@misc{AzumaKuekenshoenerMaetal.2014, author = {Azuma, Yusuke and K{\"u}kensh{\"o}ner, Tim and Ma, Guangyong and Yasunaga, Jun-ichiro and Imanishi, Miki and Tanaka, Gen and Nakase, Ikuhiko and Maruno, Takahiro and Kobayashi, Yuji and Arndt, Katja Maren and Matsuoka, Masao and Futaki, Shiroh}, title = {Controlling leucine-zipper partner recognition in cells through modification of a-g interactions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-98758}, pages = {4}, year = {2014}, abstract = {By focusing on the a-g interactions, successful design and selection were accomplished to obtain a leucine-zipper segment that discriminates the appropriate partner over another that provides very similar patterns of electrostatic interactions.}, language = {en} } @misc{PlehnMegowMay2014, author = {Plehn, Thomas and Megow, J{\"o}rg and May, Volkhard}, title = {Concerted charge and energy transfer processes in a highly flexible fullerene-dye system}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-98791}, pages = {10}, year = {2014}, abstract = {Photoinduced excitation energy transfer and accompanying charge separation are elucidated for a supramolecular system of a single fullerene covalently linked to six pyropheophorbide-a dye molecules. Molecular dynamics simulations are performed to gain an atomistic picture of the architecture and the surrounding solvent. Excitation energy transfer among the dye molecules and electron transfer from the excited dyes to the fullerene are described by a mixed quantum-classical version of the F{\"o}rster rate and the semiclassical Marcus rate, respectively. The mean characteristic time of energy redistribution lies in the range of 10 ps, while electron transfer proceeds within 150 ps. In between, on a 20 to 50 ps time-scale, conformational changes take place in the system. This temporal hierarchy of processes guarantees efficient charge separation, if the structure is exposed to a solvent. The fast energy transfer can adopt the dye excitation to the actual conformation. In this sense, the probability to achieve charge separation is large enough since any dominance of unfavorable conformations that exhibit a large dye-fullerene distance is circumvented. And the slow electron transfer may realize an averaging with respect to different conformations. To confirm the reliability of our computations, ensemble measurements on the charge separation dynamics are simulated and a very good agreement with the experimental data is obtained.}, language = {en} } @misc{SchedinaHartmannGrothetal.2014, author = {Schedina, Ina Maria and Hartmann, Stefanie and Groth, Detlef and Schlupp, Ingo and Tiedemann, Ralph}, title = {Comparative analysis of the gonadal transcriptomes of the all-female species Poecilia formosa and its maternal ancestor Poecilia mexicana}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-401420}, pages = {10}, year = {2014}, abstract = {Background The Amazon molly, Poecilia formosa (Teleostei: Poeciliinae) is an unisexual, all-female species. It evolved through the hybridisation of two closely related sexual species and exhibits clonal reproduction by sperm dependent parthenogenesis (or gynogenesis) where the sperm of a parental species is only used to activate embryogenesis of the apomictic, diploid eggs but does not contribute genetic material to the offspring. Here we provide and describe the first de novo assembled transcriptome of the Amazon molly in comparison with its maternal ancestor, the Atlantic molly Poecilia mexicana. The transcriptome data were produced through sequencing of single end libraries (100 bp) with the Illumina sequencing technique. Results 83,504,382 reads for the Amazon molly and 81,625,840 for the Atlantic molly were assembled into 127,283 and 78,961 contigs for the Amazon molly and the Atlantic molly, respectively. 63\% resp. 57\% of the contigs could be annotated with gene ontology terms after sequence similarity comparisons. Furthermore, we were able to identify genes normally involved in reproduction and especially in meiosis also in the transcriptome dataset of the apomictic reproducing Amazon molly. Conclusions We assembled and annotated the transcriptome of a non-model organism, the Amazon molly, without a reference genome (de novo). The obtained dataset is a fundamental resource for future research in functional and expression analysis. Also, the presence of 30 meiosis-specific genes within a species where no meiosis is known to take place is remarkable and raises new questions for future research.}, language = {en} } @misc{KaiserNoackCordieretal.2014, author = {Kaiser, Eurika and Noack, Bernd R. and Cordier, Laurent and Spohn, Andreas and Segond, Marc and Abel, Markus and Daviller, Guillaume and Osth, Jan and Krajnovic, Sinisa and Niven, Robert K.