A mathematical program to refine gene regulatory networks

In this paper, we propose a methodology for making sense of large, multiple time-series data sets arising in expression analysis. Specifically, we present a mathematical model to release a reduced and coherent regulatory system given a putative regulatory network. We give two equivalent formulations of the problem and prove that the problem is NP-complete. For solving large scale instances we implemented an Ant Colony Optimization procedure. A computational analysis on randomly generated test instances validates the proposed algorithm and the computations on real data concerning Saccharomyces cerevisiae show the practicability of the proposed methodology.     

A semi-Markov maintenance model with credit rating application

Email: g.damico{at}unich.it Received on 6 December 2006. Accepted on 2 April 2008. The impact of a preventive rating maintenance policy on therating process is investigated through the definition of a semi-Markovmaintenance model with imperfect repair at random times. Theresults allow us to study the rating migrations process in thetransient and the asymptotic case.     

Trapped Positrons and Electrons in the Inner Radiation Belt According to Data of the PAMELA Experiment

Measurements of secondary-electron and secondary-positron fluxes below the geomagnetic cutoff in near-Earth space were performed by means of the PAMELA magnetic spectrometer installed on board the Resurs-DK1 satellite launched on June 15, 2006, in an elliptical orbit of inclination 70° and altitude 350 to 600 km. This spectrometer permits measuring the fluxes of electrons and positrons over a wide energy range, as well as determining their spatial distributions to a precision of about 2°. A calculation of particle trajectories in the geomagnetic field makes it possible to separate electrons and positrons originating from cosmic-ray interactions in the Earth’s magnetosphere. The spatial distributions of quasitrapped, trapped, and short-lived albedo positrons and electrons of energy above 70 MeV in the radiation belt were analyzed. The ratio of the electron-to-positron fluxes and the energy spectra of the electrons and positrons in question are indicative of different productionmechanisms for stably trapped and quasitrapped secondary particles.     

Topological Invariants of Eigenvalue Intersections and Decrease of Wannier Functions in Graphene

We investigate the asymptotic decrease of the Wannier functions for the valence and conduction band of graphene, both in the monolayer and the multilayer case. Since the decrease of the Wannier functions is characterised by the structure of the Bloch eigenspaces around the Dirac points, we introduce a geometric invariant of the family of eigenspaces, baptised eigenspace vorticity. We compare it with the pseudospin winding number. For every value $n \in \mathbb {Z}$ of the eigenspace vorticity, we exhibit a canonical model for the local topology of the eigenspaces. With the help of these canonical models, we show that the single band Wannier function $w$ satisfies $|w(x)| \le {\mathrm {const}} \cdot |x|^{-2}$ as $|x| \rightarrow \infty $ , both in monolayer and bilayer graphene.     

Band-edge ultrafast pump-probe spectroscopy of core/shell CdSe/CdS rods: assessing electron delocalization by effective mass calculations

CdSe/CdS dot/rods nanocrystals show interesting physical properties related to the band-alignment at the hetero-interface, which controls the band-edge electron delocalization over the rods. Here the differential transmission spectra of CdSe/CdS nanorod samples with different core sizes have been measured using excitation resonant to the core transition. The photo bleaching ratio between dot and rod transitions increases with the dot size, indicating a trend towards electron localization. This trend has been further quantified by performing effective mass calculations in which the conduction band misalignment was varied in order to reproduce the observed bleaching feature ratio. The best agreement was found for negligible conduction band misalignment for small dots of around 2.3 nm in diameter, and about -0.1 eV misalignment was estimated for the larger dots, above 3.5 nm in diameter. This shows that the band misalignment might be dependent on the geometry of the system, and we argue that this might be related to different strain developed at the hetero-interface.     

