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

The lowest-lying baryon masses in covariant SU(3)-flavor chiral perturbation theory

We present an analysis of the baryon-octet and -decuplet masses using covariant SU(3)-flavor chiral perturbation theory up to next-to-leading order. Besides the description of the physical masses we address the problem of the lattice QCD extrapolation. Using the PACS-CS collaboration data we show that a good description of the lattice points can be achieved at next-to-leading order with the covariant loop amplitudes and phenomenologically determined values for the meson-baryon couplings. Moreover, the extrapolation to the physical point up to this order is found to be better than the linear one given at leading-order by the Gell-Mann-Okubo approach. The importance that a reliable combination of lattice QCD and chiral perturbation theory may have for hadron phenomenology is emphasized with the prediction of the pion-baryon and strange-baryon sigma terms.Comment: Typos in formulas correcte

Production of Two Pions Induced by Neutrinos

We study the threshold production of two pions induced by neutrinos in nucleon targets. The contribution of nucleon pole, pion and contact terms is calculated using a chiral Lagrangian. The contribution of the Roper resonance, neglected in earlier studies, has also been taken into account.Comment: Contribution to the proceedings of Chiral07, RCNP, Osaka, Japan. Corrected version because of problems on some pdf viewer

Weak Quasi-elastic Production of Hyperons

The quasielastic weak production of $\Lambda$ and $\Sigma$ hyperons from nucleons and nuclei induced by antineutrinos is studied in the energy region of some ongoing neutrino oscillation experiments in the intermediate energy region. The hyperon nucleon transition form factors determined from neutrino nucleon scattering and an analysis of high precision data on semileptonic decays of neutron and hyperons using SU(3) symmetry have been used. The nuclear effects due to Fermi motion and final state interaction effects due to hyperon nucleon scattering have also been studied. The numerical results for differential and total cross sections have been presented.Comment: 26 pages, 10 figure

Covariance matrices and the separability problem

We propose a unifying approach to the separability problem using covariance matrices of locally measurable observables. From a practical point of view, our approach leads to strong entanglement criteria that allow to detect the entanglement of many bound entangled states in higher dimensions and which are at the same time necessary and sufficient for two qubits. From a fundamental perspective, our approach leads to insights into the relations between several known entanglement criteria -- such as the computable cross norm and local uncertainty criteria -- as well as their limitations.Comment: 4 pages, no figures; v3: final version to appear in PR