Showing papers by "Technical University of Berlin published in 2005"

Numerical solution of saddle point problems

Abstract: Large linear systems of saddle point type arise in a wide variety of applications throughout computational science and engineering. Due to their indefiniteness and often poor spectral properties, such linear systems represent a significant challenge for solver developers. In recent years there has been a surge of interest in saddle point problems, and numerous solution techniques have been proposed for this type of system. The aim of this paper is to present and discuss a large selection of solution methods for linear systems in saddle point form, with an emphasis on iterative methods for large and sparse problems.

A database of German emotional speech.

Abstract: The article describes a database of emotional speech. Ten actors (5 female and 5 male) simulated the emotions, producing 10 German utterances (5 short and 5 longer sentences) which could be used in everyday communication and are interpretable in all applied emotions. The recordings were taken in an anechoic chamber with high-quality recording equipment. In addition to the sound electro-glottograms were recorded. The speech material comprises about 800 sentences (seven emotions * ten actors * ten sentences + some second versions). The complete database was evaluated in a perception test regarding the recognisability of emotions and their naturalness. Utterances recognised better than 80% and judged as natural by more than 60% of the listeners were phonetically labelled in a narrow transcription with special markers for voice-quality, phonatory and articulatory settings and articulatory features. The database can be accessed by the public via the internet (http://www.expressive-speech.net/emodb/).

Towards complete cofactor arrangement in the 3.0 Å resolution structure of photosystem II

Abstract: Oxygenic photosynthesis in plants, algae and cyanobacteria is initiated at photosystem II, a homodimeric multisubunit protein-cofactor complex embedded in the thylakoid membrane. Photosystem II captures sunlight and powers the unique photo-induced oxidation of water to atmospheric oxygen. Crystallographic investigations of cyanobacterial photosystem II have provided several medium-resolution structures (3.8 to 3.2 A) that explain the general arrangement of the protein matrix and cofactors, but do not give a full picture of the complex. Here we describe the most complete cyanobacterial photosystem II structure obtained so far, showing locations of and interactions between 20 protein subunits and 77 cofactors per monomer. Assignment of 11 beta-carotenes yields insights into electron and energy transfer and photo-protection mechanisms in the reaction centre and antenna subunits. The high number of 14 integrally bound lipids reflects the structural and functional importance of these molecules for flexibility within and assembly of photosystem II. A lipophilic pathway is proposed for the diffusion of secondary plastoquinone that transfers redox equivalents from photosystem II to the photosynthetic chain. The structure provides information about the Mn4Ca cluster, where oxidation of water takes place. Our study uncovers near-atomic details necessary to understand the processes that convert light to chemical energy.

Overview and recent advances in partial least squares

Abstract: Partial Least Squares (PLS) is a wide class of methods for modeling relations between sets of observed variables by means of latent variables. It comprises of regression and classification tasks as well as dimension reduction techniques and modeling tools. The underlying assumption of all PLS methods is that the observed data is generated by a system or process which is driven by a small number of latent (not directly observed or measured) variables. Projections of the observed data to its latent structure by means of PLS was developed by Herman Wold and coworkers [48,49,52].

Selected Topics in Column Generation

Abstract: Dantzig-Wolfe decomposition and column generation, devised for linear programs, is a success story in large-scale integer programming. We outline and relate the approaches, and survey mainly recent contributions, not yet found in textbooks. We emphasize the growing understanding of the dual point of view, which has brought considerable progress to the column generation theory and practice. It stimulated careful initializations, sophisticated solution techniques for the restricted master problem and subproblem, as well as better overall performance. Thus, the dual perspective is an ever recurring concept in our "selected topics."

