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Transfer entropy

David Dasenbrook, Christian Flindt
We propose a dynamical scheme for measuring the full-counting statistics in a mesoscopic conductor using an electronic Mach-Zehnder interferometer. The conductor couples capacitively to one arm of the interferometer and causes a phase shift which is proportional to the number of transferred charges. Importantly, the full-counting statistics can be obtained from average current measurements at the outputs of the interferometer. The counting field can be controlled by varying the time delay between two separate voltage signals applied to the conductor and the interferometer, respectively...
September 30, 2016: Physical Review Letters
F Vallone, E Vannini, A Cintio, M Caleo, A Di Garbo
Epilepsy is characterized by substantial network rearrangements leading to spontaneous seizures and little is known on how an epileptogenic focus impacts on neural activity in the contralateral hemisphere. Here, we used a model of unilateral epilepsy induced by injection of the synaptic blocker tetanus neurotoxin (TeNT) in the mouse primary visual cortex (V1). Local field potential (LFP) signals were simultaneously recorded from both hemispheres of each mouse in acute phase (peak of toxin action) and chronic condition (completion of TeNT effects)...
September 2016: Physical Review. E
Shota Kuwahara, Kenji Katayama
Photocatalytic reactions include several different steps and routes for photoexcited carriers, and each dynamic is closely related to the reaction efficiency. Although commonly used time-resolved techniques can reveal the kinetics of photoexcited carriers, the reaction pathways are difficult to distinguish due to decay kinetics extending over many temporal orders and various contributions from the carriers and species involved. Herein, we report the distinction of the electron dynamics in the photocatalytic processes of titanium oxide through the combination of the transient grating method and maximum entropy analysis for the estimation of time constants...
September 14, 2016: Physical Chemistry Chemical Physics: PCCP
Abhigyan Sengupta, Hsuan-Lei Sung, David J Nesbitt
In light of the current models for an early RNA-based universe, the potential influence of simple amino acids on tertiary folding of ribozymal RNA into biochemically competent structures is speculated to be of significant evolutionary importance. In the present work, the folding-unfolding kinetics of a ubiquitous tertiary interaction motif, the GAAA tetraloop-tetraloop receptor (TL-TLR), is investigated by single-molecule fluorescence resonance energy transfer spectroscopy in the presence of natural amino acids both with (e...
October 10, 2016: Journal of Physical Chemistry. B
Seraj A Ansari, Prasanta K Mohapatra, Willem Verboom, Linfeng Rao
Isothermal titration calorimetry was employed for the direct measurement of the enthalpy of extraction (ΔHextr) of Eu(NO3)3 by using a tripodal diglycolamide (T-DGA) ligand dissolved in n-dodecane containing 5% (v/v) 2-decanol. The enthalpy of extraction obtained by titration calorimetry was in good agreement with the enthalpy of extraction calculated from the temperature dependence of the distribution coefficients by using the van't Hoff equation. The Gibbs free energy and the entropy of extraction (ΔGextr and ΔSextr) for the extraction of Eu(NO3)3 by T-DGA were also obtained by solvent extraction experiments...
October 5, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Ryan E Patet, Stavros Caratzoulas, Dionisios G Vlachos
We have explored mechanically embedded three-layer QM/QM/MM ONIOM models for computational studies of binding in Al-substituted zeolites. In all the models considered, the high-level-theory layer consists of the adsorbate molecule and of the framework atoms within the first two coordination spheres of the Al atom and is treated at the M06-2X/6-311G(2df,p) level. For simplicity, flexibility and routine applicability, the outer, low-level-theory layer is treated with the UFF. We have modelled the intermediate-level layer quantum mechanically and investigated the performance of HF theory and of three DFT functionals, B3LYP, M06-2X and ωB97x-D, for different layer sizes and various basis sets, with and without BSSE corrections...
September 21, 2016: Physical Chemistry Chemical Physics: PCCP
Qin Yang, Zhuangzhu Luo, Faming Jiang, Yimin Luo, Sheng Tan, Zhibin Lu, Zhaozhu Zhang, Weimin Liu
Anti-icing surfaces/interfaces are of considerable importance in various engineering fields under natural freezing environment. Although superhydrophobic self-cleaning surfaces show good anti-icing potentials, promotion of these surfaces in engineering applications seems to enter a "bottleneck" stage. One of the key issues is the intrinsic relationship between superhydrophobicity and icephobicity is unclear, and the dynamic action mechanism of "air cushion" (a key internal factor for superhydrophobicity) on icing suppression was largely ignored...
