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An efficient 10GBASE-T ethernet LDPC decoder design with low error floorsZhengya Zhang
Venkat Anantharam
Martin J. Wainwright
Borivoje Nikolić
IEEE Journal of Solid-State Circuits2010Error floors
Iterative decoder architecture
Low-density parity-check (LDPC) code
Message-passing decoding
Post-processing
1153
Minimal energy requirements in communicationRolf LandauerScience19961151
Engineering aspects of enzymatic signal transduction: Photoreceptors in the retinaPeter B. Detwiler
Sharad Ramanathan
Anirvan Sengupta
Boris I. Shraiman
Biophysical Journal20001140
Age-related alterations in the modular organization of structural cortical network by using cortical thickness from MRIZhang J. Chen
Yong He
Pedro Rosa-Neto
Gaolang Gong
Alan C. Evans
NeuroImage20111140
Cerebellar LTD and Pattern Recognition by Purkinje CellsVolker Steuber
Wolfgang Mittmann
Freek E. Hoebeek
R. Angus Silver
Chris I. De Zeeuw
Michael Häusser
Erik De Schutter
Neuron2007MOLNEURO
SYSBIO
SYSNEURO
1130
Experimental test of the fluctuation theorem for a driven two-level system with time-dependent ratesS. Schuler
T. Speck
C. Tietz
J. Wrachtrup
Udo Seifert
Physical Review Letters20051131
Targeting olfactionPeter MombaertsCurrent Opinion in Neurobiology19961120
Genetic networks: Small numbers of big moleculesNina Fedoroff
Walter Fontana
Science20021112
Does replication‐induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli?Purnananda GuptasarmaBioEssays19951110
Diffusion of transcription factors can drastically enhance the noise in gene expressionJeroen S. Van Zon
Marco J. Morelli
Sorin Tǎnase-Nicola
Pieter Rein ten Wolde
Biophysical Journal200611110
Mutual information between input and output trajectories of biochemical networksFilipe Tostevin
Pieter Rein ten Wolde
Physical Review Letters20091116
Stochastic thermodynamics of chemical reaction networksTim Schmiedl
Udo Seifert
Journal of Chemical Physics20071119
Thermodynamics of predictionSusanne Still
David A. Sivak
Anthony J. Bell
Gavin Crooks
Physical Review Letters201211014
The Stokes efficiency for molecular motors and its applicationsHongyun Wang
G. Oster
Europhysics Letters20021090
Fifty years of the VSEPR modelR. J. GillespieCoordination Chemistry Reviews2008LCP model: Lone pairs
Molecular geometry
VSEPR model
1076
Asymmetric division of Drosophila male germline stem cell shows asymmetric histone distributionVuong Tran
Cindy Lim
Jing Xie
Xin Chen
Science20121071
A stochastic-based FPGA controller for an induction motor drive with integrated neural network algorithmsDa Zhang
Hui Li
IEEE Transactions on Industrial Electronics2008Antiwindup 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)
1078
Principles underlying mammalian neocortical scalingMark A. ChangiziBiological Cybernetics20011070
Wiring economy and volume exclusion determine neuronal placement in the Drosophila brainMarta 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 Biology20111070
Steady state thermodynamicsY Oono
Paniconi M 1998
Theor. Phys. Suppl2006Fluctuation
Nonequilibrium steady state
Thermodynamics
1071
A fluctuation theorem for currents and non-linear response coefficientsDavid Andrieux
Pierre Gaspard
Journal of Statistical Mechanics: Theory and Experiment2007Current fluctuations
Exact results
Stationary states (theory)
1066
Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysicsHao Ge
Min Qian
Hong Qian
Physics Reports2012Bistability
Enzyme kinetics
Fluctuating enzyme
Gene regulatory network
Kinetic proofreading
Signaling network
Zeroth-order ultrasensitivity
1064
Universal features in the energetics of symmetry breakingÉ Roldán
I. A. Martínez
J. M.R. Parrondo
D. Petrov
Nature Physics20141062
Multivariate information transmissionWilliam J. McGillIRE Professional Group on Information Theory19541053
Patterns and mechanisms of Ancestral Histone protein inheritance in Budding yeastMarta Radman-Livaja
Kitty F. Verzijlbergen
Assaf Weiner
Tibor van Welsem
Nir Friedman
Oliver J. Rando
Fred van Leeuwen
PLoS Biology20111050
Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurementsAmar Nath Gupta
Abhilash Vincent
Krishna Neupane
Hao Yu
Feng Wang
Michael T. Woodside
Nature Physics20111040
Histone H3 tail clipping regulates gene expressionHelena Santos-Rosa
Antonis Kirmizis
Christopher Nelson
Till Bartke
Nehme Saksouk
Jacques Cote
Tony Kouzarides
Nature Structural and Molecular Biology20091040
Application-level correctness and its impact on fault toleranceXuanhua Li
Donald Yeung
Proceedings - International Symposium on High-Performance Computer Architecture20071040
Maxwell's demon assisted thermodynamic cycle in superconducting quantum circuitsH. T. Quan
Y. D. Wang
Yu Xi Liu
C. P. Sun
Franco Nori
Physical Review Letters20061040
Specific subtypes of cortical GABA interneurons contribute to the neurovascular coupling response to basal forebrain stimulationAra Kocharyan
Priscilla Fernandes
Xin Kang Tong
Elvire Vaucher
Edith Hamel
Journal of Cerebral Blood Flow and Metabolism2008Cerebral blood vessel
Cholinergic lesion
Cortical interneuron
Hemodynamic response
Inhibitory interneuron
Microvessel
1040
Stochastic signal processing and transduction in chemotactic response of eukaryotic cellsMasahiro Ueda
Tatsuo Shibata
Biophysical Journal20071030
Grid cells generate an analog error-correcting code for singularly precise neural computationSameet Sreenivasan
Ila Fiete
Nature Neuroscience20111031
Cerebellar Golgi cells in the rat: Receptive fields and timing of responses to facial stimulationBart P. Vos
Antonia Volny-Luraghi
Erik De Schutter
European Journal of Neuroscience1999Cerebellum
Inhibitory interneurons
Mossy fibre
Parallel fibre
Somatosensory system
Trigeminal stimulation
1030
Efficiency of autonomous soft nanomachines at maximum powerUdo SeifertPhysical Review Letters20111031
Feedback control in a collective flashing ratchetFrancisco J. Cao
Luis Dinis
Juan M.R. Parrondo
Physical Review Letters20041020
A new notation for quantum mechanicsP. A.M. DiracMathematical Proceedings of the Cambridge Philosophical Society19391026
Systematic errors in free energy perturbation calculations due to a finite sample of configuration space: Sample-size hysteresisRobert H. Wood
Wolfgang C.F. Mühlbauer
Peter T. Thompson
Journal of Physical Chemistry19911023
The chromatin code of fungal secondary metabolite gene clustersAgnieszka Gacek
Joseph Strauss
Applied Microbiology and Biotechnology2012Aspergillus
Chromatin
Histone modifications
Secondary metabolism
1010
Classical and quantum limitations on energy consumption in computationK. K. LikharevInternational Journal of Theoretical Physics19821003
Delayed stochastic decoding of LDPC codesAli Naderi
Shie Mannor
Mohamad Sawan
Warren J. Gross
IEEE Transactions on Signal Processing2011Delayed stochastic decoding
iterative decoding
low-density parity-check code
stochastic decoding
1003
Relationship between subsistence and age at weaning in "preindustrial" societiesDaniel W. Sellen
Diana B. Smay
Human Nature2001Agriculture
Breastfeeding
Childcare
Comparative method
Cross-cultural studies
Cultural evolution
Horticulture
Hunter-gatherers
Pastoralists
Weanling's dilemma
Women's work
1000
Extracting work from a single heat bath through feedbackD. Abreu
Udo Seifert
EPL20111003
Calcium, the two-faced messenger of olfactory transduction and adaptationHugh R. Matthews
Johannes Reisert
Current Opinion in Neurobiology2003990
Calcium signalling and regulation in olfactory neuronsAnna MeniniCurrent Opinion in Neurobiology1999990
Experimental Verification of a Modified Fluctuation-Dissipation Relation for a Micron-Sized Particle in a Nonequilibrium Steady StateJ. R. Gomez-Solano
A. Petrosyan
S. Ciliberto
R. Chetrite
K. Gawȩdzki
Physical Review Letters2009990
Programmable energy landscapes for kinetic control of DNA strand displacementThomas E. Ouldridge
Jonathan Bath
Andrew J. Turberfield
Robert R.F. Machinek
Natalie E.C. Haley
Nature Communications2014980
Stochasticity of gene products from transcriptional pulsingSrividya Iyer-Biswas
F. Hayot
C. Jayaprakash
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2009981
Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraintsAnirikh Chakrabarti
Ljubisa Miskovic
Keng Cher Soh
Vassily Hatzimanikatis
Biotechnology Journal2013Elasticity
Mass action
Saturation
Stability
Thermodynamics
970
Chemical kinetics is turing universalMarcelo O. MagnascoPhysical Review Letters1997971
Local potential connectivity in cat primary visual cortexArmen Stepanyants
Judith A. Hirsch
Luis M. Martinez
Zoltán F. Kisvárday
Alex S. Ferecskó
Dmitri B. Chklovskii
Cerebral Cortex2008Excitatory
Inhibitory
Interlaminar connectivity
Morphology
Neurogeometry
960
Work fluctuations for a Brownian particle between two thermostatsPaolo ViscoJournal of Statistical Mechanics: Theory and Experiment2006Stochastic particle dynamics (theory)960
The Berry phase and the pump flux in stochastic chemical kineticsN. A. Sinitsyn
I. Nemenman
EPL2007960
Observable dependence of fluctuation-dissipation relations and effective temperaturesSuzanne Fielding
Peter Sollich
Physical Review Letters2002960
Efficiency of cellular information processingAndre C. Barato
David Hartich
Udo Seifert
New Journal of Physics2014cellular sensing
nonequilibrium processes
thermodynamics and information
952
Fuzzy Memoization for Floating-Point Multimedia ApplicationsCarlos Alvarez
Jesús Corbal
Mateo Valero
IEEE Transactions on Computers2005Low-power design
real-time and embedded systems
special-purpose and application-based
systems
942
Methods for quantifying the informational structure of sensory and motor dataMax Lungarella
Teresa Pegors
Daniel Bulwinkle
Olaf Sporns
Neuroinformatics2005Embodiment
Information self-structuring
Sensorimotor coordination
940
What can spontaneous fluctuations of the blood oxygenationlevel-dependent signal tell us about psychiatric disorders?Alex Fornito
Edward T. Bullmore
Current Opinion in Psychiatry2010Connectivity
Default mode
Endogenous
Networks
Oscillations
940
Global and regional brain metabolic scaling and its functional consequencesJan KarbowskiBMC Biology20079414
Predictive information and explorative behavior of autonomous robotsN. Ay
N. Bertschinger
R. Der
F. Güttler
E. Olbrich
European Physical Journal B2008932
Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesisAaron Fluitt
Elsje Pienaar
Hendrik Viljoen
Computational Biology and Chemistry2007Mistranslation frequencies
Ribosome kinetics
Translation
tRNA availability
920
Maxwell's demon and quantum-dot cellular automataJohn Timler
Craig S. Lent
