This dissertation is concerned with the potential multistability of protein concentrations in the cell that can arise in biochemical networks. That is, situations where one, or a family of, proteins may sit at one of two or more different steady state concentrations in otherwise identical cells, and in spite of them being in the same environment. Models of multisite protein phosphorylation have shown that this mechanism is able to exhibit unlimited multistability. Nevertheless, these models have not considered enzyme docking, the binding of the enzymes to one or more substrate docking sites, which are separate from the motif that is chemically modified. Enzyme docking is, however, increasingly being recognised as a method to achieve specificity in protein phosphorylation and dephosphorylation cycles. Most models in the literature for these systems are deterministic i.e. based on Ordinary Differential Equations, despite the fact that these are accurate only in the limit of large molecule numbers. For small molecule numbers, a discrete probabilistic, stochastic, approach is more suitable. However, when compared to the tools available in the deterministic framework, the tools available for stochastic analysis offer inadequate visualisation and intuition. We firstly try to bridge that gap, by developing three tools: a) a discrete `nullclines' construct applicable to stochastic systems - an analogue to the ODE nullcines, b) a stochastic tool based on a Weakly Chained Diagonally Dominant M-matrix formulation of the Chemical Master Equation and c) an algorithm that is able to construct non-reversible Markov chains with desired stationary probability distributions. We subsequently prove that, for multisite protein phosphorylation and similar models, in the deterministic domain, enzyme docking and the consequent substrate enzyme-sequestration must inevitably limit the extent of multistability, ultimately to one steady state. In contrast, bimodality can be obtained in the stochastic domain even in situations where bistability is not possible for large molecule numbers. We finally extend our results to cases where we have an autophosphorylating kinase, as for example is the case with $Ca^{2+}$/calmodulin-dependent protein kinase II (CaMKII), a key enzyme in synaptic plasticity.

Thesis (Master of Strategic Studies) -- Army War College, 2006. / Title from title screen (viewed , 2008). "March 8, 2006". "ADA448999"--URL.. Includes bibliographical references. Also issued in paper format.

Thesis (MPhil (Information Science))--University of Stellenbosch, 2006. / The Human Sciences Research Council (HSRC) is South Africa’s statutory research agency dedicated to the social sciences. Information Services (IS) plays a significant role in advancing social science research through the provision of its proactive desk research and its library service. HSRC IS is looking at implementing a library solution that will better serve its users. The existing library system no longer meets the needs of the HSRC Library staff or the research staff. The functionality and efficiency of an ILS is critical to the smooth operation of IS in fulfilling its mandate within the HSRC, i.e. to provide access to information, in an efficient, useful, and timely manner, the focus being on ease of accessibility to a whole range of library and other online resources. The ILS must be able to handle many formats, accommodate searching on the Internet, provide a variety of functions including manipulating electronic data, working with graphics and expediting resource sharing. IS identified the following three ILS solutions, together with their add-on components 1) Innovative Interfaces’ Millennium solution, 2) SIRSI’s Unicorn solution and 3) Ex Libris’s ALEPH solution. The user and system requirements for ILS at the HSRC are sketched. The unique requirements, as well as the requirements the HSRC shares with other research organisations, are pointed out. The three ILS are evaluated against the criteria established. All three the ILS suppliers specialise exclusively in library automation software and have many years of experience in the provision and support of ILS, Innovative Interfaces Inc and Ex Libris for 25 years each and SIRSI for 15 years. Innovative Interfaces Inc has the largest customer base in South Africa. Ex Libris has one academic consortium as a client (CALICO) and some smaller utilisers, while SIRSI is just breaking into the South African market. All three systems comply fully with all the Cataloguing, Serials and Acquisitions modules requirements, that is, the more traditional library functionalities. When it comes to the more ‘non-traditional’ functionalities, such as full-text searching and discussion forum functionality, these systems still fall short. It is either not supported at all, or additional modules or add-ons are required. The various systems requirements are aligned to the current information technology environment at the HSRC. The conclusion is that the actual differences between the systems are few and far between, but that there are some specific requirements and add-on possibilities which makes Millennium the most attractive choice.

