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

The relationship between IR, optical, and UV extinction

An analysis is presented for the variability of absolute IR, optical, and UV extinction, A(sub lambda), derived through the ratio of total-to-selective extinction, R, for 31 lines of sight for which reliable UV extinction parameters were derived. These data sample a wide range of environments and are characterized by 2.5 is less than or equal to R is less than or equal to 6.0. It was found that there is a strong linear dependence between extinction expressed as A(sub lambda)/A(sub V) and 1/R for 1.25 micron is less than or equal to lambda is less than or equal to 0.12 micron. Differences in the general shape of extinction curves are largely due to variations in shape of optical/near-UV extinction corresponding to changes in R, with A(sub lambda)/A(sub V) decreasing for increasing R. From a least-squares fit of the observed R-dependence as a function of wavelength for 0.8/micron is less than or greater than 1/lambda is less than or equal to 8.3/micron, an analytic expression was generated from which IR, optical, and UV extinction curves of the form A(sub lambda)/A(sub V) can be reproduced with reasonable accuracy from a knowledge of R. It was also found that the absolute bump strength normalized to A(sub V) shows a general decrease with increasing R, suggesting that some fraction of bump grains may be selectively incorporated into coagulated grains. Finally, it was found that absolute extinction normalized by suitably chosen color indices results in a minimization of the R-dependence of portions of the UV curve, allowing A(sub lambda) to be estimated for these wavelengths independent of R

Concurrent constraint programming with process mobility

We propose an extension of concurrent constraint programming with primitives for process migration within a hierarchical network, and we study its semantics. To this purpose, we first investigate a "pure " paradigm for process migration, namely a paradigm where the only actions are those dealing with transmissions of processes. Our goal is to give a structural definition of the semantics of migration; namely, we want to describe the behaviour of the system, during the transmission of a process, in terms of the behaviour of the components. We achieve this goal by using a labeled transition system where the effects of sending a process, and requesting a process, are modeled by symmetric rules (similar to handshaking-rules for synchronous communication) between the two partner nodes in the network. Next, we extend our paradigm with the primitives of concurrent constraint programming, and we show how to enrich the semantics to cope with the notions of environment and constraint store. Finally, we show how the operational semantics can be used to define an interpreter for the basic calculus.

Regulating Data Exchange in Service Oriented Applications

We define a type system for COWS, a formalism for specifying and combining services, while modelling their dynamic behaviour. Our types permit to express policies constraining data exchanges in terms of sets of service partner names attachable to each single datum. Service programmers explicitly write only the annotations necessary to specify the wanted policies for communicable data, while a type inference system (statically) derives the minimal additional annotations that ensure consistency of services initial configuration. Then, the language dynamic semantics only performs very simple checks to authorize or block communication. We prove that the type system and the operational semantics are sound. As a consequence, we have the following data protection property: services always comply with the policies regulating the exchange of data among interacting services. We illustrate our approach through a simplified but realistic scenario for a service-based electronic marketplace

The Effect of Dust Extinction on the Observed Properties of Galaxies in the Near-Infrared

Galaxies behind the Milky Way suffer size reduction and dimming due to their obscuration by dust in the disk of our Galaxy. The degree of obscuration is wavelength dependent. It decreases towards longer wavelengths. Compared to the optical, the Near InfraRed (NIR) $K_s$ band extinction is only $\approx10$ that of the $B$ band. This makes NIR surveys well suited for galaxy surveys close to the Galactic Plane where extinction is severe. While Galactic obscuration is less prominent in the NIR it is not negligible. In this paper we derive empirical relations to correct isophotal radii and magnitudes of galaxies observed in the NIR for foreground absorption. We simulate extinction in the $J$, $H$ and $K_s$ bands on 64 (unobscured) galaxies from the 2MASS Large Galaxy Atlas \citep{jarrett}. We propose two methods for the extinction correction, the first is optimized to provide the most accurate correction and the second provides a convenient statistical correction that works adequately in lower extinction regions. The optimized correction utilizes the galaxy surface brightness, either the disk central surface brightness, $\mu_0$, or the combined disk plus bulge central surface brightness, elliptical and disk/spiral Hubble types. A detailed comparison between the different methods and their accuracy is provided.Comment: 9 pages, 8 figures and 8 tables. Accepted by the MNRAS: Accepted 2009 September 18. Received 2009 September 18; in original form 2009 July 1

A Flexible and Modular Framework for Implementing Infrastructures for Global Computing

We present a Java software framework for building infrastructures to support the development of applications for systems where mobility and network awareness are key issues. The framework is particularly useful to develop run-time support for languages oriented towards global computing. It enables platform designers to customize communication protocols and network architectures and guarantees transparency of name management and code mobility in distributed environments. The key features are illustrated by means of a couple of simple case studies

Typing Copyless Message Passing

We present a calculus that models a form of process interaction based on copyless message passing, in the style of Singularity OS. The calculus is equipped with a type system ensuring that well-typed processes are free from memory faults, memory leaks, and communication errors. The type system is essentially linear, but we show that linearity alone is inadequate, because it leaves room for scenarios where well-typed processes leak significant amounts of memory. We address these problems basing the type system upon an original variant of session types.Comment: 50 page

Updating quasar bolometric luminosity corrections. II. Infrared bolometric corrections

We present infrared bolometric luminosity corrections derived from the detailed spectral energy distributions of 62 bright quasars of low- to moderate-redshift (z=0.03-1.4). At 1.5, 2, 3, 7, 12, 15, and 24 microns we provide bolometric corrections of the mathematical forms L_iso=\zeta \lambda L_\lambda and log(L_iso)=A+B log(\lambda L_\lambda). Bolometric corrections for radio-loud and radio-quiet objects are consistent within 95% confidence intervals, so we do not separate them. Bolometric luminosities estimated using these corrections are typically smaller than those derived from some commonly used in the literature. We investigate the possibility of a luminosity dependent bolometric correction and find that, while the data are consistent with such a correction, the dispersion is too large and the luminosity range too small to warrant such a detailed interpretation. Bolometric corrections at 1.5 $\mu$m are appropriate for objects with properties that fall in the range log(L_bol)=45.4-47.3 and bolometric corrections at all other wavelengths are appropriate for objects with properties that fall in the range log(L_bol)=45.1-47.0.Comment: 13 pages, 4 tables, 8 figures, accepted to MNRA