Programmability of Chemical Reaction Networks

Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a well-stirred solution according to standard chemical kinetics equations. SCRNs have been widely used for describing naturally occurring (bio)chemical systems, and with the advent of synthetic biology they become a promising language for the design of artificial biochemical circuits. Our interest here is the computational power of SCRNs and how they relate to more conventional models of computation. We survey known connections and give new connections between SCRNs and Boolean Logic Circuits, Vector Addition Systems, Petri Nets, Gate Implementability, Primitive Recursive Functions, Register Machines, Fractran, and Turing Machines. A theme to these investigations is the thin line between decidable and undecidable questions about SCRN behavior

The complexity of coverability in ν-Petri nets

We show that the coverability problem in ν-Petri nets is complete for ‘double Ackermann’ time, thus closing an open complexity gap between an Ackermann lower bound and a hyper-Ackermann upper bound. The coverability problem captures the verification of safety properties in this nominal extension of Petri nets with name management and fresh name creation. Our completeness result establishes ν-Petri nets as a model of intermediate power among the formalisms of nets enriched with data, and relies on new algorithmic insights brought by the use of well-quasi-order ideals

Vector addition systems and their applications in the verification of computer programs

Vector Addition Systems (and, equivalently, Petri nets) are a widespread formalism for modelling across a spectrum of problem domains, from logistics to hardware simulation. In this thesis, we firstly explore two classic decidability problems for these models: reachability, whether one can get to a given configuration, and coverability, whether one can exceed it. These problems are sufficent to express a wide class of verification properties for models derived from real-world use cases, including safety and deadlock-freeness. We present and implement a number of approaches for solving both the coverability and reachability problems, including KReach, the first known implementation of a complete decider for the general Petri net reachability problem. Petri nets offer a natural model of concurrent processes and one of the most common modern use cases for the model is in the verification of safety properties for software, especially sofware with concurrency. In the later half of this work we address some approaches to deciding properties of programs written in Finitary Idealized Concurrent Algol (FICA), a prototypical language combining functional, imperative, and higher-order concurrent programming. We introduce a new family of “leafy” automata models, all based on a novel representation of internal configurations as a tree structure whose semantics is inspired by game-semantic interpretations of FICA terms. We give translations from such terms to our automata and across the work derive decidability of some useful properties for successively more expressive subsets of terms, using a variety of methods including via reachability on Petri nets. We believe these models will help to unify the game- and automata-theoretic views of programming languages and provide a useful basis on which to further study the theory of concurrency

A Comprehensive Survey of Voice over IP Security Research

We present a comprehensive survey of Voice over IP security academic research, using a set of 245 publications forming a closed cross-citation set. We classify these papers according to an extended version of the VoIP Security Alliance (VoIPSA) Threat Taxonomy. Our goal is to provide a roadmap for researchers seeking to understand existing capabilities and to identify gaps in addressing the numerous threats and vulnerabilities present in VoIP systems. We discuss the implications of our findings with respect to vulnerabilities reported in a variety of VoIP products. We identify two specific problem areas (denial of service, and service abuse) as requiring significant more attention from the research community. We also find that the overwhelming majority of the surveyed work takes a black box view of VoIP systems that avoids examining their internal structure and implementation. Such an approach may miss the mark in terms of addressing the main sources of vulnerabilities, i.e., implementation bugs and misconfigurations. Finally, we argue for further work on understanding cross-protocol and cross-mechanism vulnerabilities (emergent properties), which are the byproduct of a highly complex system-of-systems and an indication of the issues in future large-scale systems

Physical mechanisms may be as important as brain mechanisms in evolution of speech [Commentary on Ackerman, Hage, & Ziegler. Brain Mechanisms of acoustic communication in humans and nonhuman primates: an evolutionary perspective]

We present two arguments why physical adaptations for vocalization may be as important as neural adaptations. First, fine control over vocalization is not easy for physical reasons, and modern humans may be exceptional. Second, we present an example of a gorilla that shows rudimentary voluntary control over vocalization, indicating that some neural control is already shared with great apes

Décidabilité et Complexité

International audienceL'informatique fondamentale est un vaste sujet, comme en témoignent les 2 283 et 3 176 pages des "Handbooks" (228; 1). Couvrir en quelques dizaines de pages, l'ensemble de l'in- formatique nous a semblé une entreprise hors de notre portée. De ce fait, nous nous sommes concentrés sur la notion de calcul, sujet qui reflète le goût et la passion des auteurs de ce chapitre. La notion de calcul est omniprésente et aussi ancienne que les mathématiques

Integration of analysis techniques in security and fault-tolerance

This thesis focuses on the study of integration of formal methodologies in security protocol analysis and fault-tolerance analysis. The research is developed in two different directions: interdisciplinary and intra-disciplinary. In the former, we look for a beneficial interaction between strategies of analysis in security protocols and fault-tolerance; in the latter, we search for connections among different approaches of analysis within the security area. In the following we summarize the main results of the research

Brain mechanisms of acoustic communication in humans and nonhuman primates: An evolutionary perspective

Any account of “what is special about the human brain” (Passingham 2008) must specify the neural basis of our unique ability to produce speech and delineate how these remarkable motor capabilities could have emerged in our hominin ancestors. Clinical data suggest that the basal ganglia provide a platform for the integration of primate-general mechanisms of acoustic communication with the faculty of articulate speech in humans. Furthermore, neurobiological and paleoanthropological data point at a two-stage model of the phylogenetic evolution of this crucial prerequisite of spoken language: (i) monosynaptic refinement of the projections of motor cortex to the brainstem nuclei that steer laryngeal muscles, presumably, as part of a “phylogenetic trend” associated with increasing brain size during hominin evolution; (ii) subsequent vocal-laryngeal elaboration of cortico-basal ganglia circuitries, driven by human-specific FOXP2 mutations.;>This concept implies vocal continuity of spoken language evolution at the motor level, elucidating the deep entrenchment of articulate speech into a “nonverbal matrix” (Ingold 1994), which is not accounted for by gestural-origin theories. Moreover, it provides a solution to the question for the adaptive value of the “first word” (Bickerton 2009) since even the earliest and most simple verbal utterances must have increased the versatility of vocal displays afforded by the preceding elaboration of monosynaptic corticobulbar tracts, giving rise to enhanced social cooperation and prestige. At the ontogenetic level, the proposed model assumes age-dependent interactions between the basal ganglia and their cortical targets, similar to vocal learning in some songbirds. In this view, the emergence of articulate speech builds on the “renaissance” of an ancient organizational principle and, hence, may represent an example of “evolutionary tinkering” (Jacob 1977)