Library

Description: We consider the problem of enforcing a toll on a transportation network with limited inspection resources. We formulate a game theoretic model to optimize the allocation of the inspectors, taking the reaction of the network users into account. The model includes several important aspects for practical operation of the control strategy, such as duty types for the inspectors. In contrast to an existing formulation using flows to describe the users' strategies we choose a path formulation and identify dominated user strategies to significantly reduce the problem size. Computational results suggest that our approach is better suited for practical instances.

Description: The operation of railways gives rise to many fundamental optimization problems. One of these problems is to cover a given set of timetabled trips by a set of rolling stock rotations. This is well known as the Rolling Stock Rotation Problem (RSRP). Most approaches in the literature focus primarily on modeling and minimizing the operational costs. However, an essential aspect for the industrial application is mostly neglected. As the RSRP follows timetabling and line planning, where periodicity is a highly desired property, it is also desired to carry over periodic structures to rolling stock rotations and following operations. We call this complex requirement regularity. Regularity turns out to be of essential interest, especially in the industrial scenarios that we tackle in cooperation with DB Fernverkehr AG. Moreover, regularity in the context of the RSRP has not been investigated thoroughly in the literature so far. We introduce three regularity patterns to tackle this requirement, namely regular trips, regular turns, and regular handouts. We present a two-stage approach in order to optimize all three regularity patterns. At first, we integrate regularity patterns into an integer programming approach for the minimization of the operational cost of rolling stock rotations. Afterwards regular handouts are computed. These handouts present the rotations of the first stage in the most regular way. Our computational results (i.e., rolling stock rotations evaluated by planners of DB Fernverkehr AG) show that the three regularity patterns and our concept are a valuable and, moreover, an essential contribution to rolling stock rotation optimization.

Description: We consider a novel partitioning of the set of non-dominated points for general multi-objective integer programs with $k$ objectives. The set of non-dominated points is partitioned into a set of non-dominated points whose efficient solutions are also efficient for some restricted subproblem with one less objective; the second partition comprises the non-dominated points whose efficient solutions are inefficient for any of the restricted subproblems. We show that the first partition has the nice property that it yields finite rectangular boxes in which the points of the second partition are located.

Description: When estimating a probability density within the empirical Bayes framework, the non-parametric maximum likelihood estimate (NPMLE) usually tends to overfit the data. This issue is usually taken care of by regularization - a penalization term is subtracted from the marginal log-likelihood before the maximization step, so that the estimate favors smooth solutions, resulting in the so-called maximum penalized likelihood estimation (MPLE). The majority of penalizations currently in use are rather arbitrary brute-force solutions, which lack invariance under transformation of the parameters(reparametrization) and measurements. This contradicts the principle that, if the underlying model has several equivalent formulations, the methods of inductive inference should lead to consistent results. Motivated by this principle and using an information-theoretic point of view, we suggest an entropy-based penalization term that guarantees this kind of invariance. The resulting density estimate can be seen as a generalization of reference priors. Using the reference prior as a hyperprior, on the other hand, is argued to be a poor choice for regularization. We also present an insightful connection between the NPMLE, the cross entropy and the principle of minimum discrimination information suggesting another method of inference that contains the doubly-smoothed maximum likelihood estimation as a special case.

Description: We introduce the shortest path problem with crossing costs (SPPCC), a shortest path problem in a directed graph, in which the objective function is the sum of arc weights and crossing costs. The former are independently paid for each arc used by the path, the latter need to be paid every time the path intersects certain sets of arcs, which we call regions. The SPPCC generalizes not only the classical shortest path problem but also variants such as the resource constrained shortest path problem and the minimum label path problem. We use the SPPCC to model the flight trajectory optimization problem with overflight costs. In this paper, we provide a comprehensive analysis of the problem. In particular, we identify efficient exact and approximation algorithms for the cases that are most relevant in practice.

Description: One of the main goals of mathematical modelling in systems medicine related to medical applications is to obtain patient-specific parameterizations and model predictions. In clinical practice, however, the number of available measurements for single patients is usually limited due to time and cost restrictions. This hampers the process of making patient-specific predictions about the outcome of a treatment. On the other hand, data are often available for many patients, in particular if extensive clinical studies have been performed. Therefore, before applying Bayes’ rule separately to the data of each patient (which is typically performed using a non-informative prior), it is meaningful to use empirical Bayes methods in order to construct an informative prior from all available data. We compare the performance of four priors - a non-informative prior and priors chosen by nonparametric maximum likelihood estimation (NPMLE), by maximum penalized lilelihood estimation (MPLE) and by doubly-smoothed maximum likelihood estimation (DS-MLE) - by applying them to a low-dimensional parameter estimation problem in a toy model as well as to a high-dimensional ODE model of the human menstrual cycle, which represents a typical example from systems biology modelling.

Description: We present a coarse-to-fine column generation approach for the workforce scheduling of teams. In addition we present a price-and-branch approach and a new hypergraph formulation for a specific workforce team problem, called the Toll Enforcement Problem.

Description: In this paper, we compare several approaches for the problem of gas network expansions using loops, that is, to build new pipelines in parallel to existing ones. We present different model formulations for the problem of continuous loop expansions as well as discrete loop expansions. We then analyze problem properties, such as the structure and convexity of the underlying feasible regions. The paper concludes with a computational study comparing the continuous and the discrete formulations.

