Process Calculi Abstractions for Biology

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-

A criterion for separating process calculi

We introduce a new criterion, replacement freeness, to discern the relative expressiveness of process calculi. Intuitively, a calculus is strongly replacement free if replacing, within an enclosing context, a process that cannot perform any visible action by an arbitrary process never inhibits the capability of the resulting process to perform a visible action. We prove that there exists no compositional and interaction sensitive encoding of a not strongly replacement free calculus into any strongly replacement free one. We then define a weaker version of replacement freeness, by only considering replacement of closed processes, and prove that, if we additionally require the encoding to preserve name independence, it is not even possible to encode a non replacement free calculus into a weakly replacement free one. As a consequence of our encodability results, we get that many calculi equipped with priority are not replacement free and hence are not encodable into mainstream calculi like CCS and pi-calculus, that instead are strongly replacement free. We also prove that variants of pi-calculus with match among names, pattern matching or polyadic synchronization are only weakly replacement free, hence they are separated both from process calculi with priority and from mainstream calculi.Comment: In Proceedings EXPRESS'10, arXiv:1011.601

Type systems for distributed programs: session communication

Distributed systems are everywhere around us and guaranteeing their correctness is of paramount importance. It is natural to expect that these systems interact and communicate among them to achieve a common task. In this work, we develop techniques based on types and type systems for the verification of correctness, consistency and safety properties related to communication in complex distributed systems. We study advanced safety properties related to communication, like deadlock or lock freedom and progress. We study session types in the pi-calculus describing distributed systems and communication-centric computation. Most importantly, we de- fine an encoding of the session pi-calculus into the standard typed pi-calculus in order to understand the expressive power of these concurrent calculi. We show how to derive in the session pi-calculus basic properties, like type safety or complex ones, like progress, by exploiting this encoding

Combining behavioural types with security analysis

Today's software systems are highly distributed and interconnected, and they increasingly rely on communication to achieve their goals; due to their societal importance, security and trustworthiness are crucial aspects for the correctness of these systems. Behavioural types, which extend data types by describing also the structured behaviour of programs, are a widely studied approach to the enforcement of correctness properties in communicating systems. This paper offers a unified overview of proposals based on behavioural types which are aimed at the analysis of security properties

Name-passing calculi and crypto-primitives: A survey

The paper surveys the literature on high-level name-passing process calculi, and their extensions with cryptographic primitives. The survey is by no means exhaustive, for essentially two reasons. First, in trying to provide a coherent presentation of different ideas and techniques, one inevitably ends up leaving out the approaches that do not fit the intended roadmap. Secondly, the literature on the subject has been growing at very high rate over the years. As a consequence, we decided to concentrate on few papers that introduce the main ideas, in the hope that discussing them in some detail will provide sufficient insight for further reading