Journal of Applied Physics2003921
Single-ensemble nonequilibrium path-sampling estimates of free energy differencesF. Marty Ytreberg
Daniel M. Zuckerman
Journal of Chemical Physics2004920
Logic gates and antisense DNA devices operating on a translator nucleic acid scaffoldBella Shlyahovsky
Yang Li
Oleg Lioubashevski
Johann Elbaz
Itamar Willner
ACS Nano2009Aptamer
DNA
DNAzyme
Logic gate
Nanomedicine
Thrombin
912
The synthesis of robust polynomial arithmetic with stochastic logicWeikang Qian
Marc D. Riedel
Proceedings - Design Automation Conference2008Polynomial arithmetic
Probabilistic logic
Stochastic logic
911
Stoichiometric network theory for nonequilibrium biochemical systemsHong Qian
Daniel A. Beard
Shou Dan Liang
European Journal of Biochemistry2003Biochemical network
Chemical potential
Flux
Nonequilibrium thermodynamics
Steady-state
911
Sensory-Evoked Intrinsic Optical Signals in the Olfactory Bulb Are Coupled to Glutamate Release and UptakeHirac Gurden
Naoshige Uchida
Zachary F. Mainen
Neuron2006MOLNEURO
SIGNALING
SYSNEURO
910
Effects of reservoir squeezing on quantum systems and work extractionX. L. Huang
Tao Wang
X. X. Yi
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2012910
A quantitative estimation of the global translational activity in logarithmically growing yeast cellsTobias von der HaarBMC Systems Biology2008900
The Value of Information for Populations in Varying EnvironmentsOlivier Rivoire
Stanislas Leibler
Journal of Statistical Physics2011Branching processes
Control
Fitness
Information
Investment
Population dynamics
Regulation
891
The berg-purcell limit revisitedKazunari Kaizu
Wiet De Ronde
Joris Paijmans
Koichi Takahashi
Filipe Tostevin
Pieter Rein ten Wolde
Biophysical Journal2014893
Stochastic thermodynamics of bipartite systems: Transfer entropy inequalities and a Maxwell's demon interpretationD. Hartich
A. C. Barato
Udo Seifert
Journal of Statistical Mechanics: Theory and Experiment2014exact results894
The Effect of Phenobarbitone Anaesthesia on Blood Flow and Oxygen Consumption in the Rat BrainLorentz Nilsson
Bo K. Siesjó
Acta Anaesthesiologica Scandinavica1975890
Effective temperature of red-blood-cell membrane fluctuationsEyal Ben-Isaac
Yongkeun Park
Gabriel Popescu
Frank L.H. Brown
Nir S. Gov
Yair Shokef
Physical Review Letters2011890
Measurement of stochastic entropy productionC. Tietz
S. Schuler
T. Speck
J. Wrachtrup
Udo Seifert
Physical Review Letters2006881
Heat generation required by information erasureKousuke ShizumePhysical Review E1995881
Dissipation-error tradeoff in proofreadingCharles H. BennettBioSystems19798813
New evidence for hominin carcass processing strategies at 1.5 Ma, Koobi Fora, KenyaBriana L. Pobiner
Michael J. Rogers
Christopher M. Monahan
John W.K. Harris
Journal of Human Evolution2008Bone modification
Butchery
Carnivory
Cut mark
Early Stone Age
Oldowan
Percussion mark
880
Efficiency of molecular motors at maximum powerT. Schmiedl
Udo Seifert
EPL2008884
Ueber die bewegende Kraft der Wärme und die Gesetze, welche sich daraus für die Wärmelehre selbst ableiten lassenR. ClausiusAnnalen der Physik1850870
The cell cycle switch computes approximate majorityLuca Cardelli
Attila Csikász-Nagy
Scientific Reports2012872
A master equation description of local fluctuationsM. Malek-Mansour
G. Nicolis
Journal of Statistical Physics1975Fluctuations
master equations
nonequilibrium thermodynamics
nonlinear systems
stochastic processes
870
Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling switchHong Qian
Timothy C. Reluga
Physical Review Letters2005872
Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equalityIoan Kosztin
Bogdan Barz
Lorant Janosi
Journal of Chemical Physics2006870
Modelling the development of cortical systems networksMarcus Kaiser
Claus C. Hilgetag
Neurocomputing2004Cortical connectivity
Cortical systems development
Network growth
Optimal wiring
862
Reaching optimal efficiencies using nanosized photoelectric devicesB. Rutten
B. Cleuren
Massimiliano Esposito
Physical Review B - Condensed Matter and Materials Physics2009862
Bidirectional single-electron counting and the fluctuation theoremY. Utsumi
D. S. Golubev
M. Marthaler
K. Saito
T. Fujisawa
Gerd Schön
Physical Review B - Condensed Matter and Materials Physics2010860
Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensationHong QianPhysical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics2002862
On rank vs. communication complexityNoam Nisan
Avi Wigderson
Combinatorica199505C50
68R05
Mathematics Subject Classification (1991): 68Q05
850
Work and heat probability distribution of an optically driven Brownian particle: Theory and experimentsA. Imparato
L. Peliti
G. Pesce
G. Rusciano
A. Sasso
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2007850
Covariation of residues in the homeodomain sequence familyNeil D. ClarkeProtein Science1995covariation
evolution
homeodomains
sequences
structure‐function
840
Engineering complex riboswitch regulation by dual genetic selectionVandana Sharma
Yoko Nomura
Yohei Yokobayashi
Journal of the American Chemical Society2008840
Unifying three perspectives on information processing in stochastic thermodynamicsA. C. Barato
Udo Seifert
Physical Review Letters20148423
Relationships between gene expression and brain wiring in the adult rodent brainLeon French
Paul Pavlidis
PLoS Computational Biology2011840
Off-equilibrium generalization of the fluctuation dissipation theorem for Ising spins and measurement of the linear response functionEugenio Lippiello
Federico Corberi
Marco Zannetti
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2005840
Dissipation and lag in irreversible processesS. Vaikuntanathan
C. Jarzynski
EPL2009840
The minimal work cost of information processingPhilippe Faist
Frédéric Dupuis
Jonathan Oppenheim
Renato Renner
Nature Communications2015833
Information thermodynamics on causal networksSosuke Ito
Takahiro Sagawa
Physical Review Letters2013832
Dietary constraints on encephalization in primatesJennifer L. Fish
Charles A. Lockwood
American Journal of Physical Anthropology2003Brain size
Comparative methods
Expensive tissue hypothesis
Independent contrasts
830
Receptive fields and functional architecture in the retinaVijay Balasubramanian
Peter Sterling
Journal of Physiology2009830
Unattainability of Carnot efficiency in the Brownian heat engineTsuyoshi Hondou
Ken Sekimoto
Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics2000820
Relative entropy: Free energy associated with equilibrium fluctuations and nonequilibrium deviationsHong QianPhysical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics2001825
Nitric oxide and adenosine mediate vasodilation during functional activation in cerebellar cortexJ. Li
C. Iadecola
Neuropharmacology1994GABA
Parallel fibers
adenosine
cerebellar blood flow
glutamate
nitric oxide
nitro-l-arginine
vasodilation
820
Thermodynamic reversibility in feedback processesJordan M. Horowitz
Juan M.R. Parrondo
EPL2011821
Two subtypes of non-pyramidal cells in rat hippocampal formation identified by intracellular recording and HRP injectionYasuo Kawaguchi
Kiyoshi Hama
Brain Research1987Dentate gyrus
Fast spiking cell
GABAergic neuron
Hippocampus
Intracellular injection of HRP
Non-pyramidal cell
Slice preparation
820
Maxwell's refrigerator: An exactly solvable modelDibyendu Mandal
H. T. Quan
Christopher Jarzynski
Physical Review Letters2013811
Exploiting correlation in stochastic circuit designArmin Alaghi
John P. Hayes
2013 IEEE 31st International Conference on Computer Design, ICCD 20132013Stochastic computing
low-power design
signal correlation
stochastic circuit design
800
Compendium of the Foundations of Classical Statistical PhysicsJos UffinkPhilosophy of Physics2007806
Optimized free energies from bidirectional single-molecule force spectroscopyDavid D.L. Minh
Artur B. Adib
Physical Review Letters2008800
Kinetics of reversible diffusion influenced reactions: The self-consistent relaxation time approximationIrina V. Gopich
Attila Szabo
Journal of Chemical Physics2002790
Maximum likelihood and the single receptorRobert G. Endres
Ned S. Wingreen
Physical Review Letters2009790
Thermodynamics of genuine nonequilibrium states under feedback controlDavid Abreu
Udo Seifert
Physical Review Letters2012796
Digital genetics: Unravelling the genetic basis of evolutionChristoph AdamiNature Reviews Genetics2006782
ERSA: Error resilient system architecture for probabilistic applicationsHyungmin Cho
Larkhoon Leem
Subhasish Mitra
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems2012Error resilience
hardware errors
probabilistic applications
reliability
robust systems
780
Fluctuation theorem for transport in mesoscopic systemsDavid Andrieux
Pierre Gaspard
Journal of Statistical Mechanics: Theory and Experiment2006Current fluctuations
Exact results
Stationary states (theory)
780
Fluctuation theorems for quantum processesTameem Albash
Daniel A. Lidar
Milad Marvian
Paolo Zanardi
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2013770
An update on the nonequilibrium linear responseM. Baiesi
C. Maes
New Journal of Physics2013770
Fluctuation theorem for a single enzym or molecular motorUdo SeifertEurophysics Letters2005773
On a hypothetical generational relationship between HCN and constituents of the reductive citric acid cycleAlbert EschenmoserChemistry and Biodiversity2007760
Perfect and near-perfect adaptation in a model of bacterial chemotaxisBernardo A. Mello
Yuhai Tu
Biophysical Journal2003760
Non-equilibrium work relationsJorge KurchanJournal of Statistical Mechanics: Theory and Experiment2007Current fluctuations
Stochastic particle dynamics (theory)
Transport processes/heat transfer (theory)
761
Stochastic thermodynamics of single enzymes and molecular motorsUdo SeifertEuropean Physical Journal E2011751
Exorcist XIV: The wrath of Maxwell's Demon. Part II. From Szilard to Landauer and beyondJohn Earman
John D. Norton
Studies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics1999751
Thermodynamic universality of quantum Carnot enginesBartłomiej Gardas
Sebastian Deffner
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2015751
Nonequilibrium work fluctuations for oscillators in non-Markovian bathsTrieu Mai
Abhishek Dhar
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2007750
Experimental study of the fluctuation theorem in a nonequilibrium steady stateG. 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 Physics2005750
Realization of a feedback controlled flashing ratchetBenjamin J. Lopez
Nathan J. Kuwada
Erin M. Craig
Brian R. Long