Description: A railway operator creates (rolling stock) rotations in order to have a precise master plan for the operation of a timetable by railway vehicles. A rotation is considered as a cycle that multiply traverses a set of operational days while covering trips of the timetable. As it is well known, the proper creation of rolling stock rotations by, e.g., optimization algorithms is challenging and still a topical research subject. Nevertheless, we study a completely different but strongly related question in this paper, i.e.: How to visualize a rotation? For this purpose, we introduce a basic handout concept, which directly leads to the visualization, i.e., handout of a rotation. In our industrial application at DB Fernverkehr AG, the handout is exactly as important as the rotation itself. Moreover, it turns out that also other European railway operators use exactly the same methodology (but not terminology). Since a rotation can have many handouts of different quality, we show how to compute optimal ones through an integer program (IP) by standard software. In addition, a construction as well as an improvement heuristic are presented. Our computational results show that the heuristics are a very reliable standalone approach to quickly find near-optimal and even optimal handouts. The efficiency of the heuristics is shown via a computational comparison to the IP approach.

Description: In the context of gas transmission in decoupled entry-exit systems, many approaches to determine the network capacity are based on the evaluation of realistic and severe transport situations. In this paper, we review the Reference Point Method, which is an algorithm used in practice to generate a set of scenarios using the so-called transport moment as a measure for severity. We introduce a new algorithm for finding severe transport situations that considers an actual routing of the flow through the network and is designed to handle issues arising from cyclic structures in a more dynamical manner. Further, in order to better approximate the physics of gas, an alternative, potential based flow formulation is proposed. The report concludes with a case study based on data from the benchmark library GasLib.

Description: Modern MIP solvers employ dozens of auxiliary algorithmic components to support the branch-and-bound search in finding and improving primal solutions and in strengthening the dual bound. Typically, all components are tuned to minimize the average running time to prove optimality. In this article, we take a different look at the run of a MIP solver. We argue that the solution process consists of three different phases, namely achieving feasibility, improving the incumbent solution, and proving optimality. We first show that the entire solving process can be improved by adapting the search strategy with respect to the phase-specific aims using different control tunings. Afterwards, we provide criteria to predict the transition between the individual phases and evaluate the performance impact of altering the algorithmic behavior of the MIP solver SCIP at the predicted phase transition points.

Description: Die Grundsätze für den Erwerb überregionaler Lizenzen, die von der Deutschen Forschungsgemeinschaft(DFG) gefördert werden (sog. Allianz-Lizenzen), beinhalten spezifische Regelungen zum Open Access. Damit wird DFG-seitig sichergestellt, dass bei Abschluss von Allianz-Verträgen die inkludierten Inhalte sowohl von Autoren als auch von den lizenznehmenden Einrichtungen unter vorteilhafteren Konditionen gegenüber den üblichen Self Archiving Policies (z.B. Verlagsversion, verkürzte Embargofrist) in Repositorien archiviert und veröffentlicht werden dürfen. Die Erfahrung der seit 2011 getätigten Allianz-Abschlüsse zeigt allerdings, dass der Kreis berechtigter Autorinnen und Autoren und Institutionen eigenständig kaum Gebrauch von ihren hierdurch erhaltenen Open-Access-Rechten macht. Entsprechend liegt ein großer Schatz wissenschaftlicher Literatur bei den Verlagen, der noch zu heben ist. Das bewilligte DFG-Projekt DeepGreen (Ausschreibung „Open-Access-Transformation“ von 2014) zielt darauf ab, die vereinbarten Open-Access-Konditionen der Allianz-Lizenzen auf technischer Ebene komfortabel auszugestalten und, wenn möglich, zu automatisieren, so dass nicht mehr Autorinnen und Autoren oder die hierzu berechtigten Bibliotheken die Publikationen manuell in Open-Access-Repositorien einpflegen müssen, sondern die Verlage selbst zyklisch über definierte Schnittstellen abliefern. Dazu bauen die Projektpartner (Universitätsbibliothek Erlangen-Nürnberg, Universitätsbibliothek TU Berlin, Helmholtz Open Science Koordinationsbüro am Deutschen GeoForschungsZentrum, Bayerische Staatsbibliothek München sowie die Verbünde Bibliotheksverbund Bayern und KooperativerBibliotheksverbund Berlin-Brandenburg) ein Dark Archive namens DeepGreen auf, in das teilnehmende Allianz-Lizenz-Verlage Publikationen und Metadaten einspeisen. DeepGreen soll im Anschluss als Datendrehscheibe für berechtigte Open-Access-Repositorien dienen. Als Pilotpartner konnten die Verlage Karger und SAGE gewonnen werden. Der vorliegende Aufsatz stellt das Projekt und den aktuellen Stand der Arbeiten vor.

Description: In this article, we study compact Mixed-Integer Programming (MIP) models for the Resource-Constrained Project Scheduling Problem (RCPSP). Compared to the classical time-indexed formulation, the size of compact models is strongly polynomial in the number of jobs. In addition to two compact models from the literature, we propose a new compact model. We can show that all three compact models are equivalent by successive linear transformations. For their LP-relaxations, however, we state a full inclusion hierarchy where our new model dominates the previous models in terms of polyhedral strength. Moreover, we reveal a polyhedral relationship to the common time-indexed model. Furthermore, a general class of valid cutting planes for the compact models is introduced and finally all models are evaluated by computational experiments.