This thesis proposes an Ecosystem perspective for the engineering of SoS and CPS and illustrates the impact of this perspective in three areas of contribution category First, from a conceptual and Systems Engineering perspective, a conceptual framework including the Ecosystems of System Unified Language Modeling (EoS-UML) profile, a set of Ecosystem Ensemble Diagrams, the Arms :Length Trust Model and the Cyber Physical Threat Model are provided. Second, having established this conceptual view of the ecosystem, we recognize unique role of the cryptographic credentials within it, towards enabling the ecosystem long-term value proposition and acting as a value transfer agent, implementing careful balance of properties meet stakeholder needs. Third, we propose that the ecosystem computers can be used as a distributed compute engine to run Collaborative Algorithms. To demonstrate, we define access control scheme, risk-balanced Cellular Access Control (rbCAC). The rbCAC algorithm defines access control within a cyber-physical environment in a manner which balances cost, risk, and net utility in a multi-authority setting. rbCAC is demonstrated it in an Air Travel and Border Services scenario. Other domains are also discussed included air traffic control threat prevention from drone identity attacks in protected airspaces. These contributions offer significant material for future development, ongoing credential and ecosystem design, including dynamic perimeters and continuous-time sampling, intelligent and self optimizing ecosystems, runtime collaborative platform design contracts and constraints, and analysis of APT attacks to SCADA systems using ecosystem approaches.

This thesis deals with issue of reliability of real-time embedded systems. Contains a summary of basic concepts related to field in real-time embedded systems and mechanisms for dependability enhancement through redundancy techniques and control flow checking. Describes the implementation of selected control flow checking mechanisms, the technique uses software watchdog timers, use of hardware n-modular redundancy in software environment and technique of process pairs using operating system uC/OS-II. The different mechanisms are validated by method injection of faults into the chosen data structures of system uC/OS-II.

The increasing number of smart systems inevitably leads to a huge number of systems that potentially provide independently designed, autonomously operating services. In near-future smart computing systems, such as smart cities, smart grids or smart mobility, independently developed and heterogeneous services need to be dynamically interconnected in order to develop their full potential in a rather complex collaboration with others. Since the services are developed independently, it is challenging to integrate them on-the-fly at run time. Due to the increasing degree of distribution, such systems operate in a decentralized and volatile environment, where central management is infeasible. Conversely, the increasing computational power of such systems also supersedes the need for central management. The four identified key problems of adaptable, collaborative Smart Service Systems are on-demand composition of complex service structures in decentralized environments, the absence of a comprehensive, serendipity-aware specification, a discontinuity from design-time specification to run-time execution, and the lack of a development methodology that separates the development of a service from that of its role essential to a collaboration. This approach utilizes role-based models, which have a collaborative nature, for automated, on-demand service composition. A rigorous two-phase development methodology is proposed in order to demarcate the development of the services from that of their role essential to a collaboration. Therein, a collaboration designer specifies the collaboration including its abstract functionality using the proposed role-based collaboration specification for Smart Service Systems. Thereof, a partial implementation is derived, which is complemented by services developed in the second phase. The proposed middleware architecture provides run-time support and bridges the gap between design and run time. It implements a protocol for coordinated, role-based composition and adaptation of Smart Service Systems. The approach is quantitatively and qualitatively evaluated by means of a case study and a performance evaluation in order to identify limitations of complex service structures and the trade-off of employing the concept of roles for composition and adaptation of Smart Service Systems.:1 Introduction 1.1 Motivation 1.2 Terminology 1.3 Problem Statement 1.4 Requirements Analysis 1.5 Research Questions and Hypothesis 1.6 Focus and Limitations 1.7 Outline 2 The Role Concept in Computer Science 2.1 What is a Role in Computer Science? 