Tuning genetic control through promoter engineering

Abstract: Gene function is typically evaluated by sampling the continuum of gene expression at only a few discrete points corresponding to gene knockout or overexpression. We argue that this characterization is incomplete and present a library of engineered promoters of varying strengths obtained through mutagenesis of a constitutive promoter. A multifaceted characterization of the library, especially at the single-cell level to ensure homogeneity, permitted quantitative assessment correlating the effect of gene expression levels to improved growth and product formation phenotypes in Escherichia coli. Integration of these promoters into the chromosome can allow for a quantitative accurate assessment of genetic control. To this end, we used the characterized library of promoters to assess the impact of phosphoenolpyruvate carboxylase levels on growth yield and deoxy-xylulose-P synthase levels on lycopene production. The multifaceted characterization of promoter strength enabled identification of optimal expression levels for ppc and dxs, which maximized the desired phenotype. Additionally, in a strain preengineered to produce lycopene, the response to deoxy-xylulose-P synthase levels was linear at all levels tested, indicative of a rate-limiting step, unlike the parental strain, which exhibited an optimum expression level, illustrating that optimal gene expression levels are variable and dependent on the genetic background of the strain. This promoter library concept is illustrated as being generalizable to eukaryotic organisms (Saccharomyces cerevisiae) and thus constitutes an integral platform for functional genomics, synthetic biology, and metabolic engineering endeavors.

Individual Risk Attitudes: New Evidence from a Large, Representative, Experimentally-Validated Survey

Abstract: This paper presents new evidence on the distribution of risk attitudes in the population, using a novel set of survey questions and a representative sample of roughly 22,000 individuals living in Germany. Using a question that asks about willingness to take risks in general, on an 11-point scale, we find evidence of heterogeneity across individuals, and show that willingness to take risks is negatively related to age and being female, and positively related to height and parental education. We test the behavioral relevance of this survey measure by conducting a complementary field experiment, based on a representative sample of 450 subjects, and find that the general risk question is a good predictor of actual risk-taking behavior. We then use a more standard lottery question to measure risk preferences in our sample of 22,000, and find similar results regarding heterogeneity and determinants of risk preferences, compared to the general risk question. The lottery question also makes it possible to estimate the coefficient of relative risk aversion for each individual in the sample. Using five questions about willingness to take risks in specific domains - car driving, financial matters, sports and leisure, career, and health - the paper also studies the impact of context on risk attitudes, finding a strong but imperfect correlation across contexts. Using data on a collection of risky behaviors from different contexts, including traffic offences, portfolio choice, smoking, occupational choice, participation in sports, and migration, the paper compares the predictive power of all of the risk measures. Strikingly, the general risk question predicts all behaviors whereas the standard lottery measure does not. The best predictor for any specific behavior is typically the corresponding context-specific measure.

Gas-phase catalysis by atomic and cluster metal ions: the ultimate single-site catalysts.

Abstract: Gas-phase experiments with state-of-the-art techniques of mass spectrometry provide detailed insights into numerous elementary processes. The focus of this Review is on elementary reactions of ions that achieve complete catalytic cycles under thermal conditions. The examples chosen cover aspects of catalysis pertinent to areas as diverse as atmospheric chemistry and surface chemistry. We describe how transfer of oxygen atoms, bond activation, and coupling of fragments can be mediated by atomic or cluster metal ions. In some cases truly unexpected analogies of the idealized gas-phase ion catalysis can be drawn with related chemical transformations in solution or the solid state, and so improve our understanding of the intrinsic operation of a practical catalyst at a strictly molecular level.

Wireless Technology in Industrial Networks

Abstract: With the success of wireless technologies in consumer electronics, standard wireless technologies are envisioned for the deployment in industrial environments as well. Industrial applications involving mobile subsystems or just the desire to save cabling make wireless technologies attractive. Nevertheless, these applications often have stringent requirements on reliability and timing. In wired environments, timing and reliability are well catered for by fieldbus systems (which are a mature technology designed to enable communication between digital controllers and the sensors and actuators interfacing to a physical process). When wireless links are included, reliability and timing requirements are significantly more difficult to meet, due to the adverse properties of the radio channels. In this paper, we thus discuss some key issues coming up in wireless fieldbus and wireless industrial communication systems: 1) fundamental problems like achieving timely and reliable transmission despite channel errors; 2) the usage of existing wireless technologies for this specific field of applications; and 3) the creation of hybrid systems in which wireless stations are incorporated into existing wired systems.

The Structure of Goal Contents Across 15 Cultures.

