scholarly journals Synchronous and Asynchronous Response in Dynamically Perturbed Proteins

2020 ◽  
Author(s):  
Albert Erkip ◽  
Aysima Hacisuleyman ◽  
Batu Erman ◽  
Burak Erman
Keyword(s):  
Network Model ◽  
Langevin Equation ◽  
Information Transfer ◽  
Loss Modulus ◽  
Periodic Perturbation ◽  
Dynamic Modulation ◽  
Dynamic Correlations ◽  
Lost Work ◽  
Gaussian Network

AbstractWe developed a Dynamic Gaussian Network Model to study perturbation and response in proteins. The model is based on the solution of the Langevin equation in the presence of noise and perturbation. A residue is perturbed periodically with a given frequency and the response of other residues is determined in terms of a storage and loss modulus of the protein. The amount of work lost upon periodic perturbation and the residues that contribute significantly to the lost work is determined. The model shows that perturbation introduces new dynamic correlations into the system with time delayed synchronous and asynchronous components. Residues whose perturbation induces large correlations in the protein and those that do not lead to correlations may be identified. The model is used to investigate the dynamic modulation of nanobodies. Despite its simplicity, the model explains several features of perturbation and response such as the role of loops and linkers in perturbation, dispersion of work of perturbation, and information transfer through preexisting pathways, all shown to be important factors in allostery.

scholarly journals Causality, Transfer Entropy and Allosteric Communication Landscapes in Proteins with Harmonic Interactions

2016 ◽  
Author(s):  
Aysima Hacisuleyman ◽  
Burak Erman
Keyword(s):  
Network Model ◽  
Protein Function ◽  
Information Transfer ◽  
Protein Activity ◽  
Additional Information ◽  
Gaussian Network Model ◽  
Allosteric Communication ◽  
Rapid Characterization ◽  
Dynamics Simulations ◽  
Gaussian Network

AbstractA fast and approximate method of generating allosteric communication landscapes is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but through an ensemble of pathways. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations has to be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. Residues that should be manipulated to control protein activity may be determined with this approach. This should be of great importance for allosteric drug design and for understanding the effects of mutations on protein function. The model is applied to determine allosteric communication in two proteins, Ubiquitin and Pyruvate Kinase. Predictions are in agreement with detailed molecular dynamics simulations and experimental evidence.SignificanceProteins perform their function by an exchange of information within themselves and with their environments through correlated fluctuations of their atoms. Fluctuations of one atom may drive the fluctuations of another. Information transmitted in this way leads to allosteric communication which is described as the process in which action at one site of the protein is transmitted to another site at which the protein performs its activity. Disruption of allosteric communication by mutation for example leads to disease. The present paper incorporates information theoretic concepts into the well known Gaussian Network Model of proteins and allows for rapid characterization of allosteric communication landscapes for normal functioning as well as malfunctioning proteins.

NATURAL SCIENTISTS AND RUSSIAN SCIENTIFIC FILMMAKING IN THE PRE-REVOLUTIONARY PERIOD (SCIENCE DIVISION OF THE A.A. KHANZHONKOV COMPANY)

2020 ◽  
Vol 42 (3) ◽  
pp. 355-368
Author(s):  
YEVGENIY ALEKSANDROV
Keyword(s):  
Information Transfer ◽  
Delayed Reaction ◽  
Russian Scientific ◽  
Physical Problems ◽  
Education Community ◽  
Future System ◽  
The Future ◽  
The Spectator ◽  
Revolutionary Period

The aim of the article is to recall the fi steps of comprehension by the scientific community of possibilities of a newly born means of the reality reflection. The means was initially oriented for obtaining reliable information and supposing a delayed reaction of the spectator in the process of communication. Recollection and understanding become more important under the distance education condition. Pre-revolutionary Russia lived anticipating changes, and the filmmaking was considered by the society as one of those progressive phenomena evidencing the coming of a new age. The scientists’ activity during the development of scientific fi in pre-revolutionary Russia was long hushed up and wasn’t considered as forming a basis for the future system of educational audio-visual communication. In this process there participated striking, creative personalities, mostly belonged to the community of Imperial Moscow University, which activity was during the age of changes. The significant contribution of pleiad of eminent scientists’ activity to the new direction formation was a reason to unify in one paper both their whole professional life data and information about their time-limited period of scientific fi In the future a more profound study of their achievements are considered to be promising. In the introduction the anterior period of the Russian fi appearance, where the scientific and education community of Russia was exploring the possibilities of a new means of information transfer for education purposes, is considered. Two main units are dedicated to the role of scientists in the development of scientific filmmaking for research and popularization of biomedical and physical problems.

