Santa Fe Institute Collaboration Platform

Thermodynamics of Computation

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M
Making molecular machines work +
1  +
T
The human connectome: A structural description of the human brain +
1  +
S
Soft computing: the convergence of emerging reasoning technologies +
1  +
I
Information theory in molecular biology +
1  +
W
Why do female primates have such long lifespans and so few babies? or Life in the slow lane +
1  +
T
The energy expansions of evolution +
1  +
D
Distributed hierarchical processing in the primate cerebral cortex +
1  +
N
Neurometabolic coupling in cerebral cortex reflects synaptic more than spiking activity +
10  +
E
Experience-dependent rescaling of entorhinal grids +
10  +
U
Universal features in the energetics of symmetry breaking +
10  +
T
Thermodynamic Costs of Information Processing in Sensory Adaptation +
10  +
E
Evolutionary tradeoffs in cellular composition across diverse bacteria +
10  +
A
A model for transmission of the H3K27me3 epigenetic mark +
10  +
P
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease +
10  +
T
The anatomy of memory: An interactive overview of the parahippocampal- hippocampal network +
10  +
A
A Simple Model of Optimal Population Coding for Sensory Systems +
10  +
S
Symbiotic relationship between brain structure and dynamics +
10  +
N
Nucleosome positioning and gene regulation: Advances through genomics +
10  +
T
The second wave of synthetic biology: From modules to systems +
10  +
The WUS homeobox-containing (WOX) protein family +
10  +
C
Chromatin proteins: Key responders to stress +
10  +
S
Strand algebras for DNA computing +
10  +
F
Failure of the work-hamiltonian connection for free-energy calculations +
100  +
R
Role of external flow and frame invariance in stochastic thermodynamics +
100  +
O
Optimized free energies from bidirectional single-molecule force spectroscopy +
100  +
R
Reversibility, heat dissipation, and the importance of the thermal environment in stochastic models of nonequilibrium steady states +
100  +
C
Counting translocations of strongly repelling particles through single channels: Fluctuation theorem for membrane transport +
100  +
E
Escorted free energy simulations: Improving convergence by reducing dissipation +
100  +
R
Revision of Dietary Reference Intakes for energy in preschool-age children +
100  +
C
Cooperativity, sensitivity, and noise in biochemical signaling +
100  +
A
Accuracy of direct gradient sensing by cell-surface receptors +
100  +
R
Receptor noise and directional sensing in eukaryotic chemotaxis +
100  +
I
Invariant quantities in shear flow +
101  +
L
Length of time's arrow +
101  +
R
Realization of a feedback controlled flashing ratchet +
101  +
D
Differential Landauer's principle +
101  +
A
An autonomous and reversible Maxwell's demon +
101  +
M
Memory erasure in small systems +
102  +
Minimal energy cost for thermodynamic information processing: Measurement and information erasure +
102  +
Mutual information between input and output trajectories of biochemical networks +
102  +
F
Fluctuation theorem for arbitrary open quantum systems +
102  +
H
Heterogeneity and Efficiency in the Brain +
103  +
N
Nonequilibrium steady-state fluctuations in actively cooled resonators +
103  +
E
Experimental Verification of a Modified Fluctuation-Dissipation Relation for a Micron-Sized Particle in a Nonequilibrium Steady State +
103  +
D
Dynamical reconnection and stability constraints on cortical network architecture +
103  +
R
Role of spatial averaging in the precision of gene expression patterns +
103  +
C
Computed tomography-estimated specific gravity of noncontused brain areas as a marker of severity in human traumatic brain injury +
103  +
M
Maximum likelihood and the single receptor +
103  +
G
Generalized fluctuation-dissipation theorem for steady-state systems +
103  +
D
Dependence of the fluctuation-Dissipation temperature on the choice of observable +
103  +
N
Nonequilibrium energetics of a single F1-ATPase molecule +
104  +
E
Entropy production of cyclic population dynamics +
104  +
F
Fluctuation theorem applied to F1-ATPase +
104  +
G
Generalized einstein or green-kubo relations for active biomolecular transport +
104  +
H
Heat conduction in a three dimensional anharmonic crystal +
104  +
O
On r- and K-Selection +
104  +
G
Generalized Jarzynski equality under nonequilibrium feedback control +
104  +
L
Limits of sensing temporal concentration changes by single cells +
104  +
C
Cooling classical particles with a microcanonical szilard engine +
104  +
S
Stochastic thermodynamics and sustainable efficiency in work production +
105  +
N
Nonequilibrium steady states in contact: Approximate thermodynamic structure and zeroth law for driven lattice gases +
105  +
F
Fluctuation relations and rare realizations of transport observables +
105  +
O
Optical realization of relativistic non-Hermitian quantum mechanics +
105  +
On the energetics of information exchange +
105  +
S
