# Category:Reference Materials

From Thermodynamics of Computation

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## Pages in category "Reference Materials"

The following 200 pages are in this category, out of 1,846 total.

(previous page) (next page)### C

- Changes in brain weights during the span of human life: Relation of brain weights to body heights and body weights
- Channel noise in neurons
- Characterization of Minimum Error Linear Coding with Sensory and Neural Noise
- Characterization of the anterior cingulate's role in the at-risk mental state using graph theory
- Characterization of the RNA content of chromatin
- Characterizing plastic depinning dynamics with the fluctuation theorem
- Chemical and mechanical efficiencies of molecular motors and implications for motor mechanisms
- Chemical implementation of finite-state machines
- Chemical implementation of neural networks and Turing machines
- Chemical kinetics is turing universal
- Chemical Paleogenetics. Molecular "Restoration Studies" of Extinct Forms of Life.
- Chemical reaction network theory for in-silico biologists
- Chemical Reaction Networks for Computing Polynomials
- Chemical sensing by nonequilibrium cooperative receptors
- Chemomechanical coupling of molecular motors: Thermodynamics, network representations, and balance conditions
- Chemotaxis in Escherichia coli analysed by three-dimensional tracking
- Childhood and the evolution of the human life course: An Introduction
- ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity
- Chromatin and epigenetic regulation of pre-mrna processing
- Chromatin computation
- Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels
- Chromatin organization marks exon-intron structure
- Chromatin proteins: Key responders to stress
- Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription
- Chromatin structure and the inheritance of epigenetic information
- Circulation and Energy Metabolism of the Brain.
- Classical and quantum fluctuation theorems for heat exchange
- Classical and quantum limitations on energy consumption in computation
- Classical Langevin dynamics of a charged particle moving on a sphere and diamagnetism: A surprise
- Classical open systems with nonlinear nonlocal dissipation and state-dependent diffusion: Dynamical responses and the Jarzynski equality
- Clinical longitudinal standards for height, weight, height velocity, weight velocity, and stages of puberty
- Closed-loop control strategy with improved current for a flashing ratchet
- CNS energy metabolism as related to function
- Coding Efficiency and the Metabolic Cost of Sensory and Neural Information
- Coding of Odors by a Receptor Repertoire
- Cognitive Effort Drives Workspace Configuration of Human Brain Functional Networks
- Cognitive fitness of cost-efficient brain functional networks
- Collective dynamics of 'small-world' networks
- Colloquium: The physics of Maxwell's demon and information
- Combinatorial complexity in chromatin structure and function: Revisiting the histone code
- Combinatorial complexity of pathway analysis in metabolic networks.
- Combinatorial displacement of DNA strands: Application to matrix multiplication and weighted sums
- Combinatorial Problems and Exercises
- Combinatorial readout of dual histone modifications by paired chromatin-associated modules
- Combined analog and action potential coding in hippocampal mossy fibers
- Comment on "Failure of the work-Hamiltonian connection for free-energy calculations" by Jose M. G. Vilar and J. Miguel Rubi
- Communication in neuronal networks
- Communication lower bounds using directional derivatives
- Communications: Can one identify nonequilibrium in a three-state system by analyzing two-state trajectories?
- Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard-sphere liquid
- Comparison of a hair bundle's spontaneous oscillations with its response to mechanical stimulation reveals the underlying active process
- Comparison of far-from-equilibrium work relations
- Comparison of work fluctuation relations
- Compartmental organization of the olfactory bulb glomerulus
- Compendium of the Foundations of Classical Statistical Physics
- Compiler optimization on instruction scheduling for low power
- Complex and detailed balancing of chemical reaction networks revisited
