile Applications | 2009 | |
Integrated information increases with fitness in the evolution of animats | Jeffrey A. Edlund Nicolas Chaumont Arend Hintze Christof Koch Giulio Tononi Christoph Adami | PLoS Computational Biology | 2011 | |
Thermodynamic constraints on kinetic proofreading in biosynthetic pathways | M. Ehrenberg C. Blomberg | Biophysical Journal | 1980 | |
Generalized detailed fluctuation theorem under nonequilibrium feedback control | M. Ponmurugan | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2010 | |
Optimal protocols for minimal work processes in underdamped stochastic thermodynamics | Alex Gomez-Marin Tim Schmiedl Udo Seifert | Journal of Chemical Physics | 2008 | |
Refined Second Law of Thermodynamics for Fast Random Processes | Erik Aurell Krzysztof Gawȩdzki Carlos Mejía-Monasterio Roya Mohayaee Paolo Muratore-Ginanneschi | Journal of Statistical Physics | 2012 | Landauer principle Monge-Kantorovich optimal mass transport Second Law of Thermodynamics |
Stochastic thermodynamics for Maxwell demon feedbacks | Massimiliano Esposito Gernot Schaller | EPL | 2012 | |
A simple rule for axon outgrowth and synaptic competition generates realistic connection lengths and filling fractions | Marcus Kaiser Claus C. Hilgetag Arjen Van Ooyen | Cerebral Cortex | 2009 | Axon growth Cortical networks Filling fraction Neural competition Neural networks |
Escorted free energy simulations: Improving convergence by reducing dissipation | Suriyanarayanan Vaikuntanathan Christopher Jarzynski | Physical Review Letters | 2008 | |
Finite-time thermodynamics for a single-level quantum dot | R. Kawai K. Lindenberg C. Van Den Broeck Massimiliano Esposito | EPL | 2010 | |
Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard-sphere liquid | Huan Xiang Zhou Attila Szabo | Journal of Chemical Physics | 1991 | |
Second-law-like inequalities with information and their interpretations | Jordan M. Horowitz Henrik Sandberg | New Journal of Physics | 2014 | feedback information theory nonequilibrium thermodynamics optimal control theory |
The role of glial glutamate transporters in maintaining the independent operation of juvenile mouse cerebellar parallel fibre synapses | Païkan Marcaggi Daniela Billups David Attwell | Journal of Physiology | 2003 | |
Invisibility in non-Hermitian tight-binding lattices | Stefano Longhi | Physical Review A - Atomic, Molecular, and Optical Physics | 2010 | |
Pumped biochemical reactions, nonequilibrium circulation, and stochastic resonance | Hong Qian Min Qian | Physical Review Letters | 2000 | |
Efficiency at maximum power output of linear irreversible Carnot-like heat engines | Yang Wang Z. C. Tu | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2012 | |
Stochastic thermodynamics and sustainable efficiency in work production | B. Gaveau M. Moreau L. S. Schulman | Physical Review Letters | 2010 | |
Optimal protocols and optimal transport in stochastic thermodynamics | Erik Aurell Carlos Mejía-Monasterio Paolo Muratore-Ginanneschi | Physical Review Letters | 2011 | |
Analog Computation by DNA Strand Displacement Circuits | Tianqi Song Sudhanshu Garg Reem Mokhtar Hieu Bui John Reif | ACS Synthetic Biology | 2016 | DNA computing DNA nanoscience DNA nanotechnology analog computation molecular programming self-assembly |
Convergence in the olfactory system: quantitative aspects of odour sensitivity | Wim van Drongelen Andre Holley Kjell B. Døving | Journal of Theoretical Biology | 1978 | |
The stochastic pump effect and geometric phases in dissipative and stochastic systems | N. A. Sinitsyn | Journal of Physics A: Mathematical and Theoretical | 2009 | |
Fluctuation theorems for a molecular refrigerator | Kyung Hyuk Kim Hong Qian | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2007 | |
Energy dissipation and violation of the fluctuation-response relation in nonequilibrium Langevin systems | Takahiro Harada Shin Ichi Sasa | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2006 | |
