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Transfer entropy

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https://www.readbyqxmd.com/read/28103546/quantifying-net-synergy-redundancy-of-spontaneous-variability-regulation-via-predictability-and-transfer-entropy-decomposition-frameworks
#1
Alberto Porta, Vlasta Bari, Beatrice De Maria, Anielle C M Takahashi, Stefano Guzzetti, Riccardo Colombo, Aparecida M Catai, Ferdinando Raimondi, Luca Faes
OBJECTIVE: Indexes assessing the balance between redundancy and synergy were hypothesized to be helpful in characterizing cardiovascular control from spontaneous beat-to-beat variations of heart period (HP), systolic arterial pressure (SAP) and respiration (R). METHODS: Net redundancy/synergy indexes were derived according to predictability and transfer entropy decomposition strategies via a multivariate linear regression approach. Indexes were tested in two protocols inducing modifications of the cardiovascular regulation via baroreflex loading/unloading (i...
January 17, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28101950/molecular-binding-of-toxic-phenothiazinium-derivatives-azures-to-bovine-serum-albumin-a-comparative-spectroscopic-calorimetric-and-in-silico-study
#2
Somnath Das, Md Maidul Islam, Gopal Chandra Jana, Anirudha Patra, Pradeep K Jha, Maidul Hossain
In this paper, the comparative binding behavior of antimalarial drug azure A, azure B and azure C with bovine serum albumin (BSA) has been studied. The interaction has been confirmed by multispectroscopic (UV, fluorescence, Fourier transform infrared (FT-IR), and circular dichroism) and molecular docking techniques. The experimental results show that azure B has the highest BSA binding affinity followed by azure A and azure C. The experimental evidence of binding showed a static quenching mechanism in the interaction azures with BSA...
January 19, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28095404/entropy-transfer-between-residue-pairs-and-allostery-in-proteins-quantifying-allosteric-communication-in-ubiquitin
#3
Aysima Hacisuleyman, Burak Erman
It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others...
January 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28079528/assessing-the-evolution-of-redundancy-synergy-of-spontaneous-variability-regulation-with-age
#4
Alberto Porta, Vlasta Bari, Beatrice De Maria, Natália Maria Perseguini, Juliana Milan, Patricia Rehder-Santos, Vinícius Minatel, Anielle Takahashi, Aparecida Catai
We exploited a model-based Wiener-Granger causality method in the information domain for the evaluation of the transfer entropy (TE) and interaction TE (ITE), the latter taken as a measure of the net balance between redundancy and synergy, to describe the interactions between the spontaneous variability of heart period (HP) and systolic arterial pressure (SAP) and the effect of respiration (R) on both variables. Cardiac control was typified via the genuine TE from SAP to HP, that from R to HP, and the ITE from SAP and R to HP, while vascular control was characterized via the genuine TE from HP to SAP, that from R to SAP, and the ITE from HP and R to SAP...
January 12, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28049370/underlying-molecular-interaction-of-bovine-serum-albumin-and-linezolid-a-biophysical-outlook
#5
Amartya Roy, Paromita Seal, Jyotirmoy Sikdar, Sanghamitra Banerjee, Rajen Haldar
Linezolid, one of the reserve antibiotic of oxazolidinone class has wide range of antimicrobial activity. Here we have conducted a fundamental study concerning the dynamics of its interaction with bovine serum albumin (BSA), and the post binding modification of the later by employing different spectroscopic (absorption, fluorescence and circular dichroism (CD) spectroscopy) and molecular docking tools. Gradual quenching of the tryptophan (Trp) fluorescence upon addition of linezolid to BSA confirms their interaction...
January 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28049340/accurate-schemes-for-calculation-of-thermodynamic-properties-of-liquid-mixtures-from-molecular-dynamics-simulations
#6
Miguel A Caro, Tomi Laurila, Olga Lopez-Acevedo
We explore different schemes for improved accuracy of entropy calculations in aqueous liquid mixtures from molecular dynamics (MD) simulations. We build upon the two-phase thermodynamic (2PT) model of Lin et al. [J. Chem. Phys. 119, 11792 (2003)] and explore new ways to obtain the partition between the gas-like and solid-like parts of the density of states, as well as the effect of the chosen ideal "combinatorial" entropy of mixing, both of which have a large impact on the results. We also propose a first-order correction to the issue of kinetic energy transfer between degrees of freedom (DoF)...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28018126/sublimation-like-behavior-of-cardiac-dynamics-in-heart-failure-a-malignant-phase-transition
#7
Ary L Goldberger, Teresa Henriques, Sara Mariani
An abrupt transition from sinus cardiac rhythm to atrial fibrillation (AF) is common in patients with chronic heart failure (CHF). We propose a conceptual framework for viewing this malignant transition in terms of a type of sublimation marked by the switch from highly periodic sinus interbeat interval dynamics characteristic of CHF to a state of random disorganization with AF. Sublimation of physical substances involves an increase in entropy via heat transfer. In contrast, the disease-related sublimation-like behavior involves a loss of information content, associated decreases in cardiac bioenergetic capacity and in multiscale entropy...
