Long-Range Structural Regularities and Collectivity of Folded Proteins

2009 ◽  
Vol 1227 ◽  
Author(s):  
Canan Atilgan ◽  
Ibrahim Inanc ◽  
Ali Rana Atilgan
Keyword(s):  
Distribution Function ◽  
Network Models ◽  
Coarse Grained ◽  
Large Set ◽  
Network Construction ◽  
Angular Distribution Function ◽  
Collective Motions ◽  
Folded Proteins ◽  
Construction Strategies

AbstractCoarse-grained network models of proteins successfully predict equilibrium properties related to collective modes of motion. In this study, the network construction strategies and their systematic application to proteins are used to explain the role of network models in defining the collective properties of the system. The analysis is based on the radial distribution function, a newly defined angular distribution function and the spectral dimensions of a large set of globular proteins. Our analysis shows that after reaching a certain threshold for cut-off distance, network construction has negligible effect on the collective motions and the fluctuation patterns of the residues.

scholarly journals HOW INDUSTRY 4.0 RESHAPES THE WORLD: RECOMMENDATIONS BASED ON COMPLEX GRAPH NETWORK ANALYSIS

2021 ◽  
Vol 1 ◽  
pp. 1755-1764
Author(s):  
Rongyan Zhou ◽  
Julie Stal-Le Cardinal
Keyword(s):  
Machine Learning ◽  
Industry 4.0 ◽  
Network Models ◽  
Global Supply Chain ◽  
Great Opportunity ◽  
Strategic Research ◽  
Complex Graph ◽  
The World ◽  
Tremendous Challenge

Abstract Industry 4.0 is a great opportunity and a tremendous challenge for every role of society. Our study combines complex network and qualitative methods to analyze the Industry 4.0 macroeconomic issues and global supply chain, which enriches the qualitative analysis and machine learning in macroscopic and strategic research. Unsupervised complex graph network models are used to explore how industry 4.0 reshapes the world. Based on the in-degree and out-degree of the weighted and unweighted edges of each node, combined with the grouping results based on unsupervised learning, our study shows that the cooperation groups of Industry 4.0 are different from the previous traditional alliances. Macroeconomics issues also are studied. Finally, strong cohesive groups and recommendations for businessmen and policymakers are proposed.

scholarly journals Unravelling the Role of Socioeconomic Forces in the Early Stage of COVID-19 Pandemic: A Global Analysis

2021 ◽  
Vol 18 (12) ◽  
pp. 6340
Author(s):  
Kostas Rontos ◽  
Maria-Eleni Syrmali ◽  
Luca Salvati
Keyword(s):  
Early Stage ◽  
Global Analysis ◽  
Healthcare Services ◽  
Large Set ◽  
Health Crisis ◽  
Transmission Mechanisms ◽  
Virus Dissemination ◽  
Sustainable Health ◽  
Background Context

The COVID-19 pandemic has rapidly evolved into an acute health crisis with extensive socioeconomic and demographic consequences. The severity of the COVID-19 pandemic requires a refined (and more comprehensive) understanding of virus dissemination over space, transmission mechanisms, clinical features, and risk factors. In line with this assumption, the present study illustrates a comparative, empirical analysis of the role of socioeconomic and demographic dimensions in the early stages of the COVID-19 pandemic grounded on a large set of indicators comparing the background context across a global sample of countries. Results indicate that—in addition to epidemiological factors—basic socioeconomic forces significantly shaped contagions as well as hospitalization and death rates across countries. As a response to the global crisis driven by the COVID-19 pandemic, all-embracing access to healthcare services should be strengthened along with the development of sustainable health systems supported by appropriate resources and skills. The empirical findings of this study have direct implications for the coordination of on-going, global efforts aimed at containing COVID-19 (and other, future) pandemics.

scholarly journals Instabilities of Uniformly Rotating Disks

1996 ◽  
Vol 169 ◽  
pp. 349-350 ◽  
Author(s):  
P. Vauterin ◽  
H. Dejonghe
Keyword(s):  
Distribution Function ◽  
Differential Rotation ◽  
Mass Concentration ◽  
Expansion Method ◽  
Rotating Disks ◽  
Central Mass ◽  
Reasonable Approximation ◽  
Central Regions ◽  
Series Expansion Method

We explore a series expansion method to calculate the instabilities and the structure of the perturbations for a variety of uniformly rotating finite stellar disks. This survey focuses on the role of the distribution function in stability analyses. Although the potential does not show differential rotation, it will in many cases be a reasonable approximation for the disk in the central regions of galaxies without massive central mass concentration.

scholarly journals Cryptic Transcription and Early Termination in the Control of Gene Expression

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Jessie Colin ◽  
Domenico Libri ◽  
Odil Porrua
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Regulatory Function ◽  
Large Set ◽  
Control Of Gene Expression ◽  
Alternative Transcription ◽  
Cryptic Transcription ◽  
Nuclear Exosome ◽  
The Impact