2.2 Roles in RoleDiSCo 3 State of the Art & Related Work 3.1 Role-based Modeling Abstractions for Software Systems 3.1.1 Classification 3.1.2 Approaches 3.1.3 Summary 3.2 Role-based Run-Time Systems 3.2.1 Classification 3.2.2 Approaches 3.2.3 Summary 3.3 Spontaneously Collaborating Run-Time Systems 3.3.1 Classification 3.3.2 Approaches 3.3.3 Summary 3.4 Summary 4 On-Demand Composition and Adaptation of Smart Service Systems 4.1 RoleDiSCo Development Methodology 4.1.1 Role-based Collaboration Specification for Smart Service Systems 4.1.2 Derived Partial Implementation 4.1.3 Player & Context Provision 4.2 RoleDiSCo Middleware Architecture for Smart Service Systems 4.2.1 Infrastructure Abstraction Layer 4.2.2 Context Management 4.2.3 Local Repositories & Knowledge 4.2.4 Discovery 4.2.5 Dispatcher 4.3 Coordinated Composition and Subsequent Adaptation 4.3.1 Initialization and Planning 4.3.2 Composition: Coordinating Subsystem 4.3.3 Composition: Non-Coordinating Subsystem 4.3.4 Competing Collaborations & Negotiation 4.3.5 Subsequent Adaptation 4.3.6 Terminating a Pervasive Collaboration 4.4 Summary 5 Implementing RoleDiSCo 5.1 RoleDiSCo Development Support 5.2 RoleDiSCo Middleware 5.2.1 Infrastructure Abstraction Layer 5.2.2 Knowledge Repositories and Local Class Discovery 5.2.3 Planner 6 Evaluation 6.1 Case Study: Distributed Slideshow 6.1.1 Scenario 6.1.2 Phase 1: Collaboration Design 6.1.3 Phase 2: Player Complementation 6.1.4 Coordinated Composition and Adaptation at Run Time 6.2 Runtime Evaluation 6.2.1 General Testbed Setup and Scenarios 6.2.2 Discovery Time 6.2.3 Composition Time 6.2.4 Discussion 6.3 The ›Role‹ of Roles 6.4 Summary 7 Conclusion 7.1 Summary 7.2 Research Results 7.3 Future Work

Verteilte, Eingebettete Systeme beeinflussen unser tägliches Leben in unzähligen Bereichen. Getrieben durch technologische Weiterentwicklungen und neue Nutzungsprofile nimmt der Vernetzungsgrad elektronischer Geräte rapide zu. Neben einem ausgeprägten Netzwerkcharakter sind aktuelle und zukünftige Anwendungsszenarien wesentlich durch einen hohen Mobilitätsgrad geprägt. Daraus ergeben sich zunehmend Problemstellungen bzgl. geeigneter Kommunikationskonzepte und der hierfür benötigten Energieressourcen. Dieses Buch befasst sich mit Technologien, Konzepten und Protokollen zur energieeffizienten Kommunikation in verteilten, ressourcenbeschränkten Systemen. Es definiert grundlegende Begrifflichkeiten und vermittelt einen umfassenden Einblick in die verschiedenen Forschungsschwerpunkte. Relevante, technologische Entwicklungen der beiden letzten Dekaden werden vorgestellt, thematisch eingeordnet und kritisch analysiert. Anschließend erfolgt die funktional getrennte Betrachtung von Kommunikationsprozessen auf Netzwerk-, Daten- sowie Energiemanagementebene. Darauf aufbauend widmet sich das Buch der Systemintegration und damit einhergehend dem komplexen Systemkonfigurationsprozess. Unter Berücksichtigung applikationsspezifischer Rahmenbedingungen sowie funktionaler Anforderungen werden gezielt geeignete Optimierungsstrategien ausgewählt und in einer ganzheitlich angepassten Systemarchitektur kombiniert. Erst durch das präzise Zusammenspiel von Kommunikationsparadigma, Kommunikationstechnologien und Kommunikationsprotokollen entsteht ein optimiertes Gesamtsystem, welches die zur Verfügung stehenden Ressourcen effizient nutzt. Zur Bewertung kommt ein neu entwickeltes, erweitertes Quantifizierungsmodell zum Einsatz, welches die kommunikativen Aspekte verteilter Applikationsszenarien vollständig einbezieht. Im Rahmen umfangreicher Fallstudien werden ausgewählte Optimierungsverfahren simulativ sowie auf Basis unterschiedlicher Hardwareplattformen evaluiert. Aus den Ergebnissen resultieren qualitative