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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 |