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

Multiform Adaptive Robot Skill Learning from Humans

Object manipulation is a basic element in everyday human lives. Robotic manipulation has progressed from maneuvering single-rigid-body objects with firm grasping to maneuvering soft objects and handling contact-rich actions. Meanwhile, technologies such as robot learning from demonstration have enabled humans to intuitively train robots. This paper discusses a new level of robotic learning-based manipulation. In contrast to the single form of learning from demonstration, we propose a multiform learning approach that integrates additional forms of skill acquisition, including adaptive learning from definition and evaluation. Moreover, going beyond state-of-the-art technologies of handling purely rigid or soft objects in a pseudo-static manner, our work allows robots to learn to handle partly rigid partly soft objects with time-critical skills and sophisticated contact control. Such capability of robotic manipulation offers a variety of new possibilities in human-robot interaction.Comment: Accepted to 2017 Dynamic Systems and Control Conference (DSCC), Tysons Corner, VA, October 11-1

Semantics and Verification of UML Activity Diagrams for Workflow Modelling

This thesis defines a formal semantics for UML activity diagrams that is suitable for workflow modelling. The semantics allows verification of functional requirements using model checking. Since a workflow specification prescribes how a workflow system behaves, the semantics is defined and motivated in terms of workflow systems. As workflow systems are reactive and coordinate activities, the defined semantics reflects these aspects. In fact, two formal semantics are defined, which are completely different. Both semantics are defined directly in terms of activity diagrams and not by a mapping of activity diagrams to some existing formal notation. The requirements-level semantics, based on the Statemate semantics of statecharts, assumes that workflow systems are infinitely fast w.r.t. their environment and react immediately to input events (this assumption is called the perfect synchrony hypothesis). The implementation-level semantics, based on the UML semantics of statecharts, does not make this assumption. Due to the perfect synchrony hypothesis, the requirements-level semantics is unrealistic, but easy to use for verification. On the other hand, the implementation-level semantics is realistic, but difficult to use for verification. A class of activity diagrams and a class of functional requirements is identified for which the outcome of the verification does not depend upon the particular semantics being used, i.e., both semantics give the same result. For such activity diagrams and such functional requirements, the requirements-level semantics is as realistic as the implementation-level semantics, even though the requirements-level semantics makes the perfect synchrony hypothesis. The requirements-level semantics has been implemented in a verification tool. The tool interfaces with a model checker by translating an activity diagram into an input for a model checker according to the requirements-level semantics. The model checker checks the desired functional requirement against the input model. If the model checker returns a counterexample, the tool translates this counterexample back into the activity diagram by highlighting a path corresponding to the counterexample. The tool supports verification of workflow models that have event-driven behaviour, data, real time, and loops. Only model checkers supporting strong fairness model checking turn out to be useful. The feasibility of the approach is demonstrated by using the tool to verify some real-life workflow models

Supporting group maintenance through prognostics-enhanced dynamic dependability prediction

Condition-based maintenance strategies adapt maintenance planning through the integration of online condition monitoring of assets. The accuracy and cost-effectiveness of these strategies can be improved by integrating prognostics predictions and grouping maintenance actions respectively. In complex industrial systems, however, effective condition-based maintenance is intricate. Such systems are comprised of repairable assets which can fail in different ways, with various effects, and typically governed by dynamics which include time-dependent and conditional events. In this context, system reliability prediction is complex and effective maintenance planning is virtually impossible prior to system deployment and hard even in the case of condition-based maintenance. Addressing these issues, this paper presents an online system maintenance method that takes into account the system dynamics. The method employs an online predictive diagnosis algorithm to distinguish between critical and non-critical assets. A prognostics-updated method for predicting the system health is then employed to yield well-informed, more accurate, condition-based suggestions for the maintenance of critical assets and for the group-based reactive repair of non-critical assets. The cost-effectiveness of the approach is discussed in a case study from the power industry

Supporting group maintenance through prognostics-enhanced dynamic dependability prediction

Condition-based maintenance strategies adapt maintenance planning through the integration of online condition monitoring of assets. The accuracy and cost-effectiveness of these strategies can be improved by integrating prognostics predictions and grouping maintenance actions respectively. In complex industrial systems, however, effective condition-based maintenance is intricate. Such systems are comprised of repairable assets which can fail in different ways, with various effects, and typically governed by dynamics which include time-dependent and conditional events. In this context, system reliability prediction is complex and effective maintenance planning is virtually impossible prior to system deployment and hard even in the case of condition-based maintenance. Addressing these issues, this paper presents an online system maintenance method that takes into account the system dynamics. The method employs an online predictive diagnosis algorithm to distinguish between critical and non-critical assets. A prognostics-updated method for predicting the system health is then employed to yield well-informed, more accurate, condition-based suggestions for the maintenance of critical assets and for the group-based reactive repair of non-critical assets. The cost-effectiveness of the approach is discussed in a case study from the power industry

Understanding the Elements of Executable Architectures Through a Multi-Dimensional Analysis Framework

The objective of this dissertation study is to conduct a holistic investigation into the elements of executable architectures. Current research in the field of Executable Architectures has provided valuable solution-specific demonstrations and has also shown the value derived from such an endeavor. However, a common theory underlying their applications has been missing. This dissertation develops and explores a method for holistically developing an Executable Architecture Specification (EAS), i.e., a meta-model containing both semantic and syntactic information, using a conceptual framework for guiding data coding, analysis, and validation. Utilization of this method resulted in the description of the elements of executable architecture in terms of a set of nine information interrogatives: an executable architecture information ontology. Once the detail-rich EAS was constructed with this ontology, it became possible to define the potential elements of executable architecture through an intermediate level meta-model. The intermediate level meta-model was further refined into an interrogative level meta-model using only the nine information interrogatives, at a very high level of abstraction