Heiner Linke
Physical Review Letters2008740
Nonequilibrium fluctuations and mechanochemical couplings of a molecular motorA. W.C. Lau
D. Lacoste
K. Mallick
Physical Review Letters2007740
Mapping out-of-equilibrium into equilibrium in one-dimensional transport modelsJulien Tailleur
Jorge Kurchan
Vivien Lecomte
Journal of Physics A: Mathematical and Theoretical2008740
Efficient turing-universal computation with DNA polymersLulu Qian
David Soloveichik
Erik Winfree
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)2011734
Physical Responses of Bacterial ChemoreceptorsAdy Vaknin
Howard C. Berg
Journal of Molecular Biology2007chemotaxis
fluorescence polarization
fluorescence resonance energy transfer
membrane proteins
receptors
730
Imitating chemical motors with optimal information motorsJordan M. Horowitz
Takahiro Sagawa
Juan M.R. Parrondo
Physical Review Letters2013731
An autonomous and reversible Maxwell's demonUdo Seifert
A. C. Barato
EPL20137326
The statistical neuroanatomy of frontal networks in the macaqueBruno B. Averbeck
Moonsang Seo
PLoS Computational Biology2008730
Motor-Driven Dynamics in Actin-Myosin NetworksLoïc Le Goff
François Amblard
Eric M. Furst
Physical Review Letters2002730
Heat conduction in a three dimensional anharmonic crystalKeiji Saito
Abhishek Dhar
Physical Review Letters2010720
Exploring the thermodynamic limits of computation in integrated systems: Magnetic memory, nanomagnetic logic, and the landauer limitBrian Lambson
David Carlton
Jeffrey Bokor
Physical Review Letters2011721
Thermodynamics of feedback controlled systemsF. J. Cao
M. Feito
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2009721
Covalent modifications of histones during mitosis and meiosisDazhong Xu
Jingxiang Bai
Qing Duan
Max Costa
Wei Dai
Cell Cycle2009Cell cycle
Covalent modifications
Histone
Meiosis
Mitosis
711
Deterministic function computation with chemical reaction networksHo Lin Chen
David Doty
David Soloveichik
Natural Computing2014Distributed computing
Molecular programming
Population protocols
Semilinear functions
Stochastic chemical kinetics
713
Alternative splicing in the nervous system: An emerging source of diversity and regulationChristopher J. Lee
Kris Irizarry
Biological Psychiatry2003Alternative splicing
Genomics
Receptors
mRNA
710
Length of time's arrowEdward H. Feng
Gavin Crooks
Physical Review Letters2008714
Entropy production in full phase space for continuous stochastic dynamicsRichard E. Spinney
Ian J. Ford
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2012710
Experimental test of the Gallavotti-Cohen fluctuation theorem in turbulent flowsS. Ciliberto
N. Garnier
S. Hernandez
C. Lacpatia
J. F. Pinton
G. Ruiz Chavarria
Physica A: Statistical Mechanics and its Applications2004Fluctuation theorem
Statistical mechanics
Turbulence
711
Deterministic Function Computation with Chemical Reaction NetworkHo Lin Chen
David Doty
David Soloveichik
Natural Computing2014Distributed computing
Molecular programming
Population protocols
Semilinear functions
Stochastic chemical kinetics
711
An introduction to population protocolsJames Aspnes
Eric Ruppert
Middleware for Network Eccentric and Mobile Applications2009704
Integrated information increases with fitness in the evolution of animatsJeffrey A. Edlund
Nicolas Chaumont
Arend Hintze
Christof Koch
Giulio Tononi
Christoph Adami
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Thermodynamic constraints on kinetic proofreading in biosynthetic pathwaysM. Ehrenberg
C. Blomberg
Biophysical Journal1980700
Generalized detailed fluctuation theorem under nonequilibrium feedback controlM. PonmuruganPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics2010690
Optimal protocols for minimal work processes in underdamped stochastic thermodynamicsAlex Gomez-Marin
Tim Schmiedl
Udo Seifert
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Refined Second Law of Thermodynamics for Fast Random ProcessesErik Aurell
Krzysztof Gawȩdzki
Carlos Mejía-Monasterio
Roya Mohayaee
Paolo Muratore-Ginanneschi
Journal of Statistical Physics2012Landauer principle
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Second Law of Thermodynamics
690
Stochastic thermodynamics for Maxwell demon feedbacksMassimiliano Esposito
Gernot Schaller
EPL2012696
A simple rule for axon outgrowth and synaptic competition generates realistic connection lengths and filling fractionsMarcus Kaiser
Claus C. Hilgetag
Arjen Van Ooyen
Cerebral Cortex2009Axon growth
Cortical networks
Filling fraction
Neural competition
Neural networks
680
Escorted free energy simulations: Improving convergence by reducing dissipationSuriyanarayanan Vaikuntanathan
Christopher Jarzynski
Physical Review Letters2008685
Finite-time thermodynamics for a single-level quantum dotR. Kawai
K. Lindenberg
C. Van Den Broeck
Massimiliano Esposito
EPL2010681
Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard-sphere liquidHuan Xiang Zhou
Attila Szabo
Journal of Chemical Physics1991671
Second-law-like inequalities with information and their interpretationsJordan M. Horowitz
Henrik Sandberg
New Journal of Physics2014feedback
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672
The role of glial glutamate transporters in maintaining the independent operation of juvenile mouse cerebellar parallel fibre synapsesPaïkan Marcaggi
Daniela Billups
David Attwell
Journal of Physiology2003670
Invisibility in non-Hermitian tight-binding latticesStefano LonghiPhysical Review A - Atomic, Molecular, and Optical Physics2010670
Pumped biochemical reactions, nonequilibrium circulation, and stochastic resonanceHong Qian
Min Qian
Physical Review Letters2000670
Efficiency at maximum power output of linear irreversible Carnot-like heat enginesYang Wang
Z. C. Tu
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Stochastic thermodynamics and sustainable efficiency in work productionB. Gaveau
M. Moreau
L. S. Schulman
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Optimal protocols and optimal transport in stochastic thermodynamicsErik Aurell
Carlos Mejía-Monasterio
Paolo Muratore-Ginanneschi
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Analog Computation by DNA Strand Displacement CircuitsTianqi Song
Sudhanshu Garg
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John Reif
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675
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Andre Holley
Kjell B. Døving
Journal of Theoretical Biology1978660
The stochastic pump effect and geometric phases in dissipative and stochastic systemsN. A. SinitsynJournal of Physics A: Mathematical and Theoretical2009660
Fluctuation theorems for a molecular refrigeratorKyung Hyuk Kim
Hong Qian
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2007660
Energy dissipation and violation of the fluctuation-response relation in nonequilibrium Langevin systemsTakahiro Harada
Shin Ichi Sasa
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2006660
Flight of the FINCH through the java wildernessMichael Orlov
Moshe Sipper
IEEE Transactions on Evolutionary Computation2011Automatic programming
Java bytecode
genetic programming (GP)
software evolution
650
Thermodynamic Costs of Information Processing in Sensory AdaptationPablo Sartori
Léo Granger
Chiu Fan Lee
Jordan M. Horowitz
PLoS Computational Biology2014651
Geometric effects on complex network structure in the cortexJ. A. Henderson
P. A. Robinson
Physical Review Letters2011651
Role of Astrocytes in Matching Blood Flow to Neuronal ActivityDanica Jakovcevic
David R. Harder
Current Topics in Developmental Biology2007650
Time-dependent pseudo-Hermitian Hamiltonians defining a unitary quantum system and uniqueness of the metric operatorAli MostafazadehPhysics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics2007Geometric phase
Inner product
Metric operator
PT-symmetry
Pseudo-Hermitian
Time-dependent Hamiltonian
Unitary
650
Symmetries of generating functionals of Langevin processes with colored multiplicative noiseCamille Aron
Giulio Biroli
Leticia F. Cugliandolo
Journal of Statistical Mechanics: Theory and Experiment2010Fluctuations (theory)
Rigorous results in statistical mechanics
Stochastic particle dynamics (theory)
Stochastic processes (theory)
650
Experimental demonstration of a latch in clocked quantum-dot cellular automataAlexei O. Orlov
Ravi K. Kummamuru
Rajagopal Ramasubramaniam
Geza Toth
Craig S. Lent
Gary H. Bernstein
Gregory L. Snider
Applied Physics Letters2001641
Chromatin and epigenetic regulation of pre-mrna processingSeth J. Brown
Peter Stoilov
Yi Xing
Human Molecular Genetics2012640
Cooperativity, sensitivity, and noise in biochemical signalingWilliam Bialek
Sima Setayeshgar
Physical Review Letters2008643
Use of mutual information to decrease entropy: Implications for the second law of thermodynamicsSeth LloydPhysical Review A1989645
Efficient behavior of small-world networksVito Latora
Massimo Marchiori
Physical Review Letters2001640
Feynman's ratchet optimization: Maximum power and maximum efficiency regimesS. Velasco
A. Medina
A. Calvo Hernandez
J. M.M. Roco
Journal of Physics D: Applied Physics2001641
Nonlinear fluctuation-dissipation relations and stochastic models in nonequilibrium thermodynamics. II. Kinetic potential and variational principles for nonlinear irreversible processesG. N. Bochkov
Yu E. Kuzovlev
Physica A: Statistical Mechanics and its Applications1981640
Pseudo-random generators for all hardnessesChristopher UmansJournal of Computer and System Sciences2003Complexity classes
Derandomization
Low-degree extension
Pseudo-random number generators
630
Fluctuation theorem for partially masked nonequilibrium dynamicsNaoto Shiraishi
Takahiro Sagawa
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2015631
The Jarzynski relation, fluctuation theorems, and stochastic thermodynamics for non-Markovian processesT. Speck
Udo Seifert
Journal of Statistical Mechanics: Theory and Experiment2007Nonequilibrium fluctuations in small systems
Stochastic processes (theory)
636
Steady-state fluctuation relations for systems driven by an external random forceJ. R. Gomez-Solano
L. Bellon
A. Petrosyan
S. Ciliberto
EPL2010630
The mechanics and fluctuation spectrum of active gelsAlex J. Levine
F. C. MacKintosh
Journal of Physical Chemistry B2009630
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Giuliano Benenti
Giulio Casati
Tomaž Prosen
Physical Review B - Condensed Matter and Materials Physics2011630
Second law of thermodynamics and quantum feedback control: Maxwell’s demon with weak measurementsKurt JacobsPhysical Review A - Atomic, Molecular, and Optical Physics2009620
