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From Thermodynamics of Computation
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List of results
- Programming DNA tube circumferences + (Peng Yin)
- Criticism of Feynman’s analysis of the ratchet as an engine + (Juan M. R. Parrondo)
- Run-time exploitation of application dynamism for energy-efficient exascale computing (READEX) + (Yury Oleynik)
- Correlated evolution of nearby residues in drosophilid proteins + (Benjamin Callahan)
- Engineering aspects of enzymatic signal transduction: Photoreceptors in the retina + (Peter B. Detwiler)
- The quiet revolution of numerical weather prediction + (Peter Bauer)
- Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality + (Daniel K. West)
- The limits of chemosensation vary across dimensions + (Brendan A. Bicknell)
- Analyzing molecular reaction networks: From pathways to chemical organizations + (Christoph Kaleta)
- Distribution of astroglia in glomeruli of the rat main olfactory bulb: Exclusion from the sensory subcompartment of neuropil + (T. Ivo Chao)
- The cost of cortical computation + (Peter Lennie)
- Drivers of bacterial maintenance and minimal energy requirements + (Peter M. van Bodegom)
- Targeting olfaction + (Peter Mombaerts)
- Brownian motors: Noisy transport far from equilibrium + (Peter Reimann)
- Propagation of histone marks and epigenetic memory during normal and interrupted DNA replication + (Peter Sarkies)
- Synergism between different germinant receptors in the germination of Bacillus subtilis spores + (Xuan Yi)
- Workshop report:Modeling the molecularmechanism of bacterial spore germination and elucidating reasons for germination heterogeneity + (Karl J. Indest)
- Molecular taxonomy of major neuronal classes in the adult mouse forebrain + (Ken Sugino)
- Observable dependence of fluctuation-dissipation relations and effective temperatures + (Suzanne Fielding)
- An intermediate level of abstraction for computational systems chemistry + (Jakob L. Andersen)
- Transitions from Nonliving to Living Matter + (Steen Rasmussen)
- Defining genes: A computational framework + (Sonja J. Prohaska)
- Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels + (Sylvia C. Tippmann)
- Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete + (Jakob L. Andersen)
- TRNAdb 2009: Compilation of tRNA sequences and tRNA genes + (Frank Jühling)
- Innovation in gene regulation: The case of chromatin computation + (Sonja J. Prohaska)
- Design of a trichromatic cone array + (Patrick Garrigan)
- Receptive fields and functional architecture in the retina + (Vijay Balasubramanian)
- How Much the Eye Tells the Brain + (Kristin Koch)
- Retina + (Peter Sterling)
- Chromatin and epigenetic regulation of pre-mrna processing + (Seth J. Brown)
- Pooled energy budgets: Resituating human energy -allocation trade-offs + (Karen L. Kramer)
- Systematic errors in free energy perturbation calculations due to a finite sample of configuration space: Sample-size hysteresis + (Robert H. Wood)
- Fluctuation theorems: Work is not an observable + (Peter Talkner)
- Erratum: Quantum fluctuation relations: Foundations and applications (Reviews of Modern Physics) + (Michele Campisi)
- Fluctuation theorem for arbitrary open quantum systems + (Michele Campisi)
- Broken symmetries and the masses of gauge bosons + (Peter W. Higgs)
- The Expensive-Tissue Hypothesis: The Brain and the Digestive System in Human and Primate Evolution + (Leslie C. Aiello)
- The anatomical distance of functional connections predicts brain network topology in health and schizophrenia + (Aaron F. Alexander-Bloch)
- Irreversibilities and efficiency at maximum power of heat engines: The illustrative case of a thermoelectric generator + (Y. Apertet)
- Small-world networks and functional connectivity in Alzheimer's disease + (C. J. Stam)
- Article for analog vector algebra computation + (Allen P. Mills)
- Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain + (Andrew J. Bannister)
- Optimum protocol for fast-switching free-energy calculations + (Philipp Geiger)
- Energetics and performance of a microscopic heat engine based on exact calculations of work and heat distributions + (Petr Chvosta)
- Thermodynamics of a physical model implementing a Maxwell demon + (Philipp Strasberg)
