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

Population structure, phenotypic information and association studies in long-generation crops

Poster presented at Generation Challenge Program Annual Research Meeting. Sao Paulo (Brazil), 12-16 Sep. 200

Lower bounds on concurrence and separability conditions

We obtain analytical lower bounds on the concurrence of bipartite quantum systems in arbitrary dimensions related to the violation of separability conditions based on local uncertainty relations and on the Bloch representation of density matrices. We also illustrate how these results complement and improve those recently derived [K. Chen, S. Albeverio, and S.-M. Fei, Phys. Rev. Lett. 95, 040504 (2005)] by considering the Peres-Horodecki and the computable cross norm or realignment criteria.Comment: 5 pages, 1 figure; minor changes, references added; final version: minor correction in proof of lemma 1, scope of theorem 2 clarified, to appear in PRA; mistake in proof of lemma 1 of published version corrected, results unchange

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

Distance of W3(OH) by VLBI annual parallax measurement

The most powerful tool for measuring distances within our Galaxy is the annual parallax. We carried out phase-referencing VLBI observations of H$_{2}$O masers in the star forming region W3(OH) with respect to the extragalactic continuum source ICRF 0244+624 to measure their absolute proper motions. The measured annual parallax is 0.484 $\pm$ 0.004 milli-arcseconds which corresponds to a distance of 2.07^{+0.01}_{-0.02}$ kpc from the sun. This distance is consistent with photometric and kinematic distances from previous observations.Comment: Proceedings of the 7th European VLBI Network Symposium (October 12-15 2004, Toledo, Spain), eds. Bachiller, R., Colomer, F., Desmurs, J. F., & de Vicente, P., 4 pages, 4 figures, needs evn2004.cl