Synthetic mechanochemical molecular swimmer +
105  +
T
Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction +
105  +
N
Nonlinear fluctuation-dissipation relations and stochastic models in nonequilibrium thermodynamics. II. Kinetic potential and variational principles for nonlinear irreversible processes +
106  +
E
Efficiency of autonomous soft nanomachines at maximum power +
106  +
N
Nonlinear fluctuation-dissipation relations and stochastic models in nonequilibrium thermodynamics. I. Generalized fluctuation-dissipation theorem +
106  +
O
Optimal protocols and optimal transport in stochastic thermodynamics +
106  +
H
Hydrodynamics and the fluctuation theorem +
106  +
Heat fluctuations in a nonequilibrium bath +
106  +
E
Effective temperature of red-blood-cell membrane fluctuations +
106  +
S
Symmetry properties of the large-deviation function of the velocity of a self-propelled polar particle +
106  +
T
Thermodynamic bounds on efficiency for systems with broken time-reversal symmetry +
106  +
Q
Quantum szilard engine +
106  +
T
The berg-purcell limit revisited +
106  +
I
Improving free-energy estimates from unidirectional work measurements: Theory and experiment +
107  +
Injected power fluctuations in Langevin equation +
107  +
G
Geometric effects on complex network structure in the cortex +
107  +
D
Dynamics of cooperativity in chemical sensing among cell-surface receptors +
107  +
E
Exploring the thermodynamic limits of computation in integrated systems: Magnetic memory, nanomagnetic logic, and the landauer limit +
107  +
N
Nonequilibrium thermodynamics of stochastic systems with odd and even variables +
108  +
F
Fluctuation theorems for an asymmetric rotor in a granular gas +
108  +
I
Inequalities generalizing the second law of thermodynamics for transitions between nonstationary states +
108  +
S
Stochastic energetics for non-Gaussian processes +
108  +
F
Fluctuation-preserving coarse graining for biochemical systems +
108  +
R
Role of hidden slow degrees of freedom in the fluctuation theorem +
108  +
Q
Quantum Measurement Bounds beyond the Uncertainty Relations +
108  +
T
Thermodynamics of genuine nonequilibrium states under feedback control +
108  +
The mesoscopic dynamics of thermodynamic systems +
109  +
B
Biased sampling of nonequilibrium trajectories: Can fast switching simulations outperform conventional free energy calculation methods? +
109  +
R
Resolution of nested neuronal representations can be exponential in the number of neurons +
109  +
F
Fluctuation theorem with information exchange: Role of correlations in stochastic thermodynamics +
109  +
T
Thermodynamics of prediction +
109  +
F
Fundamental limits on sensing chemical concentrations with linear biochemical networks +
109  +
Fundamental aspects of protein - Protein association kinetics +
109  +
Functional nucleic acid sensors +
109  +
T
Thermodynamics of information +
11  +
E
Energy as a constraint on the coding and processing of sensory information +
11  +
T
The Szilard engine revisited: Entropy, macroscopic randomness, and symmetry breaking phase transitions +
11  +
R
RAS oncogenes: Weaving a tumorigenic web +
11  +
A
An information theoretical analysis of kinase activated phosphorylation dephosphorylation cycle +
11  +
C
Chromatin structure and the inheritance of epigenetic information +
11  +
E
Experimental test of the quantum Jarzynski equality with a trapped-ion system +
11  +
C
Cerebellar Golgi cells in the rat: Receptive fields and timing of responses to facial stimulation +
11  +
D
Dissipation-error tradeoff in proofreading +
11  +
M
Microbial life under extreme energy limitation +
11  +
T
Tight estimates for eigenvalues of regular graphs +
11  +
Q
Quantum mechanics: No more fields +
11  +
M
Macromolecular crowding: An important but neglected aspect of the intracellular environment +
11  +
O
Open-system nonequilibrium steady state: Statistical thermodynamics, fluctuations, and chemical oscillations +
110  +
T
Thermodynamics of a physical model implementing a Maxwell demon +
110  +
K
Kinetic versus energetic discrimination in biological copying +
110  +
C
Chemical sensing by nonequilibrium cooperative receptors +
110  +
M
Multidimensional potentials of mean force from biased experiments along a single coordinate +
111  +
Maxwell's refrigerator: An exactly solvable model +
111  +
I
Information thermodynamics on causal networks +
111  +
H
Heat engine driven by purely quantum information +
111  +
I
Imitating chemical motors with optimal information motors +
111  +
S
Self-organization and entropy reduction in a living cell +
111  +
Second law of thermodynamics with discrete quantum feedback control +
1110  +
N
Nanoscale heat engine beyond the carnot limit +
112  +
U
Unifying three perspectives on information processing in stochastic thermodynamics +
112  +
T
The brain's default network: Anatomy, function, and relevance to disease +
1124  +
The neural correlates of consciousness: An update +
1124  +
The mechanics and fluctuation spectrum of active gels +
113  +
