Thermal Operators in Ising Percolation

We discuss a new cluster representation for the internal energy and the specific heat of the d-dimensional Ising model, obtained by studying the percolation mapping of an Ising model with an arbitrary set of antiferromagnetic links. Such a representation relates the thermal operators to the topological properties of the Fortuin-Kasteleyn clusters of Ising percolation and is a powerful tool to get new exact relations on the topological structure of FK clusters of the Ising model defined on an arbitrary graph.Comment: 17 pages, 2 figures. Improved version. Major changes in the text and in the notations. A missing term added in the specific heat representatio

Off equilibrium response function in the one dimensional random field Ising model

A thorough numerical investigation of the slow dynamics in the d=1 random field Ising model in the limit of an infinite ferromagnetic coupling is presented. Crossovers from the preasymptotic pure regime to the asymptotic Sinai regime are investigated for the average domain size, the autocorrelation function and staggered magnetization. By switching on an additional small random field at the time tw the linear off equilibrium response function is obtained, which displays as well the crossover from the nontrivial behavior of the d=1 pure Ising model to the asymptotic behavior where it vanishes identically.Comment: 12 pages, 10 figure

Dynamic heterogeneities in attractive colloids

We study the formation of a colloidal gel by means of Molecular Dynamics simulations of a model for colloidal suspensions. A slowing down with gel-like features is observed at low temperatures and low volume fractions, due to the formation of persistent structures. We show that at low volume fraction the dynamic susceptibility, which describes dynamic heterogeneities, exhibits a large plateau, dominated by clusters of long living bonds. At higher volume fraction, where the effect of the crowding of the particles starts to be present, it crosses over towards a regime characterized by a peak. We introduce a suitable mean cluster size of clusters of monomers connected by "persistent" bonds which well describes the dynamic susceptibility.Comment: 4 pages, 4 figure

Static and dynamic heterogeneities in irreversible gels and colloidal gelation

We compare the slow dynamics of irreversible gels, colloidal gels, glasses and spin glasses by analyzing the behavior of the so called non-linear dynamical susceptibility, a quantity usually introduced to quantitatively characterize the dynamical heterogeneities. In glasses this quantity typically grows with the time, reaches a maximum and then decreases at large time, due to the transient nature of dynamical heterogeneities and to the absence of a diverging static correlation length. We have recently shown that in irreversible gels the dynamical susceptibility is instead an increasing function of the time, as in the case of spin glasses, and tends asymptotically to the mean cluster size. On the basis of molecular dynamics simulations, we here show that in colloidal gelation where clusters are not permanent, at very low temperature and volume fractions, i.e. when the lifetime of the bonds is much larger than the structural relaxation time, the non-linear susceptibility has a behavior similar to the one of the irreversible gel, followed, at higher volume fractions, by a crossover towards the behavior of glass forming liquids.Comment: 9 pages, 3 figure

The Asp272-Glu282 Region of Platelet Glycoprotein Ib Interacts with the Heparin-binding Site of -Thrombin and Protects the Enzyme from the Heparin-catalyzed Inhibition by Antithrombin III

Platelet glycoprotein Ib (GpIb) mediates interaction with both von Willebrand factor and thrombin. Thrombin binds to GpIb via its heparin-binding site (HBS) (De Candia, E., De Cristofaro, R., De Marco, L., Mazzucato, M., Picozzi, M., and Landolfi, R. (1997) Thromb. Haemostasis 77, 735–740; De Cristofaro, R., De Candia, E., Croce, G., Morosetti, R., and Landolfi, R. (1998) Biochem. J. 332, 643–650). To identify the thrombin-binding domain on GpIbα, we examined the effect of GpIbα1–282, a GpIbα fragment released by the cobra venom mocarhagin on the heparin-catalyzed rate of thrombin inhibition by antithrombin III (AT). GpIbα1–282 inhibited the reaction in a dose-dependent and competitive fashion. In contrast, the GpIbα1–271 fragment, produced by exposing GpIbα1–282 to carboxypeptidase Y, had no effect on thrombin inhibition by the heparin-AT complex. Measurements of the apparent equilibrium constant of the GpIbα1–282 binding to thrombin as a function of different salts (NaCl and tetramethyl-ammonium chloride) concentration (0.1–0.2 M) indicated a large salt dependence (Γ± = −4.5), similar to that pertaining to the heparin binding to thrombin. The importance of thrombin HBS in its interaction with GpIbα was confirmed using DNA aptamers, which specifically bind to either HBS (HD22) or the fibrinogen recognition site of thrombin (HD1). HD22, but not HD1, inhibited thrombin binding to GpIbα1–282. Furthermore, the proteolytic derivative γT-thrombin, which lacks the fibrinogen recognition site, binds to GpIbα via its intact HBS in a reaction that is inhibited by HD22. Neither α- nor γT-thrombin bound to GpIbα1–271, suggesting that the Asp272–Glu282 region of GpIbα may act as a “heparin-like” ligand for the thrombin HBS, thereby inhibiting heparin binding to thrombin. It was also demonstrated that intact platelets may dose-dependently inhibit the heparin-catalyzed thrombin inhibition by AT at enzyme concentrations <5 nM. Altogether, these findings show that thrombin HBS binds to the region of GpIbα involving the Asp272–Glu282 segment, protecting the enzyme from the inactivation by the heparin-AT system

