@phdthesis{Schroeder2016,
  author    = {Schr{\"o}der, Henning},
  title     = {Ultrafast electron dynamics in Fe(CO)5 and Cr(CO)6},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-94589},
  school      = {Universit{\"a}t Potsdam},
  pages     = {v, 87},
  year      = {2016},
  abstract  = {In this thesis, the two prototype catalysts Fe(CO)₅ and Cr(CO)₆ are investigated with time-resolved photoelectron spectroscopy at a high harmonic setup. In both of these metal carbonyls, a UV photon can induce the dissociation of one or more ligands of the complex. The mechanism of the dissociation has been debated over the last decades. The electronic dynamics of the first dissociation occur on the femtosecond timescale. For the experiment, an existing high harmonic setup was moved to a new location, was extended, and characterized. The modified setup can induce dynamics in gas phase samples with photon energies of 1.55eV, 3.10eV, and 4.65eV. The valence electronic structure of the samples can be probed with photon energies between 20eV and 40eV. The temporal resolution is 111fs to 262fs, depending on the combination of the two photon energies. The electronically excited intermediates of the two complexes, as well as of the reaction product Fe(CO)₄, could be observed with photoelectron spectroscopy in the gas phase for the first time. However, photoelectron spectroscopy gives access only to the final ionic states. Corresponding calculations to simulate these spectra are still in development. The peak energies and their evolution in time with respect to the initiation pump pulse have been determined, these peaks have been assigned based on literature data. The spectra of the two complexes show clear differences. The dynamics have been interpreted with the assumption that the motion of peaks in the spectra relates to the movement of the wave packet in the multidimensional energy landscape. The results largely confirm existing models for the reaction pathways. In both metal carbonyls, this pathway involves a direct excitation of the wave packet to a metal-to-ligand charge transfer state and the subsequent crossing to a dissociative ligand field state. The coupling of the electronic dynamics to the nuclear dynamics could explain the slower dissociation in Fe(CO)₅ as compared to Cr(CO)₆.},
  language  = {en}
}
@phdthesis{Kluge2021,
  author    = {Kluge, Steven},
  title     = {Integration anorganischer F{\"u}llstoffe in Polysulfonmembranen und Auswirkungen auf die Gastransporteigenschaften},
  doi       = {10.25932/publishup-53270},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-532700},
  school      = {Universit{\"a}t Potsdam},
  pages     = {110},
  year      = {2021},
  abstract  = {In der vorliegenden Arbeit wird die Herstellung und Charakterisierung von Mixed-Matrix-Membranen (MMM) f{\"u}r die Gastrennung thematisiert. Dazu wurden verschiedene F{\"u}llstoffe genutzt, um in Verbindung mit dem Membranmaterial Polysulfon MMMs herzustellen. Als F{\"u}llstoffe wurden 3 aktive und 2 passive F{\"u}llstoffe verwendet. Die aktiven F{\"u}llstoffe besaßen Poren{\"o}ffnungen, die in der Lage sind Gase in Abh{\"a}ngigkeit der Molek{\"u}lgr{\"o}ße zu trennen. Daraus folgt ein h{\"o}herer idealer Trennfaktor f{\"u}r bestimmte Gaspaare als in Polysulfon selbst. Aufgrund der durch die Poren gebildeten permanenten Kan{\"a}le in den aktiven F{\"u}llstoffen ergibt sich ein schnellerer Gastransport (Permeabilit{\"a}t) als in Polysulfon. Es handelte sich bei den aktiven F{\"u}llstoffen um den Zeolith SAPO-34 und 2 Chargen eines Zeolitic Imidazolate Framework (ZIF) ZIF-8. Die beiden Chargen ZIF-8 unterschieden sich in ihrer spezifischen Oberfl{\"a}che, was diesen Einfluss speziell in die Untersuchungen zum Gastransport einbeziehen sollte. Bei den passiven F{\"u}llstoffen handelte es sich um ein aminofunktionalisiertes Kieselgel und unpor{\"o}se (dichte) Glask{\"u}gelchen. Das Kieselgel besaß Poren, die zu groß waren, um Gase effektiv zu trennen. Die Glask{\"u}gelchen konnten keine Gastrennung erm{\"o}glichen, da sie keine Poren besaßen. Aus der Literatur ist bekannt, dass die Einbettung von F{\"u}llstoffen oft zu Defekten in MMMs f{\"u}hrt. Ein Ziel dieser Arbeit war es daher die