Functional models for large-scale gene regulation networks: realism and fiction

High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different conditions, times, environments. We now possess a certain amount of information about these two levels of description, stored in libraries, databases and ontologies. A current challenge is to bridge the gap between topology and function, i.e. developing quantitative models aimed at characterizing the expression patterns of large sets of genes. However, approaches that work well for small networks become impossible to master at large scales, mainly because parameters proliferate. In this review we discuss the state of the art of large-scale functional network models, addressing the issue of what can be considered as realistic and what the main limitations may be. We also show some directions for future work, trying to set the goals that future models should try to achieve. Finally, we will emphasize the possible benefits in the understanding of biological mechanisms underlying complex multifactorial diseases, and in the development of novel strategies for the description and the treatment of such pathologies.Comment: to appear on Mol. BioSyst. 200

Stellar evolution and large extra dimensions

We discuss in detail the information on large extra dimensions which can be derived in the framework of stellar evolution theory and observation. The main effect of large extra dimensions arises from the production of the Kaluza-Klein (KK) excitations of the graviton. The KK-graviton and matter interactions are of gravitational strength, so the KK states never become thermalized and always freely escape. In this paper we first pay attention to the sun. Production of KK gravitons is incompatible with helioseismic constraints unless the 4+n dimensional Planck mass M_s exceeds 300 Gev/c^2. Next we show that stellar structures in their advanced phase of H burning evolution put much more severe constraints, M_s > 3-4 TeV/c^2, improving on current laboratory lower limits.Comment: 13 pages RevTeX file, 8 figures ps file

Theory for Phase Transitions in Insulating Vanadium Oxide

We show that the recently proposed S=2 bond model with orbital degrees of freedom for insulating V$_{2}$O$_{3}$ not only explains the anomalous magnetic ordering, but also other mysteries of the magnetic phase transition. The model contains an additional orbital degree of freedom that exhibits a zero temperature quantum phase transtion in the Ising universality class.Comment: 5 pages, 2 figure

Screening of Nuclear Reactions in the Sun and Solar Neutrinos

We quantitatively determine the effect and the uncertainty on solar neutrino production arising from the screening process. We present predictions for the solar neutrino fluxes and signals obtained with different screening models available in the literature and by using our stellar evolution code. We explain these numerical results in terms of simple laws relating the screening factors with the neutrino fluxes. Futhermore we explore a wider range of models for screening, obtained from the Mitler model by introducing and varying two phenomenological parameters, taking into account effects not included in the Mitler prescription. Screening implies, with respect to a no-screening case, a central temperat reduction of 0.5%, a 2% (8%) increase of Beryllium (Boron)-neutrino flux and a 2% (12%) increase of the Gallium (Chlorine) signal. We also find that uncertainties due to the screening effect ar at the level of 1% for the predicted Beryllium-neutrino flux and Gallium signal, not exceeding 3% for the Boron-neutrino flux and the Chlorine signal.Comment: postscript file 11 pages + 4 figures compressed and uuencoded we have replaced the previous paper with a uuencoded file (the text is the same) for any problem please write to [email protected]

Role of the impurity-potential range in disordered d-wave superconductors

We analyze how the range of disorder affects the localization properties of quasiparticles in a two-dimensional d-wave superconductor within the standard non-linear sigma-model approach to disordered systems. We show that for purely long-range disorder, which only induces intra-node scattering processes, the approach is free from the ambiguities which often beset the disordered Dirac-fermion theories, and gives rise to a Wess-Zumino-Novikov-Witten action leading to vanishing density of states and finite conductivities. We also study the crossover induced by internode scattering due to a short range component of the disorder, thus providing a coherent non-linear sigma-model description in agreement with all the various findings of different approaches.Comment: 38 pages, 1 figur

Multifractality: generic property of eigenstates of 2D disordered metals.

The distribution function of local amplitudes of eigenstates of a two-dimensional disordered metal is calculated. Although the distribution of comparatively small amplitudes is governed by laws similar to those known from the random matrix theory, its decay at larger amplitudes is non-universal and much slower. This leads to the multifractal behavior of inverse participation numbers at any disorder. From the formal point of view, the multifractality originates from non-trivial saddle-point solutions of supersymmetric $\sigma$-model used in calculations.Comment: 4 two-column pages, no figures, submitted to PRL

A Mixed Solar Core, Solar Neutrinos and Helioseismology

We consider a wide class of solar models with mixed core. Most of these models can be excluded as the predicted sound speed profile is in sharp disagreement with helioseismic constraints. All the remaining models predict $^7$Be and/or $^7$B neutrino fluxes at least as large as those of SSMs. In conclusion, helioseismology shows that a mixed solar core cannot account for the neutrino deficit implied by the current solar neutrino experiments.Comment: 6 pages, RevTeX, plus 5 postscript figure

Noncommutative geometry and physics: a review of selected recent results

This review is based on two lectures given at the 2000 TMR school in Torino. We discuss two main themes: i) Moyal-type deformations of gauge theories, as emerging from M-theory and open string theories, and ii) the noncommutative geometry of finite groups, with the explicit example of Z_2, and its application to Kaluza-Klein gauge theories on discrete internal spaces.Comment: Based on lectures given at the TMR School on contemporary string theory and brane physics, Jan 26- Feb 2, 2000, Torino, Italy. To be published in Class. Quant. Grav. 17 (2000). 3 ref.s added, typos corrected, formula on exterior product of n left-invariant one-forms corrected, small changes in the Sect. on integratio

N=2 Extremal Black Holes

It is shown that extremal magnetic black hole solutions of N = 2 supergravity coupled to vector multiplets $X^\Lambda$ with a generic holomorphic prepotential $F(X^\Lambda)$ can be described as supersymmetric solitons which interpolate between maximally symmetric limiting solutions at spatial infinity and the horizon. A simple exact solution is found for the special case that the ratios of the $X^\Lambda$ are real, and it is seen that the logarithm of the conformal factor of the spatial metric equals the Kahler potential on the vector multiplet moduli space. Several examples are discussed in detail.Comment: 10 pages, minor correction