Stochastic energetics of non-uniform temperature systemsMiki Matsuo
Shin Ichi Sasa
Physica A: Statistical Mechanics and its Applications2000620
Unbalanced expanders and randomness extractors from parvaresh-vardy codesVenkatesan Guruswami
Christopher Umans
Salil Vadhan
Proceedings of the Annual IEEE Conference on Computational Complexity2007Expander graphs
Randomness extractors
617
Reversible space equals deterministic spaceKlaus Jörn Lange
Pierre McKenzie
Alain Tapp
Journal of Computer and System Sciences2000611
Qubit thermometry for micromechanical resonatorsMatteo Brunelli
Stefano Olivares
Matteo G.A. Paris
Physical Review A - Atomic, Molecular, and Optical Physics2011611
Unified treatment of the quantum fluctuation theorem and the Jarzynski equality in terms of microscopic reversibilityT. MonnaiPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics2005610
On the Relation between Gradient Flows and the Large-Deviation Principle, with Applications to Markov Chains and DiffusionA. Mielke
M. A. Peletier
D. R.M. Renger
Potential Analysis2014Convex analysis
Generalized gradient flows
Large deviations
Particle systems
600
Tight coupling in thermal Brownian motorsA. Gomez-Marin
J. M. Sancho
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2006600
Attractant- and Disulfide-Induced Conformational Changes in the Ligand Binding Domain of the Chemotaxis Aspartate Receptor: A 19F NMR StudyMark A. Danielson
Joseph J. Falke
Hans Peter Biemann
Daniel E. Koshland
Biochemistry1994600
Maxwell's demon in biochemical signal transduction with feedback loopSosuke Ito
Takahiro Sagawa
Nature Communications2015602
Quantum Jarzynski-Sagawa-Ueda RelationsYohei Morikuni
Hal Tasaki
Journal of Statistical Physics2011Feedback
Jarzynski relation
Measurement
Quantum system
605
Heat engine driven by purely quantum informationJung Jun Park
Kang Hwan Kim
Takahiro Sagawa
Sang Wook Kim
Physical Review Letters2013602
Neuron-glia metabolic coupling and plasticityPierre J. MagistrettiExperimental Physiology2011600
Memory erasure in small systemsRaoul Dillenschneider
Eric Lutz
Physical Review Letters2009600
Fluctuation theorems and the nonequilibrium thermodynamics of molecular motorsDavid Andrieux
Pierre Gaspard
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2006590
BMI peak in infancy as a predictor for later BMI in the Uppsala Family StudyR. J. Silverwood
B. L. De Stavola
T. J. Cole
D. A. Leon
International Journal of Obesity2009Body mass index
Childhood obesity
Growth
Infancy
590
Role of hidden slow degrees of freedom in the fluctuation theoremJ. Mehl
B. Lander
C. Bechinger
V. Blickle
Udo Seifert
Physical Review Letters2012593
A possible classification of nonequilibrium steady statesB. Schmittmann
R. K.P. Zia
Journal of Physics A: Mathematical and General2006590
Fluctuation-dissipation theorems and entropy production in relaxational systemsLeticia F. Cugliandolo
David S. Dean
Jorge Kurchan
Physical Review Letters1997590
Computational design of nucleic acid feedback control circuitsBoyan Yordanov
Jongmin Kim
Rasmus L. Petersen
Angelina Shudy
Vishwesh V. Kulkarni
Andrew Phillips
ACS Synthetic Biology2014DNA strand displacement
DNA toolbox
feedback control
genelet
molecular programming
nucleic acid circuits
581
Extinction in neutrally stable stochastic Lotka-Volterra modelsAlexander Dobrinevski
Erwin Frey
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2012580
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Pieter Rein ten Wolde
Physical Review Letters2014585
Nonequilibrium thermodynamics of stochastic systems with odd and even variablesRichard E. Spinney
Ian J. Ford
Physical Review Letters2012580
Strand algebras for DNA computingLuca CardelliNatural Computing2011DNA computing
DNA strand displacement
Process algebra
571
Three-dimensional simulations of reversible bimolecular reactions: The simple target problemA. V. Popov
N. Agmon
Journal of Chemical Physics2001570
Sniffing and spatiotemporal coding in olfactionJohn W. ScottChemical Senses2006Electroolfactogram
Flow rate
Odorant hydrophobicity
Sorption
570
Physiological evidence for dendrodendritic synaptic interactions in the rabbit's olfactory glomerulusGordon M. ShepherdBrain Research1971570
Nonlinear response and fluctuation-dissipation relationsEugenio Lippiello
Federico Corberi
Alessandro Sarracino
Marco Zannetti
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2008571
Molecular kinetic analysis of a finite-time Carnot cycleY. Izumida
K. Okuda
EPL2008570
Distribution of work in isothermal nonequilibrium processesThomas Speck
Udo Seifert
Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics2004571
The adjustable nucleosome: An epigenetic signaling moduleBryan M. TurnerTrends in Genetics2012Chromatin
Epigenetics
Gene-environment interaction
Histone modification
Nuclear signaling
Nucleosome
560
A fluctuation theorem for non-equilibrium relaxational systems driven by external forcesFrancesco Zamponi
Federico Bonetto
Leticia F. Cugliandolo
Jorge Kurchan
Journal of Statistical Mechanics: Theory and Experiment2005Brownian motion
Driven diffusive systems (theory)
Fluctuations (theory)
Slow dynamics and ageing (theory)
564
Statistical mechanics of Monod-Wyman-Changeux (MWC) modelsSarah Marzen
Hernan G. Garcia
Rob Phillips
Journal of Molecular Biology2013Monod-Wyman-Changeux model
allostery
bacterial chemotaxis
chromatin structure
information theory
559
Self-organization and entropy reduction in a living cellPaul C.W. Davies
Elisabeth Rieper
Jack A. Tuszynski
BioSystems2013Entropy
Genetic code
Information theory
Shannon information
Thermodynamics
557
Physics of Self-Organization and EvolutionRainer Feistel
Werner Ebeling
Physics of Self-Organization and Evolution2011553
Human neoteny revisited: The case of synaptic plasticityEnric Bufill
Jordi Agustí
Rafael Blesa
American Journal of Human Biology2011551
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 1M. Wong-Riley
B. Anderson
W. Liebl
Z. Huang
Neuroscience1998Energy metabolism
Excitatory neurochemicals
Glutamate receptor
Immunohistochemistry
Impulse blockade
Primary visual cortex
550
Current, maximum power and optimized efficiency of a Brownian heat engineMesfin Asfaw
Mulugeta Bekele
European Physical Journal B2004550
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Andreas Hanke
Udo Seifert
Physical Review Letters2004550
Lower bounds on probabilistic linear decision treesMarc SnirTheoretical Computer Science1985540
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Jonathan Bath
Andrew J. Turberfield
Angewandte Chemie - International Edition2013DNA recognition
DNA structures
molecular computation
nanotechnology
strand displacement
540
Generalization of the second law for a transition between nonequilibrium statesK. Takara
H. H. Hasegawa
D. J. Driebe
Physics Letters, Section A: General, Atomic and Solid State Physics20105413
Holevo's bound from a general quantum fluctuation theoremDvir Kafri
Sebastian Deffner
Physical Review A - Atomic, Molecular, and Optical Physics2012545
An examination of the role of autocatalytic cycles in the chemistry of proposed primordial reactionsDonna G. BlackmondAngewandte Chemie - International Edition2009Autocatalysis
Autoinduction
Ligand acceleration
Prebiotic chemistry
Systems chemistry
531
Effective temperatures in driven systems: Static versus time-dependent relationsCorey S. O'Hern
Andrea J. Liu
Sidney R. Nagel
Physical Review Letters2004530
Receptor noise and directional sensing in eukaryotic chemotaxisWouter Jan Rappel
Herbert Levine
Physical Review Letters2008530
Aerobic glycolysis in the primate brain: Reconsidering the implications for growth and maintenanceAmy L. Bauernfeind
Sarah K. Barks
Tetyana Duka
Lawrence I. Grossman
Patrick R. Hof
Chet C. Sherwood
Brain Structure and Function2014Aerobic gycolysis
Brain energetics
Default mode network
Evolution
Oxidative phosphorylation
530
Measurement of damping and temperature: Precision bounds in Gaussian dissipative channelsAlex Monras
Fabrizio Illuminati
Physical Review A - Atomic, Molecular, and Optical Physics2011531
Stochastically driven single-level quantum dot: A nanoscale finite-time thermodynamic machine and its various operational modesMassimiliano Esposito
Niraj Kumar
Katja Lindenberg
Christian Van Den Broeck
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2012521
Irreversible dynamics of a massive intruder in dense granular fluidsA. Sarracino
D. Villamaina
G. Gradenigo
A. Puglisi
EPL2010520
Limits of sensing temporal concentration changes by single cellsThierry Mora
Ned S. Wingreen
Physical Review Letters2010520
Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxisSilke Neumann
Clinton H. Hansen
Ned S. Wingreen
Victor Sourjik
EMBO Journal2010FRET
bacterial chemotaxis
signal integration
signal transduction
transport
523
Thermodynamic efficiency of information and heat flowArmen E. Allahverdyan
Dominik Janzing
Guenter Mahler
Journal of Statistical Mechanics: Theory and Experiment2009Communication
Source and channel coding
Supply and information networks
521
Large deviation function for entropy production in driven one-dimensional systemsJakob Mehl
Thomas Speck
Udo Seifert
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2008523
Universal aspects of the chemomechanical coupling for molecular motorsReinhard LipowskyPhysical Review Letters2000520
Histone Segregation on Replicating Chromatin†Vaughn Jackson
Roger Chalkley
Biochemistry1985510
Histone Segregation on Replicating Chromatinâ€Vaughn Jackson
Roger Chalkley
Biochemistry1985510
On thermodynamic interpretation of transfer entropyMikhail Prokopenko
Joseph T. Lizier
Don C. Price
Entropy2013Boltzmann's principle
Causal effect
Entropy production
Information transfer
Irreversibility
Kullback-Leibler divergence
Thermodynamic equilibrium
Transfer entropy
511
The connection between logical and thermodynamic irreversibilityJames Ladyman
Stuart Presnell
Anthony J. Short
Berry Groisman
Studies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics2007Computation
Entropy
Information
Irreversibility
Landauer's principle
Thermodynamics
511
Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transductionHong QianBiophysical Chemistry2003Biological signal transduction
Kinetic analysis
Thermodynamic
510
Information-theoretic versus thermodynamic entropy production in autonomous sensory networksA. C. Barato
D. Hartich
Udo Seifert
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2013515
Generalization of the second law for a nonequilibrium initial stateH. H. Hasegawa
J. Ishikawa
K. Takara