Description: The global behavior of dynamical systems can be studied by analyzing the eigenvalues and corresponding eigenfunctions of linear operators associated with the system. Two important operators which are frequently used to gain insight into the system's behavior are the Perron-Frobenius operator and the Koopman operator. Due to the curse of dimensionality, computing the eigenfunctions of high-dimensional systems is in general infeasible. We will propose a tensor-based reformulation of two numerical methods for computing finite-dimensional approximations of the aforementioned infinite-dimensional operators, namely Ulam's method and Extended Dynamic Mode Decomposition (EDMD). The aim of the tensor formulation is to approximate the eigenfunctions by low-rank tensors, potentially resulting in a significant reduction of the time and memory required to solve the resulting eigenvalue problems, provided that such a low-rank tensor decomposition exists. Typically, not all variables of a high-dimensional dynamical system contribute equally to the system's behavior, often the dynamics can be decomposed into slow and fast processes, which is also reflected in the eigenfunctions. Thus, the weak coupling between different variables might be approximated by low-rank tensor cores. We will illustrate the efficiency of the tensor-based formulation of Ulam's method and EDMD using simple stochastic differential equations.

Description: Strong and directionally specific forward scattering from optical nanoantennas is of utmost importance for various applications in the broader context of photovoltaics and integrated light sources. Here, we outline a simple yet powerful design principle to perceive a nanoantenna that provides directional scattering into a higher index substrate based on the interference of multiple electric dipoles. A structural implementation of the electric dipole distribution is possible using plasmonic nanoparticles with a fairly simple geometry, i.e. two coupled rectangular nanoparticles, forming a dimer, on top of a substrate. The key to achieve directionality is to choose a sufficiently large size for the nanoparticles. This promotes the excitation of vertical electric dipole moments due to the bi-anisotropy of the nanoantenna. In turn, asymmetric scattering is obtained by ensuring the appropriate phase relation between the vertical electric dipole moments. The scattering strength and angular spread for an optimized nanoantenna can be shown to be broadband and robust against changes in the incidence angle. The scattering directionality is maintained even for an array configuration of the dimer. It only requires the preferred scattering direction of the isolated nanoantenna not to be prohibited by interference.

Description: Information about the behavior of dynamical systems can often be obtained by analyzing the eigenvalues and corresponding eigenfunctions of linear operators associated with a dynamical system. Examples of such operators are the Perron-Frobenius and the Koopman operator. In this paper, we will review di� fferent methods that have been developed over the last decades to compute � infinite-dimensional approximations of these in� finite-dimensional operators - in particular Ulam's method and Extended Dynamic Mode Decomposition (EDMD) - and highlight the similarities and di� fferences between these approaches. The results will be illustrated using simple stochastic di� fferential equations and molecular dynamics examples.

Description: We present the evaluation of temperature and precipitation forecasts obtained with the MiKlip decadal climate prediction system. These decadal hindcast experiments are verified with respect to the accuracy of the ensemble mean and the ensemble spread as a representative for the forecast uncertainty. The skill assessment follows the verification framework already used by the decadal prediction community, but enhanced with additional evaluation techniques like the logarithmic ensemble spread score. The core of the MiKlip system is the coupled Max Planck Institute Earth System Model. An ensemble of 10 members is initialized annually with ocean and atmosphere reanalyses of the European Centre for Medium-Range Weather Forecasts. For assessing the effect of the initialization, we compare these predictions to uninitialized climate projections with the same model system. Initialization improves the accuracy of temperature and precipitation forecasts in year 1, particularly in the Pacific region. The ensemble spread well represents the forecast uncertainty in lead year 1, except in the tropics. This estimate of prediction skill creates confidence in the respective 2014 forecasts, which depict less precipitation in the tropics and a warming almost everywhere. However, large cooling patterns appear in the Northern Hemisphere, the Pacific South America and the Southern Ocean. Forecasts for 2015 to 2022 show even warmer temperatures than for 2014, especially over the continents. The evaluation of lead years 2 to 9 for temperature shows skill globally with the exception of the eastern Pacific. The ensemble spread can again be used as an estimate of the forecast uncertainty in many regions: It improves over the tropics compared to lead year 1. Due to a reduction of the conditional bias, the decadal predictions of the initialized system gain skill in the accuracy compared to the uninitialized simulations in the lead years 2 to 9. Furthermore, we show that increasing the ensemble size improves the MiKlip decadal climate prediction system for all lead years.

Description: I consider models of operation modes for complex compressor stations (i.e., ones with several in- or outlets) in gas networks. In particular, my aim is to identify from a set of operation modes those that are infeasible or redundant. For this, I investigate optimization and network reduction based procedures. Ultimately, these procedures may be employed for data preprocessing in the context of gas network optimization.

Description: In several inital value problems with particularly expensive right hand side computation, there is a trade-off between accuracy and computational effort in evaluating the right hand sides. We consider inexact spectral deferred correction (SDC) methods for solving such non-stiff initial value problems. SDC methods are interpreted as fixed point iterations and, due to their corrective iterative nature, allow to exploit the accuracy-work-tradeoff for a reduction of the total computational effort. On one hand we derive an error model bounding the total error in terms of the right hand side evaluation errors. On the other hand, we define work models describing the computational effort in terms of the evaluation accuracy. Combining both, a theoretically optimal tolerance selection is worked out by minimizing the total work subject to achieving the requested tolerance.

Description: We revisit the mathematical models for wireless network jamming introduced by Commander et al. (2007,2008): we first point out the strong connections with classical wireless network design and then we propose a new model based on the explicit use of signal-to-interference quantities. Moreover, to ad- dress the uncertain nature of the jamming problem and tackle the peculiar right-hand-side (RHS) uncertainty of the corresponding model, we propose an original robust cutting-plane algorithm drawing inspiration from Multiband Robust Optimization. Finally, we assess the performance of the proposed cutting plane algorithm by experiments on realistic network instances.