E
Experimental observation of the role of mutual information in the nonequilibrium dynamics of a Maxwell demon +
113  +
Energy dissipation and noise correlations in biochemical sensing +
113  +
S
Stochastic thermodynamics in mesoscopic chemical oscillation systems +
113  +
H
High-precision test of Landauer's principle in a feedback trap +
113  +
T
Thermodynamics of statistical inference by cells +
113  +
F
Faster algorithms for subgraph isomorphism of k-Connected partial k-Trees +
1136  +
G
Good practices in free-energy calculations +
114  +
F
Fast-growth thermodynamic integration: Error and efficiency analysis +
114  +
A
Are Recursion Theoretic Arguments Useful in Complexity Theory? +
114  +
T
Thermodynamic Uncertainty Relation for Biomolecular Processes +
114  +
Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium +
114  +
S
Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation +
115  +
O
Optimal Prediction by Cellular Signaling Networks +
115  +
P
Physical Limit to Concentration Sensing Amid Spurious Ligands +
115  +
D
Dissipation Bound for Thermodynamic Control +
115  +
T
Three-dimensional simulations of reversible bimolecular reactions: The simple target problem +
115  +
O
On the generation of cryptographically strong pseudo-random sequences +
115 LNCS  +
K
Kinetics of reversible diffusion influenced reactions: The self-consistent relaxation time approximation +
117  +
H
High-energy behavior in quantum field theory +
118  +
Q
Quantum Simulation of Single-Qubit Thermometry Using Linear Optics +
118  +
F
Fundamental Costs in the Production and Destruction of Persistent Polymer Copies +
118  +
T
The quantum open system as a model of the heat engine +
12  +
R
Relationship between subsistence and age at weaning in "preindustrial" societies +
12  +
E
Entropy production as correlation between system and reservoir +
12  +
O
On the nature of allosteric transitions: A plausible model +
12  +
P
Progressive methylation of ageing histones by Dot1 functions as a timer +
12  +
Probabilistic algorithm for testing primality +
12  +
Pseudorandom generators for space-bounded computation +
12  +
S
Small-world brain networks +
12  +
F
Fluctuation theorem for nonequilibrium reactions +
120  +
D
Dietary constraints on encephalization in primates +
120  +
S
Single-ensemble nonequilibrium path-sampling estimates of free energy differences +
120  +
C
Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality +
124  +
F
Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality +
125  +
C
Coding of Odors by a Receptor Repertoire +
125  +
T
The Use of Information Theory in Evolutionary Biology +
1256  +
G
Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation +
126  +
S
Stochastic thermodynamics of chemical reaction networks +
126  +
F
Fluctuation theorem for currents and Schnakenberg network theory +
127  +
E
Entropy production for mechanically or chemically driven biomolecules +
128  +
H
How the nature of an observation affects single-trajectory entropies +
128  +
D
Defining genes: A computational framework +
128  +
B
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise +
129  +
O
Optimal protocols for minimal work processes in underdamped stochastic thermodynamics +
129  +
E
Entropy production and fluctuation theorem along a stochastic limit cycle +
129  +
L
Life in the slow lane revisited: Ontogenetic separation between chimpanzees and humans +
129  +
T
Theoretical Analysis of Epigenetic Cell Memory by Nucleosome Modification +
129  +
D
Deterministic Function Computation with Chemical Reaction Network +
13  +
B
Broken symmetries and the masses of gauge bosons +
13  +
O
Optical polarization evolution near a non-Hermitian degeneracy +
13  +
M
Matching coding, circuits, cells, and molecules to signals: General principles of retinal design in the fly's eye +
13  +
P
Parallel fibre receptive fields of purkinje cells and interneurons are climbing fibre-specific +
13  +
A
A test of metabolically efficient coding in the retina +
13  +
O
One-component systems dominate signal transduction in prokaryotes +
13  +
C
Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host +
13  +
R
Reachability bounds for chemical reaction networks and strand displacement systems +
13  +
D
Derandomizing polynomial identity tests means proving circuit lower bounds +
13  +
Designing optimal discrete-feedback thermodynamic engines +
13  +
T
The cost of cortical computation +
13  +
P
Probabilistic mapping and volume measurement of human primary auditory cortex +
13  +
C
Consensus paper: The cerebellum's role in movement and cognition +
13  +
A
An estimate of the total DNA in the biosphere +
13  +
A master equation description of local fluctuations +
13  +
C
Calcium, the two-faced messenger of olfactory transduction and adaptation +
13  +
D
Deterministic function computation with chemical reaction networks +
13  +
I
Image quality assessment: From error visibility to structural similarity +
13  +
P
Precis of The Emperor's New Mind +
13  +
S
Steady state thermodynamics +
