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Thermodynamics of Computation

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From Thermodynamics of Computation
 Author nameSource nameYearKeyword
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
Minimal energy requirements in communicationRolf LandauerScience1996
Engineering aspects of enzymatic signal transduction: Photoreceptors in the retinaPeter B. Detwiler
Sharad Ramanathan
Anirvan Sengupta
Boris I. Shraiman
Biophysical Journal2000
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
NeuroImage2011
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
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 Letters2005
Targeting olfactionPeter MombaertsCurrent Opinion in Neurobiology1996
Genetic networks: Small numbers of big moleculesNina Fedoroff
Walter Fontana
Science2002
Does replication‐induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli?Purnananda GuptasarmaBioEssays1995
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 Journal2006
Mutual information between input and output trajectories of biochemical networksFilipe Tostevin
Pieter Rein ten Wolde
Physical Review Letters2009
Stochastic thermodynamics of chemical reaction networksTim Schmiedl
Udo Seifert
Journal of Chemical Physics2007
Thermodynamics of predictionSusanne Still
David A. Sivak
Anthony J. Bell
Gavin Crooks
Physical Review Letters2012
The Stokes efficiency for molecular motors and its applicationsHongyun Wang
G. Oster
Europhysics Letters2002
Fifty years of the VSEPR modelR. J. GillespieCoordination Chemistry Reviews2008LCP model: Lone pairs
Molecular geometry
VSEPR model
Asymmetric division of Drosophila male germline stem cell shows asymmetric histone distributionVuong Tran
Cindy Lim
Jing Xie
Xin Chen
Science2012
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)
Principles underlying mammalian neocortical scalingMark A. ChangiziBiological Cybernetics2001
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 Biology2011
Steady state thermodynamicsY Oono
Paniconi M 1998
Theor. Phys. Suppl2006Fluctuation
Nonequilibrium steady state
Thermodynamics
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)
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
Universal features in the energetics of symmetry breakingÉ Roldán
I. A. Martínez
J. M.R. Parrondo
D. Petrov
Nature Physics2014
Multivariate information transmissionWilliam J. McGillIRE Professional Group on Information Theory1954
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 Biology2011
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 Physics2011
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 Biology2009
Application-level correctness and its impact on fault toleranceXuanhua Li
Donald Yeung
Proceedings - International Symposium on High-Performance Computer Architecture2007
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 Letters2006
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
Stochastic signal processing and transduction in chemotactic response of eukaryotic cellsMasahiro Ueda
Tatsuo Shibata
Biophysical Journal2007
Grid cells generate an analog error-correcting code for singularly precise neural computationSameet Sreenivasan
Ila Fiete
Nature Neuroscience2011
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
Efficiency of autonomous soft nanomachines at maximum powerUdo SeifertPhysical Review Letters2011
Feedback control in a collective flashing ratchetFrancisco J. Cao
Luis Dinis
Juan M.R. Parrondo
Physical Review Letters2004
A new notation for quantum mechanicsP. A.M. DiracMathematical Proceedings of the Cambridge Philosophical Society1939
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 Chemistry1991
The chromatin code of fungal secondary metabolite gene clustersAgnieszka Gacek
Joseph Strauss
Applied Microbiology and Biotechnology2012Aspergillus
Chromatin
Histone modifications
Secondary metabolism
Classical and quantum limitations on energy consumption in computationK. K. LikharevInternational Journal of Theoretical Physics1982
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
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
Extracting work from a single heat bath through feedbackD. Abreu
Udo Seifert
EPL2011
Calcium, the two-faced messenger of olfactory transduction and adaptationHugh R. Matthews
Johannes Reisert
Current Opinion in Neurobiology2003
Calcium signalling and regulation in olfactory neuronsAnna MeniniCurrent Opinion in Neurobiology1999
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 Letters2009
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 Communications2014
Stochasticity of gene products from transcriptional pulsingSrividya Iyer-Biswas
F. Hayot
C. Jayaprakash
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2009
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
Chemical kinetics is turing universalMarcelo O. MagnascoPhysical Review Letters1997
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