Gaussian Network Model Revisited: Effects of Mutation and Ligand Binding on Protein Behavior

2021 ◽  
Author(s):  
Burak Erman
Keyword(s):  
Ligand Binding ◽  
Network Model ◽  
Adjacency Matrix ◽  
In Silico ◽  
Coarse Grained ◽  
Published Data ◽  
Specific Information ◽  
Gaussian Network Model ◽  
Gaussian Network ◽  
Alpha Carbon

The coarse-grained Gaussian Network model, GNM, considers only the alpha carbons of the folded protein. Therefore it is not directly applicable to the study of mutation or ligand binding problems where atomic detail is required. This shortcoming is improved by including the local effect of heavy atoms in the neighborhood of each alpha carbon into the Kirchoff Adjacency Matrix. The presence of other atoms in the coordination shell of each alpha carbon diminishes the magnitude of fluctuations of that alpha carbon. But more importantly, it changes the graph-like connectivity structure, i.e., the Kirchoff Adjacency Matrix of the whole system which introduces amino acid specific and position specific information into the classical coarse-grained GNM which was originally modelled in analogy with phantom network theory of rubber elasticity. With this modification, it is now possible to make predictions on the effects of mutation and ligand binding on residue fluctuations and their pair-correlations. We refer to the new model as all-atom GNM. Using examples from published data we show that the all-atom GNM applied to in silico mutated proteins and to their laboratory mutated structures gives similar results. Thus, loss and gain of correlations, which may be related to loss and gain of function, may be studied by using simple in silico mutations only.

Role of Tumor Vascular Architecture in Nutrient and Drug Delivery: An Invasion Percolation-Based Network Model

1996 ◽  
Vol 51 (3) ◽  
pp. 327-346 ◽  
Author(s):  
James W. Baish ◽  
Yuval Gazit ◽  
David A. Berk ◽  
Mutsumi Nozue ◽  
Laurence T. Baxter ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Network Model ◽  
Invasion Percolation ◽  
Vascular Architecture

scholarly journals If you are feeling confident enough, do not hesitate to reveal who you really are : extension of Baker, Honea, and Russell (2004)

2017 ◽  
Author(s):  
◽  
Kyungku Lee
Keyword(s):  
Network Model ◽  
Memory Retention ◽  
Brand Name ◽  
Information Retention ◽  
Early Presentation ◽  
Brand Information ◽  
The Way

Due to the competitive advertising environment, marketers have been employing different executional factors including humor and narrative feature within the advertising. Based on the Network of Model of Memory, Baker, Honea, and Russell (2004) examined whether the brand name placement influences on the way people perceive the advertising and brand information retention. As an extension of Baker et al.'s study, this study examines the role of narrative features within the advertising, prior attitude, and brand name placement. But the present findings are not consistent with Baker et al.'s study that early presentation of the brand name does not elicit better attitude toward the advertising, brand. Findings also show that there is no significant effect on memory retention. Keywords: Brand name placement, prior attitude, narrative advertising, network model of memory

scholarly journals Near-optimal decoding of transient stimuli from coupled neuronal subpopulations

2014 ◽  
Author(s):  
James Trousdale ◽  
Samuel R. Carroll ◽  
Fabrizio Gabbiani ◽  
Krešimir Josić
Keyword(s):  
Visual Processing ◽  
Information Transfer ◽  
Partial Information ◽  
Rotation Axis ◽  
Biophysical Model ◽  
General Mechanism ◽  
Small Subset ◽  
Vertical System ◽  
Optimal Decoding

