Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Roughening of the (1+1) interfaces in two-component surface growth with an admixture of random deposition

We simulate competitive two-component growth on a one dimensional substrate of $L$ sites. One component is a Poisson-type deposition that generates Kardar-Parisi-Zhang (KPZ) correlations. The other is random deposition (RD). We derive the universal scaling function of the interface width for this model and show that the RD admixture acts as a dilatation mechanism to the fundamental time and height scales, but leaves the KPZ correlations intact. This observation is generalized to other growth models. It is shown that the flat-substrate initial condition is responsible for the existence of an early non-scaling phase in the interface evolution. The length of this initial phase is a non-universal parameter, but its presence is universal. In application to parallel and distributed computations, the important consequence of the derived scaling is the existence of the upper bound for the desynchronization in a conservative update algorithm for parallel discrete-event simulations. It is shown that such algorithms are generally scalable in a ring communication topology.Comment: 16 pages, 16 figures, 77 reference

SOTER: A Runtime Assurance Framework for Programming Safe Robotics Systems

The recent drive towards achieving greater autonomy and intelligence in robotics has led to high levels of complexity. Autonomous robots increasingly depend on third party off-the-shelf components and complex machine-learning techniques. This trend makes it challenging to provide strong design-time certification of correct operation. To address these challenges, we present SOTER, a robotics programming framework with two key components: (1) a programming language for implementing and testing high-level reactive robotics software and (2) an integrated runtime assurance (RTA) system that helps enable the use of uncertified components, while still providing safety guarantees. SOTER provides language primitives to declaratively construct a RTA module consisting of an advanced, high-performance controller (uncertified), a safe, lower-performance controller (certified), and the desired safety specification. The framework provides a formal guarantee that a well-formed RTA module always satisfies the safety specification, without completely sacrificing performance by using higher performance uncertified components whenever safe. SOTER allows the complex robotics software stack to be constructed as a composition of RTA modules, where each uncertified component is protected using a RTA module. To demonstrate the efficacy of our framework, we consider a real-world case-study of building a safe drone surveillance system. Our experiments both in simulation and on actual drones show that the SOTER-enabled RTA ensures the safety of the system, including when untrusted third-party components have bugs or deviate from the desired behavior

Robustness analysis of magnetic torquer controlled spacecraft attitude dynamics

This paper describes a systematic approach to the robustness analysis of linear periodically time-varying (LPTV) systems. The method uses the technique known as Lifting to transform the original time-varying uncertain system into linear fractional transformation (LFT) form. The stability and performance robustness of the system to structured parametric uncertainty can then be analysed non-conservatively using the structured singular value μ. The method is applied to analyse the stability robustness of an attitude control law for a spacecraft controlled by magnetic torquer bars, whose linearised dynamics can naturally be written in linear periodically time-varying form. The proposed method allows maximum allowable levels of uncertainty, as well as worst-case uncertainty combinations to be computed. The destabilising effect of these uncertain parameter combinations is verified in time-domain simulations

Algorithmic Verification of Continuous and Hybrid Systems

We provide a tutorial introduction to reachability computation, a class of computational techniques that exports verification technology toward continuous and hybrid systems. For open under-determined systems, this technique can sometimes replace an infinite number of simulations.Comment: In Proceedings INFINITY 2013, arXiv:1402.661

Collaborative Verification-Driven Engineering of Hybrid Systems

Hybrid systems with both discrete and continuous dynamics are an important model for real-world cyber-physical systems. The key challenge is to ensure their correct functioning w.r.t. safety requirements. Promising techniques to ensure safety seem to be model-driven engineering to develop hybrid systems in a well-defined and traceable manner, and formal verification to prove their correctness. Their combination forms the vision of verification-driven engineering. Often, hybrid systems are rather complex in that they require expertise from many domains (e.g., robotics, control systems, computer science, software engineering, and mechanical engineering). Moreover, despite the remarkable progress in automating formal verification of hybrid systems, the construction of proofs of complex systems often requires nontrivial human guidance, since hybrid systems verification tools solve undecidable problems. It is, thus, not uncommon for development and verification teams to consist of many players with diverse expertise. This paper introduces a verification-driven engineering toolset that extends our previous work on hybrid and arithmetic verification with tools for (i) graphical (UML) and textual modeling of hybrid systems, (ii) exchanging and comparing models and proofs, and (iii) managing verification tasks. This toolset makes it easier to tackle large-scale verification tasks