Recent studies on yeast transcriptome have revealed the presence of a large set of RNA polymerase II transcripts mapping to intergenic and antisense regions or overlapping canonical genes. Most of these ncRNAs (ncRNAs) are subject to termination by the Nrd1-dependent pathway and rapid degradation by the nuclear exosome and have been dubbed cryptic unstable transcripts (CUTs). CUTs are often considered as by-products of transcriptional noise, but in an increasing number of cases they play a central role in the control of gene expression. Regulatory mechanisms involving expression of a CUT are diverse and include attenuation, transcriptional interference, and alternative transcription start site choice. This review focuses on the impact of cryptic transcription on gene expression, describes the role of the Nrd1-complex as the main actor in preventing nonfunctional and potentially harmful transcription, and details a few systems where expression of a CUT has an essential regulatory function. We also summarize the most recent studies concerning other types of ncRNAs and their possible role in regulation.

scholarly journals The proliferation role of LH on porcine primordial germ cell‐like cells (pPGCLCs) through ceRNA network construction

2021 ◽  
Vol 11 (10) ◽  
Author(s):  
Ming‐Yu Zhang ◽  
Yu Tian ◽  
Shu‐Er Zhang ◽  
Hong‐Chen Yan ◽  
Wei Ge ◽  
...  
Keyword(s):  
Germ Cell ◽  
Primordial Germ Cell ◽  
Network Construction ◽  
Cerna Network

scholarly journals Structure and Dynamics of Zr4+ in Aqueous Solution: An Ab Initio QM/MM Molecular Dynamics Study

2015 ◽  
Vol 15 (2) ◽  
pp. 155-162 ◽  
Author(s):  
Suwardi Suwardi ◽  
Harno Dwi Pranowo ◽  
Ria Armunanto
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Distribution Function ◽  
Pair Potential ◽  
Structural Data ◽  
Angular Distribution Function ◽  
Dilute Aqueous Solution ◽  
Dynamical Properties ◽  
Experimental Values ◽  
Three Body

A QM/MM molecular dynamics (MD) simulation has been carried out using three-body corrected pair potential to investigate the structural and dynamical properties of Zr4+ in dilute aqueous solution. Structural data in the form of radial distribution function, coordination number distribution, and angular distribution function were obtained. The results indicate eight water molecules coordinate to zirconium ion and have two angles of O-Zr4+-O, i.e. 72.0° and 140.0° with a Zr4+-O distance of 2.34 Å. According to these results, the hydration structure of Zr4+ ion in water was more or less well-defined square antiprismatic geometry. The dynamical properties have been characterized by the ligand’s mean residence time (MRT) and Zr4+-O stretching frequencies. The inclusion of the three-body correction was important for the description of the hydrated Zr4+ ion, and the results indicated in good agreement with experimental values.

scholarly journals The dynamics of faculty hiring networks

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Eun Lee ◽  
Aaron Clauset ◽  
Daniel B. Larremore
Keyword(s):  
Network Models ◽  
Structural Mechanism ◽  
Faculty Hiring ◽  
Network Characteristics ◽  
Institutional Prestige ◽  
Structural Mechanisms ◽  
Global And Local ◽  
Global Placement ◽  
New Hire

AbstractFaculty hiring networks—who hires whose graduates as faculty—exhibit steep hierarchies, which can reinforce both social and epistemic inequalities in academia. Understanding the mechanisms driving these patterns would inform efforts to diversify the academy and shed new light on the role of hiring in shaping which scientific discoveries are made. Here, we investigate the degree to which structural mechanisms can explain hierarchy and other network characteristics observed in empirical faculty hiring networks. We study a family of adaptive rewiring network models, which reinforce institutional prestige within the hierarchy in five distinct ways. Each mechanism determines the probability that a new hire comes from a particular institution according to that institution’s prestige score, which is inferred from the hiring network’s existing structure. We find that structural inequalities and centrality patterns in real hiring networks are best reproduced by a mechanism of global placement power, in which a new hire is drawn from a particular institution in proportion to the number of previously drawn hires anywhere. On the other hand, network measures of biased visibility are better recapitulated by a mechanism of local placement power, in which a new hire is drawn from a particular institution in proportion to the number of its previous hires already present at the hiring institution. These contrasting results suggest that the underlying structural mechanism reinforcing hierarchies in faculty hiring networks is a mixture of global and local preference for institutional prestige. Under these dynamics, we show that each institution’s position in the hierarchy is remarkably stable, due to a dynamic competition that overwhelmingly favors more prestigious institutions. These results highlight the reinforcing effects of a prestige-based faculty hiring system, and the importance of understanding its ramifications on diversity and innovation in academia.

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