Coupling between sensory neurons impacts their tuning properties and correlations in their responses. How such coupling affects sensory representations and ultimately behavior remains unclear. We investigated the role of neuronal coupling during visual processing using a realistic biophysical model of the vertical system (VS) cell network in the blow fly. These neurons are thought to encode the horizontal rotation axis during rapid free flight manoeuvres. Experimental findings suggest neurons of the vertical system are strongly electrically coupled, and that several downstream neurons driving motor responses to ego-rotation receive inputs primarily from a small subset of VS cells. These downstream neurons must decode information about the axis of rotation from a partial readout of the VS population response. To investigate the role of coupling, we simulated the VS response to a variety of rotating visual scenes and computed optimal Bayesian estimates from the relevant subset of VS cells. Our analysis shows that coupling leads to near-optimal estimates from a subpopulation readout. In contrast, coupling between VS cells has no impact on the quality of encoding in the response of the full population. We conclude that coupling at one level of the fly visual system allows for near-optimal decoding from partial information at the subsequent, pre-motor level. Thus, electrical coupling may provide a general mechanism to achieve near-optimal information transfer from neuronal subpopulations across organisms and modalities.

WEBSITE AS A MEANS OF ADVERTISING CITIES OF THE WORLD: STRUCTURAL-SEMANTIC AND PRAGMATIC ASPECTS

2021 ◽  
pp. 131-141
Author(s):  
I. V. Ushchapovska ◽  
R. Ye. Podvalna
Keyword(s):  
Information Transfer ◽  
Target Audience ◽  
Lexical Unit ◽  
Advertising Message ◽  
The World ◽  
Pragmatic Aspects ◽  
Special Category

The article actualizes the study of websites as a means to promoting cities around the world and highlights the main structural and semantic characteristics of advertising sites hosted on Internet platforms. The pragmatic role of a lexical unit of advertising texts is investigated. The concepts of website and advertising text are defined, the main ways of information transfer through advertising text were described. Definitions of the concepts such as advertising, advertising text, strategy, website, and related concepts are provided. After researching the selected advertising texts, the structural and semantic characteristics of advertising on websites, and the main ways of transmitting information, such as verb sentences, simple nominative sentences, and elliptical sentences are analyzed. The pragmatic means of advertising campaigns on websites includes constructions, such as Top + Numeral, Must + V., Let + Inf, and so on. Examples of pragmatic websites are also considered. Samples and purposes of using this approach are given. There are various strategies for advertising and promoting cities and countries around the world on Internet platforms. The most popular and effective are the use of different language techniques (motivational, interrogative, negative sentences) and the strategy of the association. The advertising text is noted to embody a communicative and pragmatic guideline. In the advertising message, there is a presentation of the goods to the target audience. Thus, the main load is the language code, which is aimed at a special category of people. A small number of works on this topic indicate the need for a more detailed study of the issue.

Holistic Perspective of Standardization Strategies

2015 ◽  
Vol 2 (2) ◽  
pp. 54-65 ◽  
Author(s):  
Neeta Baporikar
Keyword(s):  
Information Transfer ◽  
Technological Development ◽  
Business Environment ◽  
International Communication ◽  
Economic Benefits ◽  
Theory Approach ◽  
Holistic Perspective ◽  
Common Basis ◽  
Grounded Theory Approach

Industry has become increasingly interested in assessing its economic efficiency, and thus is more interested in the role of standardization. Standardization is a premise of international communication improvement and the information transfer increase directly connected with the results of technological development. Standardization represents a way to confer superior value to product through price, quality, and distribution. Standardization brings confidence to consumer regarding certain producer's offer. Globalization has dramatically changed the international business environment. Systematic and reliable results can only be attained on a common basis. Since there is greater pressure on industry to rationalize, the costs and benefits of standardization must be examined from both economic and strategic viewpoint. This paper through grounded theory approach aims to analyze not only the economic benefits to the various stakeholders but also develop a holistic perspective of standardization strategies in the current environment.

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