}, title = {Cluster-based reduced-order modelling of a mixing layer}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {605}, issn = {1866-8372}, doi = {10.25932/publishup-41611}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-416113}, pages = {365 -- 414}, year = {2014}, abstract = {We propose a novel cluster-based reduced-order modelling (CROM) strategy for unsteady flows. CROM combines the cluster analysis pioneered in Gunzburger's group (Burkardt, Gunzburger \& Lee, Comput. Meth. Appl. Mech. Engng, vol. 196, 2006a, pp. 337-355) and transition matrix models introduced in fluid dynamics in Eckhardt's group (Schneider, Eckhardt \& Vollmer, Phys. Rev. E, vol. 75, 2007, art. 066313). CROM constitutes a potential alternative to POD models and generalises the Ulam-Galerkin method classically used in dynamical systems to determine a finite-rank approximation of the Perron-Frobenius operator. The proposed strategy processes a time-resolved sequence of flow snapshots in two steps. First, the snapshot data are clustered into a small number of representative states, called centroids, in the state space. These centroids partition the state space in complementary non-overlapping regions (centroidal Voronoi cells). Departing from the standard algorithm, the probabilities of the clusters are determined, and the states are sorted by analysis of the transition matrix. Second, the transitions between the states are dynamically modelled using a Markov process. Physical mechanisms are then distilled by a refined analysis of the Markov process, e. g. using finite-time Lyapunov exponent (FTLE) and entropic methods. This CROM framework is applied to the Lorenz attractor (as illustrative example), to velocity fields of the spatially evolving incompressible mixing layer and the three-dimensional turbulent wake of a bluff body. For these examples, CROM is shown to identify non-trivial quasi-attractors and transition processes in an unsupervised manner. CROM has numerous potential applications for the systematic identification of physical mechanisms of complex dynamics, for comparison of flow evolution models, for the identification of precursors to desirable and undesirable events, and for flow control applications exploiting nonlinear actuation dynamics.}, language = {en} } @misc{HoosLindauerSchaub2014, author = {Hoos, Holger and Lindauer, Marius and Schaub, Torsten H.}, title = {claspfolio 2}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {606}, issn = {1866-8372}, doi = {10.25932/publishup-41612}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-416129}, pages = {17}, year = {2014}, abstract = {Building on the award-winning, portfolio-based ASP solver claspfolio, we present claspfolio 2, a modular and open solver architecture that integrates several different portfolio-based algorithm selection approaches and techniques. The claspfolio 2 solver framework supports various feature generators, solver selection approaches, solver portfolios, as well as solver-schedule-based pre-solving techniques. The default configuration of claspfolio 2 relies on a light-weight version of the ASP solver clasp to generate static and dynamic instance features. The flexible open design of claspfolio 2 is a distinguishing factor even beyond ASP. As such, it provides a unique framework for comparing and combining existing portfolio-based algorithm selection approaches and techniques in a single, unified framework. Taking advantage of this, we conducted an extensive experimental study to assess the impact of different feature sets, selection approaches and base solver portfolios. In addition to gaining substantial insights into the utility of the various approaches and techniques, we identified a default configuration of claspfolio 2 that achieves substantial performance gains not only over clasp's default configuration and the earlier version of claspfolio, but also over manually tuned configurations of clasp.}, language = {en} } @misc{LiuTkachovKomberetal.2014, author = {Liu, W. and Tkachov, R. and Komber, H. and Senkovskyy, V. and Schubert, M. and Wei, Z. and Facchetti, A. and Neher, Dieter and Kiriy, A.}, title = {Chain-growth polycondensation of perylene diimide-based copolymers}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-98724}, pages = {8}, year = {2014}, abstract = {Herein, we report the chain-growth tin-free room temperature polymerization method to synthesize n-type perylene diimide-dithiophene-based conjugated polymers (PPDIT2s) suitable for solar cell and transistor applications. The palladium/electron-rich tri-tert-butylphosphine catalyst is effective to enable the chain-growth polymerization of anion-radical monomer Br-TPDIT-Br/Zn to PPDIT2 with a molecular weight up to Mw ≈ 50 kg mol-1 and moderate polydispersity. This is the second example of the polymerization of unusual anion-radical aromatic