Refine
Has Fulltext
- yes (146)
Year of publication
- 2015 (146) (remove)
Document Type
- Doctoral Thesis (146) (remove)
Language
- English (146) (remove)
Keywords
- Topologischer Isolator (8)
- Taufliege (5)
- Krebs <Medizin> (4)
- Quecksilbertellurid (4)
- Drosophila (3)
- Elektronischer Transport (3)
- Ereigniskorreliertes Potenzial (3)
- Exziton (3)
- Femtosekundenspektroskopie (3)
- Festkörperphysik (3)
Institute
- Graduate School of Life Sciences (32)
- Theodor-Boveri-Institut für Biowissenschaften (26)
- Physikalisches Institut (14)
- Institut für Mathematik (13)
- Institut für Pharmazie und Lebensmittelchemie (10)
- Institut für Physikalische und Theoretische Chemie (10)
- Institut für Psychologie (10)
- Institut für Theoretische Physik und Astrophysik (8)
- Institut für Informatik (7)
- Institut für Organische Chemie (6)
Sonstige beteiligte Institutionen
- ATLAS Collaboration (1)
- Adam Opel AG (1)
- CERN (1)
- Deutscher Akademischer Austauschdienst (DAAD) (1)
- Deutsches Zentrum für Luft- und Raumfahrt (DLR), Institut für Raumfahrtsysteme (1)
- Institut für Hygiene und Mikrobiologie (1)
- Instituto de Higiene, Universidad de la República, Montevideo, Uruguay (1)
- König-Ludwig-Haus, Orthopedic Clinic, Würzburg (1)
- Novartis AG (1)
- OTH Regensburg (1)
ResearcherID
- B-1911-2015 (1)
- C-2593-2016 (1)
- N-2030-2015 (1)
- N-3741-2015 (1)
In the present thesis the MBE growth and sample characterization of HgTe structures is investigated
and discussed. Due to the first experimental discovery of the quantum Spin Hall effect
(QSHE) in HgTe quantum wells, this material system attains a huge interest in the spintronics
society. Because of the long history of growing Hg-based heterostructures here at the Experimentelle
Physik III in Würzburg, there are very good requirements to analyze this material
system more precisely and in new directions. Since in former days only doped HgTe quantum
wells were grown, this thesis deals with the MBE growth in the (001) direction of undoped
HgTe quantum wells, surface located quantum wells and three dimensional bulk layers. All
Hg-based layers were grown on CdTe substrates which generate strain in the layer stack and
provide therefore new physical effects. In the same time, the (001) CdTe growth was investigated
on n-doped (001) GaAs:Si because the Japanese supplier of CdTe substrates had a
supply bottleneck due to the Tohoku earthquake and its aftermath in 2011.
After a short introduction of the material system, the experimental techniques were demonstrated
and explained explicitly. After that, the experimental part of this thesis is displayed.
So, the investigation of the (001) CdTe growth on (001) GaAs:Si is discussed in chapter 4.
Firstly, the surface preparation of GaAs:Si by oxide desorption is explored and analyzed.
Here, rapid thermal desorption of the GaAs oxide with following cool down in Zn atmosphere
provides the best results for the CdTe due to small holes at the surface, while e.g. an atomic
flat GaAs buffer deteriorates the CdTe growth quality. The following ZnTe layer supplies the
(001) growth direction of the CdTe and exhibits best end results of the CdTe for 30 seconds
growth time at a flux ratio of Zn/Te ~ 1/1.2. Without this ZnTe layer, CdTe will grow in the
(111) direction. However, the main investigation is here the optimization of the MBE growth
of CdTe. The substrate temperature, Cd/Te flux ratio and the growth time has to be adjusted
systematically. Therefore, a complex growth process is developed and established. This optimized
CdTe growth process results in a RMS roughness of around 2.5 nm and a FWHM value
of the HRXRD w-scan of 150 arcsec. Compared to the literature, there is no lower FWHM
value traceable for this growth direction. Furthermore, etch pit density measurements show
that the surface crystallinity is matchable with the commercial CdTe substrates (around 1x10^4
cm^(-2)). However, this whole process is not completely perfect and offers still room for improvements.