Description: We investigate the matching and perfect matching polytopes of hypergraphs having a special structure, which we call partitioned hypergraphs. We show that the integrality gap of the standard LP-relaxation is at most $2\sqrt{d}$ for partitioned hypergraphs with parts of size $\leq d$. Furthermore, we show that this bound cannot be improved to $\mathcal{O}(d^{0.5-\epsilon})$.

Description: Given two hypergraphs, representing a fine and a coarse "layer", and a cycle cover of the nodes of the coarse layer, the cycle embedding problem (CEP) asks for an embedding of the coarse cycles into the fine layer. The CEP is NP-hard for general hypergraphs, but it can be solved in polynomial time for graphs. We propose an integer rogramming formulation for the CEP that provides a complete escription of the CEP polytope for the graphical case. The CEP comes up in railway vehicle rotation scheduling. We present computational results for problem instances of DB Fernverkehr AG that justify a sequential coarse-first-fine-second planning approach.

Description: Optimization-based bound tightening (OBBT) is one of the most effective procedures to reduce variable domains of nonconvex mixed-integer nonlinear programs (MINLPs). At the same time it is one of the most expensive bound tightening procedures, since it solves auxiliary linear programs (LPs)—up to twice the number of variables many. The main goal of this paper is to discuss algorithmic techniques for an efficient implementation of OBBT. Most state-of-the-art MINLP solvers apply some restricted version of OBBT and it seems to be common belief that OBBT is beneficial if only one is able to keep its computational cost under control. To this end, we introduce three techniques to increase the efficiency of OBBT: filtering strategies to reduce the number of solved LPs, ordering heuristics to exploit simplex warm starts, and the generation of Lagrangian variable bounds (LVBs). The propagation of LVBs during tree search is a fast approximation to OBBT without the need to solve auxiliary LPs. We conduct extensive computational experiments on MINLPLib2. Our results indicate that OBBT is most beneficial on hard instances, for which we observe a speedup of 17% to 19% on average. Most importantly, more instances can be solved when using OBBT.

Description: We present the problem of planning mobile tours of inspectors on German motorways to enforce the payment of the toll for heavy good trucks. This is a special type of vehicle routing problem with the objective to conduct as good inspections as possible on the complete network. In addition, we developed a personalized crew rostering model, to schedule the crews of the tours. The planning of daily tours and the rostering are combined in a novel integrated approach and formulated as a complex and large scale Integer Program. The main focus of this paper extends our previous publications on how different requirements for the rostering can be modeled in detail. The second focus is on a bi-criteria analysis of the planning problem to find the balance between the control quality and the roster acceptance. Finally, computational results on real-world instances show the practicability of our method and how different input parameters influence the problem complexity.

Description: We utilize the theory of coherent sets to build Markov state models for non- equilibrium molecular dynamical systems. Unlike for systems in equilibrium, “meta- stable” sets in the non-equilibrium case may move as time evolves. We formalize this concept by relying on the theory of coherent sets, based on this we derive finite-time non-stationary Markov state models, and illustrate the concept and its main differences to equilibrium Markov state modeling on simple, one-dimensional examples.

Description: The problem of allocating operating rooms (OR) to surgical cases is a challenging task, involving both combinatorial aspects and uncertainty handling. We formulate this problem as a parallel machines scheduling problem, in which job durations follow a lognormal distribution, and a fixed assignment of jobs to machines must be computed. We propose a cutting-plane approach to solve the robust counterpart of this optimization problem. To this end, we develop an algorithm based on fixed-point iterations that identifies worst-case scenarios and generates cut inequalities. The main result of this article uses Hilbert's projective geometry to prove the convergence of this procedure under mild conditions. We also propose two exact solution methods for a similar problem, but with a polyhedral uncertainty set, for which only approximation approaches were known. Our model can be extended to balance the load over several planning periods in a rolling horizon. We present extensive numerical experiments for instances based on real data from a major hospital in Berlin. In particular, we find that: (i) our approach performs well compared to a previous model that ignored the distribution of case durations; (ii) compared to an alternative stochastic programming approach, robust optimization yields solutions that are more robust against uncertainty, at a small price in terms of average cost; (iii) the \emph{longest expected processing time first} (LEPT) heuristic performs well and efficiently protects against extreme scenarios, but only if a good prediction model for the durations is available. Finally, we draw a number of managerial implications from these observations.

Description: The Rosetta probe around comet 67P/Churyumov-Gerasimenko (67P) reveals an anisotropic dust distribution of the inner coma with jet-like structures. The physical processes leading to jet formation are under debate, with most models for cometary activity focusing on localised emission sources, such as cliffs or terraced regions. Here we suggest, by correlating high-resolution simulations of the dust environment around 67P with observations, that the anisotropy and the background dust density of 67P originate from dust released across the entire sunlit surface of the nucleus rather than from few isolated sources. We trace back trajectories from coma regions with high local dust density in space to the non-spherical nucleus and identify two mechanisms of jet formation: areas with local concavity in either two dimensions or only one. Pits and craters are examples of the first case, the neck region of the bilobed nucleus of 67P for the latter one. The conjunction of multiple sources in addition to dust released from all other sunlit areas results in a high correlation coefficient (∼0.8) of the predictions with observations during a complete diurnal rotation period of 67P.

Description: Modern CPU architectures require the use of vector instructions to fully exploit the available performance. State-of-the art compilers offer means to automatically vectorize program code. In this thesis these compilers are assessed on test cases and their capabilities to auto\-{}vectorize are evaluated to show strengths and weaknesses of the compilers. Run time measurements and vectorizations are compared to another and recommendations depending on the use case are presented.

