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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
Combinatorica1995Mathematics Subject Classification (1991): 68Q05
68R05
05C50
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