- Complex brain networks: graph theoretical analysis of structural and functional systems
- Complex Extension of Quantum Mechanics
- Complex network measures of brain connectivity: Uses and interpretations
- Complex parameter landscape for a complex neuron model
- Complexity, entropy and the physics of information
- Component-placement optimization in the brain
- Computation in networks of passively mobile finite-state sensors
- Computation on stochastic bit streams digital image processing case studies
- Computation with finite stochastic chemical reaction networks
- Computational Complexity of Probabilistic Turing Machines
- Computational Complexity: A Modern Approach
- Computational complexity: a modern approach
- Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
- Computational design of nucleic acid feedback control circuits
- Computational limits to binary genes.
- Computational selection of nucleic acid biosensors via a slip structure model
- Computed tomography-estimated specific gravity of noncontused brain areas as a marker of severity in human traumatic brain injury
- Computer simulation of Feynman's ratchet and pawl system
- Computers and Intractability: a guide to NP-completeness
- Computing the optimal protocol for finite-time processes in stochastic thermodynamics
- Computing with Noisy Information
- Conformational spread in a ring of proteins: A stochastic approach to allostery
- Connectivity optimization and the positioning of cortical areas
- Connectivity-driven white matter scaling and folding in primate cerebral cortex
- Consciousness as integrated information: A provisional manifesto
- Consensus paper: The cerebellum's role in movement and cognition
- Conservative logic
- Constrained maximal power in small engines
- Construction and optimization of a quantum analog of the Carnot cycle
- Construction of an in vitro bistable circuit from synthetic transcriptional switches
- Continuous time controllers using digital programmable devices
- Control of DNA strand displacement kinetics using toehold exchange
- Convergence in the olfactory system: quantitative aspects of odour sensitivity
- Cooling classical particles with a microcanonical szilard engine
- Cooperative binding of effectors by an allosteric ribozyme.
- Cooperative binding of two acetylation marks on a histone tail by a single bromodomain
- Cooperative multicomponent self-assembly of nucleic acid structures for the activation of DNAzyme cascades: A paradigm for DNA sensors and aptasensors
- Cooperativity, sensitivity, and noise in biochemical signaling
- Coordination languages and their significance
- Correcting errors beyond the Guruswami-Sudan radius in polynomial time
- Correlated evolution of nearby residues in drosophilid proteins
- Correlated morphometric and biochemical studies on the liver cell. I. Morphometric model, stereologic methods, and normal morphometric data for rat liver.
- Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis
- Cortical GABA Interneurons in Neurovascular Coupling: Relays for Subcortical Vasoactive Pathways
- Cortical Hubs Revealed by Intrinsic Functional Connectivity: Mapping, Assessment of Stability, and Relation to Alzheimer's Disease
- Cosmological experiments in superfluid helium?
- Costs of encephalization: the energy trade-off hypothesis tested on birds
- Could information theory provide an ecological theory of sensory processing?
- Counting translocations of strongly repelling particles through single channels: Fluctuation theorem for membrane transport
- Covalent modifications of histones during mitosis and meiosis
- Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis.
- Covariation of residues in the homeodomain sequence family
- CREW PRAMs and Decision Trees
- Criticism of Feynman’s analysis of the ratchet as an engine
- Crowding Effects on Diffusion in Solutions and Cells
- Cryptographic Limitations on Learning Boolean Formulae and Finite Automata
- Cube v4: From performance report explorer to performance analysis tool
- Curie's principle
- CURRENT OPINION IN STRUCTURAL BIOLOGY
- Current trends in finite-time thermodynamics
- Current, maximum power and optimized efficiency of a Brownian heat engine
- Cybernetics : Control and Communication in the Animal and the Machine --2nd. ed