Abstract: The authors investigated the structure of goal contents in a group of 1,854 undergraduates from 15 cultures around the world. Results suggested that the 11 types of goals the authors assessed were consistently organized in a circumplex fashion across the 15 cultures. The circumplex was well described by positioning 2 primary dimensions underlying the goals: intrinsic (e.g., self-acceptance, affiliation) versus extrinsic (e.g., financial success, image) and self-transcendent (e.g., spirituality) versus physical (e.g., hedonism). The circumplex model of goal contents was also quite similar in both wealthier and poorer nations, although there were some slight cross-cultural variations. The relevance of these results for several theories of motivation and personality are discussed.

Physically Based Deformable Models in Computer Graphics.

Abstract: Physically based deformable models have been widely embraced by the Computer Graphics community. Many problems outlined in a previous survey by Gibson and Mirtich [ GM97] have been addressed, thereby making these models interesting and useful for both offline and real-time applications, such as motion pictures and video games. In this paper, we present the most significant contributions of the past decade, which produce such impressive and perceivably realistic animations and simulations: finite element/difference/volume methods, mass-spring systems, meshfree methods, coupled particle systems and reduced deformable models based on modal analysis. For completeness, we also make a connection to the simulation of other continua, such as fluids, gases and melting objects. Since time integration is inherent to all simulated phenomena, the general notion of time discretization is treated separately, while specifics are left to the respective models. Finally, we discuss areas of application, such as elastoplastic deformation and fracture, cloth and hair animation, virtual surgery simulation, interactive entertainment and fluid/smoke animation, and also suggest areas for future research.

A comparison of three-level converters versus two-level converters for low-voltage drives, traction, and utility applications

Abstract: This paper evaluates three-level topologies as alternatives to two-level topologies in converters for low-voltage applications. Topologies, semiconductor losses, filter aspects, part count, initial cost, and life-cycle cost are compared for a grid interface, a conventional drive application, and a high-speed drive application.

Transport inequalities, gradient estimates, entropy and Ricci curvature

Abstract: We present various characterizations of uniform lower bounds for the Ricci curvature of a smooth Riemannian manifold M in terms of convexity properties of the entropy (considered as a function on the space of probability measures on M) as well as in terms of transportation inequalities for volume measures, heat kernels, and Brownian motions and in terms of gradient estimates for the heat semigroup. © 2004 Wiley Periodicals, Inc.

Zinc Oxide Nanoparticles with Defects

Abstract: Zinc oxide in the form of nanoscale materials can be regarded as one of the most important semiconductor oxides at present. However, the question of how chemical defects influence the properties of nanoscale zinc oxide materials has seldom been addressed. In this paper, we report on the introduction of defects into nanoscale ZnO, their comprehensive analysis using a combination of techniques (powder X-ray diffraction (PXRD), X-ray absorption spectroscopy/extended X-ray absorption fine structure (XAS/EXAFS), electron paramagnetic resonance (EPR), magic-angle spinning nuclear magnetic resonance (MAS-NMR), Fourier-transform infrared (FTIR), UV-vis, and photoluminescence (PL) spectroscopies coupled with ab-initio calculations), and the investigation of correlations between the different types of defects. It is seen that defect-rich zinc oxide can be obtained under kinetically controlled conditions of ZnO formation. This is realized by the thermolysis of molecular, organometallic precursors in which ZnO is pre-organized on a molecular scale. It is seen that these precursors form ZnO at low temperatures far from thermodynamic equilibrium. The resulting nanocrystalline ZnO is rich in defects. Depending on conditions, ZnO of high microstructural strain, high content of oxygen vacancies, and particular content of heteroatom impurities can be obtained. It is shown how the mentioned defects influence the electronic properties of the semiconductor nanoparticles.

Exciton binding energies in carbon nanotubes from two-photon photoluminescence

Abstract: Excitonic effects in the linear and nonlinear optical properties of single-walled carbon nanotubes are manifested by photoluminescence excitation experiments and ab initio calculations. One- and two-photon spectra showed a series of exciton states; their energy splitting is the fingerprint of excitonic interactions in carbon nanotubes. By ab initio calculations we determine the energies, wave functions, and symmetries of the excitonic states. Combining experiment and theory we find binding energies of $0.3\char21{}0.4\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ for nanotubes with diameters between 6.8 and $9.0\phantom{\rule{0.3em}{0ex}}\mathrm{\AA{}}$.

