A Mathematical Framework for Agent Based Models of Complex Biological Networks

Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis.Comment: To appear in Bulletin of Mathematical Biolog

Classical Knowledge for Quantum Security

We propose a decision procedure for analysing security of quantum cryptographic protocols, combining a classical algebraic rewrite system for knowledge with an operational semantics for quantum distributed computing. As a test case, we use our procedure to reason about security properties of a recently developed quantum secret sharing protocol that uses graph states. We analyze three different scenarios based on the safety assumptions of the classical and quantum channels and discover the path of an attack in the presence of an adversary. The epistemic analysis that leads to this and similar types of attacks is purely based on our classical notion of knowledge.Comment: extended abstract, 13 page

Compiling and securing cryptographic protocols

Protocol narrations are widely used in security as semi-formal notations to specify conversations between roles. We define a translation from a protocol narration to the sequences of operations to be performed by each role. Unlike previous works, we reduce this compilation process to well-known decision problems in formal protocol analysis. This allows one to define a natural notion of prudent translation and to reuse many known results from the literature in order to cover more crypto-primitives. In particular this work is the first one to show how to compile protocols parameterised by the properties of the available operations.Comment: A short version was submitted to IP

S+Net: extending functional coordination with extra-functional semantics

This technical report introduces S+Net, a compositional coordination language for streaming networks with extra-functional semantics. Compositionality simplifies the specification of complex parallel and distributed applications; extra-functional semantics allow the application designer to reason about and control resource usage, performance and fault handling. The key feature of S+Net is that functional and extra-functional semantics are defined orthogonally from each other. S+Net can be seen as a simultaneous simplification and extension of the existing coordination language S-Net, that gives control of extra-functional behavior to the S-Net programmer. S+Net can also be seen as a transitional research step between S-Net and AstraKahn, another coordination language currently being designed at the University of Hertfordshire. In contrast with AstraKahn which constitutes a re-design from the ground up, S+Net preserves the basic operational semantics of S-Net and thus provides an incremental introduction of extra-functional control in an existing language.Comment: 34 pages, 11 figures, 3 table

An algebraic basis for specifying and enforcing access control in security systems

Security services in a multi-user environment are often based on access control mechanisms. Static aspects of an access control policy can be formalised using abstract algebraic models. We integrate these static aspects into a dynamic framework considering requesting access to resources as a process aiming at the prevention of access control violations when a program is executed. We use another algebraic technique, monads, as a meta-language to integrate access control operations into a functional programming language. The integration of monads and concepts from a denotational model for process algebras provides a framework for programming of access control in security systems

A Formal Framework for Modeling Trust and Reputation in Collective Adaptive Systems

Trust and reputation models for distributed, collaborative systems have been studied and applied in several domains, in order to stimulate cooperation while preventing selfish and malicious behaviors. Nonetheless, such models have received less attention in the process of specifying and analyzing formally the functionalities of the systems mentioned above. The objective of this paper is to define a process algebraic framework for the modeling of systems that use (i) trust and reputation to govern the interactions among nodes, and (ii) communication models characterized by a high level of adaptiveness and flexibility. Hence, we propose a formalism for verifying, through model checking techniques, the robustness of these systems with respect to the typical attacks conducted against webs of trust.Comment: In Proceedings FORECAST 2016, arXiv:1607.0200

Towards an Effective Decision Procedure for LTL formulas with Constraints

This paper presents an ongoing work that is part of a more wide-ranging project whose final scope is to define a method to validate LTL formulas w.r.t. a program written in the timed concurrent constraint language tccp, which is a logic concurrent constraint language based on the concurrent constraint paradigm of Saraswat. Some inherent notions to tccp processes are non-determinism, dealing with partial information in states and the monotonic evolution of the information. In order to check an LTL property for a process, our approach is based on the abstract diagnosis technique. The concluding step of this technique needs to check the validity of an LTL formula (with constraints) in an effective way. In this paper, we present a decision method for the validity of temporal logic formulas (with constraints) built by our abstract diagnosis technique.Comment: Part of WLPE 2013 proceedings (arXiv:1308.2055

A general theory of action languages

We present a general theory of action-based languages as a paradigm, for the description, of those computational systems which include elements of concurrency and networking, and extend this approach to describe dist.ributed systems and also t,o describe the interaction of a system, with an environment. As part of this approach we introduce the Action Language as a common model for the class of nondeterministic concurrent programming languages and define its intensional and interaction semantics in terrors of continuous transformation of environment behavior. This semantics i.s specialized for programs with stores, and extended to describe distributed computations