Nelson Augusto Alves | Searcharxiv

arXiv2007

Unveiling community structures in weighted networks

Random walks on simple graphs in connection with electrical resistor networks lead to the definition of Markov chains with transition probability matrix in terms of electrical conductances. We extend this definition to an effective transition matrix $P_{ij}$ to account for the probability of going from vertex $i$ to any vertex $j$ of the original connected graph $G$. Also, we present an algorithm based on the definition of this effective transition matrix among vertices in the network to extract a topological feature related to the manner graph $G$ has been organized. This topological feature corresponds to the communities in the graph.

physics.soc-ph↗

arXiv2006

Topological features of proteins from amino acid residue networks

Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analysing one, two and three-vertex joint distribution of quantities related to the corresponding network of amino acid residues. Emphasis on the amino acid residue hydrophobicity leads to the definition of their center of mass as vertices in this contact network model with interactions represented by edges. The network analysis helps us to interpret experimental results such as hydrophobic scales and fraction of buried accessible surface area in terms of the network connectivity. To explore the vertex type dependent correlations, we build a network of hydrophobic and polar vertices. This procedure presents the wiring diagram of the topological structure of globular proteins leading to the following attachment probabilities between hydrophobic-hydrophobic 0.424(5), hydrophobic-polar 0.419(2) and polar-polar 0.157(3) residues.

physics.bio-ph↗