October 4, 2016: ACS Applied Materials & Interfaces
Michele Di Pierro, Bin Zhang, Erez Lieberman Aiden, Peter G Wolynes, José N Onuchic
In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. We report a theoretical model for chromatin (Minimal Chromatin Model) that explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops...
September 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
James E Longbotham, Samantha J O Hardman, Stefan Görlich, Nigel S Scrutton, Sam Hay
"Heavy" (isotopically labeled) enzyme isotope effects offer a direct experimental probe of the role of protein vibrations on enzyme-catalyzed reactions. Here we have developed a strategy to generate isotopologues of the flavoenzyme pentaerythritol tetranitrate reductase (PETNR) where the protein and/or intrinsic flavin mononucleotide (FMN) cofactor are isotopically labeled with (2)H, (15)N, and (13)C. Both the protein and cofactor contribute to the enzyme isotope effect on the reductive hydride transfer reaction, but their contributions are not additive and may partially cancel each other out...
October 7, 2016: Journal of the American Chemical Society
Zahra Homayoon, Subha Pratihar, Edward Dratz, Ross Snider, Riccardo Spezia, George L Barnes, Veronica Macaluso, Ana Martin Somer, William L Hase
Direct dynamics simulations, utilizing the RM1 semiempirical electronic structure theory, were performed to study the thermal dissociation of the doubly protonated tripeptide threonine-isoleucine-lysine ion, TIK(H(+))2, for temperatures of 1250-2500 K, corresponding to classical energies of 1778-3556 kJ/mol. The number of different fragmentation pathways increases with increase in temperature. At 1250 K there are only three fragmentation pathways, with one contributing 85% of the fragmentation. In contrast, at 2500 K, there are 61 pathways, and not one dominates...
October 13, 2016: Journal of Physical Chemistry. A
Ella S Dehghani, Nicholas D Spencer, Shivaprakash N Ramakrishna, Edmondo M Benetti
The introduction of different types and concentrations of crosslinks within poly(hydroxyethyl methacrylate) (PHEMA) brushes influences their interfacial, physicochemical properties, ultimately governing their adsorption of proteins. PHEMA brushes and brush-hydrogels were synthesized by surface-initiated, atom-transfer radical polymerization (SI-ATRP) from HEMA, with and without the addition of di(ethylene glycol) dimethacrylate (DEGDMA) or tetra(ethylene glycol) dimethacrylate (TEGDMA) as crosslinkers. Linear (pure PHEMA) brushes show high hydration and low modulus and additionally provide an efficient barrier against nonspecific protein adsorption...
October 11, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Zhenkun Guo, Paul G Giokas, Thomas P Cheshire, Olivia F Williams, David J Dirkes, Wei You, Andrew M Moran
Analogues of 2D photon echo methods in which two population times are sampled have recently been used to expose heterogeneity in chemical kinetics. In this work, the two population times sampled for a transition metal complex are transformed into a 2D rate spectrum using the maximum entropy method. The 2D rate spectrum suggests heterogeneity in the vibrational cooling (VC) rate within the ensemble. In addition, a cross peak associated with VC and back electron transfer (BET) dynamics reveals correlation between the two processes...
September 14, 2016: Journal of Chemical Physics
J G Sereni, M Giovannini, M Gómez Berisso, F Gastaldo
Low temperature thermal and magnetic measurements performed on ferro-magneticl (FM) alloys of composition Ce2.15(Pd1-x Ag x )1.95In0.9 are presented. Pd substitution by Ag depresses [Formula: see text] from 4.1 K down to 1.1 K for x  =  0.5, which is related to the increase of band electrons, with a critical concentration extrapolated to [Formula: see text]. The [Formula: see text] decrease is accompanied by a weakening of the magnetization of the FM phase. At high temperature (T  >  30 K) the inverse magnetic susceptibility reveals the presence of robust magnetic moments ([Formula: see text] [Formula: see text]), whereas the low value of the Curie-Weiss temperature [Formula: see text] K excludes any relevant effect from Kondo screening...