Description: Moderne CPU-Architekturen erfordern die Verwendung von Vektorinstruktionen, um die vorhandene Leistung vollständig auszuschöpfen. Aktuelle Compiler bieten Möglichkeiten zur automatischen Vektorisierung von Programmcode. Im Rahmen dieser Arbeit werden an Testfällen verschiedene Compiler auf ihre Fähigkeiten zur Autovektorisierung getestet und evaluiert, um Stärken und Schwächen der jeweiligen Compiler aufzuzeigen. Es werden Laufzeitergebnisse und Vektorisierungsvermögen miteinander verglichen und eine Empfehlung in Abhängigkeit des jeweiligen Anwendungsfalls gegeben.

Description: Viele Kulturinstitutionen nutzen bereits die Möglichkeiten, die ihnen die Digitalisierung und das Internet bieten. Bestände werden digitalisiert und digital aufbereitet, ganze Kunstgattungen gibt es bereits digital. Im heutigen 21. Jahrhundert existieren viele Kultureinrichtungen, wie Museen, Archive und Bibliotheken, bereits seit 100 Jahren oder länger. Doch was ist notwendig, um Institutionen, die vor der Erfindung des Fernsehens etabliert wurden, in der heutigen von Technologien bestimmten Welt bei ihren gesellschaftlichen Aufgaben zu unterstützen? Der vorliegende Text gibt eine Einführung in offene Kulturdaten und zeigt Möglichkeiten auf, wie Kultureinrichtungen von der offenen Bereitstellung ihrer digitalen Bestände profitieren und durch neue Kooperationen kulturinteressierte Menschen stärker an sich binden können. Es wird erklärt, was die Cultural Commons ausmacht und wie Kulturinstitutionen bei der Öffnung ihrer Daten vorgehen können. Um den gesellschaftlichen und institutionellen Wert frei nutzbarer Sammlungsbestände zu verdeutlichen, werden realisierte Projekte basierend auf offenen Kulturdaten im lokalen und internationalen Kontext vorgestellt.

Description: This paper develops a class of meshless methods that are well-suited to statistical inverse problems involving partial differential equations (PDEs). The methods discussed in this paper view the forcing term in the PDE as a random field that induces a probability distribution over the residual error of a symmetric collocation method. This construction enables the solution of challenging inverse problems while accounting, in a rigorous way, for the impact of the discretisation of the forward problem. In particular, this confers robustness to failure of meshless methods, with statistical inferences driven to be more conservative in the presence of significant solver error. In addition, (i) a principled learning-theoretic approach to minimise the impact of solver error is developed, and (ii) the challenging setting of inverse problems with a non-linear forward model is considered. The method is applied to parameter inference problems in which non-negligible solver error must be accounted for in order to draw valid statistical conclusions.

Description: Accurate quantifications of protein–ligand binding affinities by means of in silico methods increasingly gain importance in various scientific branches including toxicology and pharmacology. In silico techniques not only are generally less demanding than laboratory experiments regarding time as well as cost, in particular, if binding assays or synthesis protocols need to be developed in advance. At times, they also provide the only access to risk assessments on novel chemical compounds arising from biotic or abiotic degradation of anthropogenic substances. However, despite the continuous technological and algorithmic progress over the past decades, binding free energy estimations through molecular dynamics simulations still pose an enormous computational challenge owed to the mathematical complexity of solvated macromolecular systems often consisting of hundreds of thousands of atoms. The goals of this thesis can roughly be divided into two categories dealing with different aspects of host–guest binding quantification. On the one side algorithmic strategies for a comprehensive exploration and decomposition of conformational space in conjunction with an automated selection of representative molecular geometries and binding poses have been elaborated providing initial structures for free energy calculations. In light of the dreaded trapping problem typically associated with molecular dynamics simulations, the focus was laid on a particularly systematic generation of representatives covering a broad range of physically accessible molecular conformations and interaction modes. On the other side and ensuing from these input geometries, binding affinity models based on the linear interaction energy (LIE) method have been developed for a couple of (bio)molecular systems. The applications included a successful prediction of the liquid-chromatographic elution order as well as retention times of highly similar hexabromocyclododecane (HBCD) stereoisomers, a novel empirical LIE–QSAR hybrid binding affinity model related to the human estrogen receptor α (ERα), and, finally, the (eco)toxicological prioritization of transformation products originating from the antibiotic sulfamethoxazole with respect to their binding affinities to the bacterial enzyme dihydropteroate synthase. Altogether, a fully automated approach to binding mode and affinity estimation has been presented that is content with an arbitrary geometry of a small molecule under observation and a spatial vector specifying the binding site of a potential target molecule. According to our studies, it is superior to conventional docking and thermodynamic average methods and primarily suggesting binding free energy calculation on the basis of several heavily distinct complex geometries. Both chromatographic retention times of HBCD and binding affinities to ERα yielded squared coefficients of correlation with experimental results significantly higher than 0.8. Approximately 85 % (100 %) of predicted receptor–ligand binding modes deviated less than 1.53 Å (2.05 Å) from available crystallographic structures.

Description: In a wide range of applications, it is desirable to optimally control a system with respect to concurrent, potentially competing goals. This gives rise to a multiobjective optimal control problem where, instead of computing a single optimal solution, the set of optimal compromises, the so-called Pareto set, has to be approximated. When it is not possible to compute the entire control trajectory in advance, for instance due to uncertainties or unforeseeable events, model predictive control methods can be applied to control the system during operation in real time. In this article, we present an algorithm for the solution of multiobjective model predictive control problems. In an offline scenario, it can be used to compute the entire set of optimal compromises whereas in a real time scenario, one optimal compromise is computed according to an operator’s preference. The results are illustrated using the example of an industrial laundry. A logistics model of the laundry is developed and then utilized in the optimization routine. Results are presented for an offline as well as an online scenario

Description: One quarter of Europe's energy demand is provided by natural gas distributed through a vast pipeline network covering the whole of Europe. At a cost of 1 million Euro per km extending the European pipeline network is already a multi-billion Euro business. Therefore, automatic planning tools that support the decision process are desired. Unfortunately, current mathematical methods are not capable of solving the arising network design problems due to their size and complexity. In this article, we will show how to apply optimization methods that can converge to a proven global optimal solution. By introducing a new class of valid inequalities that improve the relaxation of our mixed-integer nonlinear programming model, we are able to speed up the necessary computations substantially.