130  +
I
Inertial effects in nonequilibrium work fluctuations by a path integral approach +
130  +
C
Chemomechanical coupling of molecular motors: Thermodynamics, network representations, and balance conditions +
130  +
O
Optimizing the switching function for nonequilibrium free-energy calculations: An on-the-fly approach +
130  +
M
Measurement of work in single-molecule pulling experiments +
130  +
N
Nonequilibrium steady state thermodynamics and fluctuations for stochastic systems +
130  +
P
Probing the Limits to Positional Information +
130  +
E
Engineering complex riboswitch regulation by dual genetic selection +
130  +
T
The work-Hamiltonian connection and the usefulness of the Jarzynski equality for free energy calculations +
130  +
D
Disrupted small-world networks in schizophrenia +
131  +
C
Control of DNA strand displacement kinetics using toehold exchange +
131  +
Communications: Can one identify nonequilibrium in a three-state system by analyzing two-state trajectories? +
132  +
R
Representation of nonequilibrium steady states in large mechanical systems +
134  +
E
Entropy production in a mesoscopic chemical reaction system with oscillatory and excitable dynamics +
134  +
D
Density-dependent analysis of nonequilibrium paths improves free energy estimates II. A Feynman-Kac formalism +
134  +
E
Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes: Theory and application to free energies, moments, and thermodynamic length in single-molecule pulling experiments +
134  +
Energy conversion by molecular motors coupled to nucleotide hydrolysis +
135  +
P
Potential and flux decomposition for dynamical systems and non-equilibrium thermodynamics: Curvature, gauge field, and generalized fluctuation-dissipation theorem +
135  +
N
Non-equilibrium spin-boson model: Counting statistics and the heat exchange fluctuation theorem +
135  +
R
Rare switching events in non-stationary systems +
136  +
M
Metabolic correlates of hominid brain evolution +
136  +
N
Nonequilibrium fluctuations in small systems: from physics to biology +
137  +
Non-equilibrium thermodynamics and topology of currents +
137  +
E
Eulerian and lagrangian pictures of non-equilibrium diffusions +
137  +
F
Fluctuation theorems for entropy production and heat dissipation in periodically driven Markov chains +
137  +
A
A C. elegans LSD1 Demethylase Contributes to Germline Immortality by Reprogramming Epigenetic Memory +
137  +
D
Defining Network Topologies that Can Achieve Biochemical Adaptation +
138  +
C
Chemical reaction network theory for in-silico biologists +
138  +
E
Effect of ligand diffusion on occupancy fluctuations of cell-surface receptors +
139  +
O
Open problems on information and feedback controlled systems +
14  +
E
Experimental implementation of a nonthermalizing quantum thermometer +
14  +
B
Brownian motion: A paradigm of soft matter and biological physics +
14  +
G
Grid cells generate an analog error-correcting code for singularly precise neural computation +
14  +
E
Erratum: Differences in auditory and physiological properties of HVc neurons between reproductively active male and female canaries (Serinus canaria) (European Journal of Neuroscience (2001) 14 (1377-1389)) +
14  +
S
Statistical Processors +
14  +
L
Leaderless deterministic chemical reaction networks +
14  +
E
Entropy and Nonlinear Nonequilibrium Thermodynamic Relation for Heat Conducting Steady States +
142  +
I
Inequalities for Non-equilibrium Fluctuations of Work +
142  +
N
Noise Filtering Strategies in Adaptive Biochemical Signaling Networks +
142  +
T
The Value of Information for Populations in Varying Environments +
142  +
Two Refreshing Views of Fluctuation Theorems Through Kinematics Elements and Exponential Martingale +
143  +
G
Gallavotti-Cohen-Type Symmetry Related to Cycle Decompositions for Markov Chains and Biochemical Applications +
143  +
Q
Quantum Jarzynski-Sagawa-Ueda Relations +
143  +
G
Glucans monomer-exchange dynamics as an open chemical network +
143  +
E
Epigenetics in alternative pre-mRNA splicing +
144  +
R
Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions +
145  +
A
A Gallavotti-Cohen-Evans-Morriss Like Symmetry for a Class of Markov Jump Processes +
146  +
I
Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification +
146  +
M
Mechanisms for the inheritance of chromatin states +
146  +
R
Refined Second Law of Thermodynamics for Fast Random Processes +
147  +
I
Information integration: Its relevance to brain function and consciousness +
148  +
D
Dynamics and memory of heterochromatin in living cells +
149  +
A
An update on the nonequilibrium linear response +
15  +
Q
Quantum speed limits-primer, perspectives, and potential future directions +
15  +
N
Neurophysiological architecture of functional magnetic resonance images of human brain +
15  +
I
In silico evolution of diauxic growth +
15  +
Q
Quantum fluctuation relations for ensembles of wave functions +
15  +
R
Role of mutual information in entropy production under information exchanges +