November 30, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Richard E Spinney, Joseph T Lizier, Mikhail Prokopenko
Recent developments have cemented the realization that many concepts and quantities in thermodynamics and information theory are shared. In this paper, we consider a highly relevant quantity in information theory and complex systems, the transfer entropy, and explore its thermodynamic role by considering the implications of time reversal upon it. By doing so we highlight the role of information dynamics on the nuanced question of observer perspective within thermodynamics by relating the temporal irreversibility in the information dynamics to the configurational (or spatial) resolution of the thermodynamics...
August 2016: Physical Review. E
Roman Krcmar, Andrej Gendiar, Tomotoshi Nishino
Phase diagram of a discrete counterpart of the classical Heisenberg model, the truncated tetrahedral model, is analyzed on the square lattice, when the interaction is ferromagnetic. Each spin is represented by a unit vector that can point to one of the 12 vertices of the truncated tetrahedron, which is a continuous interpolation between the tetrahedron and the octahedron. Phase diagram of the model is determined by means of the statistical analog of the entanglement entropy, which is numerically calculated by the corner transfer matrix renormalization group method...
August 2016: Physical Review. E
Ken Takano, Hideitsu Hino, Shotaro Akaho, Noboru Murata
This study considers the common situation in data analysis when there are few observations of the distribution of interest or the target distribution, while abundant observations are available from auxiliary distributions. In this situation, it is natural to compensate for the lack of data from the target distribution by using data sets from these auxiliary distributions-in other words, approximating the target distribution in a subspace spanned by a set of auxiliary distributions. Mixture modeling is one of the simplest ways to integrate information from the target and auxiliary distributions in order to express the target distribution as accurately as possible...
September 14, 2016: Neural Computation
Andreas Ranft, Daniel Golkowski, Tobias Kiel, Valentin Riedl, Philipp Kohl, Guido Rohrer, Joachim Pientka, Sebastian Berger, Alexander Thul, Max Maurer, Christine Preibisch, Claus Zimmer, George A Mashour, Eberhard F Kochs, Denis Jordan, Rüdiger Ilg
BACKGROUND: The neural correlates of anesthetic-induced unconsciousness have yet to be fully elucidated. Sedative and anesthetic states induced by propofol have been studied extensively, consistently revealing a decrease of frontoparietal and thalamocortical connectivity. There is, however, less understanding of the effects of halogenated ethers on functional brain networks. METHODS: The authors recorded simultaneous resting-state functional magnetic resonance imaging and electroencephalography in 16 artificially ventilated volunteers during sevoflurane anesthesia at burst suppression and 3 and 2 vol% steady-state concentrations for 700 s each to assess functional connectivity changes compared to wakefulness...
November 2016: Anesthesiology
Dinesh Pal, Brian H Silverstein, Heonsoo Lee, George A Mashour
BACKGROUND: Significant advances have been made in our understanding of subcortical processes related to anesthetic- and sleep-induced unconsciousness, but the associated changes in cortical connectivity and cortical neurochemistry have yet to be fully clarified. METHODS: Male Sprague-Dawley rats were instrumented for simultaneous measurement of cortical acetylcholine and electroencephalographic indices of corticocortical connectivity-coherence and symbolic transfer entropy-before, during, and after general anesthesia (propofol, n = 11; sevoflurane, n = 13)...
November 2016: Anesthesiology
Carsten Grabow, James Macinko, Diana Silver, Maurizio Porfiri
A universal question in network science entails learning about the topology of interaction from collective dynamics. Here, we address this question by examining diffusion of laws across US states. We propose two complementary techniques to unravel determinants of this diffusion process: information-theoretic union transfer entropy and event synchronization. In order to systematically investigate their performance on law activity data, we establish a new stochastic model to generate synthetic law activity data based on plausible networks of interactions...
August 2016: Chaos
Craig G Richter, Mariana Babo-Rebelo, Denis Schwartz, Catherine Tallon-Baudry
A fundamental feature of the temporal organization of neural activity is phase-amplitude coupling between brain rhythms at different frequencies, where the amplitude of a higher frequency varies according to the phase of a lower frequency. Here, we show that this rule extends to brain-organ interactions. We measured both the infra-slow (~0.05Hz) rhythm intrinsically generated by the stomach - the gastric basal rhythm - using electrogastrography, and spontaneous brain dynamics with magnetoencephalography during resting-state with eyes open...
August 21, 2016: NeuroImage
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