Irreversible Opinion Spreading on Scale-Free Networks

We study the dynamical and critical behavior of a model for irreversible opinion spreading on Barab\'asi-Albert (BA) scale-free networks by performing extensive Monte Carlo simulations. The opinion spreading within an inhomogeneous society is investigated by means of the magnetic Eden model, a nonequilibrium kinetic model for the growth of binary mixtures in contact with a thermal bath. The deposition dynamics, which is studied as a function of the degree of the occupied sites, shows evidence for the leading role played by hubs in the growth process. Systems of finite size grow either ordered or disordered, depending on the temperature. By means of standard finite-size scaling procedures, the effective order-disorder phase transitions are found to persist in the thermodynamic limit. This critical behavior, however, is absent in related equilibrium spin systems such as the Ising model on BA scale-free networks, which in the thermodynamic limit only displays a ferromagnetic phase. The dependence of these results on the degree exponent is also discussed for the case of uncorrelated scale-free networks.Comment: 9 pages, 10 figures; added results and discussion on uncorrelated scale-free networks; added references. To appear in PR

Estimates of multipolar coefficients to search for cosmic ray anisotropies with non-uniform or partial sky coverage

We study the possibility to extract the multipolar moments of an underlying distribution from a set of cosmic rays observed with non-uniform or even partial sky coverage. We show that if the degree is assumed to be upper bounded by $L$, each multipolar moment can be recovered whatever the coverage, but with a variance increasing exponentially with the bound $L$ if the coverage is zero somewhere. Despite this limitation, we show the possibility to test predictions of a model without any assumption on $L$ by building an estimate of the covariance matrix seen through the exposure function.Comment: 20 pages, 8 figure

Metastable states in the Blume-Emery-Griffiths spin glass model

We study the Blume-Emery-Griffiths spin glass model in presence of an attractive coupling between real replicas, and evaluate the effective potential as a function of the density overlap. We find that there is a region, above the first order transition of the model, where metastable states with a large density overlap exist. The line where these metastable states appear should correspond to a purely dynamical transition, with a breaking of ergodicity. Differently from what happens in p-spin glasses, in this model the dynamical transition would not be the precursor of a 1-step RSB transition, but (probably) of a full RSB transition.Comment: RevTeX, 4 pages, 2 fig

A Combination of Genomic Approaches Reveals the Role of <i>FOXO1a</i> in Regulating an Oxidative Stress Response Pathway

Background: While many of the phenotypic differences between human and chimpanzee may result from changes in gene regulation, only a handful of functionally important regulatory differences are currently known. As a first step towards identifying transcriptional pathways that have been remodeled in the human lineage, we focused on a transcription factor, FOXO1a, which we had previously found to be up-regulated in the human liver compared to that of three other primate species. We concentrated on this gene because of its known role in the regulation of metabolism and in longevity.Methodology: Using a combination of expression profiling following siRNA knockdown and chromatin immunoprecipitation in a human liver cell line, we identified eight novel direct transcriptional targets of FOXO1a. This set includes the gene for thioredoxin-interacting protein (TXNIP), the expression of which is directly repressed by FOXO1a. The thioredoxin-interacting protein is known to inhibit the reducing activity of thioredoxin (TRX), thereby hindering the cellular response to oxidative stress and affecting life span.Conclusions: Our results provide an explanation for the repeated observations that differences in the regulation of FOXO transcription factors affect longevity. Moreover, we found that TXNIP is down-regulated in human compared to chimpanzee, consistent with the up-regulation of its direct repressor FOXO1a in humans, and with differences in longevity between the two species.</p

Static and dynamic heterogeneities in a model for irreversible gelation

We study the structure and the dynamics in the formation of irreversible gels by means of molecular dynamics simulation of a model system where the gelation transition is due to the random percolation of permanent bonds between neighboring particles. We analyze the heterogeneities of the dynamics in terms of the fluctuations of the intermediate scattering functions: In the sol phase close to the percolation threshold, we find that this dynamical susceptibility increases with the time until it reaches a plateau. At the gelation threshold this plateau scales as a function of the wave vector $k$ as $k^{\eta -2}$, with $\eta$ being related to the decay of the percolation pair connectedness function. At the lowest wave vector, approaching the gelation threshold it diverges with the same exponent $\gamma$ as the mean cluster size. These findings suggest an alternative way of measuring critical exponents in a system undergoing chemical gelation.Comment: 4 pages, 4 figure