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

On the degree conjecture for separability of multipartite quantum states

We settle the so-called degree conjecture for the separability of multipartite quantum states, which are normalized graph Laplacians, first given by Braunstein {\it et al.} [Phys. Rev. A \textbf{73}, 012320 (2006)]. The conjecture states that a multipartite quantum state is separable if and only if the degree matrix of the graph associated with the state is equal to the degree matrix of the partial transpose of this graph. We call this statement to be the strong form of the conjecture. In its weak version, the conjecture requires only the necessity, that is, if the state is separable, the corresponding degree matrices match. We prove the strong form of the conjecture for {\it pure} multipartite quantum states, using the modified tensor product of graphs defined in [J. Phys. A: Math. Theor. \textbf{40}, 10251 (2007)], as both necessary and sufficient condition for separability. Based on this proof, we give a polynomial-time algorithm for completely factorizing any pure multipartite quantum state. By polynomial-time algorithm we mean that the execution time of this algorithm increases as a polynomial in $m,$ where $m$ is the number of parts of the quantum system. We give a counter-example to show that the conjecture fails, in general, even in its weak form, for multipartite mixed states. Finally, we prove this conjecture, in its weak form, for a class of multipartite mixed states, giving only a necessary condition for separability.Comment: 17 pages, 3 figures. Comments are welcom

Rank one discrete valuations of power series fields

In this paper we study the rank one discrete valuations of the field $k((X_1,..., X_n))$ whose center in k\lcor\X\rcor is the maximal ideal. In sections 2 to 6 we give a construction of a system of parametric equations describing such valuations. This amounts to finding a parameter and a field of coefficients. We devote section 2 to finding an element of value 1, that is, a parameter. The field of coefficients is the residue field of the valuation, and it is given in section 5. The constructions given in these sections are not effective in the general case, because we need either to use the Zorn's lemma or to know explicitly a section $\sigma$ of the natural homomorphism R_v\to\d between the ring and the residue field of the valuation $v$. However, as a consequence of this construction, in section 7, we prove that k((\X)) can be embedded into a field L((\Y)), where $L$ is an algebraic extension of $k$ and the {\em ``extended valuation'' is as close as possible to the usual order function}

Enskog Theory for Polydisperse Granular Mixtures II. Sonine Polynomial Approximation

The linear integral equations defining the Navier-Stokes (NS) transport coefficients for polydisperse granular mixtures of smooth inelastic hard disks or spheres are solved by using the leading terms in a Sonine polynomial expansion. Explicit expressions for all the NS transport coefficients are given in terms of the sizes, masses, compositions, density and restitution coefficients. In addition, the cooling rate is also evaluated to first order in the gradients. The results hold for arbitrary degree of inelasticity and are not limited to specific values of the parameters of the mixture. Finally, a detailed comparison between the derivation of the current theory and previous theories for mixtures is made, with attention paid to the implication of the various treatments employed to date.Comment: 26 pages, to be published in Phys. Rev.