15  +
O
On thermodynamic interpretation of transfer entropy +
15  +
C
Cooperative multicomponent self-assembly of nucleic acid structures for the activation of DNAzyme cascades: A paradigm for DNA sensors and aptasensors +
15  +
F
Flight of the FINCH through the java wilderness +
15  +
O
On rank vs. communication complexity +
15  +
H
Heat Release by Controlled Continuous-Time Markov Jump Processes +
150  +
T
TrxG and PcG proteins but not methylated histones remain associated with DNA through replication +
150  +
A
Asymmetrically modified nucleosomes +
151  +
R
Rate of Mutual Information Between Coarse-Grained Non-Markovian Variables +
153  +
A
A Nonequilibrium Extension of the Clausius Heat Theorem +
154  +
U
Ueber die bewegende Kraft der Wärme und die Gesetze, welche sich daraus für die Wärmelehre selbst ableiten lassen +
155  +
Q
Quantum equivalent of the Carnot cycle +
156  +
F
Fluctuation theorem for a double quantum dot coupled to a point-contact electrometer +
1566  +
T
Towards the parallel repetition conjecture +
157  +
E
Efficiency of cellular information processing +
16  +
H
Histone H3 tail clipping regulates gene expression +
16  +
How Much the Eye Tells the Brain +
16  +
S
Second-law-like inequalities with information and their interpretations +
16  +
A
An analog of the Boltzmann H-theorem (a Liapunov function) for systems of coupled chemical reactions +
16  +
Q
Quantum mechanical computers +
16  +
C
Chromatin organization marks exon-intron structure +
16  +
P
Pseudorandomness and average-case complexity via uniform reductions +
16  +
A
An intermediate level of abstraction for computational systems chemistry +
16  +
C
Chemical and mechanical efficiencies of molecular motors and implications for motor mechanisms +
17  +
D
Does replication‐induced transcription regulate synthesis of the myriad low copy number proteins of Escherichia coli? +
17  +
B
BPP and the polynomial hierarchy +
17  +
R
Randomness-efficient sampling within NC1 +
17  +
Response and habituation of the human amygdala during visual processing of facial expression +
17  +
S
Small-world networks and functional connectivity in Alzheimer's disease +
17  +
E
Energy flows in low-entropy complex systems +
17  +
B
Basal Metabolic Rate in Man +
17  +
C
Chemical Paleogenetics. Molecular "Restoration Studies" of Extinct Forms of Life. +
17 supl.  +
T
Theoretical predictions of spatiotemporal receptive fields of fly LMCs, and experimental validation +
171  +
N
Noise stability of functions with low influences: Invariance and optimality +
171  +
F
Fast and slow photoreceptors - a comparative study of the functional diversity of coding and conductances in the Diptera +
172  +
T
The superfamily of heme-copper respiratory oxidases +
176  +
Q
Quantum probabilities from quantum entanglement: Experimentally unpacking the Born rule +
18  +
T
Thermodynamics of trajectories and local fluctuation theorems for harmonic quantum networks +
18  +
R
Revealing modular architecture of human brain structural networks by using cortical thickness from MRI +
18  +
T
The microvascular system of the striate and extrastriate visual cortex of the macaque +
18  +
The emergence of human uniqueness: Characters underlying behavioral modernity +
18  +
I
Interpreting hippocampal function as recoding and forecasting +
18  +
C
Computation in networks of passively mobile finite-state sensors +
18  +
N
Neurophysiology of the BOLD fMRI Signal in Awake Monkeys +
18  +
A
ATP Consumption by Mammalian Rod Photoreceptors in Darkness and in Light +
18  +
A small world of neuronal synchrony +
18  +
L
Local potential connectivity in cat primary visual cortex +
18  +
E
Energy Cost of Proofreading to Increase Fidelity of Transfer Ribonucleic Acid Aminoacylation +
18  +
T
The free energy requirements of biological organisms; implications for evolution +
18  +
H
Higher coordination with less control-a result of information maximization in the sensorimotor loop +
18  +
A
An effect of DNA sequence on nucleosome occupancy and removal +
18  +
D
Disjointness is hard in the multiparty number-on-the-forehead model +
18  +
P
Pseudorandom generators hard for k-DNF resolution and polynomial calculus resolution +
181  +
F
Functional organization of rat olfactory bulb analysed by the 2‐deoxyglucose method +
185  +
O
Optimum walking techniques for idealized animals +
186  +
C
Cellular stoichiometry of the components of the chemotaxis signaling complex +
186  +
Q
Quantum entropy production as a measure of irreversibility +
187  +
A
A rigorous derivation of the chemical master equation +
188  +
U
Ueber die mechanischen Analogien des zweiten Hauptsatzes der Thermodynamik +
1887  +
G
Global and local thermometry schemes in coupled quantum systems +
19  +
T
The Effect of Phenobarbitone Anaesthesia on Blood Flow and Oxygen Consumption in the Rat Brain +
19  +
A
Argonaute proteins couple chromatin silencing to alternative splicing +
19  +
N
Nucleosomes are well positioned in exons and carry characteristic histone modifications +