Einbettung zu optimieren. Weiterhin sollte der Gastransport in MMMs dieser Arbeit mit dem in einer unbeladenen Polysulfonmembran verglichen werden. Aufgrund des selektiveren Trennverhaltens der aktiven F{\"u}llstoffe im Vergleich zum Membranmaterial, sollte mit der Einbettung aktiver F{\"u}llstoffe die Trennleistung der MMMs mit steigender F{\"u}llstoffbeladung immer weiter verbessert werden. Um die Eigenschaften der MMMs zu untersuchen, wurden diese mittels Rasterelektronenmikroskop (REM), Gaspermeationsmessungen (GP) und Thermogravimetrischer Analyse gekoppelt mit Massenspektrometrie (TGA-MS) charakterisiert. Untersuchungen am REM konnten eine Verbesserung der Einbettung zeigen, wenn ein polymerer Haftvermittler verwendet wurde. Verglichen wurde die optimierte Einbettung mit der Einbettung ohne Haftvermittler und Ergebnissen aus der Literatur, in der die Verwendung verschiedener Silane als Haftvermittler beschrieben wurde. Trotz der verbesserten Einbettung konnte lediglich bei geringen Beladungen an F{\"u}llstoff (10 und 20 Ma-\% bezogen auf das Membranmaterial) eine geringe Steigerung des idealen Trennfaktors in den MMMs gegen{\"u}ber der unbeladenen Polysulfonmembranen beobachtet werden. Bei h{\"o}heren F{\"u}llstoffbeladungen (30, 40 und 50 Ma-\%) war ein deutlicher Anstieg der Permeabilit{\"a}t bei stark sinkendem idealen Trennfaktor zu beobachten. Mit Hilfe von TGA-MS Messungen konnte dar{\"u}ber hinaus festgestellt werden, dass der verwendete Zeolith SAPO-34 durch Wassermolek{\"u}le blockierte Poren{\"o}ffnungen besaß. Das verhinderte den Gastransport im F{\"u}llstoff, wodurch die Trennleistung des F{\"u}llstoffes nicht ausgenutzt werden konnte. Die F{\"u}llstoffe ZIF-8 (chargenunabh{\"a}ngig) und aminofunktionalisiertes Kieselgel wiesen keine blockierten Poren auf. Dennoch zeigte sich in diesen MMMs keine Verbesserung der Gastrenn- oder Gastransporteigenschaften. MMMs mit dichten Glask{\"u}gelchen als F{\"u}llstoff zeigten dasselbe Gastrenn- und Gastransportverhalten, wie alle MMMs mit den zuvor genannten F{\"u}llstoffen. In dieser Arbeit konnte, trotz optimierter Einbettung anorganischer F{\"u}llstoffe, f{\"u}r MMMs keine Verbesserung der Gastrenn- oder Gastransporteigenschaften nachgewiesen werden. Vielmehr wurde ein Einfluss der F{\"u}llstoffmenge auf die Gastransporteigenschaften in MMMs festgestellt. Die {\"A}nderungen der MMMs gegen{\"u}ber Polysulfon stammen von den Folgen der Einbettung von F{\"u}llstoffen in das Matrixpolymer. Durch die Einbettung werden die Eigenschaften des Matrixpolymers {\"a}ndern, sodass auch der Gastransport beeinflusst wird. Des Weiteren wurde dokumentiert, dass in Abh{\"a}ngigkeit der F{\"u}llstoffbeladung die entstehende Membranstruktur beeinflusst wird. Die Beeinflussung war dabei unabh{\"a}ngig von der F{\"u}llstoffart. Es wurde eine Korrelation zwischen F{\"u}llstoffmenge und ver{\"a}nderter Membranstruktur gefunden.},
  language  = {de}
}
@phdthesis{Schirneck2022,
  author    = {Schirneck, Friedrich Martin},
  title     = {Enumeration algorithms in data profiling},
  doi       = {10.25932/publishup-55672},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-556726},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xiv, 192},
  year      = {2022},
  abstract  = {Data profiling is the extraction of metadata from relational databases. An important class of metadata are multi-column dependencies. They come associated with two computational tasks. The detection problem is to decide whether a dependency of a given type and size holds in a database. The discovery problem instead asks to enumerate all valid dependencies of that type. We investigate the two problems for three types of dependencies: unique column combinations (UCCs), functional dependencies (FDs), and inclusion dependencies (INDs). We first treat the parameterized complexity of the detection variants. We prove that the detection of UCCs and FDs, respectively, is W[2]-complete when parameterized by the size of the dependency. The detection of INDs is shown to be one of the first natural W[3]-complete problems. We further settle the enumeration complexity of the three discovery problems by presenting parsimonious equivalences with well-known enumeration