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

Neutrino Mixing Predictions of a Minimal SO(10) Model with Suppressed Proton Decay

During the past year, a minimal renormalizable supersymmetric SO(10) model has been proposed with the following properties: it predicts a naturally stable dark matter and neutrino mixing angles theta_atm and theta_13 while at the same time accommodating CKM CP violation among quarks with no SUSY CP problem. Suppression of proton decay for all allowed values of tan beta strongly restricts the flavor structure of the model making it predictive for other processes as well. We discuss the following predictions of the model in this paper, e.g. down-type quark masses, and neutrino oscillation parameters, U_e3, delta_MNSP, which will be tested by long baseline experiments such as T2K and subsequent experiments using the neutrino beam from JPARC. We also calculate lepton flavor violation and the lepton asymmetry of the Universe in this model.Comment: 22 pages, 11 figure

Suppressing Proton Decay in the Minimal SO(10) Model

We show that in a class of minimal supersymmetric SO(10) models which have been found to be quite successful in predicting neutrino mixings, all proton decay modes can be suppressed by a particular choice of Yukawa textures. This suppression works for contributions from both left and right operators for nucleon decay and for arbitrary \tan\beta. The required texture not only fits all lepton and quark masses as well as CKM parameters but it also predicts neutrino mixing parameter U_e3 and Dirac CP phase \sin|\delta_MNS| to be 0.07-0.09 and 0.3-0.7 respectively. We also discuss the relation between the GUT symmetry breaking parameters for the origin of these textures.Comment: 7 pages, 2 figure

Parallel dynamics of continuous Hopfield model revisited

We have applied the generating functional analysis (GFA) to the continuous Hopfield model. We have also confirmed that the GFA predictions in some typical cases exhibit good consistency with computer simulation results. When a retarded self-interaction term is omitted, the GFA result becomes identical to that obtained using the statistical neurodynamics as well as the case of the sequential binary Hopfield model.Comment: 4 pages, 2 figure

Symmetric sequence processing in a recurrent neural network model with a synchronous dynamics

The synchronous dynamics and the stationary states of a recurrent attractor neural network model with competing synapses between symmetric sequence processing and Hebbian pattern reconstruction is studied in this work allowing for the presence of a self-interaction for each unit. Phase diagrams of stationary states are obtained exhibiting phases of retrieval, symmetric and period-two cyclic states as well as correlated and frozen-in states, in the absence of noise. The frozen-in states are destabilised by synaptic noise and well separated regions of correlated and cyclic states are obtained. Excitatory or inhibitory self-interactions yield enlarged phases of fixed-point or cyclic behaviour.Comment: Accepted for publication in Journal of Physics A: Mathematical and Theoretica

Dynamical replica theoretic analysis of CDMA detection dynamics

We investigate the detection dynamics of the Gibbs sampler for code-division multiple access (CDMA) multiuser detection. Our approach is based upon dynamical replica theory which allows an analytic approximation to the dynamics. We use this tool to investigate the basins of attraction when phase coexistence occurs and examine its efficacy via comparison with Monte Carlo simulations.Comment: 18 pages, 2 figure

Gauge Symmetry Breaking through Soft Masses in Supersymmetric Gauge Theories

Effects of soft breaking in N=1 supersymmetric gauge theories are studied. For N_f < N_c, we include the dynamics of the non-perturbative superpotential and use the original (s)quark and gauge fields. For N_f > N_c +1, we formulate the dynamics in terms of dual (s)quarks and a dual gauge group SU(N_f-N_c). The mass squared of the squarks can be negative triggering spontaneous breakdown of flavor and color symmetry. The general condition for stability of the vacuum is derived. We determine the breaking pattern, determine the spectrum and argue that the masses vary smoothly as one crosses from the Higgs phase into the confining phase, thus exhibiting complementarity.Comment: Contribution to Inauguration Conferference of Asia Pacific Center for Theoretical Physics, 4-10 June, 1996, Seoul National University; LaTeX, no macros neede

Belief Propagation for Error Correcting Codes and Lossy Compression Using Multilayer Perceptrons

The belief propagation (BP) based algorithm is investigated as a potential decoder for both of error correcting codes and lossy compression, which are based on non-monotonic tree-like multilayer perceptron encoders. We discuss that whether the BP can give practical algorithms or not in these schemes. The BP implementations in those kind of fully connected networks unfortunately shows strong limitation, while the theoretical results seems a bit promising. Instead, it reveals it might have a rich and complex structure of the solution space via the BP-based algorithms.Comment: 18 pages, 18 figure

Proton decay and μ → e + γ connection in a renormalizable SO(10) GUT for neutrinos

Supersymmetric SO(10) grand unified models with renormalizable Yukawa couplings involving {\bf 10}, {\bf 126} and {\bf 120} Higgs fields have been shown to give a very economical theory for understanding quark-lepton flavor in a unified framework. In previous papers, we showed how nucleon decay can be suppressed in these models without invoking cancellation, by choice of Yukawa flavor texture within a type II seesaw framework for neutrinos that explains all mixings and masses including the recently observed "large" $\theta_{13}$. In this follow-up paper, we extend our earlier work to the case of type I seesaw and show that the recently measured "large" $\theta_{13}$ can be accommodated in this case while suppressing proton decay. We then point out that the two cases (type I and II) lead to different testable predictions for $B(\mu\to e+\gamma)$ and $B(\tau\to \mu (e) +\gamma)$ as well as different flavor final states in nucleon decay. In particular, we find that for the type I seesaw case, $B(\tau\to \mu +\gamma)$ can be observable while at the same time suppressing $B(\mu\to e+\gamma)$, whereas in the type II seesaw case, $B(\tau\to \mu +\gamma)$ is always suppressed whereas $B(\mu\to e+\gamma)$ is observable.Comment: 27 pages, 2 figure