Trend-based analysis of a population model of the AKAP scaffold protein

We formalise a continuous-time Markov chain with multi-dimensional discrete state space model of the AKAP scaffold protein as a crosstalk mediator between two biochemical signalling pathways. The analysis by temporal properties of the AKAP model requires reasoning about whether the counts of individuals of the same type (species) are increasing or decreasing. For this purpose we propose the concept of stochastic trends based on formulating the probabilities of transitions that increase (resp. decrease) the counts of individuals of the same type, and express these probabilities as formulae such that the state space of the model is not altered. We define a number of stochastic trend formulae (e.g. weakly increasing, strictly increasing, weakly decreasing, etc.) and use them to extend the set of state formulae of Continuous Stochastic Logic. We show how stochastic trends can be implemented in a guarded-command style specification language for transition systems. We illustrate the application of stochastic trends with numerous small examples and then we analyse the AKAP model in order to characterise and show causality and pulsating behaviours in this biochemical system

The physics models of FLUKA: status and recent development

A description of the intermediate and high energy hadronic interaction models used in the FLUKA code is given. Benchmarking against experimental data is also reported in order to validate the model performances. Finally the most recent developments and perspectives for nucleus-nucleus interactions are described together with some comparisons with experimental data.Comment: talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 10 pages, p

Modelling the influence of shielding on physical and biological organ doses.

Distributions of "physical" and "biological" dose in different organs were calculated by coupling the FLUKA MC transport code with a geometrical human phantom inserted into a shielding box of variable shape, thickness and material. While the expression "physical dose" refers to the amount of deposited energy per unit mass (in Gy), "biological dose" was modelled with "Complex Lesions" (CL), clustered DNA strand breaks calculated in a previous work based on "event-by-event" track-structure simulations. The yields of complex lesions per cell and per unit dose were calculated for different radiation types and energies, and integrated into a version of FLUKA modified for this purpose, allowing us to estimate the effects of mixed fields. As an initial test simulation, the phantom was inserted into an aluminium parallelepiped and was isotropically irradiated with 500 MeV protons. Dose distributions were calculated for different values of the shielding thickness. The results were found to be organ-dependent. In most organs, with increasing shielding thickness the contribution of primary protons showed an initial flat region followed by a gradual decrease, whereas secondary particles showed an initial increase followed by a decrease at large thickness values. Secondary particles were found to provide a substantial contribution, especially to the biological dose. In particular, the decrease of their contribution occurred at larger depths than for primary protons. In addition, their contribution to biological dose was generally greater than that of primary protons

EPR enlightening some aspects of propane ODH over VOx\u2013SiO2 and VOx\u2013Al2O3

In the oxidative dehydrogenation (ODH) of propane to propylene VOx-based catalysts prepared by name pyrolysis (FP) showed more selective than those prepared by impregnation. Furthermore, samples prepared by the same method were less active, but more selective when VOx was supported on SiO2 than on Al2O3. In order to assess V local structure, V4+ ions showed useful labels to characterise these catalysts by EPR spectroscopy. Indeed, the spectrum of a (10 wt%V2O5) FP-prepared VOx/SiO2 catalyst was typical of isolated, tetragonally distorted, paramagnetic complexes of V4+ forming a monolayer on the sample surface with a strong out-of-plane V4+-O bond. In a sample with identical composition, but prepared by impregnation, this bond showed a bit weaker. Furthermore, ferromagnetic domains of clustered V ions formed in the latter sample, hindering at least in part the accessibility to the catalytically active V-based centres. This gives evidence of the higher dispersion of V in the sample bulk provided by the FP preparation method with respect to conventional ones. A by far weaker V4+-O bond was revealed by the EPR spectrum of a (10%V2O5) VOx/Al2O3 sample, accounting for its higher oxygen availability, leading to higher activity, but lower selectivity. However, the same catalyst, when prepared by impregnation, showed a ferromagnetic resonance pattern so intense that no EPR spectrum was detectable at all and no information on the V4+-O bond strength was available in that case. Such semi-quantitative index of the V-O bond strength can be used as an index of oxygen availability, as a tool to assess catalytic activity and selectivity to the desired olefin

Scale effects for strength, ductility, and toughness in "brittle” materials

Decreasing scales effectively increase nearly all important mechanical properties of at least some "brittle” materials below 100 nm. With an emphasis on silicon nanopillars, nanowires, and nanospheres, it is shown that strength, ductility, and toughness all increase roughly with the inverse radius of the appropriate dimension. This is shown experimentally as well as on a mechanistic basis using a proposed dislocation shielding model. Theoretically, this collects a reasonable array of semiconductors and ceramics onto the same field using fundamental physical parameters. This gives proportionality between fracture toughness and the other mechanical properties. Additionally, this leads to a fundamental concept of work per unit fracture area, which predicts the critical event for brittle fracture. In semibrittle materials such as silicon, this can occur at room temperature when the scale is sufficiently small. When the local stress associated with dislocation nucleation increases to that sufficient to break bonds, an instability occurs resulting in fractur

The oxygen-assisted transformation of propane to COx/H2 through combined oxidation and WGS reactions catalyzed by vanadium oxide-based catalysts