Description: In Deutschland wurden 2011 wichtige Akzente für die Umsetzung des Grünen Wegs der Open-Access-Bewegung gesetzt: Mit finanzieller Unterstützung der Deutschen Forschungsgemeinschaft (DFG) haben Bibliotheken sogenannte Allianz-Lizenzen mit Verlagen verhandelt, in denen weitreichende Rechte hinsichtlich der Open-Access-Archivierung verankert sind. Autorinnen und Autoren zugriffsberechtigter Einrichtungen können ihre Artikel, die in diesen lizenzierten Zeitschriften erschienen sind, ohne oder mit nur kurzer Embargofrist in geeigneten Repositorien ihrer Wahl frei zugänglich machen. Allerdings macht der Kreis berechtigter Autorinnen und Autoren nur sehr zögerlich von seinen Open-Access-Rechten Gebrauch. Auch die Bibliotheken – als Betreiber der Repositorien und damit Vertreter für die berechtigten Autorinnen und Autoren – nutzen dieses Recht nur unzureichend. Mit DeepGreen verfolgen die Antragssteller das Ziel, einen Großteil jener Publikationen, die unter den speziell im DFG-geförderten Kontext verhandelten Bedingungen grün online gehen dürften, auch tatsächlich online abrufbar zu machen. Im Rahmen des Projektes wird prototypisch mit Allianzverlagen und berechtigten Bibliotheken ein möglichst stark automatisierter Workflow entwickelt, in dem rechtssichere Verlagsdaten inklusive der Volltexte abgeliefert und von Repositorien eingespielt werden. Ein technischer Baustein ist dabei ein intermediäres Repositorium, das als Datenverteiler dient. Das nationale Projektkonsortium besteht aus den zwei Bibliotheksverbünden Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV) und Bibliotheksverbund Bayern (BVB), den zwei Universitätsbibliotheken der Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) und der Technische Universität Berlin (TU Berlin), zusätzlich die Bayerische Staatsbibliothek (BSB) und eine außeruniversitäre Forschungseinrichtung - das Helmholtz Open Science Koordinationsbüro am Deutschen GeoForschungsZentrum (GFZ). Das Projekt startet zum 01. Januar 2016. Hier vorliegend finden Sie den Projektantrag zum Nachlesen.

Description: Real World networks often exhibit a significant number of vertices which are sparsely and irregularly connected to other vertices in the network. For clustering theses networks with a model based algorithm, we propose the Stochastic Block Model with Irrelevant Vertices (SBMIV) for weighted net- works. We propose an original Variational Bayesian Expectation Maximiza- tion inference algorithm for the SBMIV which is an advanced version of our Blockloading algorithm for the Stochastic Block Model. We introduce a model selection criterion for the number of clusters of the SBMIV which is based on the lower variational bound of the model likelihood. We propose a fully Bayesian inference process, based on plausible informative priors, which is independent of other algorithms for preprocessing start values for the cluster assignment of vertices. Our inference methods allow for a multi level identification of irrelevant vertices which are hard to cluster reliably ac- cording to the SBM. We demonstrate that our methods improve on the normal Stochastic Block model by applying it to to Earthquake Networks which are an example of networks with a large number of sparsely and irregularly con- nected vertices.

Description: Bus rapid transit systems in developing and newly industrialized countries often consist of a trunk with a path topology. On this trunk, several overlapping lines are operated which provide direct connections. The demand varies heavily over the day, with morning and afternoon peaks typically in reverse directions. We propose an integer programming model for this problem, derive a structural property of line plans in the static (or single period) ``unimodal demand'' case, and consider approaches to the solution of the multi-period version that rely on clustering the demand into peak and off-peak service periods. An application to the Metrobüs system of Istanbul is discussed.

Description: The introduction of the near-field quantity of optical chirality has emerged in various numerical and few experimental studies of local chirality enhancement due to its relation to the excitation rate of chiral molecules. This time-even pseudoscalar has been dismissed as being a higher-order version of helicity. Nevertheless, we revisit the derivation of the underlying conservation law and define optical chirality in media similar to. We identify the mechanism of chirality conversion by either inhomogeneous or anisotropic space to complement the conservation of optical chirality. The conservation law of optical chirality in arbitrary space enables the extension of the concept of polarization to the near-field where no distiniguished propagation direction of light is present. We show that the connection of electromagnetic energy and optical chirality provide the ability to define a circular polarization basis in time-harmonic near-field analysis. In order to illustrate our theory, we present electromagnetic field simulations of simple as well as more complex nanostructures. Results using the well-known far-field polarization concept are readily reproduced and extended from the point of view of chirality conversion.

Description: Optical 3D simulations in many-query and real-time contexts require new solution strategies. We study an adaptive, error controlled reduced basis method for solving parametrized time-harmonic optical scattering problems. Application fields are, among others, design and optimization problems of nano-optical devices as well as inverse problems for parameter reconstructions occuring e. g. in optical metrology. The reduced basis method presented here relies on a finite element modeling of the scattering problem with parametrization of materials, geometries and sources.