D. J. Driebe
Physics Letters, Section A: General, Atomic and Solid State Physics2010515
The selfish brain: Competition for energy resourcesAchim PetersAmerican Journal of Human Biology2011512
The stochastic chemomechanics of the F1-ATPase molecular motorP. Gaspard
E. Gerritsma
Journal of Theoretical Biology2007Arrhenius kinetics
F1-ATPase
Mechanochemical coupling
Molecular motor
Stochastic process
510
Nonequilibrium steady-state fluctuations in actively cooled resonatorsM. Bonaldi
L. Conti
P. De Gregorio
L. Rondoni
G. Vedovato
A. Vinante
M. Bignotto
M. Cerdonio
P. Falferi
N. Liguori
S. Longo
R. Mezzena
A. Ortolan
G. A. Prodi
F. Salemi
L. Taffarello
S. Vitale
J. P. Zendri
Physical Review Letters2009510
Failure of the work-hamiltonian connection for free-energy calculationsJ. Miguel Rubi
Jose M.G. Vilar
Physical Review Letters2008510
Pseudorandomness and average-case complexity via uniform reductionsLuca Trevisan
Salil Vadhan
Computational Complexity2007Average-case complexity
Derandomization
Instance checkers
Pseudorandomness
500
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Alexander A. Razborov
Annual Symposium on Foundations of Computer Science - Proceedings2001500
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Charles K. Fisher
Thierry Mora
Pankaj Mehta
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Assessing the nonequilibrium thermodynamics in a quenched quantum many-body system via single projective measurementsL. Fusco
S. Pigeon
A. Xuereb
L. Mazzola
M. Campisi
A. Ferraro
M. Paternostro
G. De Chiara
T. J.G. Apollaro
Physical Review X2014500
Large deviations of heat flow in harmonic chainsAnupam Kundu
Sanjib Sabhapandit
Abhishek Dhar
Journal of Statistical Mechanics: Theory and Experiment2011current fluctuations
heat conduction
large deviations in non-equilibrium systems
500
Fluctuations of internal energy flow in a vibrated granular gasAndrea Puglisi
Paolo Visco
Alain Barrat
Emmanuel Trizac
Frédéric Van Wijland
Physical Review Letters2005500
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L. Peliti
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2006500
Relevance of initial and final conditions for the fluctuation relation in Markov processesA. Puglisi
L. Rondoni
A. Vulpiani
Journal of Statistical Mechanics: Theory and Experiment2006Current fluctuations
Fluctuations (theory)
Granular matter
Stochastic processes (theory)
500
Fluctuation-dissipation relations for Markov processesGregor DiezemannPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics2005500
Compiler optimization on instruction scheduling for low powerChingren Lee
Jenq Kuen Lee
Ting Ting Hwang
Shi Chun Tsai
Proceedings of the International Symposium on System Synthesis2000Capacitance
Circuits
Computer architecture
Costs
Energy consumption
Greedy algorithms
Optimizing compilers
Processor scheduling
Software performance
VLIW
500
Computing the optimal protocol for finite-time processes in stochastic thermodynamicsHolger Then
Andreas Engel
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2008490
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Martin Howard
Pieter Rein ten Wolde
Physical Review Letters2009490
Kinetic versus energetic discrimination in biological copyingPablo Sartori
Simone Pigolotti
Physical Review Letters2013490
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Michael J. Berry
Network: Computation in Neural Systems2002492
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Stefano Olivares
Mauro Paternostro
Matteo G.A. Paris
Physical Review A - Atomic, Molecular, and Optical Physics2012491
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Martin Spichty
Martin Karplus
Physical Review Letters2006490
Comparison of work fluctuation relationsJordan Horowitz
Christopher Jarzynski
Journal of Statistical Mechanics: Theory and Experiment2007Nonequilibrium fluctuations in small systems493
Fluctuation relations and coarse-grainingSaar Rahav
Christopher Jarzynski
Journal of Statistical Mechanics: Theory and Experiment2007Nonequilibrium fluctuations in small systems
Stochastic particle dynamics (theory)
486
Quantifying noise levels of intercellular signalsKai Wang
Wouter Jan Rappel
Rex Kerr
Herbert Levine
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2007480
A general framework for non-equilibrium phenomena: The master equation and its formal consequencesBernard Gaveau
L. S. Schulman
Physics Letters, Section A: General, Atomic and Solid State Physics1997482
Neurochemical organization of the macaque retina: Effect of TTX on levels and gene expression of cytochrome oxidase and nitric oxide synthase and on the immunoreactivity of Na+ K+ ATPase and NMDA receptor subunit IMargaret T.T. Wong-Riley
Zifang Huang
Wendy Liebl
Feng Nie
Haiyun Xu
Chenyang Zhang
Vision Research1998Cytochrome oxidase
NMDA receptor
Na+ K+ ATPase
Nitric oxide synthase
cDNA
480
Dynamical reconnection and stability constraints on cortical network architectureP. A. Robinson
J. A. Henderson
E. Matar
P. Riley
R. T. Gray
Physical Review Letters2009481
A mathematical theorem as the basis for the second law: Thomson's formulation applied to equilibriumA. E. Allahverdyan
Th M. Nieuwenhuizen
Physica A: Statistical Mechanics and its Applications2002Mathematical proof
Perpetual motion
Persistent currents
Second law
Thomson formulation
480
Entropy production for mechanically or chemically driven biomoleculesTim Schmiedl
Thomas Speck
Udo Seifert
Journal of Statistical Physics2007Biomolecules
Brownian motion
Chemical kinetics in biological systems
Fluctuation phenomena
Random processes
Thermodynamics
480
Potential and flux decomposition for dynamical systems and non-equilibrium thermodynamics: Curvature, gauge field, and generalized fluctuation-dissipation theoremHaidong Feng
Jin Wang
Journal of Chemical Physics2011470
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Jason Mars
Xiao Zhang
Robert Hagmann
Robert Hundt
Eric Tune
Proceedings - International Symposium on High-Performance Computer Architecture2013471
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Christopher C. Govern
Pieter Rein ten Wolde
Physical Review X2017Biological physics
Chemical physics
Statistical physics
474
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David Wolpert
Eric Libby
Jan Amend
Tori Hoehler
Chris Kempes
Frontiers in Microbiology2017Basal power requirement
Maintenance metabolism
Metabolic ecology
4710
The scaling of white matter to gray matter in cerebellum and neocortexEliot C. Bush
John M. Allman
Brain, Behavior and Evolution2003Cerebellum
Mammals
Neocortex
Scaling
White matter
470
Designing optimal discrete-feedback thermodynamic enginesJordan M. Horowitz
Juan M.R. Parrondo
New Journal of Physics2011473
Thermodynamics of Computational Copying in Biochemical SystemsThomas E. Ouldridge
Christopher C. Govern
Pieter Rein ten Wolde
Physical Review X2017Biological physics
Chemical physics
Statistical physics
479
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Simon B. Laughlin
Vision Research2000Blue cones
Colour
Contrast gain
Frequency response
Photoreceptor
SNR
Vision
470
Binary Multiplication with PN SequencesP. K. Gupta
R. Kumaresan
IEEE Transactions on Acoustics, Speech, and Signal Processing1988464
Efficient checking of computationsRichard J. LiptonLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)1990460
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Dinshaw J. Patel
Journal of Biological Chemistry2011460
RetinaPeter Sterling
Jonathan B. Demb
The Synaptic Organization of the Brain2004Eyes
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Vision
Visual information
460
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Kim Hill
Oskar Burger
A. Magdalena Hurtado
American Journal of Physical Anthropology2006Ache foragers
Chimpanzees
Growth rates
Human life history
461
Wiring cost in the organization of a biological neuronal networkYong Yeol Ahn
Hawoong Jeong
Beom Jun Kim
Physica A: Statistical Mechanics and its Applications2006Biological network
Neuronal network
Wiring cost
461
Power fluctuations in stochastic models of dissipative systemsJean FaragoPhysica A: Statistical Mechanics and its Applications2004Brownian motion
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Noise
Probability theory
Random processes
Statistics
Stochastic processes
460
Non-equilibrium spin-boson model: Counting statistics and the heat exchange fluctuation theoremLena Nicolin
Dvira Segal
Journal of Chemical Physics2011461
Two Refreshing Views of Fluctuation Theorems Through Kinematics Elements and Exponential MartingaleRaphaël Chetrite
Shamik Gupta
Journal of Statistical Physics2011Fluctuation Relations
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Martingales
Non-equilibrium Markov Process
460
Morphisms of reaction networks that couple structure to functionLuca CardelliBMC Systems Biology2014Biological networks
Chemical reaction networks
Influence networks
Morphisms
450
Irreversible effects of memoryA. Puglisi
D. Villamaina
Europhysics Letters2009450
Symmetry properties of the large-deviation function of the velocity of a self-propelled polar particleNitin Kumar
Sriram Ramaswamy
A. K. Sood
Physical Review Letters2011450
Fluctuation dissipation relations far from equilibriumFederico Corberi
Eugenio Lippiello
Marco Zannetti
Journal of Statistical Mechanics: Theory and Experiment2007Coarsening processes (theory)450
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X. Sunney Xie
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2006450
Generalizing Landauer's principleO. J.E. MaroneyPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics2009452
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Seth Lloyd
Lorenzo MacCone
Physical Review Letters2012453
Inertial effects in Büttiker-Landauer motor and refrigerator at the overdamped limitRonald Benjamin
Ryoichi Kawai
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2008450
The Use of Information Theory in Evolutionary BiologyChristoph AdamiAnnals of the New York Academy of Sciences2012Animat evolution
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Information theory
Protein evolution
451
Disjointness is hard in the multiparty number-on-the-forehead modelTroy Lee
Adi Shraibman
Computational Complexity2009Communication complexity
Disjointness
Number-on-the-forehead model
Proof complexity
440
A generalization of Wegscheider's condition. Implications for properties of steady states and for quasi-steady-state approximationStefan Schuster
Ronny Schuster
Journal of Mathematical Chemistry1989446
