Propagation of fluctuations in interaction networks governed by the law of mass action

Using an example of physical interactions between proteins, we study how perturbations propagate in interconnected networks whose equilibrium state is governed by the law of mass action. We introduce a comprehensive matrix formalism which predicts the response of this equilibrium to small changes in total concentrations of individual molecules, and explain it using a heuristic analogy to a current flow in a network of resistors. Our main conclusion is that on average changes in free concentrations exponentially decay with the distance from the source of perturbation. We then study how this decay is influenced by such factors as the topology of a network, binding strength, and correlations between concentrations of neighboring nodes. An exact analytic expression for the decay constant is obtained for the case of uniform interactions on the Bethe lattice. Our general findings are illustrated using a real biological network of protein-protein interactions in baker's yeast with experimentally determined protein concentrations.Comment: 4 pages; 2 figure

Promise and Pitfalls of Extending Google's PageRank Algorithm to Citation Networks

We review our recent work on applying the Google PageRank algorithm to find scientific "gems" among all Physical Review publications, and its extension to CiteRank, to find currently popular research directions. These metrics provide a meaningful extension to traditionally-used importance measures, such as the number of citations and journal impact factor. We also point out some pitfalls of over-relying on quantitative metrics to evaluate scientific quality.Comment: 3 pages, 1 figure, invited comment for the Journal of Neuroscience. The arxiv version is microscopically different from the published versio

On the superfluidity of classical liquid in nanotubes

In 2001, the author proposed the ultra second quantization method. The ultra second quantization of the Schr\"odinger equation, as well as its ordinary second quantization, is a representation of the N-particle Schr\"odinger equation, and this means that basically the ultra second quantization of the equation is the same as the original N-particle equation: they coincide in 3N-dimensional space. We consider a short action pairwise potential V(x_i -x_j). This means that as the number of particles tends to infinity, $N\to\infty$, interaction is possible for only a finite number of particles. Therefore, the potential depends on N in the following way: $V_N=V((x_i-x_j)N^{1/3})$. If V(y) is finite with support $\Omega_V$, then as $N\to\infty$ the support engulfs a finite number of particles, and this number does not depend on N. As a result, it turns out that the superfluidity occurs for velocities less than $\min(\lambda_{\text{crit}}, \frac{h}{2mR})$, where $\lambda_{\text{crit}}$ is the critical Landau velocity and R is the radius of the nanotube.Comment: Latex, 20p. The text is presented for the International Workshop "Idempotent and tropical mathematics and problems of mathematical physics", Independent University of Moscow, Moscow, August 25--30, 2007 and to be published in the Russian Journal of Mathematical Physics, 2007, vol. 15, #

Expansion Around the Mean-Field Solution of the Bak-Sneppen Model

We study a recently proposed equation for the avalanche distribution in the Bak-Sneppen model. We demonstrate that this equation indirectly relates $\tau$,the exponent for the power law distribution of avalanche sizes, to $D$, the fractal dimension of an avalanche cluster.We compute this relation numerically and approximate it analytically up to the second order of expansion around the mean field exponents. Our results are consistent with Monte Carlo simulations of Bak-Sneppen model in one and two dimensions.Comment: 5 pages, 2 ps-figures iclude