Safety‐oriented discrete event model for airport A‐SMGCS reliability assessment

A detailed analysis of State of the Art Technologies and Procedures into Airport Advanced-Surface Movement Guidance and Control Systems has been provided in this thesis, together with the review ofStatistical Monte Carlo Analysis, Reliability Assessment and Petri Nets theories. This practical and theoretical background has lead the author to the conclusion that there is a lack of linkage in between these fields. At the same of time the rapid increasing of Air Traffic all over the world, has brought in evidence the urgent need of practical instruments able to identify and quantify the risks connected with Aircraft operations on the ground, since the Airport has shown to be the actual ‘bottle neck’ of the entire Air Transport System. Therefore, the only winning approach to such a critical matter has to be multi-disciplinary, sewing together apparently different subjects, coming from the most disparate areas of interest and trying to fulfil the gap. The result of this thesis work has come to a start towards the end, when a Timed Coloured Petri Net (TCPN) model of a ‘sample’ Airport A-SMGCS has been developed, that is capable of taking into account different orders of questions arisen during these recent years and tries to give them some good answers. The A-SMGCS Airport model is, in the end, a parametric tool relying on Discrete Event System theory, able to perform a Reliability Analysis of the system itself, that: • uses a Monte Carlo Analysis applied to a Timed Coloured Petri Net, whose purpose is to evaluate the Safety Level of Surface Movements along an Airport • lets the user to analyse the impact of Procedures and Reliability Indexes of Systems such as Surface Movement Radars, Automatic Dependent Surveillance-Broadcast, Airport Lighting Systems, Microwave Sensors, and so on… onto the Safety Level of Airport Aircraft Transport System • not only is a valid instrument in the Design Phase, but it is useful also into the Certifying Activities an in monitoring the Safety Level of the above mentioned System with respect to changes to Technologies and different Procedures.This TCPN model has been verified against qualitative engineering expectations by using simulation experiments and occupancy time schedules generated a priori. Simulation times are good, and since the model has been written into Simulink/Stateflow programming language, it can be compiled to run real-time in C language (Real-time workshop and Stateflow Coder), thus relying on portable code, able to run virtually on any platform, giving even better performances in terms of execution time. One of the most interesting applications of this work is the estimate, for an Airport, of the kind of A-SMGCS level of implementation needed (Technical/Economical convenience evaluation). As a matter of fact, starting from the Traffic Volume and choosing the kind of Ground Equipment to be installed, one can make predictions about the Safety Level of the System: if the value is compliant with the TLS required by ICAO, the A-SMGCS level of Implementation is sufficiently adequate. Nevertheless, even if the Level of Safety has been satisfied, some delays due to reduced or simplified performances (even if Safety is compliant) of some of the equipment (e.g. with reference to False Alarm Rates) can lead to previously unexpected economical consequences, thus requiring more accurate systems to be installed, in order to meet also Airport economical constraints. Work in progress includes the analysis of the effect of weather conditions and re-sequencing of a given schedule. The effect of re-sequencing a given schedule is not yet enough realistic since the model does not apply inter arrival and departure separations. However, the model might show some effect on different sequences based on runway occupancy times. A further developed model containing wake turbulence separation conditions would be more sensitive for this case. Hence, further work will be directed towards: • The development of On-Line Re-Scheduling based on the available actual runway/taxiway configuration and weather conditions. • The Engineering Safety Assessment of some small Italian Airport A-SMGCSs (Model validation with real data). • The application of Stochastic Differential Equations systems in order to evaluate the collision risk on the ground inside the Place alone on the Petri Net, in the event of a Short Term Conflict Alert (STCA), by adopting Reich Collision Risk Model. • Optimal Air Traffic Control Algorithms Synthesis (Adaptive look-ahead Optimization), by Dynamically Timed Coloured Petri Nets, together with the implementation of Error-Recovery Strategies and Diagnosis Functions

A formalism for describing and simulating systems with interacting components.

This thesis addresses the problem of descriptive complexity presented by systems involving a high number of interacting components. It investigates the evaluation measure of performability and its application to such systems. A new description and simulation language, ICE and it's application to performability modelling is presented. ICE (Interacting ComponEnts) is based upon an earlier description language which was first proposed for defining reliability problems. ICE is declarative in style and has a limited number of keywords. The ethos in the development of the language has been to provide an intuitive formalism with a powerful descriptive space. The full syntax of the language is presented with discussion as to its philosophy. The implementation of a discrete event simulator using an ICE interface is described, with use being made of examples to illustrate the functionality of the code and the semantics of the language. Random numbers are used to provide the required stochastic behaviour within the simulator. The behaviour of an industry standard generator within the simulator and different methods of number allocation are shown. A new generator is proposed that is a development of a fast hardware shift register generator and is demonstrated to possess good statistical properties and operational speed. For the purpose of providing a rigorous description of the language and clarification of its semantics, a computational model is developed using the formalism of extended coloured Petri nets. This model also gives an indication of the language's descriptive power relative to that of a recognised and well developed technique. Some recognised temporal and structural problems of system event modelling are identified. and ICE solutions given. The growing research area of ATM communication networks is introduced and a sophisticated top down model of an ATM switch presented. This model is simulated and interesting results are given. A generic ICE framework for performability modelling is developed and demonstrated. This is considered as a positive contribution to the general field of performability research