CNDO/2 Study of C2H2 + H2O System

Different configurations of the C2H2 + H2O system obtained by various translations and rotations of H2O around the C2H2 molecule were studied. The two molecules were found to form not only hydrogen bond but also a charge transfer complex

CNDO/2 Study of C2H2 + H2O System

Different configurations of the C2H2 + H2O system obtained by various translations and rotations of H2O around the C2H2 molecule were studied. The two molecules were found to form not only hydrogen bond but also a charge transfer complex

How Information Theory Met Chemical Graph Theory in Ruđer Bošković Institute

Reminiscence for the years of collaboration with the jubilee On the occasion of the 80th Anniversary of Prof. Dr. Nenad Trinajstić This work is licensed under a Creative Commons Attribution 4.0 International License

A survey of current software for network analysis in molecular biology

Software for network motifs and modules is briefly reviewed, along with programs for network comparison. The three major software packages for network analysis, CYTOSCAPE, INGENUITY and PATHWAY STUDIO, and their associated databases, are compared in detail. A comparative test evaluated how these software packages perform the search for key terms and the creation of network from those terms and from experimental expression data

Network Topology Analysis of Post-Mortem Brain Microarrays Identifies More Alzheimer’s Related Genes and MicroRNAs and Points to Novel Routes for Fighting with the Disease

Network-based approaches are powerful and beneficial tools to study complex systems in their entirety, elucidating the essential factors that turn the multitude of individual elements into a functional system. In this study we used critical network topology descriptors and guilt-by-association rule to explore and understand the significant molecular players, drug targets and underlying biological mechanisms of Alzheimer’s disease. Analyzing two post-mortem brain gene microarrays (GSE4757 and GSE28146) with Pathway Studio software package we constructed and analyzed a set of protein-protein interaction, as well as miRNA-target networks. In a 4-step procedure the expression datasets were normalized using Robust Multi-array Average approach, while the modulation of gene expression by the disease was statistically evaluated by the empirical Bayes method from the limma Bioconductor package. Representative set of 214 seed-genes (p\u3c0.01) common for the three brain sections of the two microarrays was thus created. The Pathway Studio analysis of the networks built identified 15 new potential AD-related genes and 17 novel AD-involved microRNAs. Using KEGG pathways relevant in Alzheimer’s disease we built an integrated mechanistic network from the interactions between the overlapping genes in these pathways. Routes of possible disease initiation process were thus revealed through the CD4, DCN, and IL8 extracellular ligands. DAVID and IPA enrichment analysis uncovered a number of deregulated biological processes and pathways including neuron projection/differentiation, aging, oxidative stress, chemokine/ neurotrophin signaling, long-term potentiation and others. The findings in this study offer information of interest for subsequent experimental studies

Information inequalities and Generalized Graph Entropies

In this article, we discuss the problem of establishing relations between information measures assessed for network structures. Two types of entropy based measures namely, the Shannon entropy and its generalization, the R\'{e}nyi entropy have been considered for this study. Our main results involve establishing formal relationship, in the form of implicit inequalities, between these two kinds of measures when defined for graphs. Further, we also state and prove inequalities connecting the classical partition-based graph entropies and the functional-based entropy measures. In addition, several explicit inequalities are derived for special classes of graphs.Comment: A preliminary version. To be submitted to a journa

Information Theory in Describing the Electronic Structures of Atoms

An information approach to the description of atoms by introducing »differential« entropy characteristics of chemical elements has been developed. These quantities clearly reflect the horizontal and vertical structure of the periodic table, and the main features of atomic electron structures, such as delay in filling d- and f-subshells, the action of Hund\u27s first rule, the anomalies in the electronic structure of some atoms, the appearance of the first electron having a given value of some quantum number, etc. The necessity of change in the position of lanthanides and actinides in the periodic table is discussed