- Asymmetrically modified nucleosomes + (Philipp Voigt)
- Role of the polycomb protein EED in the propagation of repressive histone marks + (Raphael Margueron)
- The minimal work cost of information processing + (Philippe Faist)
- Optimal information storage and the distribution of synaptic weights: Perceptron versus Purkinje cell + (Nicolas Brunel)
- Argonaute proteins couple chromatin silencing to alternative splicing + (Maya Ameyar-Zazoua)
- Biased sampling of nonequilibrium trajectories: Can fast switching simulations outperform conventional free energy calculation methods? + (Harald Oberhofer)
- Untangling Complex Systems: A Grand Challenge for Science + (Pier Luigi Gentili)
- Soft computing: the convergence of emerging reasoning technologies + (Piero P. Bonissone)
- Computed tomography-estimated specific gravity of noncontused brain areas as a marker of severity in human traumatic brain injury + (Vincent Degos)
- Data Center Efficiency Assessment + (Pierre Delforge)
- Fluctuation theorem for currents and Schnakenberg network theory + (David Andrieux)
- Fluctuation theorem for nonequilibrium reactions + (Pierre Gaspard)
- Fluctuation theorem for transport in mesoscopic systems + (David Andrieux)
- Fluctuation theorems and the nonequilibrium thermodynamics of molecular motors + (David Andrieux)
- Network and thermodynamic conditions for a single macroscopic current fluctuation theorem + (David Andrieux)
- A fluctuation theorem for currents and non-linear response coefficients + (David Andrieux)
- Neuron-glia metabolic coupling and plasticity + (Pierre J. Magistretti)
- Probability density functions of work and heat near the stochastic resonance of a colloidal particle + (Alberto Imparato)
- Reversible space equals deterministic space + (Klaus Jörn Lange)
- Entropic tension in crowded membranes + (Martin Lindén)
- Thermodynamics of Computational Copying in Biochemical Systems + (Thomas E. Ouldridge)
- Thermodynamics of computational copying in biochemical systems + (Thomas E. Ouldridge)
- Fundamental limits on sensing chemical concentrations with linear biochemical networks + (Christopher C. Govern)
- Energy dissipation and noise correlations in biochemical sensing + (Christopher C. Govern)
- Mutual information between input and output trajectories of biochemical networks + (Filipe Tostevin)
- The berg-purcell limit revisited + (Kazunari Kaizu)
- Lower bound on the precision of transcriptional regulation and why facilitated diffusion can reduce noise in gene expression + (Joris Paijmans)
- Rare switching events in non-stationary systems + (Nils B. Becker)
- Forward flux sampling for rare event simulations + (Rosalind J. Allen)
- Effect of feedback on the fidelity of information transmission of time-varying signals + (Wiet Hendrik De Ronde)
- Fundamental Costs in the Production and Destruction of Persistent Polymer Copies + (Thomas E. Ouldridge)
- Role of spatial averaging in the precision of gene expression patterns + (Thorsten Erdmann)
- Diffusion of transcription factors can drastically enhance the noise in gene expression + (Jeroen S. Van Zon)
- Optimal Prediction by Cellular Signaling Networks + (Nils B. Becker)
- On the connection between computational and biochemical measurement + (Thomas E Ouldridge)
- Advocating noise as an agent for ultra-low energy computing: Probabilistic complementary metal-oxide-semiconductor devices and their characteristics + (Pinar Korkmaz)
- Using profile information to assist classic code optimizations + (Pohua P. Chang)
- Histone modifications at human enhancers reflect global cell-type-specific gene expression + (Nathaniel D. Heintzman)
- How the nature of an observation affects single-trajectory entropies + (Ying Li)
- Tolerating Soft Errors in Processor Cores Using CLEAR (Cross-Layer Exploration for Architecting Resilience) + (Eric Cheng)
- Stretching the limits of clock-gating efficiency in server-class processors + (Hans Jacobson)
- On the shoulders of giants: Properties of the stellar halo and the milky way mass distribution + (Prajwal Raj Kafle)
- The ManyBugs and IntroClass Benchmarks for Automated Repair of C Programs + (Claire Le Goues)
- The second wave of synthetic biology: From modules to systems + (Priscilla E.M. Purnick)
