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/

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

Logics for Unranked Trees: An Overview

Labeled unranked trees are used as a model of XML documents, and logical languages for them have been studied actively over the past several years. Such logics have different purposes: some are better suited for extracting data, some for expressing navigational properties, and some make it easy to relate complex properties of trees to the existence of tree automata for those properties. Furthermore, logics differ significantly in their model-checking properties, their automata models, and their behavior on ordered and unordered trees. In this paper we present a survey of logics for unranked trees

Abundance determinations in HII regions: model fitting versus Te-method

The discrepancy between the oxygen abundances in high-metallicity HII regions determined through the Te-method (and/or through the corresponding "strong lines - oxygen abundance" calibration) and that determined through the model fitting (and/or through the corresponding "strong lines - oxygen abundance" calibration) is discussed. It is suggested to use the interstellar oxygen abundance in the solar vicinity, derived with very high precision from the high-resolution observations of the weak interstellar absorption lines towards the stars, as a "Rosetta stone" to verify the validity of the oxygen abundances derived in HII regions with the Te-method at high abundances. The agreement between the value of the oxygen abundance at the solar galactocentric distance traced by the abundances derived in HII regions through the Te-method and that derived from the interstellar absorption lines towards the stars is strong evidence in favor of that i) the two-zone model for Te seems to be a realistic interpretation of the temperature structure within HII regions, and ii) the classic Te-method provides accurate oxygen abundances in HII regions. It has been concluded that the "strong lines - oxygen abundance" calibrations must be based on the HII regions with the oxygen abundances derived with the Te-method but not on the existing grids of the models for HII regions.Comment: 5 pages, 3 figures, accepted for publication in Astronomy and Astrophysic

Lazy Mobile Intruders

We present a new technique for analyzing platforms that execute potentially malicious code, such as web-browsers, mobile phones, or virtualized infrastructures. Rather than analyzing given code, we ask what code an intruder could create to break a security goal of the platform. To avoid searching the infinite space of programs that the intruder could come up with (given some initial knowledge) we adapt the lazy intruder technique from protocol verification: the code is initially just a process variable that is getting instantiated in a demand-driven way during its execution. We also take into account that by communication, the malicious code can learn new information that it can use in subsequent operations, or that we may have several pieces of malicious code that can exchange information if they “meet”. To formalize both the platform and the malicious code we use the mobile ambient calculus, since it provides a small, abstract formalism that models the essence of mobile code. We provide a decision procedure for security against arbitrary intruder processes when the honest processes can only perform a bounded number of steps and without path constraints in communication. We show that this problem is NP-complete

High-Resolution Observations of Interstellar Ca I Absorption -- Implications for Depletions and Electron Densities in Diffuse Clouds

We present high-resolution (FWHM ~ 0.3-1.5 km/s) spectra of interstellar Ca I absorption toward 30 Galactic stars. Comparisons of the column densities of Ca I, Ca II, K I, and other species -- for individual components identified in the line profiles and also when integrated over entire lines of sight -- yield information on relative electron densities and depletions. There is no obvious relationship between the ratio N(Ca I)/N(Ca II) [equal to n_e/(Gamma/alpha_r) for photoionization equilibrium] and the fraction of hydrogen in molecular form f(H2) (often taken to be indicative of the local density n_H). For a smaller sample of sightlines for which the thermal pressure (n_H T) and local density can be estimated via analysis of the C I fine-structure excitation, the average electron density inferred from C, Na, and K (assuming photoionization equilibrium) seems to be independent of n_H and n_H T. While the n_e obtained from the ratio N(Ca I)/N(Ca II) is often significantly higher than the values derived from other elements, the patterns of relative n_e derived from different elements show both similarities and differences for different lines of sight -- suggesting that additional processes besides photoionization and radiative recombination commonly and significantly affect the ionization balance of heavy elements in diffuse IS clouds. Such additional processes may also contribute to the (apparently) larger than expected fractional ionizations (n_e/n_H) found for some lines of sight with independent determinations of n_H. In general, inclusion of ``grain-assisted'' recombination does reduce the inferred n_e, but it does not reconcile the n_e estimated from different elements. The depletion of calcium may have a much weaker dependence on density than was suggested by earlier comparisons with CH and CN.Comment: aastex, 70 pages, accepted to ApJ

Unveiling the nature of IGR J16283-4838

Context. One of the most striking discoveries of the INTEGRAL observatory is the existence of a previously unknown population of X-ray sources in the inner arms of the Galaxy. The investigations of the optical/NIR counterparts of some of them have provided evidence that they are highly absorbed high mass X-ray binaries hosting supergiants. Aims. We aim to identify the optical/NIR counterpart of one of the newly discovered INTEGRAL sources, IGR J16283-4838, and determine the nature of this system. Methods. We present optical and NIR observations of the field of IGR J16283-4838, and use the astrometry and photometry of the sources within it to identify its counterpart. We obtain its NIR spectrum, and its optical/NIR spectral energy distribution by means of broadband photometry. We search for the intrinsic polarization of its light, and its short and long-term photometric variability. Results. We demonstrate that this source is a highly absorbed HMXB located beyond the Galactic center, and that it may be surrounded by a variable circumstellar medium.Comment: 6 pages, 5 figures, accepted for publication in Astronomy & Astrophysic

A Taxonomy of Causality-Based Biological Properties

We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a theoretical point of view, biochemical reactions are abstractly represented as causal implications and the produced metabolites as causal consequences of the implication representing the corresponding reaction. The fact that a reactant is produced is represented by means of the chain of reactions that have made it exist. Such representation abstracts away from quantities, stoichiometric and thermodynamic parameters and constitutes the basis for the characterization of our properties. Moreover, we propose an effective method for verifying our properties based on an abstract model of system dynamics. This consists of a new abstract semantics for the system seen as a concurrent network and expressed using the Chemical Ground Form calculus. We illustrate an application of this framework to a portion of a real metabolic pathway