und quantitative Rückschlüsse auf das mögliche Optimierungspotential unter realen Einsatzbedingungen. Die gewonnenen Erkenntnisse dienen als wichtige Richtgrößen für zukünftige Entwicklungen im Bereich eingebetteter, ressourcenbeschränkter Kommunikationssysteme. / Embedded systems are used in almost every domain of our daily lives. Actual research and development activities focus on wireless connected and mobile system architectures. The resulting network topologies represent embedded, distributed systems, which are able to process complex tasks in a collaborative way. Most of the respective hardware platforms are energy self-sufficient with strongly limited resources for data processing, data storage and communication. With focus on the energy resources, communication tasks have a huge impact on the systems power consumption. In order to optimise the energy efficiency of these communication tasks, one key challenge for engineers is the application-specific integration of adapted communication concepts, radio technologies, and protocol stacks into an all-embracing communication architecture. This book critically discusses energy efficiency in distributed, embedded systems with focus on the communication aspects. The first part introduces basic definitions as well as a novel estimation model for quantifying energy efficiency on both local (system) and global (network) layer. In the second part, this book proposes several optimisation approaches for energy-efficient, resource-limited communication systems. This include hardware approaches as well as software approaches to optimise the runtime environment and the data processing tasks. Each approach operates on different abstraction layers within the system architecture. The last part of the book deals with the evaluation of specific optimisation strategies under real-world conditions. The test cases includes simulation scenarios as well as hardware test benches within a heterogeneous network environment. The respective results and analyses represent important guidelines for future developments in field of distributed, embedded communication platforms.

Verteilte, Eingebettete Systeme beeinflussen unser tägliches Leben in unzähligen Bereichen. Getrieben durch technologische Weiterentwicklungen und neue Nutzungsprofile nimmt der Vernetzungsgrad elektronischer Geräte rapide zu. Neben einem ausgeprägten Netzwerkcharakter sind aktuelle und zukünftige Anwendungsszenarien wesentlich durch einen hohen Mobilitätsgrad geprägt. Daraus ergeben sich zunehmend Problemstellungen bzgl. geeigneter Kommunikationskonzepte und der hierfür benötigten Energieressourcen. Dieses Buch befasst sich mit Technologien, Konzepten und Protokollen zur energieeffizienten Kommunikation in verteilten, ressourcenbeschränkten Systemen. Es definiert grundlegende Begrifflichkeiten und vermittelt einen umfassenden Einblick in die verschiedenen Forschungsschwerpunkte. Relevante, technologische Entwicklungen der beiden letzten Dekaden werden vorgestellt, thematisch eingeordnet und kritisch analysiert. Anschließend erfolgt die funktional getrennte Betrachtung von Kommunikationsprozessen auf Netzwerk-, Daten- sowie Energiemanagementebene. Darauf aufbauend widmet sich das Buch der Systemintegration und damit einhergehend dem komplexen Systemkonfigurationsprozess. Unter Berücksichtigung applikationsspezifischer Rahmenbedingungen sowie funktionaler Anforderungen werden gezielt geeignete Optimierungsstrategien ausgewählt und in einer ganzheitlich angepassten Systemarchitektur kombiniert. Erst durch das präzise Zusammenspiel von Kommunikationsparadigma, Kommunikationstechnologien und Kommunikationsprotokollen entsteht ein optimiertes Gesamtsystem, welches die zur Verfügung stehenden Ressourcen effizient nutzt. Zur Bewertung kommt ein neu entwickeltes, erweitertes Quantifizierungsmodell zum Einsatz, welches die kommunikativen Aspekte verteilter Applikationsszenarien vollständig einbezieht. Im Rahmen umfangreicher Fallstudien werden ausgewählte Optimierungsverfahren simulativ sowie auf Basis unterschiedlicher Hardwareplattformen evaluiert. Aus den Ergebnissen resultieren qualitative und quantitative Rückschlüsse auf das mögliche Optimierungspotential unter realen Einsatzbedingungen. Die gewonnenen Erkenntnisse dienen als wichtige Richtgrößen für