November 2016: Complexity
https://www.readbyqxmd.com/read/27993392/an-inverse-gas-chromatographic-methodology-for-studying-gas-liquid-mass-transfer
#8
A Paloglou, K Martakidis, D Gavril
A novel methodology of reversed flow inverse gas chromatography (RF-IGC) is presented. It permits the simultaneous determination of mass transfer coefficients across the gas liquid interface as well as the respective solubility parameters and thermodynamic functions of dissolution of gases into liquids. The standard deviation of the experimentally determined parameters is estimated for first time, which combined with the successful comparison of the values of the present parameters with other literature ones ascertain the reliability of the methodology...
January 13, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27973836/hofmeister-anion-effects-on-thermodynamics-of-caffeine-partitioning-between-aqueous-and-cyclohexane-phases
#9
Bradley A Rogers, Tye S Thompson, Yanjie Zhang
Specific anion effects on the thermodynamics of caffeine partitioning between aqueous and cyclohexane phases were studied in the presence of 11 sodium salts by utilizing UV-vis spectroscopy. It is observed that weakly hydrated anions such as ClO4(-), SCN(-), and I(-) salt caffeine into the aqueous phase and increase the standard Gibbs free energy for caffeine transfer. On the other hand, well-hydrated anions such as CO3(2-) and SO4(2-) salt caffeine molecules out of the aqueous solution and promote the transfer process...
December 15, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27973805/substrate-sulfoxidation-by-an-iron-iv-oxo-complex-benchmarking-computationally-calculated-barrier-heights-to-experiment
#10
Fabián G Cantú Reinhard, Abayomi S Faponle, Sam P de Visser
High-valent metal-oxo oxidants are common reactive species in synthetic catalysts as well as heme and nonheme iron enzymes. In general, they efficiently react with substrates through oxygen atom transfer, and for a number of cases, experimental rate constants have been determined. However, because these rate constants are generally measured in a polar solution, it has been found difficult to find computational methodologies to reproduce experimental trends and reactivities. In this work, we present a detailed computational study into para-substituted thioanisole sulfoxidation by a nonheme iron(IV)-oxo complex...
December 15, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27967176/onsager-coefficients-for-systems-with-periodic-potentials
#11
Alexandre Rosas, Christian Van den Broeck, Katja Lindenberg
We carry out the thermodynamic analysis of a Markovian stochastic engine, driven by a spatially and temporally periodic modulation in a d-dimensional space. We derive the analytic expressions for the Onsager coefficients characterizing the linear response regime for the isothermal transfer of one type of work (a driver) to another (a load), mediated by a stochastic time-periodic machine. As an illustration, we obtain the explicit results for a Markovian kangaroo process coupling two orthogonal directions and find extremely good agreement with numerical simulations...
November 2016: Physical Review. E
https://www.readbyqxmd.com/read/27967120/information-flow-and-causality-as-rigorous-notions-ab-initio
#12
X San Liang
Information flow or information transfer the widely applicable general physics notion can be rigorously derived from first principles, rather than axiomatically proposed as an ansatz. Its logical association with causality is firmly rooted in the dynamical system that lies beneath. The principle of nil causality that reads, an event is not causal to another if the evolution of the latter is independent of the former, which transfer entropy analysis and Granger causality test fail to verify in many situations, turns out to be a proven theorem here...
November 2016: Physical Review. E
https://www.readbyqxmd.com/read/27951677/combining-simulations-and-solution-experiments-as-a-paradigm-for-rna-force-field-refinement
#13
Andrea Cesari, Alejandro Gil-Ley, Giovanni Bussi
Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA oligomers and suggest that molecular dynamics should be complemented with experimental data. We here propose a scheme based on the maximum entropy principle to combine simulations with bulk experiments. In the proposed scheme, the noise arising from both the measurements and the forward models used to back-calculate the experimental observables is explicitly taken into account...