19  +
A
Aerobic glycolysis in the human brain is associated with development and neotenous gene expression +
19  +
A simple rule for axon outgrowth and synaptic competition generates realistic connection lengths and filling fractions +
19  +
P
Pooled energy budgets: Resituating human energy -allocation trade-offs +
19  +
C
Component-placement optimization in the brain +
19  +
M
Making copies of chromatin: the challenge of nucleosomal organization and epigenetic information +
19  +
P
Perceiving the epigenetic landscape through histone readers +
19  +
S
Synergism between different germinant receptors in the germination of Bacillus subtilis spores +
193  +
Stochastic arithmetic implementations of neural networks with in situ learning +
1993-January  +
G
Gene expression of Caenorhabditis elegans neurons carries information on their synaptic connectivity +
2  +
C
Complex parameter landscape for a complex neuron model +
2  +
N
Nonoptimal component placement, but short processing paths, due to long-distance projections in neural systems +
2  +
I
Identification and classification of hubs in brain networks +
2  +
R
Role of mechanical factors in the morphology of the primate cerebral cortex +
2  +
D
Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase +
2  +
E
Equalities and Inequalities: Irreversibility and the Second Law of Thermodynamics at the Nanoscale +
2  +
A
A quantitative estimation of the global translational activity in logarithmically growing yeast cells +
2  +
T
The cell cycle switch computes approximate majority +
2  +
M
Mapping information flow in sensorimotor networks +
2  +
C
Construction of an in vitro bistable circuit from synthetic transcriptional switches +
2  +
M
Modulation of Chemical Composition and Other Parameters of the Cell by Growth Rate +
2  +
L
Low-Power Digital Systems Based on Adiabatic-Switching Principles +
2  +
E
Evolving Coordinated Behavior by Maximizing Information Structure +
2  +
L
Laser cooling of atoms +
20  +
M
Mej´ıa-Monasterio C 2007 Fluctuations in nonequilibrium statistical mechanics: models +
20  +
A
Analyzing friction forces with the Jarzynski equality +
20  +
T
The TAU parallel performance system +
20  +
P
Physics of chemoreception +
20  +
C
Characterization of the RNA content of chromatin +
20  +
Compiler optimization on instruction scheduling for low power +
2000-January  +
T
The unique games conjecture, integrality gap for cut problems and embeddability of negative type metrics into l 1 +
2005  +
C
Correcting errors beyond the Guruswami-Sudan radius in polynomial time +
2005  +
Comparison of work fluctuation relations +
2007  +
O
On the work - Hamiltonian connection in manipulated systems +
2008  +
P
Probability density functions of work and heat near the stochastic resonance of a colloidal particle +
2008  +
T
The stochastic pump current and the non-adiabatic geometrical phase +
2008  +
W
Work fluctuations in a nematic liquid crystal +
2009  +
O
Optimal operation of feedback flashing ratchets +
2009  +
D
Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes +
2009  +
T
Thermodynamic efficiency of information and heat flow +
2009  +
D
Dynamic force spectroscopy of DNA hairpins: II. Irreversibility and dissipation +
2009  +
S
Statistical properties of entropy production derived from fluctuation theorems +
2010  +
N
Nonequilibrium statistical mechanics of shear flow: Invariant quantities and current relations +
2010  +
E
Entropy production and fluctuation relations for a KPZ interface +
2010  +
S
Symmetries of generating functionals of Langevin processes with colored multiplicative noise +
2010  +
E
Energetics and performance of a microscopic heat engine based on exact calculations of work and heat distributions +
2010  +
D
Dynamical fluctuations for periodically driven diffusions +
2010  +
F
Fluctuations and response in a non-equilibrium micron-sized system +
2011  +
N
Non-equilibrium steady states: Maximization of the Shannon entropy associated with the distribution of dynamical trajectories in the presence of constraints +
2011  +
S
Single-molecule thermodynamics: The heat distribution function of a charged particle in a static magnetic field +
2011  +
O
On anomalous diffusion and the out of equilibrium response function in one-dimensional models +
2011  +
M
Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics +
2011  +
L
Large deviations of heat flow in harmonic chains +
2011  +
A
A bound particle coupled to two thermostats +
2011  +
M
Modified fluctuation-dissipation theorem near non-equilibrium states and applications to the Glauber-Ising chain +
2011  +
E
Entropy production and fluctuation theorems under feedback control: The molecular refrigerator model revisited +
2012  +
H
Heat flow in chains driven by thermal noise +
2012  +
N
Non-equilibrium equalities with unital quantum channels +
2013  +
T
Thermodynamic and logical reversibilities revisited +
2014  +
S
Stochastic thermodynamics of bipartite systems: Transfer entropy inequalities and a Maxwell's demon interpretation +