Bounds of efficiency at maximum power for linear, superlinear and sublinear irreversible Carnot-like heat enginesYang Wang
Z. C. Tu
EPL2012440
Geometrical expression of excess entropy productionTakahiro Sagawa
Hisao Hayakawa
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2011445
Fluctuation theorems for non-linear generalized Langevin systemsTakahiro Ohkuma
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Journal of Statistical Mechanics: Theory and Experiment2007Fluctuations (theory)
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Stochastic processes (theory)
4410
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Tim Jacobs
Christian Maes
Nikos S. Skantzos
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2006440
Lower bounds on dissipation upon coarse grainingA. Gomez-Marin
J. M.R. Parrondo
C. Van Den Broeck
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2008440
Efficient measurement of linear susceptibilities in molecular simulations: Application to aging supercooled liquidsLudovic BerthierPhysical Review Letters2007440
Jarzynski equality for quantum stochastic mapsAlexey E. Rastegin
Karol Ayczkowski
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2014430
A simple theory of motor protein kinetics and energetics. IIHong QianBiophysical Chemistry2000431
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Chemomechanical coupling of molecular motors: Thermodynamics, network representations, and balance conditionsReinhard Lipowsky
Steffen Liepelt
Journal of Statistical Physics2008Cytoskeletal motors
Energy transduction
Entropy production
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431
Entropy production theorems and some consequencesArnab Saha
Sourabh Lahiri
A. M. Jayannavar
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Intra-well motion
Phase lag
Stochastic energetics
Stochastic resonance
434
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Landauer's principle
Natural selection
Thermodynamics
433
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Christopher Jarzynski
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Bilge E.S. Akgul
Krishna V. Palem
Lakshmi N. Chakrapani
Japanese Journal of Applied Physics, Part 1: Regular Papers and Short Notes and Review Papers2006Low-energy computing
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423
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Rob Phillips
PLoS Computational Biology2012420
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Udo Seifert
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2014424
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Gideon Dror
Isaac Meilijson
Eytan Ruppin
PLoS Computational Biology2006421
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H. Ouerdane
C. Goupil
Ph Lecoeur
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Extended fluctuation-dissipation theorem for soft matter in stationary flowThomas Speck
Udo Seifert
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2009420
Nonequilibrium steady state of a nanometric biochemical system: Determining the thermodynamic driving force from single enzyme turnover time tracesWei Min
Liang Jiang
Ji Yu
S. C. Kou
Hong Qian
X. Sunney Xie
Nano Letters2005422
Transmission gate-based approximate adders for inexact computingZhixi Yang
Jie Han
Fabrizio Lombardi
Proceedings of the 2015 IEEE/ACM International Symposium on Nanoscale Architectures, NANOARCH 20152015approximate adder
approximate computing
error distance
error rate
low power
412
Transforming probabilities with combinational logicWeikang Qian
Marc D. Riedel
Hongchao Zhou
Jehoshua Bruck
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems2011Logic synthesis
probabilistic logic
probabilistic signals
random bit streams
stochastic bit streams
411
Role of mutual information in entropy production under information exchangesTakahiro Sagawa
Masahito Ueda
New Journal of Physics2013411
Thermodynamic work gain from entanglementKen Funo
Yu Watanabe
Masahito Ueda
Physical Review A - Atomic, Molecular, and Optical Physics2013410
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Michael R. Deweese
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2014410
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Juan Pablo Paz
Wojciech H. Zurek
Physical Review E2016418
Generating function formula of heat transfer in harmonic networksKeiji Saito
Abhishek Dhar
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Dissipated work in driven harmonic diffusive systems: General solution and application to stretching Rouse polymersT. Speck
Udo Seifert
European Physical Journal B2005410
Intensive thermodynamic parameters in nonequilibrium systemsEric Bertin
Kirsten Martens
Olivier Dauchot
Michel Droz
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2007400
Random-Pulse MachinesSergio T. RibeiroIEEE Transactions on Electronic Computers1967Arithmetic operations
logical gate
neuromime systems
parallel processors
pulse-rate analog coding
random-pulse sequences
400
An analog of the Boltzmann H-theorem (a Liapunov function) for systems of coupled chemical reactionsDavid ShearJournal of Theoretical Biology1967400
The (absence of a) relationship between thermodynamic and logical reversibilityO. J.E. MaroneyStudies in History and Philosophy of Science Part B - Studies in History and Philosophy of Modern Physics2005Computation
Information
Landauer's principle
Maxwell's demon
Statistical mechanics
Thermodynamics
401
The energy expansions of evolutionOlivia P. JudsonNature Ecology and Evolution2017403
Discriminatory proofreading regimes in nonequilibrium systemsArvind Murugan
David A. Huse
Stanislas Leibler
Physical Review X2014Biological physics
Materials science
Statistical physics
400
Thermodynamic and logical reversibilities revisitedTakahiro SagawaJournal of Statistical Mechanics: Theory and Experiment2014driven di-usive systems (theory)407
Humans are not cooperative breeders but practice biocultural reproductionBarry Bogin
Jared Bragg
Christopher Kuzawa
Annals of Human Biology2014Alloparenting
Childhood
Human life history
Lifetime reproductive effort
Longevity
408
On LICQ and the uniqueness of Lagrange multipliersGerd WachsmuthOperations Research Letters2013Constraint qualification
Lagrange multiplier
Optimality conditions
409
Free energy for protein folding from nonequilibrium simulations using the Jarzynski equalityDaniel K. West
Peter D. Olmsted
Emanuele Paci
Journal of Chemical Physics2006400
Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapesA. Mossa
M. Manosas
N. Forns
J. M. Huguet
F. Ritort
Journal of Statistical Mechanics: Theory and Experiment2009Bio-polymers) (experiment)
Bio-polymers) (theory)
Fluctuations (experiment)
Fluctuations (theory)
Mechanical properties (DNA
Membranes
RNA
400
Representation of nonequilibrium steady states in large mechanical systemsTeruhisa S. Komatsu
Naoko Nakagawa
Shin Ichi Sasa
Hal Tasaki
Journal of Statistical Physics2009Excess entropy production
Nonequilibrium steady state
Probability distribution
400
Easiness Assumptions and Hardness Tests: Trading Time for Zero ErrorValentine KabanetsJournal of Computer and System Sciences2001390
Progressive methylation of ageing histones by Dot1 functions as a timerDirk De Vos
Floor Frederiks
Marit Terweij
Tibor Van Welsem
Kitty F. Verzijlbergen
Ekaterina Iachina
Erik L. De Graaf
A. F. Maarten Altelaar
Gideon Oudgenoeg
Albert J.R. Heck
Jeroen Krijgsveld
Barbara M. Bakker
Fred Van Leeuwen
EMBO Reports2011H3K4
H3K79
Set1
cell cycle
chromatin
390
Logical computation on stochastic bit streams with linear finite-state machinesPeng Li
David J. Lilja
Weikang Qian
Marc D. Riedel
Kia Bazargan
IEEE Transactions on Computers2014Stochastic computing
finite-state machine (FSM)
stochastic bit streams
390
Effect of ligand diffusion on occupancy fluctuations of cell-surface receptorsAlexander M. Berezhkovskii
Attila Szabo
Journal of Chemical Physics2013390
Transfer entropy and transient limits of computationMikhail Prokopenko
Joseph T. Lizier
Scientific Reports2014393
Jarzynski equation for a simple quantum system: Comparing two definitions of workA. Engel
R. Nolte
EPL2007390
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noisePaul Maragakis
Felix Ritort
Carlos Bustamante
Martin Karplus
Gavin Crooks
Journal of Chemical Physics2008397
Onsager coefficients of a Brownian Carnot cycleY. Izumida
K. Okuda
European Physical Journal B2010390
Role of external flow and frame invariance in stochastic thermodynamicsThomas Speck
Jakob Mehl
Udo Seifert
Physical Review Letters2008391
Heat fluctuations in a nonequilibrium bathJ. R. Gomez-Solano
A. Petrosyan
S. Ciliberto
Physical Review Letters2011380
Computational selection of nucleic acid biosensors via a slip structure modelBradley Hall
Jay R. Hesselberth
Andrew D. Ellington
Biosensors and Bioelectronics2007Aptamer beacon
Aptazyme
Computational selection
Signaling aptamer
Slip structure
380
Generating Binary Sequences for Stochastic ComputingP. Jeavons
D. A. Cohen
J. Shawe-Taylor
IEEE Transactions on Information Theory1994Stochastic computing
neural networks
pseudorandom sequences
381
SRAM for error-tolerant applications with dynamic energy-quality management in 28 nm CMOSFabio Frustaci
Mahmood Khayatzadeh
David Blaauw
Dennis Sylvester
Massimo Alioto
IEEE Journal of Solid-State Circuits2015Error-tolerant
SRAM
approximate computing
energy-quality tradeoff
error-free
near-threshold
resiliency
ultra-low power processing
381
Accuracy of direct gradient sensing by cell-surface receptorsRobert G. Endres
Ned S. Wingreen
Progress in Biophysics and Molecular Biology2009Chemotaxis
Fluctuation-dissipation theorem
Gradient sensing
Ligand-receptor binding
Noise
380
Reducing Intrinsic Biochemical Noise in Cells and Its Thermodynamic LimitHong QianJournal of Molecular Biology2006kinetics
nonequilibrium steady-state
phosphorylation energy hypothesis
proofreading
protein specificity
383
Improving free-energy estimates from unidirectional work measurements: Theory and experimentMatteo Palassini
Felix Ritort
Physical Review Letters2011380
An effect of DNA sequence on nucleosome occupancy and removalXin Wang
Gene O. Bryant
Monique Floer
Dan Spagna
Mark Ptashne
Nature Structural and Molecular Biology2011371
Dynamics of cooperativity in chemical sensing among cell-surface receptorsMonica Skoge
Yigal Meir
Ned S. Wingreen
Physical Review Letters2011370
Finite-time erasing of information stored in fermionic bitsGiovanni Diana
G. Baris Bagci
Massimiliano Esposito
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2013371
Entropy production of cyclic population dynamicsBenjamin Andrae