Flight of the FINCH through the java wilderness | Michael Orlov Moshe Sipper | IEEE Transactions on Evolutionary Computation | 2011 | Automatic programming Java bytecode genetic programming (GP) software evolution |
Thermodynamic Costs of Information Processing in Sensory Adaptation | Pablo Sartori Léo Granger Chiu Fan Lee Jordan M. Horowitz | PLoS Computational Biology | 2014 | |
Geometric effects on complex network structure in the cortex | J. A. Henderson P. A. Robinson | Physical Review Letters | 2011 | |
Role of Astrocytes in Matching Blood Flow to Neuronal Activity | Danica Jakovcevic David R. Harder | Current Topics in Developmental Biology | 2007 | |
Time-dependent pseudo-Hermitian Hamiltonians defining a unitary quantum system and uniqueness of the metric operator | Ali Mostafazadeh | Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | 2007 | Geometric phase Inner product Metric operator PT-symmetry Pseudo-Hermitian Time-dependent Hamiltonian Unitary |
Symmetries of generating functionals of Langevin processes with colored multiplicative noise | Camille Aron Giulio Biroli Leticia F. Cugliandolo | Journal of Statistical Mechanics: Theory and Experiment | 2010 | Fluctuations (theory) Rigorous results in statistical mechanics Stochastic particle dynamics (theory) Stochastic processes (theory) |
Experimental demonstration of a latch in clocked quantum-dot cellular automata | Alexei O. Orlov Ravi K. Kummamuru Rajagopal Ramasubramaniam Geza Toth Craig S. Lent Gary H. Bernstein Gregory L. Snider | Applied Physics Letters | 2001 | |
Chromatin and epigenetic regulation of pre-mrna processing | Seth J. Brown Peter Stoilov Yi Xing | Human Molecular Genetics | 2012 | |
Cooperativity, sensitivity, and noise in biochemical signaling | William Bialek Sima Setayeshgar | Physical Review Letters | 2008 | |
Use of mutual information to decrease entropy: Implications for the second law of thermodynamics | Seth Lloyd | Physical Review A | 1989 | |
Efficient behavior of small-world networks | Vito Latora Massimo Marchiori | Physical Review Letters | 2001 | |
Feynman's ratchet optimization: Maximum power and maximum efficiency regimes | S. Velasco A. Medina A. Calvo Hernandez J. M.M. Roco | Journal of Physics D: Applied Physics | 2001 | |
Nonlinear fluctuation-dissipation relations and stochastic models in nonequilibrium thermodynamics. II. Kinetic potential and variational principles for nonlinear irreversible processes | G. N. Bochkov Yu E. Kuzovlev | Physica A: Statistical Mechanics and its Applications | 1981 | |
Pseudo-random generators for all hardnesses | Christopher Umans | Journal of Computer and System Sciences | 2003 | Complexity classes Derandomization Low-degree extension Pseudo-random number generators |
Fluctuation theorem for partially masked nonequilibrium dynamics | Naoto Shiraishi Takahiro Sagawa | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2015 | |
The Jarzynski relation, fluctuation theorems, and stochastic thermodynamics for non-Markovian processes | T. Speck Udo Seifert | Journal of Statistical Mechanics: Theory and Experiment | 2007 | Nonequilibrium fluctuations in small systems Stochastic processes (theory) |
Steady-state fluctuation relations for systems driven by an external random force | J. R. Gomez-Solano L. Bellon A. Petrosyan S. Ciliberto | EPL | 2010 | |
The mechanics and fluctuation spectrum of active gels | Alex J. Levine F. C. MacKintosh | Journal of Physical Chemistry B | 2009 | |
Thermopower with broken time-reversal symmetry | Keiji Saito Giuliano Benenti Giulio Casati Tomaž Prosen | Physical Review B - Condensed Matter and Materials Physics | 2011 | |
Second law of thermodynamics and quantum feedback control: Maxwell’s demon with weak measurements | Kurt Jacobs | Physical Review A - Atomic, Molecular, and Optical Physics | 2009 | |