2014  +
E
Energy dissipation in an adaptive molecular circuit +
2015  +
H
Housekeeping entropy in continuous stochastic dynamics with odd-parity variables +
2016  +
Holographic Second Laws of Black Hole Thermodynamics +
2018  +
P
Path integrals with generalized Grassmann variables +
207  +
T
The thermodynamics of computation-a review +
21  +
D
Defect and error tolerance in the presence of massive numbers of defects +
21  +
S
Self-Organization in a Perceptual Network +
21  +
A
A simple population protocol for fast robust approximate majority +
21  +
U
Using information theory to search for co-evolving residues in proteins +
21  +
C
Classical and quantum limitations on energy consumption in computation +
21  +
I
Influence of combinatorial histone modifications on antibody and effector protein recognition +
21  +
F
Fast computation by population protocols with a leader +
21  +
W
Wiring economy and volume exclusion determine neuronal placement in the Drosophila brain +
21  +
Weight consistency specifies regularities of macaque cortical networks +
21  +
D
Darwinian demons, evolutionary complexity, and information maximization +
21  +
F
Forward flux sampling for rare event simulations +
21  +
C
Challenges for complexity measures: A perspective from social dynamics and collective social computation +
21  +
Conservative logic +
21  +
Chromatin and epigenetic regulation of pre-mrna processing +
21  +
R
Readers of histone modifications +
21  +
C
Curie's principle +
21  +
Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing +
21  +
U
Using profile information to assist classic code optimizations +
21  +
C
Consciousness as integrated information: A provisional manifesto +
215  +
T
The physical nature of information +
217  +
A
Aerobic glycolysis in the primate brain: Reconsidering the implications for growth and maintenance +
219  +
F
Functional connectivity between anatomically unconnected areas is shaped by collective network-level effects in the macaque cortex +
22  +
C
Could information theory provide an ecological theory of sensory processing? +
22  +
T
The computer as a physical system: A microscopic quantum mechanical Hamiltonian model of computers as represented by Turing machines +
22  +
C
Computational selection of nucleic acid biosensors via a slip structure model +
22  +
U
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements +
22  +
C
Combinatorial complexity in chromatin structure and function: Revisiting the histone code +
22  +
R
RNA sequence analysis using covariance models +
22  +
D
Directing reprogramming to pluripotency by transcription factors +
22  +
A
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions +
22  +
C
Computation on stochastic bit streams digital image processing case studies +
22  +
H
Human brain networks in health and disease +
22  +
T
The neural code of the retina +
22  +
E
Expanders, randomness, or time versus space: Extended abstract +
223 LNCS  +
F
Free energy transduction in a chemical motor model +
228  +
T
Thermodynamic constraints for biochemical networks +
228  +
A
A general framework for non-equilibrium phenomena: The master equation and its formal consequences +
229  +
C
Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes +
23  +
Channel noise in neurons +
23  +
W
What can spontaneous fluctuations of the blood oxygenationlevel-dependent signal tell us about psychiatric disorders? +
23  +
T
The selfish brain: Competition for energy resources +
23  +
H
Human neoteny revisited: The case of synaptic plasticity +
23  +
D
Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMENTHYLASE3 +
23  +
P
Programmable ligand-controlled riboregulators of eukaryotic gene expression +
23  +
S
Silencing of transgene transcription precedes methylation of promoter DNA and histone H3 lysine 9 +
23  +
T
The anatomical distance of functional connections predicts brain network topology in health and schizophrenia +
23  +
D
Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex +
234  +
C
Chemotaxis in Escherichia coli analysed by three-dimensional tracking +
239  +
E
Energetics of functional activation in neural tissues +
24  +
H
Heterochromatin formation involves changes in histone modifications over multiple cell generations +
24  +
Histone Segregation on Replicating Chromatin†+
24  +
A
A Hitchhiker's guide to statistical tests for assessing randomized algorithms in software engineering +
24  +
H
Histone Segregation on Replicating Chromatin† +
24  +
F
Finite time thermodynamic optimization or entropy generation minimization of energy systems +
24  +
T
Tracking uncertainty with probabilistic logic circuit testing +
24  +
The Datacenter as a Computer +
24  +
The stochastic chemomechanics of the F1-ATPase molecular motor +
247  +
The neural basis of functional brain imaging signals +
25  +
E
Energy allocation between brain and body during ontogenetic development +
25  +
S
Sparse complete sets for NP: Solution of a conjecture of Berman and Hartmanis +
25  +
T
