A type system for components

In modern distributed systems, dynamic reconfiguration, i.e., changing at runtime the communication pattern of a program, is chal- lenging. Generally, it is difficult to guarantee that such modifications will not disrupt ongoing computations. In a previous paper, a solution to this problem was proposed by extending the object-oriented language ABS with a component model allowing the programmer to: i) perform up- dates on objects by means of communication ports and their rebinding; and ii) precisely specify when such updates can safely occur in an object by means of critical sections. However, improper rebind operations could still occur and lead to runtime errors. The present paper introduces a type system for this component model that extends the ABS type system with the notion of ports and a precise analysis that statically enforces that no object will attempt illegal rebinding

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

Programming chemistry in DNA-addressable bioreactors

We present a formal calculus, termed the chemtainer calculus, able to capture the complexity of compartmentalized reaction systems such as populations of possibly nested vesicular compartments. Compartments contain molecular cargo as well as surface markers in the form of DNA single strands. These markers serve as compartment addresses and allow for their targeted transport and fusion, thereby enabling reactions of previously separated chemicals. The overall system organization allows for the set-up of programmable chemistry in microfluidic or other automated environments. We introduce a simple sequential programming language whose instructions are motivated by state-of-the-art microfluidic technology. Our approach integrates electronic control, chemical computing and material production in a unified formal framework that is able to mimic the integrated computational and constructive capabilities of the subcellular matrix. We provide a non-deterministic semantics of our programming language that enables us to analytically derive the computational and constructive power of our machinery. This semantics is used to derive the sets of all constructable chemicals and supermolecular structures that emerge from different underlying instruction sets. Because our proofs are constructive, they can be used to automatically infer control programs for the construction of target structures from a limited set of resource molecules. Finally, we present an example of our framework from the area of oligosaccharide synthesis

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.

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

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

Strange magnification pattern in the large separation lens SDSS J1004+4112 from optical to X-rays

We present simultaneous XMM-Newton UV and X-ray observations of the quadruply lensed quasar SDSS J1004+4112 (RBS 825). Simultaneously with the XMM-Newton observations we also performed integral field spectroscopy on the two closest lens images A and B using the Calar Alto PMAS spectrograph. In X-rays the widely spaced components C and D are clearly resolved, while the closer pair of images A and B is marginally resolved in the XMM-EPIC images. The integrated X-ray flux of the system has decreased by a factor of 6 since it was observed in the ROSAT All Sky Survey in 1990, while the X-ray spectrum became much harder with the power law index evolving from Gamma=-2.3 to -1.86. By deblending the X-ray images of the lensed QSO we find that the X-ray flux ratios between the lens images A and B are significantly different from the simultaneously obtained UV ratios and previously measured optical flux ratios. Our optical spectrum of lens image A shows an enhancement in the blue emission line wings, which has been observed in previous epochs as a transient feature. We propose a scenario where intrinsic UV and X-ray variability gives rise to line variations which are selectively magnified in image A by microlensing. The extended emission of the lensing cluster of galaxies is clearly detected in the EPIC images, we measure a 0.5-2.0 keV luminosity of 1.4 E44 erg/s. Based on the cluster X-ray properties, we estimate a mass of 2-6 E14 solar masses.Comment: 11 pages, 10 figures, accepted for publication in Astronomy & Astrophysic

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