problems. Namely, the discovery of UCCs is equivalent to the famous transversal hypergraph problem of enumerating the hitting sets of a hypergraph. The discovery of FDs is equivalent to the simultaneous enumeration of the hitting sets of multiple input hypergraphs. Finally, the discovery of INDs is shown to be equivalent to enumerating the satisfying assignments of antimonotone, 3-normalized Boolean formulas. In the remainder of the thesis, we design and analyze discovery algorithms for unique column combinations. Since this is as hard as the general transversal hypergraph problem, it is an open question whether the UCCs of a database can be computed in output-polynomial time in the worst case. For the analysis, we therefore focus on instances that are structurally close to databases in practice, most notably, inputs that have small solutions. The equivalence between UCCs and hitting sets transfers the computational hardness, but also allows us to apply ideas from hypergraph theory to data profiling. We devise an discovery algorithm that runs in polynomial space on arbitrary inputs and achieves polynomial delay whenever the maximum size of any minimal UCC is bounded. Central to our approach is the extension problem for minimal hitting sets, that is, to decide for a set of vertices whether they are contained in any minimal solution. We prove that this is yet another problem that is complete for the complexity class W[3], when parameterized by the size of the set that is to be extended. We also give several conditional lower bounds under popular hardness conjectures such as the Strong Exponential Time Hypothesis (SETH). The lower bounds suggest that the running time of our algorithm for the extension problem is close to optimal. We further conduct an empirical analysis of our discovery algorithm on real-world databases to confirm that the hitting set perspective on data profiling has merits also in practice. We show that the resulting enumeration times undercut their theoretical worst-case bounds on practical data, and that the memory consumption of our method is much smaller than that of previous solutions. During the analysis we make two observations about the connection between databases and their corresponding hypergraphs. On the one hand, the hypergraph representations containing all relevant information are usually significantly smaller than the original inputs. On the other hand, obtaining those hypergraphs is the actual bottleneck of any practical application. The latter often takes much longer than enumerating the solutions, which is in stark contrast to the fact that the preprocessing is guaranteed to be polynomial while the enumeration may take exponential time. To make the first observation rigorous, we introduce a maximum-entropy model for non-uniform random hypergraphs and prove that their expected number of minimal hyperedges undergoes a phase transition with respect to the total number of edges. The result also explains why larger databases may have smaller hypergraphs. Motivated by the second observation, we present a new kind of UCC discovery algorithm called Hitting Set Enumeration with Partial Information and Validation (HPIValid). It utilizes the fast enumeration times in practice in order to speed up the computation of the corresponding hypergraph. This way, we sidestep the bottleneck while maintaining the advantages of the hitting set perspective. An exhaustive empirical evaluation shows that HPIValid outperforms the current state of the art in UCC discovery. It is capable of processing databases that were previously out of reach for data profiling.},
  language  = {en}
}
@phdthesis{Derežanin2023,
  author    = {Derežanin, Lorena},
  title     = {Contribution of structural variation to adaptive evolution of mammalian genomes},
  doi       = {10.25932/publishup-59144},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-591443},
  school      = {Universit{\"a}t Potsdam},
  pages     = {188},
  year      = {2023},