Work fluctuations for a Brownian particle between two thermostatsPaolo ViscoJournal of Statistical Mechanics: Theory and Experiment2006Stochastic particle dynamics (theory)
The Berry phase and the pump flux in stochastic chemical kineticsN. A. Sinitsyn
I. Nemenman
EPL2007
Observable dependence of fluctuation-dissipation relations and effective temperaturesSuzanne Fielding
Peter Sollich
Physical Review Letters2002
Efficiency of cellular information processingAndre C. Barato
David Hartich
Udo Seifert
New Journal of Physics2014cellular sensing
nonequilibrium processes
thermodynamics and information
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
Methods for quantifying the informational structure of sensory and motor dataMax Lungarella
Teresa Pegors
Daniel Bulwinkle
Olaf Sporns
Neuroinformatics2005Embodiment
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 Psychiatry2010Connectivity
Default mode
Endogenous
Networks
Oscillations
Global and regional brain metabolic scaling and its functional consequencesJan KarbowskiBMC Biology2007
Predictive information and explorative behavior of autonomous robotsN. Ay
N. Bertschinger
R. Der
F. Güttler
E. Olbrich
European Physical Journal B2008
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
Maxwell's demon and quantum-dot cellular automataJohn Timler
Craig S. Lent
Journal of Applied Physics2003
Single-ensemble nonequilibrium path-sampling estimates of free energy differencesF. Marty Ytreberg
Daniel M. Zuckerman
Journal of Chemical Physics2004
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
The synthesis of robust polynomial arithmetic with stochastic logicWeikang Qian
Marc D. Riedel
Proceedings - Design Automation Conference2008Polynomial arithmetic
Probabilistic logic
Stochastic logic
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
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
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 Physics2012
A quantitative estimation of the global translational activity in logarithmically growing yeast cellsTobias von der HaarBMC Systems Biology2008
The Value of Information for Populations in Varying EnvironmentsOlivier Rivoire
Stanislas Leibler
Journal of Statistical Physics2011Branching processes
Control
Fitness
Information
Investment
Population dynamics
Regulation
The berg-purcell limit revisitedKazunari Kaizu
Wiet De Ronde
Joris Paijmans
Koichi Takahashi
Filipe Tostevin
Pieter Rein ten Wolde
Biophysical Journal2014
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 results
The Effect of Phenobarbitone Anaesthesia on Blood Flow and Oxygen Consumption in the Rat BrainLorentz Nilsson
Bo K. Siesjó
Acta Anaesthesiologica Scandinavica1975
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 Letters2011
Measurement of stochastic entropy productionC. Tietz
S. Schuler
T. Speck
J. Wrachtrup
Udo Seifert
Physical Review Letters2006
Heat generation required by information erasureKousuke ShizumePhysical Review E1995
Dissipation-error tradeoff in proofreadingCharles H. BennettBioSystems1979
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
Efficiency of molecular motors at maximum powerT. Schmiedl
Udo Seifert
EPL2008
Ueber die bewegende Kraft der Wärme und die Gesetze, welche sich daraus für die Wärmelehre selbst ableiten lassenR. ClausiusAnnalen der Physik1850
The cell cycle switch computes approximate majorityLuca Cardelli
Attila Csikász-Nagy
Scientific Reports2012
A master equation description of local fluctuationsM. Malek-Mansour
G. Nicolis
Journal of Statistical Physics1975Fluctuations
master equations
nonequilibrium thermodynamics
nonlinear systems
stochastic processes
Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling switchHong Qian
Timothy C. Reluga
Physical Review Letters2005
Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equalityIoan Kosztin
Bogdan Barz
Lorant Janosi
Journal of Chemical Physics2006
Modelling the development of cortical systems networksMarcus Kaiser
Claus C. Hilgetag
Neurocomputing2004Cortical connectivity
Cortical systems development
Network growth
Optimal wiring
Reaching optimal efficiencies using nanosized photoelectric devicesB. Rutten
B. Cleuren
Massimiliano Esposito
Physical Review B - Condensed Matter and Materials Physics2009
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 Physics2010
Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensationHong QianPhysical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics2002
On rank vs. communication complexityNoam Nisan
Avi Wigderson
Combinatorica199505C50
68R05
Mathematics Subject Classification (1991): 68Q05
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 Physics2007
Covariation of residues in the homeodomain sequence familyNeil D. ClarkeProtein Science1995covariation
evolution
homeodomains
sequences
structure‐function
Engineering complex riboswitch regulation by dual genetic selectionVandana Sharma
Yoko Nomura
Yohei Yokobayashi
Journal of the American Chemical Society2008
Unifying three perspectives on information processing in stochastic thermodynamicsA. C. Barato
Udo Seifert
Physical Review Letters2014