The growth of undoped HgTe quantum wells was also a new direction in research in contrast
to the previous n-doped grown HgTe quantum wells. Here in chapter 5, the goal of very low
carrier densities was achieved and therefore it is now possible to do transport experiments in
the n - and p - region by tuning the gate voltage. To achieve this high sample quality, very precise
growth of symmetric HgTe QWs and their HRXRD characterization is examined. Here,
the quantum well thickness can now determined accurate to under 0.3 nm. Furthermore, the transport analysis of different quantum well thicknesses shows that the carrier density and
mobility increase with rising HgTe layer thickness. However, it is found out that the band
gap of the HgTe QW closes indirectly at a thickness of 11.6 nm. This is caused by the tensile
strained growth on CdTe substrates. Moreover, surface quantum wells are studied. These
quantum wells exhibit no or a very thin HgCdTe cap. Though, oxidization and contamination
of the surface reduces here the carrier mobility immensely and a HgCdTe layer of around 5 nm
provides the pleasing results for transport experiments with superconductors connected to the
topological insulator [119]. A completely new achievement is the realization of MBE growth
of HgTe quantum wells on CdTe/GaAs:Si substrates. This is attended by the optimization of
the CdTe growth on GaAs:Si. It exposes that HgTe quantum wells grown in-situ on optimized
CdTe/GaAs:Si show very nice transport data with clear Hall plateaus, SdH oscillations, low
carrier densities and carrier mobilities up to 500 000 cm^2/Vs. Furthermore, a new oxide etching
process is developed and analyzed which should serve as an alternative to the standard
HCl process which generates volcano defects at some time. However, during the testing time
the result does not differ in Nomarski, HRXRD, AFM and transport measurements. Here,
long-time tests or etching and mounting in nitrogen atmosphere may provide new elaborate
results.
The main focus of this thesis is on the MBE growth and standard characterization of HgTe bulk
layers and is discussed in chapter 6. Due to the tensile strained growth on lattice mismatched
CdTe, HgTe bulk opens up a band gap of around 22 meV at the G-point and exhibits therefore
its topological surface states. The analysis of surface condition, roughness, crystalline quality,
carrier density and mobility via Nomarski, AFM, XPS, HRXRD and transport measurements
is therefore included in this work. Layer thickness dependence of carrier density and mobility
is identified for bulk layer grown directly on CdTe substrates. So, there is no clear correlation
visible between HgTe layer thickness and carrier density or mobility. So, the carrier density is
almost constant around 1x10^11 cm^(-2) at 0 V gate voltage. The carrier mobility of these bulk
samples however scatters between 5 000 and 60 000 cm^2/Vs almost randomly. Further experiments
should be made for a clearer understanding and therefore the avoidance of unusable
bad samples.But, other topological insulator materials show much higher carrier densities and
lower mobility values. For example, Bi2Se3 exhibits just density values around 1019 cm^(-2)
and mobility values clearly below 5000 cm2/Vs. The carrier density however depends much
on lithography and surface treatment after growth. Furthermore, the relaxation behavior and
critical thickness of HgTe grown on CdTe is determined and is in very good agreement with
theoretical prediction (d_c = 155 nm). The embedding of the HgTe bulk layer between HgCdTe
layers created a further huge improvement. Similar to the quantum well structures the carrier
mobility increases immensely while the carrier density levels at around 1x10^11 cm^(-2) at 0
V gate voltage as well. Additionally, the relaxation behavior and critical thickness of these
barrier layers has to be determined. HgCdTe grown on commercial CdTe shows a behavior as
predicted except the critical thickness which is slightly higher than expected (d_c = 850 nm).
Otherwise, the relaxation of HgCdTe grown on CdTe/GaAs:Si occurs in two parts. The layer
is fully strained up to 250 nm. Between 250 nm and 725 nm the HgCdTe film starts to relax
randomly up to 10 %. The relaxation behavior for thicknesses larger than 725 nm occurs than
linearly to the inverse layer thickness. A explanation is given due to rough interface conditions
and crystalline defects of the CdTe/GaAs:Si compared to the commercial CdTe substrate. HRXRD and AFM data support this statement. Another point is that the HgCdTe barriers protect the active HgTe layer and because of the high carrier mobilities the Hall measurements provide new transport data which have to be interpreted more in detail in the future. In addition, HgTe bulk samples show very interesting transport data by gating the sample from the top and the back. It is now possible to manipulate the carrier densities of the top and bottom surface states almost separately. The back gate consisting of the n-doped GaAs substrate and the thick insulating CdTe buffer can tune the carrier density for Delta(n) ~ 3x10^11 cm^(-2). This is sufficient to tune the Fermi energy from the p-type into the n-type region [138].