Stochastic energetics of non-uniform temperature systems | Miki Matsuo Shin Ichi Sasa | Physica A: Statistical Mechanics and its Applications | 2000 | |
Unbalanced expanders and randomness extractors from parvaresh-vardy codes | Venkatesan Guruswami Christopher Umans Salil Vadhan | Proceedings of the Annual IEEE Conference on Computational Complexity | 2007 | Expander graphs Randomness extractors |
Reversible space equals deterministic space | Klaus Jörn Lange Pierre McKenzie Alain Tapp | Journal of Computer and System Sciences | 2000 | |
Qubit thermometry for micromechanical resonators | Matteo Brunelli Stefano Olivares Matteo G.A. Paris | Physical Review A - Atomic, Molecular, and Optical Physics | 2011 | |
Unified treatment of the quantum fluctuation theorem and the Jarzynski equality in terms of microscopic reversibility | T. Monnai | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2005 | |
On the Relation between Gradient Flows and the Large-Deviation Principle, with Applications to Markov Chains and Diffusion | A. Mielke M. A. Peletier D. R.M. Renger | Potential Analysis | 2014 | Convex analysis Generalized gradient flows Large deviations Particle systems |
Tight coupling in thermal Brownian motors | A. Gomez-Marin J. M. Sancho | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2006 | |
Attractant- and Disulfide-Induced Conformational Changes in the Ligand Binding Domain of the Chemotaxis Aspartate Receptor: A 19F NMR Study | Mark A. Danielson Joseph J. Falke Hans Peter Biemann Daniel E. Koshland | Biochemistry | 1994 | |
Maxwell's demon in biochemical signal transduction with feedback loop | Sosuke Ito Takahiro Sagawa | Nature Communications | 2015 | |
Quantum Jarzynski-Sagawa-Ueda Relations | Yohei Morikuni Hal Tasaki | Journal of Statistical Physics | 2011 | Feedback Jarzynski relation Measurement Quantum system |
Heat engine driven by purely quantum information | Jung Jun Park Kang Hwan Kim Takahiro Sagawa Sang Wook Kim | Physical Review Letters | 2013 | |
Neuron-glia metabolic coupling and plasticity | Pierre J. Magistretti | Experimental Physiology | 2011 | |
Memory erasure in small systems | Raoul Dillenschneider Eric Lutz | Physical Review Letters | 2009 | |
Fluctuation theorems and the nonequilibrium thermodynamics of molecular motors | David Andrieux Pierre Gaspard | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2006 | |
BMI peak in infancy as a predictor for later BMI in the Uppsala Family Study | R. J. Silverwood B. L. De Stavola T. J. Cole D. A. Leon | International Journal of Obesity | 2009 | Body mass index Childhood obesity Growth Infancy |
Role of hidden slow degrees of freedom in the fluctuation theorem | J. Mehl B. Lander C. Bechinger V. Blickle Udo Seifert | Physical Review Letters | 2012 | |
A possible classification of nonequilibrium steady states | B. Schmittmann R. K.P. Zia | Journal of Physics A: Mathematical and General | 2006 | |
Fluctuation-dissipation theorems and entropy production in relaxational systems | Leticia F. Cugliandolo David S. Dean Jorge Kurchan | Physical Review Letters | 1997 | |
Computational design of nucleic acid feedback control circuits | Boyan Yordanov Jongmin Kim Rasmus L. Petersen Angelina Shudy Vishwesh V. Kulkarni Andrew Phillips | ACS Synthetic Biology | 2014 | DNA strand displacement DNA toolbox feedback control genelet molecular programming nucleic acid circuits |
Extinction in neutrally stable stochastic Lotka-Volterra models | Alexander Dobrinevski Erwin Frey | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2012 | |
Energy dissipation and noise correlations in biochemical sensing | Christopher C. Govern Pieter Rein ten Wolde | Physical Review Letters | 2014 | |
Nonequilibrium thermodynamics of stochastic systems with odd and even variables | Richard E. Spinney Ian J. Ford | Physical Review Letters | 2012 | |