- Specific subtypes of cortical GABA interneurons contribute to the neurovascular coupling response to basal forebrain stimulation + (Ara Kocharyan)
- The lac repressor displays facilitated diffusion in living cells + (Petter Hammar)
- Nonequilibrium steady states in contact: Approximate thermodynamic structure and zeroth law for driven lattice gases + (Punyabrata Pradhan)
- Nonequilibrium fluctuation theorems in the presence of local heating + (Punyabrata Pradhan)
- Does replication‐induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli? + (Purnananda Guptasarma)
- Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase + (Qi Wang)
- Theory of Nonequilibrium Steady States + (D-Q Jiang)
- Understanding quantum work in a quantum many-body system + (Qian Wang)
- A Map of the Interactome Network of the Metazoan C. elegans + (Siming Li)
- Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification + (Minjia Tan)
- Covalent modifications of histones during mitosis and meiosis + (Dazhong Xu)
- Uncovering intrinsic modular organization of spontaneous brain activity in humans + (Yong He)
- Reviews of nonlinear dynamics and complexity Nonequilibrium Statistical Physics of Small Systems: Fluctuation Relations and Beyond (Weinheim: Wiley-VCH) + (R Klages)
- Precis of The Emperor's New Mind + (R Penrose)
- Reversibility, heat dissipation, and the importance of the thermal environment in stochastic models of nonequilibrium steady states + (R. A. Blythe)
- The quantum open system as a model of the heat engine + (R. Alicki)
- Cerebellar LTD and Pattern Recognition by Purkinje Cells + (Volker Steuber)
- Experimental implementation of a nonthermalizing quantum thermometer + (C. Raitz)
- The superfamily of heme-copper respiratory oxidases + (J. A. Garcia-Horsman)
- Reversible electronic logic using switches + (R. C. Merkle)
- On the symmetry of current probability distributions in jump processes + (R. Chetrite)
- Entropy production and fluctuation relations for a KPZ interface + (R. Chetrite)
- Experimental Verification of a Modified Fluctuation-Dissipation Relation for a Micron-Sized Particle in a Nonequilibrium Steady State + (R. Chetrite)
- Ueber die bewegende Kraft der Wärme und die Gesetze, welche sich daraus für die Wärmelehre selbst ableiten lassen + (R. Clausius)
- Measurement of 'true' glucose production rates in infancy and childhood with 6,6-dideuteroglucose + (D. M. Bier)
- Histone modifications at human enhancers reflect global cell-type-specific gene expression + (Nathaniel D. Heintzman)
- Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome + (Nathaniel D. Heintzman)
- Predictive information and explorative behavior of autonomous robots + (N. Ay)
- Observation of non-Hermitian degeneracies in a chaotic exciton-polariton billiard + (T. Gao)
- The fundamental plan of the retina + (R. H. Masland)
- Clinical longitudinal standards for height, weight, height velocity, weight velocity, and stages of puberty + (J. M. Tanner)
- Macromolecular crowding: An important but neglected aspect of the intracellular environment + (R. J. Ellis)
- Fifty years of the VSEPR model + (R. J. Gillespie)
- Fluctuation theorems for stochastic dynamics + (R. J. Harris)
- Number of parallel fiber synapses on an individual Purkinje cell in the cerebellum of the rat + (R. M.A. Napper)
- BMI peak in infancy as a predictor for later BMI in the Uppsala Family Study + (R. J. Silverwood)
- Efficiency of Brownian motors in terms of entropy production rate + (Min Qian)
- General mass action kinetics + (F. Horn)
- Non-equilibrium statistical mechanics: From a paradigmatic model to biological transport + (T. Chou)
- Probability currents as principal characteristics in the statistical mechanics of non-equilibrium steady states + (R. K.P. Zia)
- A possible classification of nonequilibrium steady states + (B. Schmittmann)
- Finite-time thermodynamics for a single-level quantum dot + (R. Kawai)
- Jarzynski equality for the Jepsen gas + (I. Bena)
- Binary Multiplication with PN Sequences + (P. K. Gupta)
- Experimental test of environment-assisted invariance + (L. Vermeyden)
- Operation modes of the molecular motor kinesin + (S. Liepelt)
- Steady-state balance conditions for molecular motor cycles and stochastic nonequilibrium processes + (S. Liepelt)