Jonas Cremer
Tobias Reichenbach
Erwin Frey
Physical Review Letters2010372
On the generation of cryptographically strong pseudo-random sequencesAdi ShamirLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)1981361
Work fluctuations for a harmonic oscillator driven by an external random forceSanjib SabhapanditEPL2011361
A spectral transform approach to stochastic circuitsArmin Alaghi
John P. Hayes
Proceedings - IEEE International Conference on Computer Design: VLSI in Computers and Processors2012Design methodology
logic synthesis
probabilistic methods
stochastic computing
360
Stochastic energetics for non-Gaussian processesKiyoshi Kanazawa
Takahiro Sagawa
Hisao Hayakawa
Physical Review Letters2012361
Test of steady-state fluctuation theorem in turbulent Rayleigh- Bénard convectionX. D. Shang
P. Tong
K. Q. Xia
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2005360
On universality in ageing ferromagnetsChristophe ChatelainJournal of Statistical Mechanics: Theory and Experiment2004coarseningpro cesses (theory)360
Heat and work fluctuations for a harmonic oscillatorSanjib SabhapanditPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics2012350
Dynamics of a tracer granular particle as a nonequilibrium Markov processAndrea Puglisi
Paolo Visco
Emmanuel Trizac
Frédéric Van Wijland
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Thermodynamic cost of measurementsLéo Granger
Holger Kantz
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2011351
Fluctuation theorem for the flashing ratchet model of molecular motorsD. Lacoste
K. Mallick
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2009340
Estimate of the free energy difference in mechanical systems from work fluctuations: Experiments and modelsF. Douarche
S. Ciliberto
A. Petrosyan
Journal of Statistical Mechanics: Theory and Experiment2005Dynamical processes (experiment)
Fluctuations (experiment)
Fluctuations (theory)
Mechanical properties (DNA
RNA
biopolymers) (experiment)
membranes
340
Stochastic arithmetic implementations of neural networks with in situ learningJeffrey A. Dickson
Robert D. McLeod
Howard C. Card
IEEE International Conference on Neural Networks - Conference Proceedings1993342
Seflab: A lab for measuring software energy footprintsMiguel A. Ferreira
Eric Hoekstra
Bo Merkus
Bram Visser
Joost Visser
2013 2nd International Workshop on Green and Sustainable Software, GREENS 2013 - Proceedings2013Energy efficiency
Green products
Sotlware Engineering
lndex 1erms
345
Jarzynski equality for the Jepsen gasI. Bena
C. Van Den Broeck
R. Kawai
Europhysics Letters2005340
Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levelsSylvia C. Tippmann
Robert Ivanek
Dimos Gaidatzis
Anne Schöler
Leslie Hoerner
Erik Van Nimwegen
Michael B. Stadler
Dirk Schübeler
Peter Stadler
Molecular Systems Biology2012RNA decay
chromatin
histone modifications
microRNA
transcriptional regulation
340
A graph-theoretical approach for the analysis and model reduction of complex-balanced chemical reaction networksShodhan Rao
Arjan van der Schaft
Bayu Jayawardhana
Journal of Mathematical Chemistry2013Equilibria
Linkage classes
Persistence conjecture
Schur complement
Weighted Laplacian matrix
Zero-deficiency networks
340
Fluctuation theorems in the presence of information gain and feedbackSourabh Lahiri
Shubhashis Rana
A. M. Jayannavar
Journal of Physics A: Mathematical and Theoretical2012340
Entropy production and fluctuation theorems under feedback control: The molecular refrigerator model revisitedT. Munakata
M. L. Rosinberg
Journal of Statistical Mechanics: Theory and Experiment2012large deviations in non-equilibrium systems
stationary states
stochastic particle dynamics (theory)
340
Entropy and Nonlinear Nonequilibrium Thermodynamic Relation for Heat Conducting Steady StatesTeruhisa S. Komatsu
Naoko Nakagawa
Shin ichi Sasa
Hal Tasaki
Journal of Statistical Physics2011Clausius relation
Excess heat
Nonequilibrium steady states
340
Higher coordination with less control-a result of information maximization in the sensorimotor loopKeyan Zahedi
Nihat Ay
Ralf Der
Adaptive Behavior2010embodied artificial intelligence
information theory
predictive information
self-organized learning
sensorimotor loop
331
Effect of feedback on the fidelity of information transmission of time-varying signalsWiet Hendrik De Ronde
Filipe Tostevin
Pieter Rein ten Wolde
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2010333
Determining cortical landscapesJack W. ScannellNature1997330
Interpreting hippocampal function as recoding and forecastingWilliam B. Levy
Ashlie B. Hocking
Xiangbao Wu
Neural Networks2005CA3
Chaotic
Chunking
Cognition
Cognitive mapping
Context
Prediction
Randomization
Recoding
Synaptic modification
Trace conditioning
Transitive inference
Transverse patterning
330
Resolution of nested neuronal representations can be exponential in the number of neuronsAlexander Mathis
Andreas V.M. Herz
Martin B. Stemmler
Physical Review Letters2012330
Steady-state balance conditions for molecular motor cycles and stochastic nonequilibrium processesS. Liepelt
R. Lipowsky
EPL2007330
Synthetic mechanochemical molecular swimmerRamin GolestanianPhysical Review Letters2010330
Factoring numbers in O(logn) arithmetic stepsAdi ShamirInformation Processing Letters1979Factoring algorithms
arithmetic complexity
prime numbers
3210
A bound particle coupled to two thermostatsHans C. Fogedby
Alberto Imparato
Journal of Statistical Mechanics: Theory and Experiment2011current fluctuations
exact results
large deviations in non-equilibrium systems
stochastic particle dynamics (theory)
320
A Simple Histone Code Opens Many Paths to EpigeneticsKim Sneppen
Ian B. Dodd
PLoS Computational Biology2012322
Optical polarization evolution near a non-Hermitian degeneracyM. V. BerryJournal of Optics2011Stokes phenomenon
adiabatic
asymptotics
crystal optics
exceptional point
propagation
two-state
320
Work and dissipation fluctuations near the stochastic resonance of a colloidal particleP. Jop
A. Petrosyan
S. Ciliberto
EPL2008320
STRAUSS: Spectral Transform Use in Stochastic Circuit SynthesisArmin Alaghi
John P. Hayes
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems2015Logic synthesis
design methodology
probabilistic methods
stochastic circuit optimization
stochastic computing
320
Jarzynski equality modified in the linear feedback systemYouhei Fujitani
Hiroyuki Suzuki
Journal of the Physical Society of Japan2010Helmholtz free-energy
Separation theorem
The second law
Time-reversal process
321
Bona fide stochastic resonance: A view point from stochastic energeticsDebasis Dan
A. M. Jayannavar
Physica A: Statistical Mechanics and its Applications2005Bona fide resonance
Stochastic energetics
Stochastic resonance
320
Architecture and Statistical Model of a Pulse-Mode Digital Multilayer Neural NetworkYoung Chul Kim
Michael A. Shanblatt
IEEE Transactions on Neural Networks1995310
Correlated evolution of nearby residues in drosophilid proteinsBenjamin Callahan
Richard A. Neher
Doris Bachtrog
Peter Andolfatto
Boris I. Shraiman
PLoS Genetics2011310
Helical logicRalph C. Merkle
K. Eric Drexler
Nanotechnology1996313
Optimal Prediction by Cellular Signaling NetworksNils B. Becker
Andrew Mugler
Pieter Rein ten Wolde
Physical Review Letters2015310
Physical Limit to Concentration Sensing Amid Spurious LigandsThierry MoraPhysical Review Letters2015310
Darwinian demons, evolutionary complexity, and information maximizationDavid C. KrakauerChaos2011312
Energy Cost of Proofreading to Increase Fidelity of Transfer Ribonucleic Acid AminoacylationMichael A. Savageau
Rolf R. Freter
Biochemistry1979310
Could information theory provide an ecological theory of sensory processing?Joseph J. AtickNetwork: Computation in Neural Systems2011310
Quantum speed limits-primer, perspectives, and potential future directionsMichael R. FreyQuantum Information Processing2016Entanglement
Geometrical state space perspective
Krotov algorithm
Mandelstam–Tamm inequality
Margolus–Levitin inequality
Non-unitary evolution
Open systems
Quantum Fisher information
Quantum brachistochrone
Quantum control
Quantum speed limit
Quantum state evolution
319
Performance of quantum Otto refrigerators with squeezingRui Long
Wei Liu
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2015310
Transient fluctuation relations for time-dependent particle transportAlexander Altland
Alessandro De Martino
Reinhold Egger
Boris Narozhny
Physical Review B - Condensed Matter and Materials Physics2010310
Far-from-equilibrium measurements of thermodynamic lengthEdward H. Feng
Gavin Crooks
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2009311
Article for analog vector algebra computationAllen P. Mills
Bernard Yurke
Philip M. Platzman
BioSystems1999DNA computing
Hopfield network
Neural networks
301
Digital and analog gene circuits for biotechnologyNathaniel Roquet
Timothy K. Lu
Biotechnology Journal2014Analog gene circuit
Digital gene circuit
Memory
Metabolic engineering
Synthetic biology
300
Stretching the limits of clock-gating efficiency in server-class processorsHans Jacobson
Pradip Bose
Zhigang Hu
Alper Buyuktosunoglu
Victor Zyuban
Rick Eickemeyer
Lee Eisen
John Griswell
Doug Logan
Balaram Sinharoy
Joel Tendier
Proceedings - International Symposium on High-Performance Computer Architecture2005301
Adapt locally and act globally: Strategy to maintain high chemoreceptor sensitivity in complex environmentsGanhui Lan
Sonja Schulmeister
Victor Sourjik
Yuhai Tu
Molecular Systems Biology2011bacterial chemotaxis
high sensitivity to multiple signals
methylation crosstalk
mixed receptor cluster
sensory adaptation
300
Quantum dynamical field theory for nonequilibrium phase transitions in driven open systemsJamir Marino
Sebastian Diehl
Physical Review B2016301
Nonequilibrium work distributions for a trapped Brownian particle in a time-dependent magnetic fieldArnab Saha
A. M. Jayannavar
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2008300
Non-equilibrium steady states: Maximization of the Shannon entropy associated with the distribution of dynamical trajectories in the presence of constraintsCécile MonthusJournal of Statistical Mechanics: Theory and Experiment2011current fluctuations
optimization under uncertainty
stationary states
statistical inference
300
Closed-loop control strategy with improved current for a flashing ratchetL. Dinis
J. M.R. Parrondo
F. J. Cao
Europhysics Letters2005300
Sampling adsorbing staircase walks using a new Markov chain decomposition methodRussell A. Martin
Dana Randall