Dimension Reduction of Large-Scale Systems

Abstract: In the past decades, model reduction has become an ubiquitous tool in analysis and simulation of dynamical systems, control design, circuit simulation, structural dynamics, CFD, and many other disciplines dealing with complex physical models. The aim of this book is to survey some of the most successful model reduction methods in tutorial style articles and to present benchmark problems from several application areas for testing and comparing existing and new algorithms. As the discussed methods have often been developed in parallel in disconnected application areas, the intention of the mini-workshop in Oberwolfach and its proceedings is to make these ideas available to researchers and practitioners from all these different disciplines.

Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes

Abstract: Dehalococcoides ethenogenes is the only bacterium known to reductively dechlorinate the groundwater pollutants, tetrachloroethene (PCE) and trichloroethene, to ethene. Its 1,469,720-base pair chromosome contains large dynamic duplicated regions and integrated elements. Genes encoding 17 putative reductive dehalogenases, nearly all of which were adjacent to genes for transcription regulators, and five hydrogenase complexes were identified. These findings, plus a limited repertoire of other metabolic modes, indicate that D. ethenogenes is highly evolved to utilize halogenated organic compounds and H2. Diversification of reductive dehalogenase functions appears to have been mediated by recent genetic exchange and amplification. Genome analysis provides insights into the organism's complex nutrient requirements and suggests that an ancestor was a nitrogen-fixing autotroph.

Synchronization is Enhanced in Weighted Complex Networks

Abstract: The propensity for synchronization of complex networks with directed and weighted links is considered. We show that a weighting procedure based upon the global structure of network pathways enhances complete synchronization of identical dynamical units in scale-free networks. Furthermore, we numerically show that very similar conditions hold also for phase synchronization of nonidentical chaotic oscillators.

The need for a pressure-term representation in empirical Galerkin models of incompressible shear flows

Abstract: Low-dimensional empirical Galerkin models are developed for spatially evolving laminar and transitional shear layers, based on a Karhunen–Loeve decomposition of incompressible two- and three-dimensional Navier–Stokes simulations. It is shown that the key to an accurate Galerkin model is a novel analytical pressure-term representation. The effect of the pressure term is elucidated by a modal energy-flow analysis in a mixing layer, which generalizes the framework developed by Rempfer (1991). In convectively unstable shear layers, it is shown in particular that neglecting small energy terms leads to large amplitude errors in the Galerkin model. The effect of the pressure term and small neglected energy flows is very important for a two-dimensional mixing layer, is less pronounced for the three-dimensional analogue, and can be considered as small in an absolutely unstable wake flow.

A Primer in Column Generation

Abstract: We give a didactic introduction to the use of the column generation technique in linear and in particular in integer programming. We touch on both, the relevant basic theory and more advanced ideas which help in solving large scale practical problems. Our discussion includes embedding Dantzig-Wolfe decomposition and Lagrangian relaxation within a branch-and-bound framework, deriving natural branching and cutting rules by means of a so-called compact formulation, and understanding and influencing the behavior of the dual variables during column generation. Most concepts are illustrated via a small example. We close with a discussion of the classical cutting stock problem and some suggestions for further reading.

Radial breathing mode of single-walled carbon nanotubes: Optical transition energies and chiral-index assignment

Abstract: We present a comprehensive study of the chiral-index assignment of carbon nanotubes in aqueous suspensions by resonant Raman scattering of the radial breathing mode. We determine the energies of the first optical transition in metallic tubes and of the second optical transition in semiconducting tubes for more than 50 chiral indices. The assignment is unique and does not depend on empirical parameters. The systematics of the so-called branches in the Kataura plot are discussed; many properties of the tubes are similar for members of the same branch. We show how the radial breathing modes observed in a single Raman spectrum can be easily assigned based on these systematics. In addition, empirical fits provide the energies and radial breathing modes for all metallic and semiconducting nanotubes with diameters between 0.6 and 1.5 nm. We discuss the relation between the frequency of the radial breathing mode and tube diameter. Finally, from the Raman intensities we obtain information on the electron-phonon coupling.