zukünftige Entwicklungen im Bereich eingebetteter, ressourcenbeschränkter Kommunikationssysteme. / Embedded systems are used in almost every domain of our daily lives. Actual research and development activities focus on wireless connected and mobile system architectures. The resulting network topologies represent embedded, distributed systems, which are able to process complex tasks in a collaborative way. Most of the respective hardware platforms are energy self-sufficient with strongly limited resources for data processing, data storage and communication. With focus on the energy resources, communication tasks have a huge impact on the systems power consumption. In order to optimise the energy efficiency of these communication tasks, one key challenge for engineers is the application-specific integration of adapted communication concepts, radio technologies, and protocol stacks into an all-embracing communication architecture. This book critically discusses energy efficiency in distributed, embedded systems with focus on the communication aspects. The first part introduces basic definitions as well as a novel estimation model for quantifying energy efficiency on both local (system) and global (network) layer. In the second part, this book proposes several optimisation approaches for energy-efficient, resource-limited communication systems. This include hardware approaches as well as software approaches to optimise the runtime environment and the data processing tasks. Each approach operates on different abstraction layers within the system architecture. The last part of the book deals with the evaluation of specific optimisation strategies under real-world conditions. The test cases includes simulation scenarios as well as hardware test benches within a heterogeneous network environment. The respective results and analyses represent important guidelines for future developments in field of distributed, embedded communication platforms.

<p>Predmet istraživanja ove doktorske disertacije je mogućnost uspostavljanja modela Big Data sistema sa pripadajućom softversko &ndash;&nbsp; hardverskom arhitekturom za podr&scaron;ku senzorskim mrežama i IoT uređajima. Razvijeni model počiva na energetsko efikasnim, heterogenim, masovno paralelizovaim SoC hardverskim platformama, uz podr&scaron;ku softverske aplikativne arhitekture (poput OpenCL) za unifikovan rad.<br />Pored aktuelnih hardverskih, softverskih i mrežnih računarskih tehnologija i arhitektura namenjenih za rad podkomponenata modelovanog sistema u radu je predstavljen istorijski osvrt na njihov razvoj. Time je nagla&scaron;ena tendencija cikličnog kretanja koncepcijskih paradigmi računarstva, kroz svojevrstne ere centralizacije &ndash; decentralizacije computinga. U radu su predstavljene tehnologije i metode za ubrzavanje operacija&nbsp; u bazama i skladi&scaron;tima podataka. Istražene su mogućnosti za bolju pripremu Big Data informacionih sistema&nbsp; koji treba da zadovolje potrebe&nbsp; novo najavljene informatičke revolucije op&scaron;te primene računarstva tzv. Ubiquitous computing-a i Interneta stvari (IoT).</p> / <p>The research topic of this doctoral thesis is the possibility of establishing a model for Big Data System with corresponding software-hardware architecture to support sensor networks and IoT devices.&nbsp; The developed model is based on energy efficient, heterogeneous, massively parallelized SoC hardware platforms, with the support of software application architecture. (Such as an open CL) for unified operation.&nbsp; In addition to current hardware, software and network computing technologies, and architecture intended to operate subcomponents of the system modeled in this paper is presented as an historical overview of their development.&nbsp; Which emphasizes the tendency of the cyclic movement of the conceptual paradigm of computing, through the unique era of centralization/decentralization of computing. The thesis presents the technology and methods to accelerate operations in databases and data warehouses. We also investigate the possibilities for a better preparation of Big Data information systems to meet the needs of the newly announced IT revolution in the announced general application of computing called Ubiquitous computing and the Internet of Things (IoT).</p>