### D

- Darwinian demons, evolutionary complexity, and information maximization
- Data Center Efficiency Assessment
- Decoherence, einselection, and the quantum origins of the classical
- Defect and error tolerance in the presence of massive numbers of defects
- Defining genes: A computational framework
- Defining Network Topologies that Can Achieve Biochemical Adaptation
- Delayed stochastic decoding of LDPC codes
- Demons, Engines and the Second Law
- Dendrosomatic voltage and charge transfer in rat neocortical pyramidal cells
- Density-dependent analysis of nonequilibrium paths improves free energy estimates II. A Feynman-Kac formalism
- Dental and skeletal growth in early fossil hominins
- Dental evidence for ontogenetic differences between modern humans and Neanderthals
- Deoxyribozymes that recode sequence information
- Dependence of the fluctuation-Dissipation temperature on the choice of observable
- Derandomizing polynomial identity tests means proving circuit lower bounds
- Derivation of quantum master equation with counting fields by monitoring a probe
- Design and analysis of synthetic carbon fixation pathways.
- Design of 1-tape 2-symbol reversible Turing machines based on reversible logic elements
- Design of a Neuronal Array
- Design of a trichromatic cone array
- Design principles of a bacterial signalling network
- Designing logic circuits for probabilistic computation in the presence of noise
- Designing optimal discrete-feedback thermodynamic engines
- Detecting Activity in Olfactory Bulb Glomeruli with Astrocyte Recording
- Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex
- Determining cortical landscapes
- Deterministic Function Computation with Chemical Reaction Network
- Deterministic function computation with chemical reaction networks
- Development of Gap Junctions in Hippocampal Astrocytes: Evidence That Whole Cell Electrophysiological Phenotype Is an Intrinsic Property of the Individual Cell
- Development of large-scale functional brain networks in children
- Dietary constraints on encephalization in primates
- Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis
- Differential Landauer's principle
- Diffusion of transcription factors can drastically enhance the noise in gene expression
- Diffusion Tensor Tractography Reveals Abnormal Topological Organization in Structural Cortical Networks in Alzheimer's Disease
- Digital and analog gene circuits for biotechnology
- Digital genetics: Unravelling the genetic basis of evolution
- Digitalized Signatures and Public-Key Functions as Intractable as Factorization
- Directing reprogramming to pluripotency by transcription factors
- Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome
- Discriminatory proofreading regimes in nonequilibrium systems
- Disjointness is hard in the multiparty number-on-the-forehead model
- Disrupted axonal fiber connectivity in schizophrenia
- Disrupted Modularity and Local Connectivity of Brain Functional Networks in Childhood-Onset Schizophrenia
- Disrupted small-world networks in schizophrenia
- Dissipated work in driven harmonic diffusive systems: General solution and application to stretching Rouse polymers
- Dissipation and lag in irreversible processes
- Dissipation and noise immunity in computation and communication
- Dissipation Bound for Thermodynamic Control
- Dissipation-error tradeoff in proofreading
- Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
- Distinctive features of dinoflagellate chromatin. Absence of nucleosomes in a primitive species Prorocentrum micans E.
- Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase
- Distributed hierarchical processing in the primate cerebral cortex
- Distribution of astroglia in glomeruli of the rat main olfactory bulb: Exclusion from the sensory subcompartment of neuropil
- Distribution of entropy production for a colloidal particle in a nonequilibrium steady state
- Distribution of oxygen tension on the surface of arterioles, capillaries and venules of brain cortex and in tissue in normoxia: An experimental study on rats
- Distribution of work in isothermal nonequilibrium processes
- Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator
- DNA as a universal substrate for chemical kinetics (Extended Abstract)
- DNA COMPUTING
- Does replication‐induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli?
- Drivers of bacterial maintenance and minimal energy requirements
- Dropbox Quick Start
- Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMENTHYLASE3
- Dynamic DNA nanotechnology using strand-displacement reactions
- Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes
- Dynamic force spectroscopy of DNA hairpins: II. Irreversibility and dissipation
- Dynamic mapping at the laminar level of odor-elicited responses in rat olfactory bulb by functional MRI.
- Dynamic reconfiguration of human brain networks during learning
- Dynamical consequences of lesions in cortical networks
- Dynamical ensembles in nonequilibrium statistical mechanics
- Dynamical fluctuations for periodically driven diffusions
- Dynamical reconnection and stability constraints on cortical network architecture
- Dynamics and memory of heterochromatin in living cells
- Dynamics of a tracer granular particle as a nonequilibrium Markov process
- Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations.
- Dynamics of cooperativity in chemical sensing among cell-surface receptors
- Dynamics of inherently bounded histone modification domains
- Dynamics of market correlations: Taxonomy and portfolio analysis
- Dynamo: Amazon’s Highly Available Key-value Store