December 13, 2016: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/27951518/interaction-of-an-antiepileptic-drug-lamotrigine-with-human-serum-albumin-hsa-application-of-spectroscopic-techniques-and-molecular-modeling-methods
#14
Fatemeh Poureshghi, Parisa Ghandforoushan, Azam Safarnejad, Somaieh Soltani
Lamotrigine (an epileptic drug) interaction with human serum albumin (HSA) was investigated by fluorescence, UV-Vis, FTIR, CD spectroscopic techniques, and molecular modeling methods. Binding constant (Kb) of 5.74×10(3) and number of binding site of 0.97 showed that there is a slight interaction between lamotrigine and HSA. Thermodynamic studies was constructed using the flourimetric titrations in three different temperatures and the resulted data used to calculate the parameters using Vant Hoff equation. Decreased Stern Volmer quenching constant by enhanced temperature revealed the static quenching mechanism...
January 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/27934051/ultrafast-long-range-charge-separation-in-organic-photovoltaics-promotion-by-off-diagonal-vibronic-couplings-and-entropy-increase
#15
Yao Yao, Xiaoyu Xie, Haibo Ma
The exciton dissociation in a model donor/acceptor heterojunction with electron-phonon couplings is simulated by a full quantum dynamical method, in which ultrafast long-range charge separation is observed. Such a novel scenario does not undergo short-range interfacial (pinned) charge transfer states, but can be mainly ascribed to the quantum resonance between local Frenkel excited states and a broad array of long-range charge transfer (LRCT) states assisted by the moderate off-diagonal vibronic couplings. The entropy-increasing effect associated with the very dense density of states for LRCT states is also found to be beneficial for lowering the free energy barrier for charge generation in organic solar cells...
December 1, 2016: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/27930289/unified-framework-for-information-integration-based-on-information-geometry
#16
Masafumi Oizumi, Naotsugu Tsuchiya, Shun-Ichi Amari
Assessment of causal influences is a ubiquitous and important subject across diverse research fields. Drawn from consciousness studies, integrated information is a measure that defines integration as the degree of causal influences among elements. Whereas pairwise causal influences between elements can be quantified with existing methods, quantifying multiple influences among many elements poses two major mathematical difficulties. First, overestimation occurs due to interdependence among influences if each influence is separately quantified in a part-based manner and then simply summed over...
December 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27924257/a-unified-statistical-model-of-protein-multiple-sequence-alignment-integrating-direct-coupling-and-insertions
#17
Akira R Kinjo
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically model the MSA incorporating both short-range and long-range correlations as well as insertions, I have derived a lattice gas model of the MSA based on the principle of maximum entropy. The partition function, obtained by the transfer matrix method with a mean-field approximation, accounts for all possible alignments with all possible sequences...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27908118/free-energy-calculations-along-entropic-pathways-i-homogeneous-vapor-liquid-nucleation-for-atomic-and-molecular-systems
#18
Caroline Desgranges, Jerome Delhommelle
Using the entropy S as a reaction coordinate, we determine the free energy barrier associated with the formation of a liquid droplet from a supersaturated vapor for atomic and molecular fluids. For this purpose, we develop the μVT-S simulation method that combines the advantages of the grand-canonical ensemble, that allows for a direct evaluation of the entropy, and of the umbrella sampling method, that is well suited to the study of an activated process like nucleation. Applying this approach to an atomic system such as Ar allows us to test the method...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27908002/computing-algebraic-transfer-entropy-and-coupling-directions-via-transcripts
#19
José M Amigó, Roberto Monetti, Beata Graff, Grzegorz Graff
Most random processes studied in nonlinear time series analysis take values on sets endowed with a group structure, e.g., the real and rational numbers, and the integers. This fact allows to associate with each pair of group elements a third element, called their transcript, which is defined as the product of the second element in the pair times the first one. The transfer entropy of two such processes is called algebraic transfer entropy. It measures the information transferred between two coupled processes whose values belong to a group...
November 2016: Chaos
https://www.readbyqxmd.com/read/27833120/backward-transfer-entropy-informational-measure-for-detecting-hidden-markov-models-and-its-interpretations-in-thermodynamics-gambling-and-causality
#20
Sosuke Ito
The transfer entropy is a well-established measure of information flow, which quantifies directed influence between two stochastic time series and has been shown to be useful in a variety fields of science. Here we introduce the transfer entropy of the backward time series called the backward transfer entropy, and show that the backward transfer entropy quantifies how far it is from dynamics to a hidden Markov model. Furthermore, we discuss physical interpretations of the backward transfer entropy in completely different settings of thermodynamics for information processing and the gambling with side information...
November 11, 2016: Scientific Reports
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