complexes formed in a reaction of active Zn and electron-deficient diimide-based aryl halides. As such, the discovered polymerization method is not a specific reactivity feature of the naphthalene-diimide derivatives but is rather a general polymerization tool. This is an important finding, given the significantly higher maximum external quantum efficiency that can be reached with PDI-based copolymers (32-45\%) in all-polymer solar cells compared to NDI-based materials (15-30\%). Our studies revealed that PPDIT2 synthesized by the new method and the previously published polymer prepared by step-growth Stille polycondensation show similar electron mobility and all-polymer solar cell performance. At the same time, the polymerization reported herein has several technological advantages as it proceeds relatively fast at room temperature and does not involve toxic tin-based compounds. Because several chain-growth polymerization reactions are well-suited for the preparation of well-defined multi-functional polymer architectures, the next target is to explore the utility of the discovered polymerization in the synthesis of end-functionalized polymers and block copolymers. Such materials would be helpful to improve the nanoscale morphology of polymer blends in all-polymer solar cells.}, language = {en} } @misc{BechiHerterMcKennaetal.2014, author = {Bechi, Beatrice and Herter, Susanne and McKenna, Shane and Riley, Christopher and Leimk{\"u}hler, Silke and Turner, Nicholas J. and Carnell, Andrew J.}, title = {Catalytic bio-chemo and bio-bio tandem oxidation reactions for amide and carboxylic acid synthesis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-99414}, year = {2014}, abstract = {A catalytic toolbox for three different water-based one-pot cascades to convert aryl alcohols to amides and acids and cyclic amines to lactams, involving combination of oxidative enzymes (monoamine oxidase, xanthine dehydrogenase, galactose oxidase and laccase) and chemical oxidants (TBHP or CuI(cat)/H2O2) at mild temperatures, is presented. Mutually compatible conditions were found to afford products in good to excellent yields.}, language = {en} } @misc{EhlertUngerSaalfrank2014, author = {Ehlert, Christopher and Unger, Wolfgang E. S. and Saalfrank, Peter}, title = {C K-edge NEXAFS spectra of graphene with physical and chemical defects}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-74429}, pages = {14083 -- 14095}, year = {2014}, abstract = {Recently, C K-edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of graphite (HOPG) surfaces have been measured for the pristine material, and for HOPG treated with either bromine or krypton plasmas (Lippitz et al., Surf. Sci., 2013, 611, L1). Changes of the NEXAFS spectra characteristic for physical (krypton) and/or chemical/physical modifications of the surface (bromine) upon plasma treatment were observed. Their molecular origin, however, remained elusive. In this work we study by density functional theory, the effects of selected point and line defects as well as chemical modifications on NEXAFS carbon K-edge spectra of single graphene layers. For Br-treated surfaces, also Br 3d X-ray Photoelectron Spectra (XPS) are simulated by a cluster approach, to identify possible chemical modifications. We observe that some of the defects related to plasma treatment lead to characteristic changes of NEXAFS spectra, similar to those in experiment. Theory provides possible microscopic origins for these changes.}, language = {en} } @misc{Kronauer2014, author = {Kronauer, J{\"o}rg}, title = {Beziehungen am Scheideweg? : Die NSA-Aff{\"a}re und das deutschamerikanische Verh{\"a}ltnis}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-71845}, year = {2014}, abstract = {Enth{\"u}llungen {\"u}ber groß angelegte NSA-Lauschangriffe auf die Bundesrepublik, die auch vor dem Mobiltelefon der Bundeskanzlerin nicht haltmachten, haben mit neuer Intensit{\"a}t nicht nur die Frage nach dem deutsch-amerikanischen Verh{\"a}ltnis auf die Tagesordnung gesetzt. Bedeutet diese Massenspionage, dass Grundrechte in Deutschland von ausw{\"a}rtigen Diensten umstandslos außer Kraft gesetzt werden k{\"o}nnen? Oder ist sie der Vorbote eines aufziehenden Hegemonialkonflikts zwischen der EU und den USA?}, language = {de} } @misc{Germano2014, author = {Germano, Gustavo}, title = {Aus{\^e}ncias Brasil}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-71139}, year = {2014}, abstract = {Von der Milit{\"a}rdiktatur ermordet und spurlos verschwunden - diese Ausstellung greift zur{\"u}ck auf Fotoalben der Familienangeh{\"o}rigen von Brasilianern, die der systematischen Repression, Folter und Verschleppung der brasilianischen Milit{\"a}rdiktatur (1964-1985) zum Opfer gefallen sind: Arbeiter, Stadtguerilleros, Studenten, Akademiker, ganze Familien.}, language = {de} }