Strand algebras for DNA computing | Luca Cardelli | Natural Computing | 2011 | DNA computing DNA strand displacement Process algebra |
Three-dimensional simulations of reversible bimolecular reactions: The simple target problem | A. V. Popov N. Agmon | Journal of Chemical Physics | 2001 | |
Sniffing and spatiotemporal coding in olfaction | John W. Scott | Chemical Senses | 2006 | Electroolfactogram Flow rate Odorant hydrophobicity Sorption |
Physiological evidence for dendrodendritic synaptic interactions in the rabbit's olfactory glomerulus | Gordon M. Shepherd | Brain Research | 1971 | |
Nonlinear response and fluctuation-dissipation relations | Eugenio Lippiello Federico Corberi Alessandro Sarracino Marco Zannetti | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2008 | |
Molecular kinetic analysis of a finite-time Carnot cycle | Y. Izumida K. Okuda | EPL | 2008 | |
Distribution of work in isothermal nonequilibrium processes | Thomas Speck Udo Seifert | Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics | 2004 | |
The adjustable nucleosome: An epigenetic signaling module | Bryan M. Turner | Trends in Genetics | 2012 | Chromatin Epigenetics Gene-environment interaction Histone modification Nuclear signaling Nucleosome |
A fluctuation theorem for non-equilibrium relaxational systems driven by external forces | Francesco Zamponi Federico Bonetto Leticia F. Cugliandolo Jorge Kurchan | Journal of Statistical Mechanics: Theory and Experiment | 2005 | Brownian motion Driven diffusive systems (theory) Fluctuations (theory) Slow dynamics and ageing (theory) |
Statistical mechanics of Monod-Wyman-Changeux (MWC) models | Sarah Marzen Hernan G. Garcia Rob Phillips | Journal of Molecular Biology | 2013 | Monod-Wyman-Changeux model allostery bacterial chemotaxis chromatin structure information theory |
Self-organization and entropy reduction in a living cell | Paul C.W. Davies Elisabeth Rieper Jack A. Tuszynski | BioSystems | 2013 | Entropy Genetic code Information theory Shannon information Thermodynamics |
Physics of Self-Organization and Evolution | Rainer Feistel Werner Ebeling | Physics of Self-Organization and Evolution | 2011 | |
Human neoteny revisited: The case of synaptic plasticity | Enric Bufill Jordi Agustí Rafael Blesa | American Journal of Human Biology | 2011 | |
Neurochemical organization of the macaque striate cortex: Correlation of cytochrome oxidase with Na+K+ATPase, NADPH-diaphorase, nitric oxide synthase, and N-methyl-D-aspartate receptor subunit 1 | M. Wong-Riley B. Anderson W. Liebl Z. Huang | Neuroscience | 1998 | Energy metabolism Excitatory neurochemicals Glutamate receptor Immunohistochemistry Impulse blockade Primary visual cortex |
Current, maximum power and optimized efficiency of a Brownian heat engine | Mesfin Asfaw Mulugeta Bekele | European Physical Journal B | 2004 | |
Probing molecular free energy landscapes by periodic loading | Oliver Braun Andreas Hanke Udo Seifert | Physical Review Letters | 2004 | |
Lower bounds on probabilistic linear decision trees | Marc Snir | Theoretical Computer Science | 1985 | |
Combinatorial displacement of DNA strands: Application to matrix multiplication and weighted sums | Anthony J. Genot Jonathan Bath Andrew J. Turberfield | Angewandte Chemie - International Edition | 2013 | DNA recognition DNA structures molecular computation nanotechnology strand displacement |
Generalization of the second law for a transition between nonequilibrium states | K. Takara H. H. Hasegawa D. J. Driebe | Physics Letters, Section A: General, Atomic and Solid State Physics | 2010 | |
Holevo's bound from a general quantum fluctuation theorem | Dvir Kafri Sebastian Deffner | Physical Review A - Atomic, Molecular, and Optical Physics | 2012 | |
An examination of the role of autocatalytic cycles in the chemistry of proposed primordial reactions | Donna G. Blackmond | Angewandte Chemie - International Edition | 2009 | Autocatalysis Autoinduction Ligand acceleration Prebiotic chemistry Systems chemistry |