Relationships between gene expression and brain wiring in the adult rodent brainLeon French
Paul Pavlidis
PLoS Computational Biology2011
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 Physics2005
Dissipation and lag in irreversible processesS. Vaikuntanathan
C. Jarzynski
EPL2009
The minimal work cost of information processingPhilippe Faist
Frédéric Dupuis
Jonathan Oppenheim
Renato Renner
Nature Communications2015
Information thermodynamics on causal networksSosuke Ito
Takahiro Sagawa
Physical Review Letters2013
Dietary constraints on encephalization in primatesJennifer L. Fish
Charles A. Lockwood
American Journal of Physical Anthropology2003Brain size
Comparative methods
Expensive tissue hypothesis
Independent contrasts
Receptive fields and functional architecture in the retinaVijay Balasubramanian
Peter Sterling
Journal of Physiology2009
Unattainability of Carnot efficiency in the Brownian heat engineTsuyoshi Hondou
Ken Sekimoto
Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics2000
Relative entropy: Free energy associated with equilibrium fluctuations and nonequilibrium deviationsHong QianPhysical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics2001
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
Thermodynamic reversibility in feedback processesJordan M. Horowitz
Juan M.R. Parrondo
EPL2011
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
Maxwell's refrigerator: An exactly solvable modelDibyendu Mandal
H. T. Quan
Christopher Jarzynski
Physical Review Letters2013
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
Compendium of the Foundations of Classical Statistical PhysicsJos UffinkPhilosophy of Physics2007
Optimized free energies from bidirectional single-molecule force spectroscopyDavid D.L. Minh
Artur B. Adib
Physical Review Letters2008
Kinetics of reversible diffusion influenced reactions: The self-consistent relaxation time approximationIrina V. Gopich
Attila Szabo
Journal of Chemical Physics2002
Maximum likelihood and the single receptorRobert G. Endres
Ned S. Wingreen
Physical Review Letters2009
Thermodynamics of genuine nonequilibrium states under feedback controlDavid Abreu
Udo Seifert
Physical Review Letters2012
Digital genetics: Unravelling the genetic basis of evolutionChristoph AdamiNature Reviews Genetics2006
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
Fluctuation theorem for transport in mesoscopic systemsDavid Andrieux
Pierre Gaspard
Journal of Statistical Mechanics: Theory and Experiment2006Current fluctuations
Exact results
Stationary states (theory)
Fluctuation theorems for quantum processesTameem Albash
Daniel A. Lidar
Milad Marvian
Paolo Zanardi
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2013
An update on the nonequilibrium linear responseM. Baiesi
C. Maes
New Journal of Physics2013
Fluctuation theorem for a single enzym or molecular motorUdo SeifertEurophysics Letters2005
On a hypothetical generational relationship between HCN and constituents of the reductive citric acid cycleAlbert EschenmoserChemistry and Biodiversity2007
Perfect and near-perfect adaptation in a model of bacterial chemotaxisBernardo A. Mello
Yuhai Tu
Biophysical Journal2003
Non-equilibrium work relationsJorge KurchanJournal of Statistical Mechanics: Theory and Experiment2007Current fluctuations
Stochastic particle dynamics (theory)
Transport processes/heat transfer (theory)
Stochastic thermodynamics of single enzymes and molecular motorsUdo SeifertEuropean Physical Journal E2011
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 Physics1999
Thermodynamic universality of quantum Carnot enginesBartłomiej Gardas
Sebastian Deffner
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2015
Nonequilibrium work fluctuations for oscillators in non-Markovian bathsTrieu Mai
Abhishek Dhar
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2007
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 Physics2005
Realization of a feedback controlled flashing ratchetBenjamin J. Lopez
Nathan J. Kuwada
Erin M. Craig
Brian R. Long
Heiner Linke
Physical Review Letters2008
Nonequilibrium fluctuations and mechanochemical couplings of a molecular motorA. W.C. Lau
D. Lacoste
K. Mallick
Physical Review Letters2007
Mapping out-of-equilibrium into equilibrium in one-dimensional transport modelsJulien Tailleur
Jorge Kurchan
Vivien Lecomte
Journal of Physics A: Mathematical and Theoretical2008
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)2011
Physical Responses of Bacterial ChemoreceptorsAdy Vaknin
Howard C. Berg
Journal of Molecular Biology2007chemotaxis
fluorescence polarization
fluorescence resonance energy transfer
membrane proteins
receptors
Imitating chemical motors with optimal information motorsJordan M. Horowitz
Takahiro Sagawa
Juan M.R. Parrondo
Physical Review Letters2013
An autonomous and reversible Maxwell's demonUdo Seifert
A. C. Barato
EPL2013
The statistical neuroanatomy of frontal networks in the macaqueBruno B. Averbeck
Moonsang Seo
PLoS Computational Biology2008
Motor-Driven Dynamics in Actin-Myosin NetworksLoïc Le Goff
François Amblard