  abstract  = {Following the extinction of dinosaurs, the great adaptive radiation of mammals occurred, giving rise to an astonishing ecological and phenotypic diversity of mammalian species. Even closely related species often inhabit vastly different habitats, where they encounter diverse environmental challenges and are exposed to different evolutionary pressures. As a response, mammals evolved various adaptive phenotypes over time, such as morphological, physiological and behavioural ones. Mammalian genomes vary in their content and structure and this variation represents the molecular mechanism for the long-term evolution of phenotypic variation. However, understanding this molecular basis of adaptive phenotypic variation is usually not straightforward. The recent development of sequencing technologies and bioinformatics tools has enabled a better insight into mammalian genomes. Through these advances, it was acknowledged that mammalian genomes differ more, both within and between species, as a consequence of structural variation compared to single-nucleotide differences. Structural variant types investigated in this thesis - such as deletion, duplication, inversion and insertion, represent a change in the structure of the genome, impacting the size, copy number, orientation and content of DNA sequences. Unlike short variants, structural variants can span multiple genes. They can alter gene dosage, and cause notable gene expression differences and subsequently phenotypic differences. Thus, they can lead to a more dramatic effect on the fitness (reproductive success) of individuals, local adaptation of populations and speciation. In this thesis, I investigated and evaluated the potential functional effect of structural variations on the genomes of mustelid species. To detect the genomic regions associated with phenotypic variation I assembled the first reference genome of the tayra (Eira barbara) relying on linked-read sequencing technology to achieve a high level of genome completeness important for reliable structural variant discovery. I then set up a bioinformatics pipeline to conduct a comparative genomic analysis and explore variation between mustelid species living in different environments. I found numerous genes associated with species-specific phenotypes related to diet, body condition and reproduction among others, to be impacted by structural variants. Furthermore, I investigated the effects of artificial selection on structural variants in mice selected for high fertility, increased body mass and high endurance. Through selective breeding of each mouse line, the desired phenotypes have spread within these populations, while maintaining structural variants specific to each line. In comparison to the control line, the litter size has doubled in the fertility lines, individuals in the high body mass lines have become considerably larger, and mice selected for treadmill performance covered substantially more distance. Structural variants were found in higher numbers in these trait-selected lines than in the control line when compared to the mouse reference genome. Moreover, we have found twice as many structural variants spanning protein-coding genes (specific to each line) in trait-selected lines. Several of these variants affect genes associated with selected phenotypic traits. These results imply that structural variation does indeed contribute to the evolution of the selected phenotypes and is heritable. Finally, I suggest a set of critical metrics of genomic data that should be considered for a stringent structural variation analysis as comparative genomic studies strongly rely on the contiguity and completeness of genome assemblies. Because most of the available data used to represent reference genomes of mammalian species is generated using short-read sequencing technologies, we may have incomplete knowledge of genomic features. Therefore, a cautious structural variation analysis is required to minimize the effect of technical constraints. The impact of structural variants on the adaptive evolution of mammalian genomes is slowly gaining more focus but it is still incorporated in only a small number of population studies. In my thesis, I advocate the inclusion of structural variants in studies of genomic diversity for a more comprehensive insight into genomic variation within and between species, and its effect on adaptive evolution.},
  language  = {en}
}