keyword
MENU ▼
Read by QxMD icon Read
search

Transfer entropy

keyword
https://www.readbyqxmd.com/read/27924257/a-unified-statistical-model-of-protein-multiple-sequence-alignment-integrating-direct-coupling-and-insertions
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/27832153/inferring-weighted-directed-association-network-from-multivariate-time-series-with-a-synthetic-method-of-partial-symbolic-transfer-entropy-spectrum-and-granger-causality
#5
Yanzhu Hu, Huiyang Zhao, Xinbo Ai
Complex network methodology is very useful for complex system explorer. However, the relationships among variables in complex system are usually not clear. Therefore, inferring association networks among variables from their observed data has been a popular research topic. We propose a synthetic method, named small-shuffle partial symbolic transfer entropy spectrum (SSPSTES), for inferring association network from multivariate time series. The method synthesizes surrogate data, partial symbolic transfer entropy (PSTE) and Granger causality...
2016: PloS One
https://www.readbyqxmd.com/read/27830402/synthesis-and-crystal-structures-of-novel-copper-ii-complexes-with-glycine-and-substituted-phenanthrolines-reactivity-towards-dna-bsa-and-in-vitro-cytotoxic-and-antimicrobial-evaluation
#6
Duygu İnci, Rahmiye Aydın, Özgür Vatan, Tuba Sevgi, Dilek Yılmaz, Yunus Zorlu, Yusuf Yerli, Bünyemin Çoşut, Elif Demirkan, Nilüfer Çinkılıç
New copper(II) complexes-dimeric-[Cu(nphen)(gly)(H2O)](+) (1) and [Cu(dmphen)(gly)(NO3)(H2O)] (2) (nphen = 5-nitro-1,10-phenanthroline, dmphen = 4,7-dimethyl-1,10-phenanthroline, and gly = glycine)-have been synthesized and characterized by CHN analysis, single-crystal X-ray diffraction techniques, FTIR, EPR spectroscopy, and cyclic voltammetry. The CT-DNA-binding properties of these complexes have been investigated by thermal denaturation measurements and both absorption and emission spectroscopy. The DNA cleavage activity of these complexes has been studied on supercoiled pUC19 plasmid DNA by gel electrophoresis experiments in the absence and presence of H2O2...
November 10, 2016: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/27819088/collective-proton-transfer-in-ordinary-ice-local-environments-temperature-dependence-and-deuteration-effects
#7
Christof Drechsel-Grau, Dominik Marx
The transfer of multiple protons in hydrogen-bonded networks usually occurs one proton at a time. At sufficiently high temperatures, each proton transfers via thermally activated hopping along its hydrogen bond, thereby moving a charge defect through the network. At low temperatures, quantum-mechanical tunnelling might set in instead, thus avoiding hopping over the energy barriers. In the case of several transferring protons, independent thermal hopping or quantum tunnelling of the individual protons becomes less favourable because of a significant creation of charge defects...
November 7, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27808463/interaction-and-energy-transfer-studies-between-bovine-serum-albumin-and-cdte-quantum-dots-conjugates-cdte-qds-as-energy-acceptor-probes
#8
M G Kotresh, L S Inamdar, M A Shivkumar, K S Adarsh, B N Jagatap, B G Mulimani, G M Advirao, S R Inamdar
In this paper, a systematic investigation of the interaction of bovine serum albumin (BSA) with water-soluble CdTe quantum dots (QDs) of two different sizes capped with carboxylic thiols is presented based on steady-state and time-resolved fluorescence measurements. Efficient Förster resonance energy transfer (FRET) was observed to occur from BSA donor to CdTe acceptor as noted from reduction in the fluorescence of BSA and enhanced fluorescence from CdTe QDs. FRET parameters such as Förster distance, spectral overlap integral, FRET rate constant and efficiency were determined...
November 3, 2016: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/27802274/topology-cross-frequency-and-same-frequency-band-interactions-shape-the-generation-of-phase-amplitude-coupling-in-a-neural-mass-model-of-a-cortical-column
#9
Roberto C Sotero
Phase-amplitude coupling (PAC), a type of cross-frequency coupling (CFC) where the phase of a low-frequency rhythm modulates the amplitude of a higher frequency, is becoming an important indicator of information transmission in the brain. However, the neurobiological mechanisms underlying its generation remain undetermined. A realistic, yet tractable computational model of the phenomenon is thus needed. Here we analyze a neural mass model of a cortical column, comprising fourteen neuronal populations distributed across four layers (L2/3, L4, L5 and L6)...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27775537/can-a-soft-robotic-probe-use-stiffness-control-like-a-human-finger-to-improve-efficacy-of-haptic-perception
#10
Nantachai Sornkarn, Thrishantha Nanayakkara
When humans are asked to palpate a soft tissue to locate a hard nodule, they regulate the stiffness, speed, and force of the finger during examination. If we understand the relationship between these behavioral variables and haptic information gain (transfer entropy) during manual probing, we can improve the efficacy of soft robotic probes for soft tissue palpation, such as in tumor localization in minimally invasive surgery. Here, we recorded the muscle co-contraction activity of the finger using EMG sensors to address the question as to whether joint stiffness control during manual palpation plays an important role in the haptic information gain...
