19,228 research outputs found
Petri nets for systems and synthetic biology
We give a description of a Petri net-based framework for
modelling and analysing biochemical pathways, which uniÂŻes 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 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
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 Ό. 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
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
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
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