This paper reports about the gas-phase oxidation of propane catalyzed by bulk vanadium oxide and by alumina- and silica-supported vanadium oxide. The reaction was studied with the aim of finding conditions at which the formation of H2 and CO2 is preferred over that of CO, H2O and of products of alkane partial oxidation. It was found that with bulk V2O5 considerable amounts of H2 are produced above 400 8C, the temperature at which the limiting reactant, oxygen, is totally consumed. The formation of H2 derived from the combination of: (i) oxidation reactions, with generation of CO, CO2, oxygenates (mainly acetic acid), propylene and H2O, all occurring in the fraction of catalytic bed that operated in the presence of gas-phase oxygen, and (ii) WGS reaction, propane dehydrogenation and coke formation, that instead occurred in the fraction of bed operating under anaerobic conditions. This combination of different reactions in a single catalytic bed was possible because of the reduction of V2O5 to V2O3 at high temperature, in the absence of gas-phase oxygen. In fact, vanadium sesquioxide was found to be an effective catalyst for the WGS, while V2O5 was inactive in this reaction. The same combination of reactions was not possible when vanadium oxide was supported over high-surface area silica or alumina; this was attributed to the fact that in these catalysts vanadium was not reduced below the oxidation state V4+, even under reaction conditions leading to total oxygen conversion. In consequence, these catalysts produced less H2 than bulk vanadium oxide

The colored Hanbury Brown--Twiss effect

The Hanbury Brown--Twiss effect is one of the celebrated phenomenologies of modern physics that accommodates equally well classical (interferences of waves) and quantum (correlations between indistinguishable particles) interpretations. The effect was discovered in the late thirties with a basic observation of Hanbury Brown that radio-pulses from two distinct antennas generate signals on the oscilloscope that wiggle similarly to the naked eye. When Hanbury Brown and his mathematician colleague Twiss took the obvious step to propose bringing the effect in the optical range, they met with considerable opposition as single-photon interferences were deemed impossible. The Hanbury Brown--Twiss effect is nowadays universally accepted and, being so fundamental, embodies many subtleties of our understanding of the wave/particle dual nature of light. Thanks to a novel experimental technique, we report here a generalized version of the Hanbury Brown--Twiss effect to include the frequency of the detected light, or, from the particle point of view, the energy of the detected photons. In addition to the known tendencies of indistinguishable photons to arrive together on the detector, we find that photons of different colors present the opposite characteristic of avoiding each others. We postulate that fermions can be similarly brought to exhibit positive (boson-like) correlations by frequency filtering.Comment: 18 pages, includes supplementary material of the derivation

Vortex and half-vortex dynamics in a spinor quantum fluid of interacting polaritons

Spinorial or multi-component Bose-Einstein condensates may sustain fractional quanta of circulation, vorticant topological excitations with half integer windings of phase and polarization. Matter-light quantum fluids, such as microcavity polaritons, represent a unique test bed for realising strongly interacting and out-of-equilibrium condensates. The direct access to the phase of their wavefunction enables us to pursue the quest of whether half vortices ---rather than full integer vortices--- are the fundamental topological excitations of a spinor polariton fluid. Here, we are able to directly generate by resonant pulsed excitations, a polariton fluid carrying either the half or full vortex states as initial condition, and to follow their coherent evolution using ultrafast holography. Surprisingly we observe a rich phenomenology that shows a stable evolution of a phase singularity in a single component as well as in the full vortex state, spiraling, splitting and branching of the initial cores under different regimes and the proliferation of many vortex anti-vortex pairs in self generated circular ripples. This allows us to devise the interplay of nonlinearity and sample disorder in shaping the fluid and driving the phase singularities dynamicsComment: New version complete with revised modelization, discussion and added material. 8 pages, 7 figures. Supplementary videos: https://drive.google.com/folderview?id=0B0QCllnLqdyBfmc2ai0yVF9fa2g2VnZodGUwemVkLThBb3BoOVRKRDJMS2dUdjlZdkRTQk

ERK1 and ERK2 are involved in recruitment and maturation of human mesenchymal stem cells induced to adipogenic differentiation

Adipocytes' biology and the mechanisms that control adipogenesis have gained importance because of the need to develop therapeutic strategies to control obesity and the related pathologies. Human mesenchymal stem cells (hMSCs), undifferentiated stem cells present in the bone marrow that are physiological precursors of adipocytes, were induced to adipogenic differentiation. The molecular mechanisms on the basis of the adipogenesis were evaluated, focusing on the MAPKinases ERK1 and ERK2, which are involved in many biological and cellular processes. ERK1 and ERK2 phosphorylation was reduced with different timing and intensity for the two isoforms in treated hMSCs in comparison with control cells until day 10 and then at 14-28 days, it reached the level of untreated cultures. The total amount of ERK1 was also decreased up to day 10 and then was induced to the level of untreated cultures, whereas the expression of ERK2 was not changed following adipogenic induction. Treatment with the specific ERK1/2 inhibitor U0126 during the whole differentiation period hampered hMSCs' adipogenic differentiation, as lipid droplets appeared in very few cells and were reduced in number and size. When U0126 was administered only during the initial phase of differentiation, the number of hMSCs recruited to adipogenesis was reduced while, when it was administered later, hMSCs did not acquire a mature adipocytic phenotype. ERK1 and ERK2 are important for hMSC adipogenic differentiation since any alteration to the correct timing of their phosphorylation affects either the recruitment into the differentiation program and the extent of their maturation