Syntactic Markovian Bisimulation for Chemical Reaction Networks

In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time Markov chains (CTMCs), the typically large populations of species cause combinatorially large state spaces. This makes the analysis very difficult in practice and represents the major bottleneck for the applicability of minimization techniques based, for instance, on lumpability. In this paper we present syntactic Markovian bisimulation (SMB), a notion of bisimulation developed in the Larsen-Skou style of probabilistic bisimulation, defined over the structure of a CRN rather than over its underlying CTMC. SMB identifies a lumpable partition of the CTMC state space a priori, in the sense that it is an equivalence relation over species implying that two CTMC states are lumpable when they are invariant with respect to the total population of species within the same equivalence class. We develop an efficient partition-refinement algorithm which computes the largest SMB of a CRN in polynomial time in the number of species and reactions. We also provide an algorithm for obtaining a quotient network from an SMB that induces the lumped CTMC directly, thus avoiding the generation of the state space of the original CRN altogether. In practice, we show that SMB allows significant reductions in a number of models from the literature. Finally, we study SMB with respect to the deterministic semantics of CRNs based on ordinary differential equations (ODEs), where each equation gives the time-course evolution of the concentration of a species. SMB implies forward CRN bisimulation, a recently developed behavioral notion of equivalence for the ODE semantics, in an analogous sense: it yields a smaller ODE system that keeps track of the sums of the solutions for equivalent species.Comment: Extended version (with proofs), of the corresponding paper published at KimFest 2017 (http://kimfest.cs.aau.dk/

Process algebra modelling styles for biomolecular processes

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed

Optical Observations of PSR J0205+6449

PSR J0205+6449 is a X-ray and radio pulsar in supernova remnant 3C 58. We report on observations of the central region of 3C 58 using the 4.2-m William Herschel Telescope with the intention of identifying the optical counterpart of PSR J0205+6449 and characterising its pulsar wind nebula. Around the pulsar position we identified extended emission with a magnitude of B = 23 \fm 97 \pm 0.10, V = 22 \fm 95 \pm 0.05 and R = 22 \fm 15 \pm 0.03 consistent with a pulsar wind nebula. From the R-band image we identified three knots with $m_R$ = 24 \fm 08 \pm 0.07 (o1), 24 \fm 15 \pm 0.07 (o2) and 24 \fm 24 \pm 0.08 (o3). We confirm the presence of an optical pulsar wind nebula around PSR J0205+6449 and give an upper limit of $m_R \approx$ 24 for the optical magnitude of the pulsar. Furthermore we make the tentative suggestion that our object o1, with an $m_R \approx$ 24.08 is the optical counterpart. If confirmed the pulsar would have an $L_R/L_x\approx 0.004$ and an optical efficiency of about 5% of the Crab pulsar. Such a low efficiency is more consistent with the characteristic age of the pulsar rather than that of SN 1181.Comment: The paper contains 3 figures and 3 tables, accepted for publication in MNRA

Graphical Encoding of a Spatial Logic for the pi-Calculus

This paper extends our graph-based approach to the verification of spatial properties of π-calculus specifications. The mechanism is based on an encoding for mobile calculi where each process is mapped into a graph (with interfaces) such that the denotation is fully abstract with respect to the usual structural congruence, i.e., two processes are equivalent exactly when the corresponding encodings yield isomorphic graphs. Behavioral and structural properties of π-calculus processes expressed in a spatial logic can then be verified on the graphical encoding of a process rather than on its textual representation. In this paper we introduce a modal logic for graphs and define a translation of spatial formulae such that a process verifies a spatial formula exactly when its graphical representation verifies the translated modal graph formula

Combined color indexes and photometric structure of galaxies NGC 834 and NGC 1134

We present the results of BVRI photometry of two galaxies with active star formation: NGC 834 and NGC 1134. Combined color index Q_{BVI} was used to investigate the photometrical structure of the galaxies. Index Q_{BVI} is not affected by internal extinction and is sensitive to the presence of blue stars. Ring-like region with active star formation at 15" from the center reveals itself in the Q_{BVI} map of NGC 834. Three-arm spiral structure is well-seen on the Q_{BVI} map of NGC 1134. We propose to use the combined indexes Q_{BVI} and similarly defined indices as a tracers of Star Formation activity and structure of dusty galaxies.Comment: 3 pages, 4 embedded figures, LaTeX2e, using the EslabStyle.cls file, presented as a poster in the 33rd ESLAB Symp. "Star formation from the small to the large scale", Noordwijk, The Netherlands, 2-5 November 1999, (F. Favata, A.A. Kaas & A. Wilson eds, ESA SP-445

Review of the ELI-NP-GBS low level rf and synchronization systems

The Gamma Beam System (GBS) of ELI-NP is a linac based gamma-source in construction at Magurele (RO) by the European consortium EuroGammaS led by INFN. Photons with tunable energy and with intensity and brilliance well beyond the state of the art will be produced by Compton back-scattering between a high quality electron beam (up to 740 MeV) and a 515 nm intense laser pulse. Production of very intense photon flux with narrow bandwidth requires multi-bunch operation at 100 Hz repetition rate. A total of 13 klystrons, 3 S-band (2856 MHz) and 10 C-band (5712 MHz) will power a total of 14 Travelling Wave accelerating sections (2 S-band and 12 C-band) plus 3 S-band Standing Wave cavities (a 1.6 cell RF gun and 2 RF deflectors). Each klystron is individually driven by a temperature stabilized LLRF module, for a maximum flexibility in terms of accelerating gradient, arbitrary pulse shaping (e.g. to compensate beam loading effects in multi-bunch regime) and compensation of long-term thermal drifts. In this paper, the whole LLRF system architecture and bench test results, the RF reference generation and distribution together with an overview of the synchronization system will be described

