As any RNA sequence can be folded in many different ways, there are lots of different possible secondary structures for a given sequence. Most computational prediction methods based on free energy minimization compute a number of suboptimal foldings and we have to identify the native structures among all these possible secondary structures. For this reason, much effort has been made to develop approaches for identifying good predictions of RNA secondary structure. Using the abstract shapes approach as introduced by Giegerich et al., each class of similar secondary structures is represented by one shape and the native structures can be found among the top shape representatives. In this article, we derive some interesting results answering enumeration problems for abstract shapes and secondary structures of RNA. We start by computing symptotical representations for the number of shape representations of length n. Our main goal is to find out how much the search space can be reduced by using the concept of abstract shapes. To reach this goal, we analyze the number of secondary structures and shapes compatible with an RNA sequence of length n under the assumption that base pairing is allowed between arbitrary pairs of bases analytically and compare their exponential growths. Additionally, we analyze the number of secondary structures compatible with an RNA sequence of length n under the assumptions that base pairing is allowed only between certain pairs of bases and that the structures meet some appropriate conditions. The exponential growth factors of the resulting asymptotics are compared to the corresponding experimentally obtained value as given by Giegerich et al.
Guaranteeing correctness of compilation is a ma jor precondition for correct software. Code generation can be one of the most error-prone tasks in a compiler. One way to achieve trusted compilation is certifying compilation. A certifying compiler generates for each run a proof that it has performed the compilation run correctly. The proof is checked in a separate theorem prover. If the theorem prover is content with the proof, one can be sure that the compiler produced correct code. This paper presents a certifying code generation phase for a compiler translating an intermediate language into assembler code. The time spent for checking the proofs is the bottleneck of certifying compilation. We exhibit an improved framework for certifying compilation and considerable advances to overcome this bottleneck. We compare our implementation featuring the Coq theorem prover to an older implementation. Our current implementation is feasible for medium to large sized programs.
Abstraction is intensively used in the verification of large, complex or infinite-state systems. With abstractions getting more complex it is often difficult to see whether they are valid. However, for using abstraction in model checking it has to be ensured that properties are preserved. In this paper, we use a translation validation approach to verify property preservation of system abstractions. We formulate a correctness criterion based on simulation between concrete and abstract system for a property to be verified. For each distinct run of the abstraction procedure the correctness is verified in the theorem prover Isabelle/HOL. This technique is applied in the verification of embedded adaptive systems. This paper is an extended version a previously published work.
The Super-Peer Selection Problem is an optimization problem in network topology construction. It may be cast as a special case of a Hub Location Problem, more exactly an Uncapacitated Single Allocation p-Hub Median Problem with equal weights. We show that this problem is still NP-hard by reduction from Max Clique.
Selbstorganisation ist eine interessante und vielversprechende Möglichkeit, um die Komplexität verteilter Systeme beherrschbar zu machen. In diesem Beitrag schlagen wir ein leistungsfähiges Rechnersystem auf Basis von rekonfigurierbarer Hardware vor, welches aufgrund seiner Flexibilität in vielen Bereichen eingesetzt werden kann. Es wird die geplante Systemarchitektur und Systemsoftware beschrieben und ein intelligentes, verteiltes Kamerasystem vorgestellt, welches wir als Anwendung mit dem vorgeschlagenen System realisieren wollen, um Selbstorganisation in verteilten Systemen näher zu untersuchen.
The provision of network Quality-of-Service (network QoS) in wireless (ad-hoc) networks is a major challenge in the development of future communication systems. Before designing and implementing these systems, the network QoS requirements are to be specified. Since QoS functionalities are integrated across layers and hence QoS specifications exist on different system layers, a QoS mapping technique is needed to translate the specifications into each other. In this paper, we formalize the relationship between layers. Based on a comprehensive and holistic formalization of network QoS requirements, we define two kinds of QoS mappings. QoS domain mappings associate QoS domains of two abstraction levels. QoS scalability mappings associate utility and cost functions of two abstraction levels. We illustrate our approach by examples from the case study Wireless Video Transmission.
The provision of network Quality-of-Service (network QoS) in wireless (ad-hoc) networks is a major challenge in the development of future communication systems. Before designing and implementing these systems, the network QoS requirements are to be specified. Existing approaches to the specification of network QoS requirements are mainly focused on specific domains or individual system layers. In this paper, we present a holistic, comprehensive formalization of network QoS requirements, across layers. QoS requirements are specified on each layer by defining QoS domain, consisting of QoS performance, reliability, and guarantee, and QoS scalability, with utility and cost functions. Furthermore, we derive preorders on multi-dimensional QoS domains, and present criteria to reduce these domains, leading to a manageable subset of QoS values that is sufficient for system design and implementation. We illustrate our approach by examples from the case study Wireless Video Transmission.
Web-based authentication is a popular mechanism implemented by Wireless Internet Service Providers (WISPs) because it allows a simple registration and authentication of customers, while avoiding the high resource requirements of the new IEEE 802.11i security standard and the backward compatibility issues of legacy devices. In this work we demonstrate two different and novel attacks against web-based authentication. One attack exploits operational anomalies of low- and middle-priced devices in order to hijack wireless clients, while the other exploits an already known vulnerability within wired-networks, which in dynamic wireless environments turns out to be even harder to detect and protect against.
Over a period of 30 years, ITU-T’s Specification and Description Language (SDL) has matured to a sophisticated formal modelling language for distributed systems and communication protocols. The language definition of SDL-2000, the latest version of SDL, is complex and difficult to maintain. Full tool support for SDL is costly to implement. Therefore, only subsets of SDL are currently supported by tools. These SDL subsets - called SDL profiles - already cover a wide range of systems, and are often suffcient in practice. In this report, we present our approach for extracting the formal semantics for SDL profiles from the complete SDL semantics. We then formalise the approach, present our SDL-profile tool, and report on our experiences.
This document introduces the extension of Katja to support position structures and explains the subtleties of their application as well as the design decisions made and problems solved with respect to their implementation. The Katja system was first introduced by Jan Schäfer in the context of his project work and is based on the MAX system developed by Arnd Poetzsch-Heffter.