Eric M. Furst
Physical Review Letters2002
Heat conduction in a three dimensional anharmonic crystalKeiji Saito
Abhishek Dhar
Physical Review Letters2010
Exploring the thermodynamic limits of computation in integrated systems: Magnetic memory, nanomagnetic logic, and the landauer limitBrian Lambson
David Carlton
Jeffrey Bokor
Physical Review Letters2011
Thermodynamics of feedback controlled systemsF. J. Cao
M. Feito
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2009
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
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
Alternative splicing in the nervous system: An emerging source of diversity and regulationChristopher J. Lee
Kris Irizarry
Biological Psychiatry2003Alternative splicing
Genomics
Receptors
mRNA
Length of time's arrowEdward H. Feng
Gavin Crooks
Physical Review Letters2008
Entropy production in full phase space for continuous stochastic dynamicsRichard E. Spinney
Ian J. Ford
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2012
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
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
An introduction to population protocolsJames Aspnes
Eric Ruppert
Middleware for Network Eccentric and Mobile Applications2009
Integrated information increases with fitness in the evolution of animatsJeffrey A. Edlund
Nicolas Chaumont
Arend Hintze
Christof Koch
Giulio Tononi
Christoph Adami
PLoS Computational Biology2011
Thermodynamic constraints on kinetic proofreading in biosynthetic pathwaysM. Ehrenberg
C. Blomberg
Biophysical Journal1980
Generalized detailed fluctuation theorem under nonequilibrium feedback controlM. PonmuruganPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics2010
Optimal protocols for minimal work processes in underdamped stochastic thermodynamicsAlex Gomez-Marin
Tim Schmiedl
Udo Seifert
Journal of Chemical Physics2008
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
Monge-Kantorovich optimal mass transport
Second Law of Thermodynamics
Stochastic thermodynamics for Maxwell demon feedbacksMassimiliano Esposito
Gernot Schaller
EPL2012
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
Escorted free energy simulations: Improving convergence by reducing dissipationSuriyanarayanan Vaikuntanathan
Christopher Jarzynski
Physical Review Letters2008
Finite-time thermodynamics for a single-level quantum dotR. Kawai
K. Lindenberg
C. Van Den Broeck
Massimiliano Esposito
EPL2010
Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard-sphere liquidHuan Xiang Zhou
Attila Szabo
Journal of Chemical Physics1991
Second-law-like inequalities with information and their interpretationsJordan M. Horowitz
Henrik Sandberg
New Journal of Physics2014feedback
information theory
nonequilibrium thermodynamics
optimal control theory
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 Physiology2003
Invisibility in non-Hermitian tight-binding latticesStefano LonghiPhysical Review A - Atomic, Molecular, and Optical Physics2010
Pumped biochemical reactions, nonequilibrium circulation, and stochastic resonanceHong Qian
Min Qian
Physical Review Letters2000
Efficiency at maximum power output of linear irreversible Carnot-like heat enginesYang Wang
Z. C. Tu
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2012
Stochastic thermodynamics and sustainable efficiency in work productionB. Gaveau
M. Moreau
L. S. Schulman
Physical Review Letters2010
Optimal protocols and optimal transport in stochastic thermodynamicsErik Aurell
Carlos Mejía-Monasterio
Paolo Muratore-Ginanneschi
Physical Review Letters2011
Analog Computation by DNA Strand Displacement CircuitsTianqi Song
Sudhanshu Garg
Reem Mokhtar
Hieu Bui
John Reif
ACS Synthetic Biology2016DNA computing
DNA nanoscience
DNA nanotechnology
analog computation
molecular programming
self-assembly
Convergence in the olfactory system: quantitative aspects of odour sensitivityWim van Drongelen
Andre Holley
Kjell B. Døving
Journal of Theoretical Biology1978
The stochastic pump effect and geometric phases in dissipative and stochastic systemsN. A. SinitsynJournal of Physics A: Mathematical and Theoretical2009
Fluctuation theorems for a molecular refrigeratorKyung Hyuk Kim
Hong Qian
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics2007
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 Physics2006
Flight of the FINCH through the java wildernessMichael Orlov
Moshe Sipper
IEEE Transactions on Evolutionary Computation2011Automatic programming
Java bytecode
genetic programming (GP)
software evolution
Thermodynamic Costs of Information Processing in Sensory AdaptationPablo Sartori
Léo Granger
Chiu Fan Lee
Jordan M. Horowitz
PLoS Computational Biology2014
Geometric effects on complex network structure in the cortexJ. A. Henderson
P. A. Robinson
Physical Review Letters2011
Role of Astrocytes in Matching Blood Flow to Neuronal ActivityDanica Jakovcevic
David R. Harder
Current Topics in Developmental Biology2007
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
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