X‐ray‐Raman‐scattering‐based EXAFS beyond the dipole limit

X‐ray Raman scattering (XRS) provides a bulk‐sensitive method of measuring the extended X‐ray absorption fine structure (EXAFS) of soft X‐ray absorption edges. Accurate measurements and data analysis procedures for the determination of XRS‐EXAFS of polycrystalline diamond are described. The contributions of various angular‐momentum components beyond the dipole limit to the atomic background and the EXAFS oscillations are incorporated using self‐consistent real‐space multiple‐scattering calculations. The properly extracted XRS‐EXAFS oscillations are in good agreement with calculations and earlier soft X‐ray EXAFS results. It is shown, however, that under certain conditions multiple‐scattering contributions to XRS‐EXAFS deviate from those in standard EXAFS, leading to noticeable changes in the real‐space signal at higher momentum transfers owing to non‐dipole contributions. These results pave the way for the accurate application of XRS‐EXAFS to previously inaccessible light‐element systems.     

Cavitand-functionalized porous silicon as an active surface for organophosphorus vapor detection

This paper reports on the preparation of a porous silicon-based material covalently functionalized with cavitand receptors suited for the detection of organophosphorus vapors. Two different isomeric cavitands, both containing one acid group at the upper rim, specifically designed for covalent anchoring on silicon, were grafted on H-terminated porous silicon (PSi) by thermal hydrosilylation. The covalently functionalized surfaces and their complexation properties were characterized by combining different analytical techniques, namely X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), and mass spectroscopy analysis coupled with thermal desorption experiments. Complexation experiments were performed by exposing both active surfaces and a control surface consisting of PSi functionalized with a structurally similar but inactive methylene-bridged cavitand (MeCav) to dimethyl methylphosphonate (DMMP) vapors. Comparison between active and inactive surfaces demonstrated the recognition properties of the new surfaces. Finally, the nature of the involved interactions, the energetic differences between active and inactive surfaces toward DMMP complexation, and the comparison with a true nerve gas agent (sarin) were studied by DFT modeling. The results revealed the successful grafting reaction, the specific host-guest interactions of the PSi-bonded receptors, and the reversibility of the guest complexation.     

Spectral and kinetic evidence for attack at coordinated phenanthroline in the reaction between aliphatic amines and transition metal complexes of 5-nitro-1,10-phenanthroline

Various transition metal complexes of 5-nitro-1,10-phenanthroline react with aliphatic amines in dipolar aprotic solvents to give deeply coloured species. The spectral changes, which can be reversed upon addition of acid or of the appropriate protonated amine, do not depend either on the nature of the metal and the ancillary ligands or on the geometry of the complexes; this has been taken as evidence that the colour forming process is due to a specific interaction of aliphatic amines with coordinated phenanthroline. While the rate of reaction of [Pt(5-NO₂phen)Cl₂] and [Pd(5-NO₂phen)Cl₂] with Br^?, which is known to displace Cl^? in the substrates, depends strongly on the nature of the central atom, the second order rate constant at 25°C being 3.2 × 10^?4 dm³mol^?1s^?1 and 1.35 dm³mol^?1s^?1 for the platinum and the palladium derivative respectively, the rate of reaction with n-propylamine has a comparable value for both substrates. This is further evidence that amines attack the coordinated phenanthroline, rather than the central atom. On the basis of the spectral features and the reaction stoicheiometry, the adducts of metal complexes of 5-NO₂phen and aliphatic amines are presumably Meisenheimer-like complexes.     

Possible Tests of Curvature Effects in Weak Gravitational Fields

The possibility of performing in proximity of the Earth experiments to test the predictions of general relativity for the trajectories of particles and photons in weak gravitational fields is studied. Three experiments are analyzed, all based on optical detection methods. The first experiment would allow to detect the tidal acceleration using a freely-falling Michelson interferometer. In a second experiment, based on laser-ranging methods, the relativistic correction to the classical gravity acceleration could be detected. Finally, the possibility of detecting light deflection induced by space curvature in an optical cavity with high-reflectivity mirrors is discussed.