The expected degree distribution in transient duplication divergence models

Background: The basic building block of a body is protein which is a complex system whose structure plays a key role in activation, catalysis, messaging and disease states. Therefore, careful investigation of protein structure is necessary for the diagnosis of diseases and for the drug designing. Protein structures are described at their different levels of complexity: primary (chain), secondary (helical), tertiary (3D), and quaternary structure. Analyzing complex 3D structure of protein is a difficult task but it can be analyzed as a network of interconnection between its component, where amino acids are considered as nodes and interconnection between them are edges. Objective: Many literature works have proven that the small world network concept provides many new opportunities to investigate network of biological systems. The objective of this paper is analyzing the protein structure using small world concept. Methods: Protein is analyzed using small world network concept, specifically where extreme condition is having a degree distribution which follows power law. For the correct verification of the proposed approach, dataset of the Oncogene protein structure is analyzed using Python programming. Results: Protein structure is plotted as network of amino acids (Residue Interaction Graph (RIG)) using distance matrix of nodes with given threshold, then various centrality measures (i.e., degree distribution, Degree-Betweenness correlation, and Betweenness-Closeness correlation) are calculated for 1323 nodes and graphs are plotted. Conclusion: Ultimately, it is concluded that there exist hubs with higher centrality degree but less in number, and they are expected to be robust toward harmful effects of mutations with new functions.

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Models of network formation

10.1093/oso/9780198805090.003.0013 ◽

2018 ◽

Author(s):

Mark Newman

Keyword(s):

Degree Distribution ◽

Network Formation ◽

Preferential Attachment ◽

Network Size ◽

Large Network ◽

Citation Networks ◽

Airline Networks ◽

Attachment Model ◽

Delivery Networks

This chapter describes models of the growth or formation of networks, with a particular focus on preferential attachment models. It starts with a discussion of the classic preferential attachment model for citation networks introduced by Price, including a complete derivation of the degree distribution in the limit of large network size. Subsequent sections introduce the Barabasi-Albert model and various generalized preferential attachment models, including models with addition or removal of extra nodes or edges and models with nonlinear preferential attachment. Also discussed are node copying models and models in which networks are formed by optimization processes, such as delivery networks or airline networks.

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The structure of co-publications multilayer network

Computational Social Networks ◽

10.1186/s40649-021-00089-w ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Ghislain Romaric Meleu ◽

Paulin Yonta Melatagia

Keyword(s):

Power Law ◽

Degree Distribution ◽

Preferential Attachment ◽

Small World ◽

Generation Model ◽

Small World Network ◽

Power Law Distribution ◽

Multilayer Networks ◽

Multilayer Network ◽

Scientific Papers

AbstractUsing the headers of scientific papers, we have built multilayer networks of entities involved in research namely: authors, laboratories, and institutions. We have analyzed some properties of such networks built from data extracted from the HAL archives and found that the network at each layer is a small-world network with power law distribution. In order to simulate such co-publication network, we propose a multilayer network generation model based on the formation of cliques at each layer and the affiliation of each new node to the higher layers. The clique is built from new and existing nodes selected using preferential attachment. We also show that, the degree distribution of generated layers follows a power law. From the simulations of our model, we show that the generated multilayer networks reproduce the studied properties of co-publication networks.

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