October 19, 2016: IEEE Transactions on Haptics
https://www.readbyqxmd.com/read/27770675/two-step-transfer-entropy-an-estimator-of-delayed-directional-couplings-between-multivariate-eeg-time-series
#11
Maryam Songhorzadeh, Karim Ansari-Asl, Alimorad Mahmoudi
Quantifying delayed directional couplings between electroencephalographic (EEG) time series requires an efficient method of causal network inference. This is especially due to the limited knowledge about the underlying dynamics of the brain activity. Recent methods based on information theoretic measures such as Transfer Entropy (TE) made significant progress on this issue by providing a model-free framework for causality detection. However, TE estimation from observed data is not a trivial task, especially when the number of variables is large which is the case in a highly complex system like human brain...
October 14, 2016: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/27769993/transferring-entropy-to-the-realm-of-gxg-interactions
#12
Paola G Ferrario, Inke R König
Genome-wide association studies are moving to genome-wide interaction studies, as the genetic background of many diseases appears to be more complex than previously supposed. Thus, many statistical approaches have been proposed to detect gene-gene (GxG) interactions, among them numerous information theory-based methods, inspired by the concept of entropy. These are suggested as particularly powerful and, because of their nonlinearity, as better able to capture nonlinear relationships between genetic variants and/or variables...
October 21, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27768952/a-biophysical-investigation-on-the-binding-of-proflavine-with-human-hemoglobin-insights-from-spectroscopy-thermodynamics-and-afm-studies
#13
Anirban Basu, Gopinatha Suresh Kumar
Interaction of proflavine with hemoglobin (Hgb) was studied employing spectroscopy, calorimetry, and atomic force microscopy. The equilibrium constant was found to be of the order 10(4)M(-1). The quenching of Hgb fluorescence by proflavine was due to the complex formation. Calculation of the molecular distance (r) between the donor (β-Trp37 of Hgb) and acceptor (proflavine) suggested that energy can be efficiently transferred from the β-Trp37 residue at the α1β2 interface of the protein to the dye. Proflavine induced significant secondary structural changes in Hgb...
October 12, 2016: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/27768950/molecular-mechanism-of-the-binding-of-3-4-5-tri-o-caffeoylquinic-acid-to-human-serum-albumin-saturation-transfer-difference-nmr-multi-spectroscopy-and-docking-studies
#14
Bin Tang, Yanmei Huang, Hongqin Yang, Peixiao Tang, Hui Li
As a natural dietary polyphenol, 3,4,5-tri-O-caffeoylquinic acid (3,4,5-triCQA) exhibits numerous stronger pharmacological activities than that of its analogues. Studies on interaction between 3,4,5-triCQA and protein are very helpful for understanding the mechanism of these enhanced biological functions. In this study, (1)H saturation transfer difference NMR ((1)H STD-NMR) combined with multi-spectroscopy were used to probe the interaction of 3,4,5-triCQA with human serum albumin (HSA). Both qualitative and quantitative (1)H STD-NMR indicated that 3,4,5-triCQA can specifically bind to HSA at the favored Sudlow's site II with caffeoyl groups as the main recognizable moiety...
October 17, 2016: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/27740844/dynamical-scheme-for-interferometric-measurements-of-full-counting-statistics
#15
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
https://www.readbyqxmd.com/read/27739854/time-evolution-of-interhemispheric-coupling-in-a-model-of-focal-neocortical-epilepsy-in-mice
#16
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
https://www.readbyqxmd.com/read/27722579/distinction-of-electron-pathways-at-titanium-oxide-liquid-interfaces-in-photocatalytic-processes-and-co-catalyst-effects
#17
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
https://www.readbyqxmd.com/read/27718572/amino-acid-specific-effects-on-rna-tertiary-interactions-single-molecule-kinetic-and-thermodynamic-studies
#18
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
https://www.readbyqxmd.com/read/27711776/thermodynamics-of-biphasic-lanthanide-extraction-by-tripodal-diglycolamide-a-solution-calorimetry-study
#19
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
https://www.readbyqxmd.com/read/27711545/adsorption-in-zeolites-using-mechanically-embedded-oniom-clusters
#20
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
keyword
keyword
114539
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"