- Hydrodynamics and the fluctuation theorem + (M. Belushkin)
- Longitudinal gradients in periarteriolar oxygen tension. A possible mechanism for the participation of oxygen in local regulation of blood flow. + (B. R. Duling)
- Principles of Population Genetics. + (R. M. Cormack)
- Nonequilibrium statistical mechanics of shear flow: Invariant quantities and current relations + (A. Baule)
- Invariant quantities in shear flow + (A. Baule)
- Optimum walking techniques for idealized animals + (A. S. Jayes)
- Nonequilibrium steady-state fluctuations in actively cooled resonators + (M. Bonaldi)
- Incremental growth tables: Supplementary to previously published charts + (R. N. Baumgartner)
- Reversible Quantum Brownian Heat Engines for Electrons + (T. E. Humphrey)
- Observation of the Kibble-Zurek scaling law for defect formation in ion crystals + (S. Ulm)
- Jarzynski equation for a simple quantum system: Comparing two definitions of work + (A. Engel)
- Zur Quantentheorie der Molekeln + (M. Born)
- Ramanujan graphs + (A. Lubotzky)
- Invariant visual representation by single neurons in the human brain + (R. Quian Quiroga)
- Weight consistency specifies regularities of macaque cortical networks + (N. T. Markov)
- Of dreaming and wakefulness + (R. R. Llinás)
- Experimental implementation of a nonthermalizing quantum thermometer + (C. Raitz)
- Dynamical reconnection and stability constraints on cortical network architecture + (P. A. Robinson)
- Stochastic thermodynamics for linear kinetic equations + (C. Van Den Broeck)
- Extension of the fluctuation theorem + (R. van Zon)
- Stationary and transient work-fluctuation theorems for a dragged Brownian particle + (R. van Zon)
- Extended heat-fluctuation theorems for a system with deterministic and stochastic forces + (R. van Zon)
- Human neoteny revisited: The case of synaptic plasticity + (Enric Bufill)
- Work distribution functions for hysteresis loops in a single-spin system + (Rahul Marathe)
- Cooling classical particles with a microcanonical szilard engine + (Rahul Marathe)
- Synthetic analog computation in living cells + (Ramiz Daniel)
- Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing + (Gunnar Schotta)
- Physics of Self-Organization and Evolution + (Rainer Feistel)
- Experimental demonstration of a latch in clocked quantum-dot cellular automata + (Alexei O. Orlov)
- An efficient graph theory based method to identify every minimal reaction set in a metabolic network + (Sudhakar Jonnalagadda)
- Introduction to Automata Theory, Languages, and Computation + (John E. Hopcroft)
- Neuroscience: Hemodynamic signals correlate tightly with synchronized gamma oscillations + (Jörn Niessing)
- Higher coordination with less control-a result of information maximization in the sensorimotor loop + (Keyan Zahedi)
- Signal focusing through active transport + (Aljaž Godec)
- Helical logic + (Ralph C. Merkle)
- Neurometabolic coupling in cerebral cortex reflects synaptic more than spiking activity + (Ahalya Viswanathan)
- Self-Organization in a Perceptual Network + (Ralph Linsker)
- Synthetic mechanochemical molecular swimmer + (Ramin Golestanian)
- Observation of parity-time symmetry in optics + (Christian E. Rüter)
- The brain's default network: Anatomy, function, and relevance to disease + (Randy L. Buckner)
- Response and habituation of the human amygdala during visual processing of facial expression + (Hans C. Breiter)
- Experimental verification of Landauer's principle linking information and thermodynamics + (Antoine Bérut)
- Memory erasure in small systems + (Raoul Dillenschneider)
- Role of the polycomb protein EED in the propagation of repressive histone marks + (Raphael Margueron)
- Two Refreshing Views of Fluctuation Theorems Through Kinematics Elements and Exponential Martingale + (Raphaël Chetrite)
- A Gallavotti-Cohen-Evans-Morriss Like Symmetry for a Class of Markov Jump Processes + (Andre Cardoso Barato)
- Eulerian and lagrangian pictures of non-equilibrium diffusions + (Raphaël Chetrite)
- Inequalities generalizing the second law of thermodynamics for transitions between nonstationary states + (Gatien Verley)
- Modified fluctuation-dissipation theorem near non-equilibrium states and applications to the Glauber-Ising chain + (Gatien Verley)
