@misc{Rieche2003, type = {Master Thesis}, author = {Rieche, Simon}, title = {Lastbalancierung in Peer-to-Peer Systemen}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10048}, school = {Zuse Institute Berlin (ZIB)}, year = {2003}, abstract = {Peer-to-Peer (P2P) Systeme werden u.a. zur Verwaltung von großen Datenmengen benutzt, die auf verschiedene Rechner verteilt sind. Benutzern soll damit der Zugriff auf Daten innerhalb des Systems leicht erm{\"o}glicht werden. Damit in P2P Systemen die Daten effizient verteilt und gesucht werden k{\"o}nnen, existieren Distributed Hash Tables. Distributed Hash Tables (DHT) sind eine Methode, um globale Informationen persistent speichern zu k{\"o}nnen. Der Wertebereich der Hashfunktion, welche die zu ver{\"o}ffentlichenden Eintr{\"a}ge auf Werte abbildet, wird in Abschnitte aufgeteilt, die einzelnen Knoten zugeteilt werden. Die meisten DHTs haben aber ein Problem bei der Verteilung der Last. Die verschiedenen DHT Systeme beruhen meist auf einem identischen Ansatz der Lastverteilung. Die Last wird nur mit Hilfe einer Hashfunktion verteilt. Es wird davon ausgegangen, dass diese Funktion die Last gleichm{\"a}ßig verteilt. Im Rahmen dieser Arbeit wurde ein Verfahren zur Last Verteilung entwickelt, simuliert und implementiert. Bei dem Verfahren wird die Last wie bei der Verteilung von W{\"a}rme an die Umgebung abgegeben. Es wird mit existierenden Lastbalancierungsalgorithmen verglichen. Mit diesem neuen Verfahren ist es m{\"o}glich, Last in DHTs besser zu verteilen ohne große {\"A}nderungen an den DHTs vorzunehmen. Es wird gezeigt, wie mit dem Verfahren zus{\"a}tzlich die Fehlertoleranz des P2P Systems erh{\"o}ht werden kann.}, language = {de} } @misc{Menne2003, type = {Master Thesis}, author = {Menne, Ulrich}, title = {LP approaches to survivable networks with single path routing}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9989}, school = {Zuse Institute Berlin (ZIB)}, year = {2003}, language = {en} } @misc{Kroeller2003, type = {Master Thesis}, author = {Kr{\"o}ller, Alexander}, title = {Network Optimization: Integration of Hardware Configuration and Capacity Dimensioning}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9952}, school = {Zuse Institute Berlin (ZIB)}, year = {2003}, language = {en} } @misc{Tuchscherer2003, type = {Master Thesis}, author = {Tuchscherer, Andreas}, title = {Dynamical Configuration of Transparent Optical Telecommunication Networks}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10214}, school = {Zuse Institute Berlin (ZIB)}, year = {2003}, abstract = {All-optical telecommunication networks allow for switching connections by lightpaths which can pass several network links without any opto-electronic conversion. Upon arrival of a connection request, it must be decided online, i.e., without knowledge of future requests, if it is accepted and in that case on which lightpaths the connection is routed. This online problem with the goal of maximizing the total profit gained by accepted requests is called Dynamic Singleclass Call Admission Problem (DSCA). We present existing and new algorithms for the DSCA as well as their theoretical and practical evaluation.}, language = {en} } @misc{Orlowski2003, type = {Master Thesis}, author = {Orlowski, Sebastian}, title = {Local and global restoration of node and link failures in telecommunication networks}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10008}, school = {Zuse Institute Berlin (ZIB)}, year = {2003}, abstract = {This diploma thesis deals with the restoration problem in telecommunication networks. The goal is to find a cost minimal capacity capacity assignment on the edges and nodes of a network such that given demands can be satisfied even in case of the failure of an edge or node in the network. Moreover, restrictions on the routing paths (like length restrictions) and hardware constraints have to be satisfied. A Mixed Integer Programming model is presented which takes into account restoration requirements as well as hardware constraints and which abstracts from a particular restoration protocol and failure situation. This abstraction provides new insight into the structure of the network restoration problem and shows that from a mathematical point of view, the commonly used restoration techniques Link Restoration, Path Restoration and Reservation are not as different as they seem to be from a practical point of view. In addition, our model allows (but is not limited to) optimizing working capacity, intended for normal use, and spare capacity, intended for rerouting purposes in case of a failure, in one step. Furthermore, our formulation of capacity cost allows taking into account the effects of discrete, non-linear cost structures which are common in practice. Up to our knowledge, no publication in the existing literature covers all these aspects, let alone in one model, although they are of major practical interest. The model has been implemented in a Branch and Cut framework. The theoretical background of the algorithmic procedure is presented in detail, including computational complexity investigations on the pricing problem. The abstraction from a particular restoration protocol turns out to be useful both from a theoretical and computational point of view. In fact, our investigations suggest a distinction into Local Restoration and Global Restoration rather than into Link Restoration,Path Restoration, Reservation and mixtures of these concepts. In addition to the theoretical aspects of the algorithmic procedure, some implementational details are briefly discussed. Our implementation has been tested on 14 real world instances, which is described in detail. One part of the computational results consists of a comparison of optimal network cost values using diffeent restoration mechanisms, applied to securing either all single node failures, all single edge failures or both. In addition, the effects of a discrete cost structure are investigated, which has rarely been considered yet in literature. Furthermore, the cost ifference between joint and successive working and spare capacity optimization is investigated. In the second part of the computational results, several heuristics for the network restoration problem are compared with respect to both solution quality and time. This diploma thesis deals with the restoration problem in telecommunication networks. The goal is to find a cost minimal capacity capacity assignment on the edges and nodes of a network such that given demands can be satisfied even in case of the failure of an edge or node in the network. Moreover, restrictions on the routing paths (like length restrictions) and hardware constraints have to be satisfied. A Mixed Integer Programming model is presented which takes into account restoration requirements as well as hardware constraints and which abstracts from a particular restoration protocol and failure situation. This abstraction provides new insight into the structure of the network restoration problem and shows that from a mathematical point of view, the commonly used restoration techniques Link Restoration, Path Restoration and Reservation are not as different as they seem to be from a practical point of view. In addition, our model allows (but is not limited to) optimizing working capacity, intended for normal use, and spare capacity, intended for rerouting purposes in case of a failure, in one step. Furthermore, our formulation of capacity cost allows taking into account the effects of discrete, non-linear cost structures which are common in practice. Up to our knowledge, no publication in the existing literature covers all these aspects, let alone in one model, although they are of major practical interest. The model has been implemented in a Branch and Cut framework. The theoretical background of the algorithmic procedure is presented in detail, including computational complexity investigations on the pricing problem. The abstraction from a particular restoration protocol turns out to be useful both from a theoretical and computational point of view. In fact, our investigations suggest a distinction into Local Restoration and Global Restoration rather than into Link Restoration, Path Restoration, Reservation and mixtures of these concepts. In addition to the theoretical aspects of the algorithmic procedure, some implementational details are briefly discussed. Our implementation has been tested on 14 real world instances, which is described in detail. One part of the computational results consists of a comparison of optimal network cost values using different restoration mechanisms, applied to securing either all single node failures, all single edge failures or both. In addition, the effects of a discrete cost structure are investigated, which has rarely been considered yet in literature. Furthermore, the cost difference between joint and successive working and spare capacity optimization is investigated. In the second part of the computational results, several heuristics for the network restoration problem are compared with respect to both solution quality and time.}, language = {en} } @misc{KroellerWessaely2003, author = {Kr{\"o}ller, Alexander and Wess{\"a}ly, Roland}, title = {Integrated Optimization of Hardware Configuration and Capacity. Dimensioning in SDH and opaque WDM networks}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7714}, number = {03-49}, year = {2003}, abstract = {We suggest a new model for the design of telecommunication networks which integrates decisions about the topology, configuration of the switching hardware, link dimensioning, and protected routing of communication demands. Applying the branch-and-cut-algorithm implemented in our network planning and optimization tool DISCNET, we demonstrate that real-world based network planning instances of such an enhanced model can be solved.}, language = {en} } @misc{Koch2003, author = {Koch, Thorsten}, title = {Verteilter Dokumenten-Speicher, Erfahrungen mit den Kluwer-Daten des Friedrich-Althoff-Konsortiums}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7726}, number = {03-50}, year = {2003}, abstract = {Dieser Bericht beschreibt die Erfahrungen und Schlussfolgerungen,die im Rahmen der VDS-Vorstudie bei der Speicherung der vom Friedrich-Althoff-Konsortium lizenzierten Zeitschriften des Kluwer-Verlages gewonnen wurden.}, language = {de} } @misc{Weber2003, author = {Weber, Marcus}, title = {Clustering by using a simplex structure}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7782}, number = {04-03}, year = {2003}, abstract = {In this paper we interpret clustering as a mapping of data into a simplex. If the data itself has simplicial struture this mapping becomes linear. Spectral analysis is an often used tool for clustering data. We will show that corresponding singular vectors or eigenvectors comprise simplicial structure. Therefore they lead to a cluster algorithm, which consists of a simple linear mapping. An example for this kind of algorithms is the Perron cluster analysis (PCCA). We have applied it in practice to identify metastable sets of molecular dynamical systems. In contrast to other algorithms, this kind of approach provides an a priori criterion to determine the number of clusters. In this paper we extend the ideas to more general problems like clustering of bipartite graphs.}, language = {en} } @misc{MayEisenhardtSchmidtEhrenbergetal.2003, author = {May, Andreas and Eisenhardt, Steffen and Schmidt-Ehrenberg, Johannes and Cordes, Frank}, title = {Rigid body docking for Virtual Screening}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7690}, number = {03-47}, year = {2003}, abstract = {A recently developed algorithm allows Rigid Body Docking of ligands to proteins, regardless of the accessibility and location of the binding site. The Docking procedure is divided into three subsequent optimization phases, two of which utilize rigid body dynamics. The last one is applied with the ligand already positioned inside the binding pocket and accounts for full flexibility. Initially, a combination of geometrical and force-field based methods is used as a Coarse Docking strategy, considering only Lennard-Jones interactions between the target and pharmaceutically relevant atoms or functional groups. The protein is subjected to a Hot Spot Analysis, which reveals points of high affinity in the protein environment towards these groups. The hot spots are distributed into different subsets according to their group affiliation. The ligand is described as a complementary point set, consisting of the same subsets. Both sets are matched in \$\mathrm{I\!R}^{3}\$, by superimposing members of the same subsets. In the first instance, steric inhibition is nearly neglected, preventing the system's trajectory from trapping in local minima and thus from finding false positive solutions. Hence the exact location of the binding site can be determined fast and reliably without any additional information. Subsequently, errors resulting from approximations are minimized via finetuning, this time considering both Lennard-Jones and Coulomb forces. Finally, the potential energy of the whole complex is minimized. In a first evaluation, results are rated by a reduced scoring function considering only noncovalent interaction energies. Exemplary Screening results will be given for specific ligands.}, language = {en} } @misc{BoitCordes2003, author = {Boit, Alice and Cordes, Frank}, title = {RNA 3D-Modeling}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7708}, number = {03-48}, year = {2003}, abstract = {This article presents a new computational approach to the three-dimensional (3D) modeling of ribonucleic acid (RNA) sequences with unknown spatial structure. The main concept is a mapping of the query sequence onto the 3D structures of a suitable template RNA molecule. This technique called \textit{threading} has originally been developed for the modeling of protein 3D structures. The application to RNA systems bridges the information gap between the growing mass of RNA sequence data and the relatively limited number of available 3D structures. The new RNA threading method is demonstrated on a tRNA model system because sufficient representative 3D structures have experimentally been elucidated and deposited in the public databases. Nevertheless, the method is in principle transferable on all other RNA species. Algorithms are developed that decompose these template structures into their secondary structure elements and gather this information in a specific template database. The best template is chosen with public alignment and secondary structure prediction tools which are integrated in the RNA modeling module. The structural information gathered from the template and the best alignment is combined to establish a comprehensive 3D model of the query sequence. A range of complete tRNA structures has successfully been modeled with the RNA threading method. The prototype module visualizes the models and provides convenient access to the proposed 3D structures. Therefore, the method could give new insight into a variety of RNA systems which in the recent years have become increasingly important as potential new pharmaceutical agents.}, language = {en} } @misc{DeuflhardChairs2003, author = {Deuflhard, Peter and (Chairs), Hyung Yong Ra}, title = {Korean-German Bilateral Symposium on Scientific Computing}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7778}, number = {04-02}, year = {2003}, abstract = {Collection of abstracts of the Korean-German Bilateral Symposium on Scientific Computing, Berlin January 15/16, 2004}, language = {en} }