Heavy metal load and effects on biochemical properties in urban soils of a medium-sized city, Ancona, Italy

none6noUrban soils are often mixed with extraneous materials and show a high spatial variability that determine great differences from their agricultural or natural counterparts. The soils of 18 localities of a medium-sized city (Ancona, Italy) were analysed for their main physicochemical and biological properties, and for chromium (Cr), copper (Cu), cobalt (Co), lead (Pb), nickel (Ni), zinc (Zn), and mercury (Hg) total content, distribution among particle-size fractions, and extractability. Because of the absence of thresholds defining a hot spot for heavy metal pollution in urban soils, we defined a “threshold of attention” (ToA) for each heavy metal aiming to bring out hot spot soils where it is more impellent to intervene to mitigate or avoid potential environmental concerns. In several city locations, the soil displayed sub-alkaline pH, large contents of clay-size particles, and higher TOC, total N, and available P with respect to the surrounding rural areas, joined with high contents of total heavy metals, but low availability. The C biomass, basal respiration, qCO2, and enzyme activities were compared to that detected in the near rural soils, and results suggested that heavy metals content has not substantially compromised the soil ecological services. We conclude that ToA can be considered as a valuable tool to highlight soil hot spots especially for cities with a long material history and, for a proper risk assessment in urban soils, we suggest considering the content of available heavy metals (rather than the total content) and soil functions.openSerrani D.; Ajmone-Marsan F.; Corti G.; Cocco S.; Cardelli V.; Adamo P.Serrani, D.; Ajmone-Marsan, F.; Corti, G.; Cocco, S.; Cardelli, V.; Adamo, P

The G292.0+1.8 pulsar wind nebula in the mid-infrared

G292.0+1.8 is a Cas A-like supernova remnant that contains the young pulsar PSR J1124-5916 powering a compact torus-like pulsar wind nebula visible in X-rays. A likely counterpart to the nebula has been detected in the optical VRI bands. To confirm the counterpart candidate nature, we examined archival mid-infrared data obtained with the Spitzer Space Telescope. Broad-band images taken at 4.5, 8, 24, and 70 microns were analyzed and compared with available optical and X-ray data. The extended counterpart candidate is firmly detected in the 4.5 and 8 micron bands. It is brighter and more extended in the bands than in the optical, and its position and morphology agree well with the coordinates and morphology of the torus-like pulsar wind nebula in X-rays. The source is not visible in 24 and 70 micron images, which are dominated by bright emission from the remnant shell and filaments. We compiled the infrared fluxes of the nebula, which probably contains a contribution from an unresolved pulsar in its center, with the optical and X-ray data. The resulting unabsorbed multiwavelength spectrum is described by power laws of significantly steeper slope in the infrared-optical than in X-rays, implying a double-knee spectral break between the optical and X-rays. The 24 and 70 microns flux upper limits suggest a second break and a flatter spectrum at the long wavelength limit. These features are common to two other pulsar wind nebulae associated with the remnants B0540-69.3 and 3C 58 and observed in all three ranges. The position, morphology, and spectral properties of the detected source allow us to comfirm that it is the infrared-optical counterpart to both the pulsar and its wind nebula system in the G292.0+1.8 supernova remnant.Comment: 5 pages, 2 figure

Automated search for galactic star clusters in large multiband surveys: I. Discovery of 15 new open clusters in the Galactic anticenter region

Aims: According to some estimations, there are as many as 100000 open clusters in the Galaxy, but less than 2000 of them have been discovered, measured, and cataloged. We plan to undertake data mining of multiwavelength surveys to find new star clusters. Methods: We have developed a new method to search automatically for star clusters in very large stellar catalogs, which is based on convolution with density functions. We have applied this method to a subset of the Two Micron All Sky Survey catalog toward the Galactic anticenter. We also developed a method to verify whether detected stellar groups are real star clusters, which tests whether the stars that form the spatial density peak also fall onto a single isochrone in the color-magnitude diagram. By fitting an isochrone to the data, we estimate at the same time the main physical parameters of a cluster: age, distance, color excess. Results: For the present paper, we carried out a detailed analysis of 88 overdensity peaks detected in a field of $16\times16$ degrees near the Galactic anticenter. From this analysis, 15 overdensities were confirmed to be new open clusters and the physical and structural parameters were determined for 12 of them; 10 of them were previously suspected to be open clusters by Kronberger (2006) and Froebrich (2007). The properties were also determined for 13 yet-unstudied known open clusters, thus almost tripling the sample of open clusters with studied parameters in the anticenter. The parameters determined with this method showed a good agreement with published data for a set of well-known clusters.Comment: accepted to A&