Generating functional analysis of complex formation and dissociation in large protein interaction networks

We analyze large systems of interacting proteins, using techniques from the non-equilibrium statistical mechanics of disordered many-particle systems. Apart from protein production and removal, the most relevant microscopic processes in the proteome are complex formation and dissociation, and the microscopic degrees of freedom are the evolving concentrations of unbound proteins (in multiple post-translational states) and of protein complexes. Here we only include dimer-complexes, for mathematical simplicity, and we draw the network that describes which proteins are reaction partners from an ensemble of random graphs with an arbitrary degree distribution. We show how generating functional analysis methods can be used successfully to derive closed equations for dynamical order parameters, representing an exact macroscopic description of the complex formation and dissociation dynamics in the infinite system limit. We end this paper with a discussion of the possible routes towards solving the nontrivial order parameter equations, either exactly (in specific limits) or approximately.Comment: 14 pages, to be published in Proc of IW-SMI-2009 in Kyoto (Journal of Phys Conference Series

Chiral Symmetry and s-wave Low-Lying Meson-Baryon Resonances

The $s-$wave meson-baryon scattering is analyzed for the isospin-strangeness $I=1/2, S=0$ and $I=0,S=-1$ sectors, in a Bethe-Salpeter coupled channel formalism incorporating Chiral Symmetry. For both sectors, four channels have been considered: $\pi N$, $\eta N$, $K \Lambda$, $K \Sigma$ and $\pi \Sigma$, $\bar K N$, $\eta \Lambda$, $K \Xi$, respectively. The needed two particle irreducible matrix amplitudes are taken from lowest order Chiral Perturbation Theory in a relativistic formalism. There appear undetermined low energy constants, as a consequence of the renormalization of the amplitudes, which are obtained from fits to the available data: elastic $\pi N$ phase-shifts, $\pi^- p \to \eta n$ and $\pi^- p \to K^0 \Lambda$ cross sections and to $\pi\Sigma\to\pi\Sigma$ mass-spectrum, the elastic $\bar K N \to \bar K N$ and $\bar K N\to \pi \Sigma$ $t$--matrices and to the $K^- p \to \eta \Lambda$ cross section data. The position and residues of the complex poles in the second Riemann sheet of the scattering amplitude determine masses, widths and branching ratios of the $S_{11}-$ $N$(1535) and $-N$(1650) and $S_{01}-$ $\Lambda$(1405) and $-\Lambda$(1670) resonances, in reasonable agreement with experiment. A good overall description of data, from threshold up to around 2 GeV is achieved despite the fact that three-body channels have not been explicitly included.Comment: 5 Pages, 2 figures, invited contribution to Focus Session on Nature of Threshold N*, to be published in Proceedings of Nstar 2002, Pittsburgh, USA, October 9-12, 2002 (World Scientific