Description: Maxwell solvers based on the hp-adaptive finite element method allow for accurate geometrical modeling and high numerical accuracy. These features are indispensable for the optimization of optical properties or reconstruction of parameters through inverse processes. High computational complexity prohibits the evaluation of the solution for many parameters. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem allowing to compute solutions for a parameter configuration orders of magnitude faster. The RBM allows to evaluate linear and nonlinear outputs of interest like Fourier transform or the enhancement of the electromagnetic field in milliseconds. We apply the RBM to compute light-scattering off two dimensional photonic crystal structures made of silicon and reconstruct geometrical parameters.

Description: Maxwell solvers based on the hp-adaptive finite element method allow for accurate geometrical modeling and high numerical accuracy. These features are indispensable for the optimization of optical properties or reconstruction of parameters through inverse processes. High computational complexity prohibits the evaluation of the solution for many parameters. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem allowing to compute solutions for a parameter configuration orders of magnitude faster. The RBM allows to evaluate linear and nonlinear outputs of interest like Fourier transform or the enhancement of the electromagnetic field in milliseconds. We apply the RBM to compute light-scattering off two dimensional photonic crystal structures made of silicon and reconstruct geometrical parameters.

Description: Fields such as optical metrology and computational lithography require fast and efficient methods for solving the time-harmonic Maxwell’s equation. Highly accurate geometrical modeling and numerical accuracy atcomputational costs are a prerequisite for any simulation study of complex nano-structured photonic devices. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem based on the hp-adaptive finite element solver JCMsuite capable of handling geometric and non-geometric parameter dependencies allowing for online evaluations in milliseconds. We apply the RBM to compute light-scatteringoptical wavelengths off periodic arrays of fin field-effect transistors (FinFETs) where geometrical properties such as the width and height of the fin and gate can vary in a large range.

Description: We summarize the basics and first results of the analyses within our ZIB Bridge Project and give an outlook on further studies broadening the usage of hardware acceleration within the Finite Element Method (FEM) based solution of Maxwell’s equations.

Description: Optical 3D simulations in many-query and real-time contexts require new solution strategies. We study an adaptive, error controlled reduced basis method for solving parametrized time-harmonic optical scattering problems. Application fields are, among others, design and optimization problems of nano-optical devices as well as inverse problems for parameter reconstructions occurring e. g. in optical metrology. The reduced basis method pre- sented here relies on a finite element modeling of the scattering problem with parametrization of materials, geometries and sources.

Description: Fields such as optical metrology and computational lithography require fast and efficient methods for solving the time-harmonic Maxwell's equation. Highly accurate geometrical modelling and numerical accuracy at low computational costs are a prerequisite for any simulation study of complex nano-structured photonic devices. We present a reduced basis method (RBM) for the time-harmonic electromagnetic scattering problem based on the hp-adaptive finite element solver JCMsuite capable of handling geometric and non-geometric parameter dependencies allowing for online evaluations in milliseconds. We apply the RBM to compute light-scattering at optical wavelengths of periodic arrays of fin field-effect transistors (FinFETs) where geometrical properties such as the width and height of the fin and gate can vary in a large range.

Description: Many scientific applications deal with data from a multitude of different sources, e.g., measurements, imaging and simulations. Each source provides an additional perspective on the phenomenon of interest, but also comes with specific limitations, e.g. regarding accuracy, spatial and temporal availability. Effectively combining and analyzing such multimodal and partially incomplete data of limited accuracy in an integrated way is challenging. In this work, we outline an approach for an integrated analysis and visualization of the atmospheric impact of volcano eruptions. The data sets comprise observation and imaging data from satellites as well as results from numerical particle simulations. To analyze the clouds from the volcano eruption in the spatiotemporal domain we apply topological methods. Extremal structures reveal structures in the data that support clustering and comparison. We further discuss the robustness of those methods with respect to different properties of the data and different parameter setups. Finally we outline open challenges for the effective integrated visualization using topological methods.

Description: Biological erosion is a key process for the recycling of carbonate and the formation of calcareous sediments in the oceans. Experimental studies showed that bioerosion is subject to distinct temporal variability, but previous long-term studies were restricted to tropical waters. Here, we present results from a 14-year bioerosion experiment that was carried out along the rocky limestone coast of the island of Rhodes, Greece, in the Eastern Mediterranean Sea, in order to monitor the pace at which bioerosion affects carbonate substrate and the sequence of colonisation by bioeroding organisms. Internal macrobioerosion was visualised and quantified by micro-computed tomography and computer-algorithm-based segmentation procedures. Analysis of internal macrobioerosion traces revealed a dominance of bioeroding sponges producing eight types of characteristic Entobia cavity networks, which were matched to five different clionaid sponges by spicule identification in extracted tissue. The morphology of the entobians strongly varied depending on the species of the producing sponge, its ontogenetic stage, available space, and competition by other bioeroders. An early community developed during the first 5 years of exposure with initially very low macrobioerosion rates and was followed by an intermediate stage when sponges formed large and more diverse entobians and bioerosion rates increased. After 14 years, 30 % of the block volumes were occupied by boring sponges, yielding maximum bioerosion rates of 900 g m^−2 yr^−1. A high spatial variability in macrobioerosion prohibited clear conclusions about the onset of macrobioerosion equilibrium conditions. This highlights the necessity of even longer experimental exposures and higher replication at various factor levels in order to better understand and quantify temporal patterns of macrobioerosion in marine carbonate environments.

