Fibroblast-Specific Protein-Protein Interactions for Myocardial Fibrosis from MetaCore Network.

Myocardial fibrosis is a major pathologic disorder associated with a multitude of cardiovascular diseases (CVD). The pathogenesis is complex and encompasses multiple molecular pathways. Integration of fibrosis-associated genes into the global MetaCore network of protein-protein interactions (PPI) offers opportunities to identify PPI with functional and therapeutic significance.

Random matrix model of Kolmogorov-Zakharov turbulence.

We introduce and study a random matrix model of Kolmogorov-Zakharov turbulence in a nonlinear purely dynamical finite-size system with many degrees of freedom. For the case of a direct cascade, the energy and norm pumping takes place at low energy scales with absorption at high energies. For a pumping strength above a certain chaos border, a global chaotic attractor appears with a stationary energy flow through a Hamiltonian inertial energy interval.

Goal quest for an intelligent surfer moving in a chaotic flow.

We consider a model of an intelligent surfer moving on the Ulam network generated by a chaotic dynamics in the Chirikov standard map. This directed network is obtained by the Ulam method with a division of the phase space in cells of fixed size forming the nodes of a Markov chain. The goal quest for this surfer is to determine the network path from an initial node A to a final node B with minimal resistance given by the sum of inverse transition probabilities.

Nonlinear Perturbation of Random Matrix Theory.

We consider a system of linear oscillators, or quantum states, described by random matrix theory and analyze how its time evolution is affected by a nonlinear perturbation. Our numerical results show that above a certain chaos border a weak or moderate nonlinearity leads to a dynamical thermalization of a finite number of degrees of freedom with energy equipartition over linear eigenmodes as expected from the laws of classical statistical mechanics. The system temperature is shown to change in a broad range from positive to negative values, and the dependence of system characteristics on the initial injected energy is determined.

Fibrosis Protein-Protein Interactions from Google Matrix Analysis of MetaCore Network.

Protein-protein interactions is a longstanding challenge in cardiac remodeling processes and heart failure. Here, we use the MetaCore network and the Google matrix algorithms for prediction of protein-protein interactions dictating cardiac fibrosis, a primary cause of end-stage heart failure. The developed algorithms allow identification of interactions between key proteins and predict new actors orchestrating fibroblast activation linked to fibrosis in mouse and human tissues.

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network.

English Wikipedia, containing more than five millions articles, has approximately eleven thousands web pages devoted to proteins or genes most of which were generated by the Gene Wiki project. These pages contain information about interactions between proteins and their functional relationships. At the same time, they are interconnected with other Wikipedia pages describing biological functions, diseases, drugs and other topics curated by independent, not coordinated collective efforts.

Google matrix of the citation network of Physical Review.

We study the statistical properties of spectrum and eigenstates of the Google matrix of the citation network of Physical Review for the period 1893-2009. The main fraction of complex eigenvalues with largest modulus is determined numerically by different methods based on high-precision computations with up to p = 16384 binary digits that allow us to resolve hard numerical problems for small eigenvalues. The nearly nilpotent matrix structure allows us to obtain a semianalytical computation of eigenvalues.

Diffusion and localization for the Chirikov typical map.

We consider the classical and quantum properties of the "Chirikov typical map," proposed by Boris Chirikov in 1969. This map is obtained from the well-known Chirikov standard map by introducing a finite-number T of random phase-shift angles. These angles induce a random behavior for small time-scales (tT) .