Invariant computations in local cortical networks with balanced excitation and inhibition

Abstract: Cortical computations critically involve local neuronal circuits. The computations are often invariant across a cortical area yet are carried out by networks that can vary widely within an area according to its functional architecture. Here we demonstrate a mechanism by which orientation selectivity is computed invariantly in cat primary visual cortex across an orientation preference map that provides a wide diversity of local circuits. Visually evoked excitatory and inhibitory synaptic conductances are balanced exquisitely in cortical neurons and thus keep the spike response sharply tuned at all map locations. This functional balance derives from spatially isotropic local connectivity of both excitatory and inhibitory cells. Modeling results demonstrate that such covariation is a signature of recurrent rather than purely feed-forward processing and that the observed isotropic local circuit is sufficient to generate invariant spike tuning.

Measuring round trip times to determine the distance between WLAN nodes

Abstract: This publication explores the degree of accuracy to which the propagation delay of WLAN packets can be measured using today's commercial, inexpensive equipment. The aim is to determine the distance between two wireless nodes for location sensing applications. We conducted experiments in which we measured the time difference between sending a data packet and receiving the corresponding immediate acknowledgement. We found the propagation delays correlate closely with distance, having only a measurement error of a few meters. Furthermore, they are more precise than received signal strength indications. To overcome the low time resolution of the given hardware timers, various statistical methods are applied, developed and analyzed. For example, we take advantage of drifting clocks to determine propagation delays that are forty times smaller than the clocks' quantization resolution. Our approach also determines the frequency offset between remote and local crystal clocks.

Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1

Abstract: Dehalococcoides species are strictly anaerobic bacteria, which catabolize many of the most toxic and persistent chlorinated aromatics and aliphatics by reductive dechlorination and are used for in situ bioremediation of contaminated sites. Our sequencing of the complete 1,395,502 base pair genome of Dehalococcoides strain CBDB1 has revealed the presence of 32 reductive-dehalogenase-homologous (rdh) genes, possibly conferring on the bacteria an immense dehalogenating potential. Most rdh genes were associated with genes encoding transcription regulators such as two-component regulatory systems or transcription regulators of the MarR-type. Four new paralog groups of rdh-associated genes without known function were detected. Comparison with the recently sequenced genome of Dehalococcoides ethenogenes strain 195 reveals a high degree of gene context conservation (synteny) but exceptionally high plasticity in all regions containing rdh genes, suggesting that these regions are under intense evolutionary pressure.

Design and comparison of 4.16 kV neutral point clamped, flying capacitor and series connected H-bridge multi-level converters

Abstract: This paper describes the design of a (4-kV, 4.16-MVA) three-level neutral-point-clamped-, three-level flying-capacitor-, four-level flying-capacitor-, and nine-level seriesconnected H-bridge voltage-source converter on the basis of state-of-the-art 6.5-, 4.5-, 3.3- and 1.7-kV insulated gate bipolar transistors. The semiconductor loss distribution and the design of semiconductors and passive components are compared for a medium switching frequency assuming a constant converter efficiency of about 99%. To evaluate the converter characteristics in high switching frequency applications, a second comparison is realized for the maximum switching frequencies assuming a constant expense of semiconductors in all converters.

Risk-sensitive reinforcement learning applied to control under constraints

Abstract: In this paper, we consider Markov Decision Processes (MDPs) with error states. Error states are those states entering which is undesirable or dangerous. We define the risk with respect to a policy as the probability of entering such a state when the policy is pursued. We consider the problem of finding good policies whose risk is smaller than some user-specified threshold, and formalize it as a constrained MDP with two criteria. The first criterion corresponds to the value function originally given. We will show that the risk can be formulated as a second criterion function based on a cumulative return, whose definition is independent of the original value function. We present a model free, heuristic reinforcement learning algorithm that aims at finding good deterministic policies. It is based on weighting the original value function and the risk. The weight parameter is adapted in order to find a feasible solution for the constrained problem that has a good performance with respect to the value function. The algorithm was successfully applied to the control of a feed tank with stochastic inflows that lies upstream of a distillation column. This control task was originally formulated as an optimal control problem with chance constraints, and it was solved under certain assumptions on the model to obtain an optimal solution. The power of our learning algorithm is that it can be used even when some of these restrictive assumptions are relaxed.