Description: The Ammonoidea is a group of extinct cephalopods ideal to study evolution through deep time. The evolution of the planispiral shell and complexly folded septa in ammonoids has been thought to have increased the functional surface area of the chambers permitting enhanced metabolic functions such as: chamber emptying, rate of mineralization and increased growth rates throughout ontogeny. Using nano-computed tomography and synchrotron radiation based micro-computed tomography, we present the first study of ontogenetic changes in surface area to volume ratios in the phragmocone chambers of several phylogenetically distant ammonoids and extant cephalopods. Contrary to the initial hypothesis, ammonoids do not possess a persistently high relative chamber surface area. Instead, the functional surface area of the chambers is higher in earliest ontogeny when compared to Spirula spirula. The higher the functional surface area the quicker the potential emptying rate of the chamber; quicker chamber emptying rates would theoretically permit faster growth. This is supported by the persistently higher siphuncular surface area to chamber volume ratio we collected for the ammonite Amauroceras sp. compared to either S. spirula or nautilids. We demonstrate that the curvature of the surface of the chamber increases with greater septal complexity increasing the potential refilling rates. We further show a unique relationship between ammonoid chamber shape and size that does not exist in S. spirula or nautilids. This view of chamber function also has implications for the evolution of the internal shell of coleoids, relating this event to the decoupling of soft-body growth and shell growth.

Description: The endoskeletons of sharks and rays are composed of an unmineralized cartilaginous core, covered in an outer layer of mineralized tiles called tesserae. The tessellated layer is vital to the growth as well as the material properties of the skeletal element, providing both flexibility and strength. However, characterizing the relationship between tesseral size and shape, and skeletal growth and mechanics is challenging because tesserae are small (a few hundred micrometers wide), anchored to the surrounding tissue in complex three-dimensional ways, and occur in huge numbers. Using a custom-made semi-automatic segmentation algorithm, we present the first quantitative and three-dimensional description of tesserae in micro-CT scans of whole skeletal elements. Our segmentation algorithm relies on aspects we have learned of general tesseral morphology. We exploit the distance map of the mineralized layer to separate individual tiles using a hierarchical watershed algorithm. Additionally, we have developed post-processing techniques to quickly correct segmentation errors. Our data reveals that the tessellation is not regular, with tesserae showing a great range of shapes, sizes and number of neighbors. This is partly region-dependent: for example, thick, columnar tesserae are arranged in series along convex edges with small radius of curvature (RoC), whereas more brick-or disc-shaped tesserae are found in planar areas. We apply our newly developed techniques on the left and right hyomandibula (skeletal elements supporting the jaws) from four different ages of a stingray species, to clarify how tiling patterns develop across ontogeny and differ within and between individuals. We evaluate the functional consequences of tesseral morphologies using finite element analysis and 3d-printing, for a better understanding of shark skeletal mechanics, but also to extract fundamental engineering design principles of tiling arrangements on load-bearing three-dimensional objects.

Description: A framework is proposed for extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance. The minima of the acceleration magnitude, i.e. a superset of the acceleration zeros, are extracted and discriminated into vortices and saddle points --- based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These features are tracked in time with a robust algorithm for tracking features. Thus a space-time hierarchy of the minima is built and vortex merging events are detected. The acceleration feature extraction strategy is applied to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of pressure field and minima of λ2.

Description: SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Rather than using bespoke analog or digital hardware, the basic computational unit of a SpiNNaker system is a general-purpose ARM processor, allowing it to be programmed to simulate a wide variety of neuron and synapse models. This flexibility is particularly valuable in the study of biological plasticity phenomena. A recently proposed learning rule based on the Bayesian Confidence Propagation Neural Network (BCPNN) paradigm offers a generic framework for modeling the interaction of different plasticity mechanisms using spiking neurons. However, it can be computationally expensive to simulate large networks with BCPNN learning since it requires multiple state variables for each synapse, each of which needs to be updated every simulation time-step. We discuss the trade-offs in efficiency and accuracy involved in developing an event-based BCPNN implementation for SpiNNaker based on an analytical solution to the BCPNN equations, and detail the steps taken to fit this within the limited computational and memory resources of the SpiNNaker architecture. We demonstrate this learning rule by learning temporal sequences of neural activity within a recurrent attractor network which we simulate at scales of up to 2.0 × 10^4 neurons and 5.1 × 10^7 plastic synapses: the largest plastic neural network ever to be simulated on neuromorphic hardware. We also run a comparable simulation on a Cray XC-30 supercomputer system and find that, if it is to match the run-time of our SpiNNaker simulation, the super computer system uses approximately 45× more power. This suggests that cheaper, more power efficient neuromorphic systems are becoming useful discovery tools in the study of plasticity in large-scale brain models.

Description: A novel multi-criteria optimization framework for matching of partially visible shapes in multiple images using joint geometric graph embedding is proposed. The proposed framework achieves matching of partial shapes in images that exhibit extreme variations in scale, orientation, viewpoint and illumination and also instances of occlusion; conditions which render impractical the use of global contour-based descriptors or local pixel-level features for shape matching. The proposed technique is based on optimization of the embedding distances of geometric features obtained from the eigenspectrum of the joint image graph, coupled with regularization over values of the mean pixel intensity or histogram of oriented gradients. It is shown to obtain successfully the correspondences denoting partial shape similarities as well as correspondences between feature points in the images. A new benchmark dataset is proposed which contains disparate image pairs with extremely challenging variations in viewing conditions when compared to an existing dataset [18]. The proposed technique is shown to significantly outperform several state-of-the-art partial shape matching techniques on both datasets.

Description: ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wave function, as well as several grid-independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by user-written modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT offers routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is open-source under GNU-LGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations.