scholarly journals How many bits of information can be transferred between residues in a protein and how fast?

2022 ◽  
Author(s):  
Aysima Hacisuleyman ◽  
Burak Erman
Keyword(s):  
Information Transfer ◽  
Activity Time ◽  
Perfect Agreement ◽  
Time Resolved ◽  
Transfer Rates ◽  
Entropy Transfer ◽  
Raman And Infrared Spectroscopy ◽  
Ultraviolet Resonance Raman ◽  
Basic Features ◽  
Gaussian Network

Time resolved Raman and infrared spectroscopy experiments show the basic features of information transfer between residues in proteins. Here, we present the theoretical basis of information transfer using a simple elastic net model and recently developed entropy transfer concept in proteins. Mutual information between two residues is a measure of communication in proteins which shows the maximum amount of information that may be transferred between two residues. However, it does not explain the actual amount of transfer nor the transfer rate of information between residues. For this, dynamic equations of the system are needed. We used the Schreiber theory of information transfer and the Gaussian network Model of proteins, together with the solution of the Langevin equation, to quantify allosteric information transfer. Results of the model are in perfect agreement with ultraviolet resonance Raman measurements. Analysis of the allosteric protein Human NAD-dependent isocitrate dehydrogenase shows that a multitude of paths contribute collectively to information transfer. While the peak values of information transferred are small relative to information content of residues, considering the estimated transfer rates, which are in the order of megabits per second, sustained transfer during the activity time-span of proteins may be significant.

scholarly journals Hierarchical coupling between ATP hydrolysis and Hsp90’s client binding site

2020 ◽  
Author(s):  
Steffen Wolf ◽  
Benedikt Sohmen ◽  
Björn Hellenkamp ◽  
Johann Thurn ◽  
Gerhard Stock ◽  
...  
Keyword(s):  
Binding Site ◽  
Single Molecule ◽  
Information Transfer ◽  
Atp Hydrolysis ◽  
Structural Information ◽  
Substrate Binding ◽  
Signal Propagation ◽  
Nonequilibrium Molecular Dynamics ◽  
Time Resolved ◽  
Substrate Binding Site

I.ABSTRACTSeveral indicators for a signal propagation from a binding site to a distant functional site have been found in the Hsp90 dimer. Here we determined a time-resolved pathway from ATP hydrolysis to changes in a distant folding substrate binding site. This was possible by combining single-molecule fluorescence-based methods with extensive atomistic nonequilibrium molecular dynamics simulations. We find that hydrolysis of one ATP effects a structural asymmetry in the full Hsp90 dimer that leads to the collapse of a central folding substrate binding site. Arg380 is the major mediator in transferring structural information from the nucleotide to the substrate binding site. This allosteric process occurs via hierarchical dynamics that involve timescales from picoto milliseconds and length scales from Ångstroms to several nanometers. We presume that similar hierarchical mechanisms are fundamental for information transfer through many other proteins.

scholarly journals Excitation of Spectra of Multiply Ionized Atoms by Capacitor Discharges

1974 ◽  
Vol 28 (3) ◽  
pp. 223-234 ◽  
Author(s):  
Cornelius H. H. Van Deurzen ◽  
John G. Conway
Keyword(s):  
Differential Equation ◽  
Electrical Circuit ◽  
Spectral Lines ◽  
Circuit Parameter ◽  
Excitation Energies ◽  
Time Resolved ◽  
Transfer Rates ◽  
Line Intensities ◽  
Relative Line ◽  
Varied Intensity

Spectra of vanadium have been produced in a vacuum sliding spark, and their relative line intensities have been measured as parameters of the electrical circuit were varied. Intensity maxima of the spectral lines are interpreted as representing excitation energies and have been found to depend in a definitive manner on the power delivered to the source and on the duration of the discharge. The differential equation of the circuit is solved for the charge and energy transfer rates from the capacitor to the source, and two functions of the continuous circuit parameter [Formula: see text] are defined which greatly assist in interpreting the effect of the circuit parameters on the excitation in the source. A relationship was found between the excitation in the source and the electrical circuit parameters. By means of this relationship one may obtain a good estimate of the excitation gained in the spark source. It is shown that by exercising careful control over the circuit parameters it is possible to separate spectra of neighboring ionization stages through either total pulse or time-resolved observations.

Time-resolved ultraviolet resonance Raman studies of protein structure: application to bacteriorhodopsin

Biochemistry ◽  
1992 ◽  
Vol 31 (23) ◽  
pp. 5328-5334 ◽  
Author(s):  
James B. Ames ◽  
Marianne Ros ◽  
Jan Raap ◽  
Johan Lugtenburg ◽  
Richard A. Mathies
Keyword(s):  
Protein Structure ◽  
Resonance Raman ◽  
Time Resolved ◽  
Ultraviolet Resonance Raman

scholarly journals New Insights into Synthetic Copper Greens: The Search for Specific Signatures by Raman and Infrared Spectroscopy for Their Characterization in Medieval Artworks

Heritage ◽  
2019 ◽  
Vol 2 (2) ◽  
pp. 1614-1629 ◽  
Author(s):  
Juliana Buse ◽  
Vanessa Otero ◽  
Maria Melo
Keyword(s):  
Infrared Spectroscopy ◽  
Copper Chloride ◽  
Systematic Investigation ◽  
Perfect Agreement ◽  
Crown Of Aragon ◽  
Green Component ◽  
Raman And Infrared Spectroscopy ◽  
Group 2 ◽  
Art Research ◽  
Green Pigments

A systematic investigation of medieval copper green pigments was carried out based on written sources: 21 manuscripts, dating from 50–70 to 1755 AD, were sourced and 77 recipes were selected, translating into 44 experiments. Reconstructions from medieval recipes were prepared and characterized through a multianalytical approach to disclose the original pigment formulation that is often described as verdigris. Based on the results obtained, we propose three main groups of copper green pigments, group 1, in which only Cu(CH3COO)2·H2O is formed; group 2, where this acetate is found together with copper oxalates; group 3, in which atacamite is present as the major green component or as a signature compound. The products formed are in perfect agreement with that predicted by the state-of-the-art research on the mechanisms of atmospheric corrosion of copper. This knowledge, together with our experience on craft recipes to prepare medieval paint materials, allowed us to recover a lost medieval recipe to produce a copper green pigment based mainly on atacamite, a basic copper chloride, which has been recently detected, by Raman and infrared spectroscopy, in artworks ranging from Catalonia and the Crown of Aragon panel painting to Islamic manuscripts.

scholarly journals A Hybrid Speller Design Using Eye Tracking and SSVEP Brain–Computer Interface

Sensors ◽  
2020 ◽  
Vol 20 (3) ◽  
pp. 891 ◽  
Author(s):  
Malik M. Naeem Mannan ◽  
M. Ahmad Kamran ◽  
Shinil Kang ◽  
Hak Soo Choi ◽  
Myung Yung Jeong
Keyword(s):  
Eye Tracking ◽  
Classification Accuracy ◽  
Information Transfer ◽  
High Speed ◽  
Communication Channel ◽  
Computer Interface ◽  
Stimuli Responsive ◽  
Transfer Rates ◽  
Computer Interfaces ◽  
Large Numbers

Steady-state visual evoked potentials (SSVEPs) have been extensively utilized to develop brain–computer interfaces (BCIs) due to the advantages of robustness, large number of commands, high classification accuracies, and information transfer rates (ITRs). However, the use of several simultaneous flickering stimuli often causes high levels of user discomfort, tiredness, annoyingness, and fatigue. Here we propose to design a stimuli-responsive hybrid speller by using electroencephalography (EEG) and video-based eye-tracking to increase user comfortability levels when presented with large numbers of simultaneously flickering stimuli. Interestingly, a canonical correlation analysis (CCA)-based framework was useful to identify target frequency with a 1 s duration of flickering signal. Our proposed BCI-speller uses only six frequencies to classify forty-eight targets, thus achieve greatly increased ITR, whereas basic SSVEP BCI-spellers use an equal number of frequencies to the number of targets. Using this speller, we obtained an average classification accuracy of 90.35 ± 3.597% with an average ITR of 184.06 ± 12.761 bits per minute in a cued-spelling task and an ITR of 190.73 ± 17.849 bits per minute in a free-spelling task. Consequently, our proposed speller is superior to the other spellers in terms of targets classified, classification accuracy, and ITR, while producing less fatigue, annoyingness, tiredness and discomfort. Together, our proposed hybrid eye tracking and SSVEP BCI-based system will ultimately enable a truly high-speed communication channel.

Optimizing information‐transfer rates for human communication

2006 ◽  
Vol 119 (5) ◽  
pp. 3237-3237
Author(s):  
Charlotte M. Reed ◽  
Nathaniel I. Durlach ◽  
Hong Z. Tan
Keyword(s):  
Information Transfer ◽  
Human Communication ◽  
Transfer Rates

scholarly journals Brain–Computer Interface Spellers for Communication: Why We Need to Address Their Security and Authenticity

2020 ◽  
Vol 10 (3) ◽  
pp. 139
Author(s):  
Anirban Dutta
Keyword(s):  
Research And Development ◽  
Information Transfer ◽  
Brain Computer Interface ◽  
Computer Interface ◽  
Brain Computer Interfaces ◽  
Transfer Rates ◽  
Computer Interfaces ◽  
Significant Research

Brain–Computer Interfaces (BCI) have witnessed significant research and development in the last 20 years where the main aim was to improve their accuracy and increase their information transfer rates (ITRs), while still making them portable and easy to use by a broad range of users [...]

scholarly journals INFORMATION TRANSFER RATES IN SPIN QUANTUM CHANNELS

2007 ◽  
Vol 05 (04) ◽  
pp. 439-455 ◽  
Author(s):  
DAVIDE ROSSINI ◽  
VITTORIO GIOVANNETTI ◽  
ROSARIO FAZIO
Keyword(s):  
Quantum Information ◽  
Information Transfer ◽  
Transmission Efficiency ◽  
Spin Chains ◽  
Quantum Channels ◽  
Transfer Rates ◽  
Temporal Correlations ◽  
Spin Quantum ◽  
Communication Efficiency

We analyze the communication efficiency of quantum information transfer along unmodulated spin chains by computing the communication rates of various protocols. The effects of temporal correlations are discussed, showing that they can be exploited to boost the transmission efficiency.

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