Annual Symposium on Foundations of Computer Science - Proceedings2000291
Increasing utilization in modern warehouse-scale computers using Bubble-UpJason Mars
Lingjia Tang
Kevin Skadron
Mary Lou Soffa
Robert Hundt
IEEE Micro2012Bubble-up
performance degradation
quality of service
warehouse-scale computer
290
Innovation in gene regulation: The case of chromatin computationSonja J. Prohaska
David C. Krakauer
Peter Stadler
Journal of Theoretical Biology2010Chromatin
Evolution
Gene regulation
290
Feed-forward loops and diamond motifs lead to tunable transmission of information in the frequency domainW. H. De Ronde
F. Tostevin
P. R. Ten Wolde
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2012292
Integral quantum fluctuation theorems under measurement and feedback controlKen Funo
Yu Watanabe
Masahito Ueda
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2013290
Fluctuation theorems for an asymmetric rotor in a granular gasSylvain Joubaud
Detlef Lohse
Devaraj Van Der Meer
Physical Review Letters2012290
Fluctuations of the total entropy production in stochastic systemsS. Joubaud
N. B. Garnier
S. Ciliberto
EPL2008290
Exactly solvable model for driven dissipative systemsYair Srebro
Dov Levine
Physical Review Letters2004280
Heat flow in chains driven by thermal noiseHans C. Fogedby
Alberto Imparato
Journal of Statistical Mechanics: Theory and Experiment2012heat conduction
large deviations in non-equilibrium systems
280
The lag-phase during diauxic growth is a trade-off between fast adaptation and high growth rateDominique Chu
David J. Barnes
Scientific Reports2016282
Barriers and silencers: A theoretical toolkit for control and containment of nucleosome-based epigenetic statesIan B. Dodd
Kim Sneppen
Journal of Molecular Biology2011bistability
chromatin
nucleosome modification
positive feedback
stochastic modeling
281
Fundamental limits on sensing chemical concentrations with linear biochemical networksChristopher C. Govern
Pieter Rein ten Wolde
Physical Review Letters2012283
An estimate of the total DNA in the biosphereHanna K.E. Landenmark
Duncan H. Forgan
Charles S. Cockell
PLoS Biology2015280
Rate of Mutual Information Between Coarse-Grained Non-Markovian VariablesAndre C. Barato
David Hartich
Udo Seifert
Journal of Statistical Physics2013Entropy production
Mutual information
Non-Markov processes
284
An information-theoretic equality implying the Jarzynski relationVlatko VedralJournal of Physics A: Mathematical and Theoretical2012280
Dental and skeletal growth in early fossil homininsM. Christopher Dean
Victoria S. Lucas
Annals of Human Biology2009Enamel
Growth
Hominin
Incremental markings
Teeth
280
Beyond Feast-Famine: Brain evolution, human life history, and the metabolic syndromeChristopher W. KuzawaHuman Evolutionary Biology2010281
Measurement of work in single-molecule pulling experimentsAlessandro Mossa
Sara De Lorenzo
Josep Maria Huguet
Felix Ritort
Journal of Chemical Physics2009280
Injected power and entropy flow in a heated granular gasP. Visco
A. Puglisi
A. Barrat
E. Trizac
F. Van Wljland
Europhysics Letters2005280
On the work - Hamiltonian connection in manipulated systemsLuca PelitiJournal of Statistical Mechanics: Theory and Experiment2008Large deviations in non-equilibrium systems280
Invariant quantities in shear flowA. Baule
R. M.L. Evans
Physical Review Letters2008280
Microrheology and the fluctuation theorem in dense colloidsL. G. Wilson
A. W. Harrison
W. C.K. Poon
A. M. Puertas
EPL2011270
Effective temperatures of a heated Brownian particleL. Joly
S. Merabia
J. L. Barrat
EPL2011270
Curie's principleA. F. ChalmersBritish Journal for the Philosophy of Science1970270
The hidden simplicity of biologyPaul C.W. Davies
Sara Imari Walker
Reports on Progress in Physics2016biological laws
complexity
emergence
276
Uniform approximation and Bernstein polynomials with coefficients in the unit intervalWeikang Qian
Marc D. Riedel
Ivo Rosenberg
European Journal of Combinatorics2011270
How Far is Complex Balancing from Detailed Balancing?Alicia Dickenstein
Mercedes Pérez Millán
Bulletin of Mathematical Biology2011Complex balancing
Detailed balancing
General kinetics
Mass action
270
Chemical sensing by nonequilibrium cooperative receptorsMonica Skoge
Sahin Naqvi
Yigal Meir
Ned S. Wingreen
Physical Review Letters2013270
Complex and detailed balancing of chemical reaction networks revisitedArjan van der Schaft
Shodhan Rao
Bayu Jayawardhana
Journal of Mathematical Chemistry2015Complex balancing
Detailed balancing
Mass action kinetics
Reaction networks
Stability
Wegscheider conditions
273
Quantum discord and Maxwell’s demonsWojciech Hubert ZurekPhysical Review A - Atomic, Molecular, and Optical Physics2003270
On the efficiency of path sampling methods for the calculation of free energies from non-equilibrium simulationsWolfgang Lechner
Christoph Dellago
Journal of Statistical Mechanics: Theory and Experiment2007Driven diffusive systems (theory)
Exact results
270
Inertial effects in nonequilibrium work fluctuations by a path integral approachTooru Taniguchi
E. G.D. Cohen
Journal of Statistical Physics2008Critical mass
Inertial effects
Laboratory and comoving frames
Nonequilibrium work fluctuations and theorem
Path integration
270
Dissipation Bound for Thermodynamic ControlBenjamin B. MachtaPhysical Review Letters2015260
How much non-coding DNA do eukaryotes require?Sebastian E. Ahnert
Andrei Zinovyev
Thomas M.A. Fink
Journal of Theoretical Biology2008Accelerated networks
Genetic networks
Minimum
Prokaryotes
260
Quantum Extension of the Jarzynski Relation: Analogy with Stochastic DephasingShaul MukamelPhysical Review Letters2003260
The stochastic pump current and the non-adiabatic geometrical phaseJun OhkuboJournal of Statistical Mechanics: Theory and Experiment2008New applications of statistical mechanics
Transport processes/heat transfer (theory)
260
Fluctuation-preserving coarse graining for biochemical systemsBernhard Altaner
Jürgen Vollmer
Physical Review Letters2012260
Probability density functions of work and heat near the stochastic resonance of a colloidal particleAlberto Imparato
Pierre Jop
Artyom Petrosyan
Sergio Ciliberto
Journal of Statistical Mechanics: Theory and Experiment2008Brownian motion
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Stochastic particle dynamics (theory)
fluctuations (theory)
260
Generalized einstein or green-kubo relations for active biomolecular transportUdo SeifertPhysical Review Letters2010250
Directing reprogramming to pluripotency by transcription factorsKenjiro Adachi
Hans R. Schöler
Current Opinion in Genetics and Development2012250
Dynamic force spectroscopy of DNA hairpins: II. Irreversibility and dissipationM. Manosas
A. Mossa
N. Forns
J. M. Huguet
F. Ritort
Journal of Statistical Mechanics: Theory and Experiment2009Bio-polymers) (theory)
Fluctuations (experiment)
Fluctuations (theory)
Mechanical properties (DNA
Membranes
RNA
bio-polymers) (experiment)
250
Information and maximum power in a feedback controlled Brownian ratchetM. Feito
F. J. Cao
European Physical Journal B2007250
Recovery of state-specific potential of molecular motor from single-molecule trajectoryShoichi Toyabe
Hiroshi Ueno
Eiro Muneyuki
EPL2012251
Experimental accessibility of generalized fluctuation-dissipation relations for nonequilibrium steady statesJakob Mehl
Valentin Blickle
Udo Seifert
Clemens Bechinger
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2010251
Generalised Einstein relation for hot Brownian motionD. Chakraborty
M. V. Gnann
D. Rings
J. Glaser
F. Otto
F. Cichos
K. Kroy
EPL2011250
Reconstructing the free-energy landscape of a mechanically unfolded model proteinAlberto Imparato
Stefano Luccioli
Alessandro Torcini
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Ueber die mechanischen Analogien des zweiten Hauptsatzes der ThermodynamikLudwig BoltzmannJournal fur die Reine und Angewandte Mathematik1887241
Resolution lower bounds for the weak functional pigeonhole principleAlexander A. RazborovTheoretical Computer Science2003240
Variational formula for experimental determination of high-order correlations of current fluctuations in driven systemsTakahiro Nemoto
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Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2011240
Exact path-integral evaluation of the heat distribution function of a trapped Brownian oscillatorDebarati Chatterjee
Binny J. Cherayil
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Reversible programming languages
241
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Jan P. Amend
John Doyle
Tori Hoehler
Chris Kempes
ISME Journal2016240
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Charles P. Ratliff
Jennifer M. Klein
Peter Sterling
David H. Brainard
Vijay Balasubramanian
PLoS Computational Biology2010240
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Paul Dean
PLoS Computational Biology2008240
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Michio Otsuki
Hisao Hayakawa
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Artyom Petrosyan
Sergio Ciliberto
Christian Maes
Journal of Statistical Mechanics: Theory and Experiment2011Brownian motion
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240
Asymptotics of work distributions in nonequilibrium systemsA. EngelPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics2009240
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Keshab K. Parhi
Marc D. Riedel
ACS Synthetic Biology2017DNA strand-displacement reaction
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Polynomials
242
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Landauer's principle
Natural selection
Thermodynamics
240
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A. Puglisi
A. Vulpiani
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Stochastic particle dynamics (theory)
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230
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M. Feito
H. Touchette
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Closed-loop
Feedback
Information
Ratchet
230
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Derandomization
Pseudorandomness
Random walks on expander graphs
221
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220
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220
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C. Piazza
A. Policriti
M. Simeoni
B. Mishra
Theoretical Computer Science2004Biochemical models
Bisimulation
Collapsing
Hybrid automata
210
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211
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