Effective temperatures in driven systems: Static versus time-dependent relations | Corey S. O'Hern Andrea J. Liu Sidney R. Nagel | Physical Review Letters | 2004 | |
Receptor noise and directional sensing in eukaryotic chemotaxis | Wouter Jan Rappel Herbert Levine | Physical Review Letters | 2008 | |
Aerobic glycolysis in the primate brain: Reconsidering the implications for growth and maintenance | Amy L. Bauernfeind Sarah K. Barks Tetyana Duka Lawrence I. Grossman Patrick R. Hof Chet C. Sherwood | Brain Structure and Function | 2014 | Aerobic gycolysis Brain energetics Default mode network Evolution Oxidative phosphorylation |
Measurement of damping and temperature: Precision bounds in Gaussian dissipative channels | Alex Monras Fabrizio Illuminati | Physical Review A - Atomic, Molecular, and Optical Physics | 2011 | |
Stochastically driven single-level quantum dot: A nanoscale finite-time thermodynamic machine and its various operational modes | Massimiliano Esposito Niraj Kumar Katja Lindenberg Christian Van Den Broeck | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2012 | |
Irreversible dynamics of a massive intruder in dense granular fluids | A. Sarracino D. Villamaina G. Gradenigo A. Puglisi | EPL | 2010 | |
Limits of sensing temporal concentration changes by single cells | Thierry Mora Ned S. Wingreen | Physical Review Letters | 2010 | |
Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis | Silke Neumann Clinton H. Hansen Ned S. Wingreen Victor Sourjik | EMBO Journal | 2010 | FRET bacterial chemotaxis signal integration signal transduction transport |
Thermodynamic efficiency of information and heat flow | Armen E. Allahverdyan Dominik Janzing Guenter Mahler | Journal of Statistical Mechanics: Theory and Experiment | 2009 | Communication Source and channel coding Supply and information networks |
Large deviation function for entropy production in driven one-dimensional systems | Jakob Mehl Thomas Speck Udo Seifert | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2008 | |
Universal aspects of the chemomechanical coupling for molecular motors | Reinhard Lipowsky | Physical Review Letters | 2000 | |
Histone Segregation on Replicating Chromatin† | Vaughn Jackson Roger Chalkley | Biochemistry | 1985 | |
Histone Segregation on Replicating Chromatinâ | Vaughn Jackson Roger Chalkley | Biochemistry | 1985 | |
On thermodynamic interpretation of transfer entropy | Mikhail Prokopenko Joseph T. Lizier Don C. Price | Entropy | 2013 | Boltzmann's principle Causal effect Entropy production Information transfer Irreversibility Kullback-Leibler divergence Thermodynamic equilibrium Transfer entropy |
The connection between logical and thermodynamic irreversibility | James Ladyman Stuart Presnell Anthony J. Short Berry Groisman | Studies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics | 2007 | Computation Entropy Information Irreversibility Landauer's principle Thermodynamics |
Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction | Hong Qian | Biophysical Chemistry | 2003 | Biological signal transduction Kinetic analysis Thermodynamic |
Information-theoretic versus thermodynamic entropy production in autonomous sensory networks | A. C. Barato D. Hartich Udo Seifert | Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | 2013 | |
Generalization of the second law for a nonequilibrium initial state | H. H. Hasegawa J. Ishikawa K. Takara D. J. Driebe | Physics Letters, Section A: General, Atomic and Solid State Physics | 2010 | |
The selfish brain: Competition for energy resources | Achim Peters | American Journal of Human Biology | 2011 | |
The stochastic chemomechanics of the F1-ATPase molecular motor | P. Gaspard E. Gerritsma | Journal of Theoretical Biology | 2007 | Arrhenius kinetics F1-ATPase Mechanochemical coupling Molecular motor Stochastic process |