Molecular Model of Dynamic Social Network Based on E-mail communication

In this work we consider an application of physically inspired sociodynamical model to the modelling of the evolution of email-based social network. Contrary to the standard approach of sociodynamics, which assumes expressing of system dynamics with heuristically defined simple rules, we postulate the inference of these rules from the real data and their application within a dynamic molecular model. We present how to embed the n-dimensional social space in Euclidean one. Then, inspired by the Lennard-Jones potential, we define a data-driven social potential function and apply the resultant force to a real e-mail communication network in a course of a molecular simulation, with network nodes taking on the role of interacting particles. We discuss all steps of the modelling process, from data preparation, through embedding and the molecular simulation itself, to transformation from the embedding space back to a graph structure. The conclusions, drawn from examining the resultant networks in stable, minimum-energy states, emphasize the role of the embedding process projecting the non–metric social graph into the Euclidean space, the significance of the unavoidable loss of information connected with this procedure and the resultant preservation of global rather than local properties of the initial network. We also argue applicability of our method to some classes of problems, while also signalling the areas which require further research in order to expand this applicability domain

Sodium Ion Cycle in Bacterial Pathogens: Evidence from Cross-Genome Comparisons

Analysis of the bacterial genome sequences shows that many human and animal pathogens encode primary membrane Na(+) pumps, Na(+)-transporting dicarboxylate decarboxylases or Na(+)-translocating NADH:ubiquinone oxidoreductase, and a number of Na(+)-dependent permeases. This indicates that these bacteria can utilize Na(+) as a coupling ion instead of or in addition to the H(+) cycle. This capability to use a Na(+) cycle might be an important virulence factor for such pathogens as Vibrio cholerae, Neisseria meningitidis, Salmonella enterica serovar Typhi, and Yersinia pestis. In Treponema pallidum, Chlamydia trachomatis, and Chlamydia pneumoniae, the Na(+) gradient may well be the only energy source for secondary transport. A survey of preliminary genome sequences of Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans, and Treponema denticola indicates that these oral pathogens also rely on the Na(+) cycle for at least part of their energy metabolism. The possible roles of the Na(+) cycling in the energy metabolism and pathogenicity of these organisms are reviewed. The recent discovery of an effective natural antibiotic, korormicin, targeted against the Na(+)-translocating NADH:ubiquinone oxidoreductase, suggests a potential use of Na(+) pumps as drug targets and/or vaccine candidates. The antimicrobial potential of other inhibitors of the Na(+) cycle, such as monensin, Li(+) and Ag(+) ions, and amiloride derivatives, is discussed