Thermodynamics of natural selection III: Landauer’s principle in computation and chemistry +
252  +
Thermodynamics of natural selection I: Energy flow and the limits on organization +
252  +
Thermodynamics of natural selection II: Chemical Carnot cycles +
252  +
H
How much non-coding DNA do eukaryotes require? +
252  +
T
Thermodynamics of natural selection III: Landauer's principle in computation and chemistry +
252  +
F
Fifty years of the VSEPR model +
252  +
R
Reversible Computation and Reversible Programming Languages +
253  +
P
Path integral formulation of general diffusion processes +
26  +
Principles of control thermodynamics +
26  +
A
A (sub)graph isomorphism algorithm for matching large graphs +
26  +
M
Measurement of 'true' glucose production rates in infancy and childhood with 6,6-dideuteroglucose +
26  +
F
Facilitated target location in biological systems +
264  +
I
Innovation in gene regulation: The case of chromatin computation +
265  +
L
Longitudinal gradients in periarteriolar oxygen tension. A possible mechanism for the participation of oxygen in local regulation of blood flow. +
27  +
P
Parallel simulation of compressible flow using automatic differentiation and PETSc +
27  +
E
Energetic basis of brain activity: Implications for neuroimaging +
27  +
V
Visual DSD: A design and analysis tool for DNA strand displacement systems +
27  +
S
Stoichiometric network theory for nonequilibrium biochemical systems +
270  +
M
Minimal energy requirements in communication +
272  +
N
Number of parallel fiber synapses on an individual Purkinje cell in the cerebellum of the rat +
274  +
S
Stochastic energetics of non-uniform temperature systems +
276  +
F
Forward and backward propagation of dendritic impulses and their synaptic control in mitral cells +
278  +
O
Optimal Process Paths for Endoreversible Systems +
28  +
S
Specific subtypes of cortical GABA interneurons contribute to the neurovascular coupling response to basal forebrain stimulation +
28  +
P
Parallel mechanisms of epigenetic reprogramming in the germline +
28  +
R
Regulation of chromatin structure by long noncoding RNAs: Focus on natural antisense transcripts +
28  +
T
The complexity of facets (and some facets of complexity) +
28  +
The adjustable nucleosome: An epigenetic signaling module +
28  +
S
Split decision: What happens to nucleosomes during DNA replication? +
280  +
A
A systems perspective on early olfactory coding +
286  +
P
Phosphorylation and regulation of Raf by Akt (protein kinase B) +
286  +
C
Combinatorial readout of dual histone modifications by paired chromatin-associated modules +
286  +
T
The olfactory bulb: Coding and processing of odor molecule information +
286  +
S
Sparse coding and decorrelation in primary visual cortex during natural vision +
287  +
Structure and function of a human TAF(II)250 double bromodomain module +
288  +
D
Dynamical consequences of lesions in cortical networks +
29  +
R
RELATION BETWEEN PHYSIOLOGICAL FUNCTION AND ENERGY METABOLISM IN THE CENTRAL NERVOUS SYSTEM +
29  +
D
Differences in signalling by directly and indirectly binding ligands in bacterial chemotaxis +
29  +
T
Translating the histone code +
293  +
E
Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality +
296  +
S
Solution of a 20-variable 3-SAT problem on a DNA computer +
296  +
H
Hamiltonian derivations of the generalized Jarzynski equalities under feedback control +
297  +
G
Genetic networks: Small numbers of big molecules +
297  +
E
Extracting work from a single heat bath via vanishing quantum coherence +
299  +
O
Olfactory network dynamics and the coding of multidimensional signals +
3  +
M
Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete +
3  +
Monotone Circuits for Connectivity Require Super-Logarithmic Depth +
3  +
E
Efficiency and cost of economical brain functional networks +
3  +
I
Information processing and the second law of thermodynamics: An inclusive, Hamiltonian approach +
3  +
Q
Quantum techniques for studying equilibrium in reaction networks +
3  +
A
A generalization of Wegscheider's condition. Implications for properties of steady states and for quasi-steady-state approximation +
3  +
D
Dynamic DNA nanotechnology using strand-displacement reactions +
3  +
L
Logic gates and antisense DNA devices operating on a translator nucleic acid scaffold +
3  +
M
Methods for quantifying the informational structure of sensory and motor data +
3  +
C
Computational design of nucleic acid feedback control circuits +
3  +
E
Exorcist XIV: The wrath of Maxwell's Demon. Part II. From Szilard to Landauer and beyond +
30  +
I
Insect olfactory receptors. +
30  +
E
Efficient extraction of free energy profiles from nonequilibrium experiments +
30  +
S
Small-world properties of nonlinear brain activity in schizophrenia +
30  +
T
Transforming probabilities with combinational logic +
30  +
R
Rethinking mammalian brain evolution +
30  +
S
Study of stochastic resonance by method of stochastic energetics +
300  +
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