- Chromatin structure and the inheritance of epigenetic information + (Raphaël Margueron)
- Computational design of nucleic acid feedback control circuits + (Boyan Yordanov)
- Solution of a 20-variable 3-SAT problem on a DNA computer + (Ravinderjit S. Braich)
- Structure and function of a human TAF(II)250 double bromodomain module + (Raymond H. Jacobson)
- Neurophysiological architecture of functional magnetic resonance images of human brain + (Raymond Salvador)
- Non-equilibrium thermodynamics and topology of currents + (Vladimir Y. Chernyak)
- Analog Computation by DNA Strand Displacement Circuits + (Tianqi Song)
- Energy conversion by molecular motors coupled to nucleotide hydrolysis + (Reinhard Lipowsky)
- Universal aspects of the chemomechanical coupling for molecular motors + (Reinhard Lipowsky)
- Chemomechanical coupling of molecular motors: Thermodynamics, network representations, and balance conditions + (Reinhard Lipowsky)
- Transient fluctuation relations for time-dependent particle transport + (Alexander Altland)
- Fluctuation relations and rare realizations of transport observables + (Alexander Altland)
- Epigenetics in alternative pre-mRNA splicing + (Reini F. Luco)
- The thermodynamic meaning of negative entropy + (Lídia Del Rio)
- The minimal work cost of information processing + (Philippe Faist)
- Energy use constrains brain information processing + (Julia J. Harris)
- Modular and hierarchically modular organization of brain networks + (David Meunier)
- On the solution to numerical problems using stochastic arithmetic + (René Alt)
- Computation in networks of passively mobile finite-state sensors + (Dana Angluin)
- Mapping the structural core of human cerebral cortex + (Patric Hagmann)
- Superfamilies of Evolved and Designed Networks + (Ron Milo)
- The anatomical distance of functional connections predicts brain network topology in health and schizophrenia + (Aaron F. Alexander-Bloch)
- Quantifying noise levels of intercellular signals + (Kai Wang)
- A Map of the Interactome Network of the Metazoan C. elegans + (Siming Li)
- Improving fast-switching free energy estimates by dynamical freezing + (Paolo Nicolini)
- Glucans monomer-exchange dynamics as an open chemical network + (Riccardo Rao)
- Correlated evolution of nearby residues in drosophilid proteins + (Benjamin Callahan)
- Representations of Odor in the Piriform Cortex + (Dan D. Stettler)
- RNA sequence analysis using covariance models + (Sean R. Eddy)
- Second-order selection for evolvability in a large Escherichia coli population + (Robert J. Woods)
- The evolutionary origin of complex features + (Richard E. Lenski)
- Genome evolution and adaptation in a long-term experiment with Escherichia coli + (Jeffrey E. Barrick)
- Nonequilibrium thermodynamics of stochastic systems with odd and even variables + (Richard E. Spinney)
- Entropy production in full phase space for continuous stochastic dynamics + (Richard E. Spinney)
- Efficient checking of computations + (Richard J. Lipton)
- Reducibility among combinatorial problems + (Richard M. Karp)
- Quantum mechanical computers + (Richard P. Feynman)
- Influence of combinatorial histone modifications on antibody and effector protein recognition + (Stephen M. Fuchs)
- Stretching the limits of clock-gating efficiency in server-class processors + (Hans Jacobson)
- Programmable and autonomous computing machine made of biomolecules + (Yaakov Benenson)
- Programming DNA tube circumferences + (Peng Yin)
- Novel algorithms for fast statistical analysis of scaled circuits + (Amith Singhee)
- Entropic tension in crowded membranes + (Martin Lindén)
- Statistical mechanics of Monod-Wyman-Changeux (MWC) models + (Sarah Marzen)
- Holographic Second Laws of Black Hole Thermodynamics + (Alice Bernamonti)
- Stochastic arithmetic implementations of neural networks with in situ learning + (Jeffrey A. Dickson)
- Increased accuracy of ligand sensing by receptor diffusion on cell surface + (Gerardo Aquino)
- Maximum likelihood and the single receptor + (Robert G. Endres)
- Accuracy of direct gradient sensing by cell-surface receptors + (Robert G. Endres)
- Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells + (Giovanna de Palo)
- Memory improves precision of cell sensing in fluctuating environments + (Gerardo Aquino)