In this thesis it is shown that strained HgTe bulk layers exhibit superior transport data by embedding between HgCdTe barrier layers. The n-doped GaAs can here serve as a back gate.
Furthermore, MBE growth of high crystalline, undoped HgTe quantum wells shows also new
and extended transport output. Finally, it is notable that due to the investigated CdTe growth
on GaAs the Hg-based heterostructure MBE growth is partially independent from commercial
suppliers.
Identification of human host cell factors involved in \(Staphylococcus\) \(aureus\) 6850 infection
(2015)
Staphylococcus aureus is both a human commensal and a pathogen. 20%-30% of all individuals are permanently or occasionally carriers of S. aureus without any symptoms. In contrast to this, S. aureus can cause life-threatening diseases e.g. endocarditis, osteomyelitis or sepsis. Here, the increase in antibiotic resistances makes it more and more difficult to treat these infections and hence the number of fatalities rises constantly. Since the pharmaceutical industry has no fundamentally new antibiotics in their pipeline, it is essential to better understand the interplay between S. aureus and the human host cell in order to find new, innovative treatment options.
In this study, a RNA interference based whole genome pool screen was performed to identify human proteins, which play a role during S. aureus infections. Since 1,600 invasion and 2,271 cell death linked factors were enriched at least 2 fold, the big challenge was to filter out the important ones. Here, a STRING pathway analysis proved to be the best option. Subsequently, the identified hits were validated with the help of inhibitors and a second, individualised small interfering RNA-based screen.
In the course of this work two important steps were identified, that are critical for host cell death: the first is bacterial invasion, the second phagosomal escape. The second step is obligatory for intracellular bacterial replication and subsequent host cell death. Invasion in turn is determining for all following events. Accordingly, the effect of the identified factors towards these two crucial steps was determined. Under screening conditions, escape was indirectly measured via intracellular replication. Three inhibitors (JNKII, Methyl-beta-cyclodeytrin, 9-Phenantrol) could be identified for the invasion process. In addition, siRNAs targeted against 16 different genes (including CAPN2, CAPN4 and PIK3CG), could significantly reduce bacterial invasion. Seven siRNAs (FPR2, CAPN4, JUN, LYN, HRAS, AKT1, ITGAM) were able to inhibit intracellular replication significantly. Further studies showed that the IP3 receptor inhibitor 2-APB, the calpain inhibitor calpeptin and the proteasome inhibitor MG-132 are able to prevent phagosomal escape and as a consequence intracellular replication and host cell death.
In this context the role of calpains, calcium, the proteasome and the mitochondrial membrane potential was further investigated in cell culture. Here, an antagonistic behaviour of calpain 1 and 2 during bacterial invasion was observed. Intracellular calcium signalling plays a major role, since its inhibition protects host cells from death. Beside this, the loss of mitochondrial membrane potential is characteristic for S. aureus infection but not responsible for host cell death. The reduction of membrane potential can be significantly diminished by the inhibition of the mitochondrial Na+/Ca2+ exchanger.
All together, this work shows that human host cells massively contribute to different steps in S. aureus infection rather than being simply killed by bacterial pore-forming toxins. Various individual host cell factors were identified, which contribute either to invasion or to phagosomal escape and therefore to S. aureus induced cytotoxicity. Finally, several inhibitors of S. aureus infection were identified. One of them, 2-APB, was already tested in a sepsis mouse model and reduced bacterial load of kidneys.
Thus, this study shows valuable evidence for novel treatment options against S. aureus infections, based on the manipulation of host cell signalling cascades.
Pavlovian fear conditioning describes a form of associative learning in which a previously neutral stimulus elicits a conditioned fear response after it has been temporally paired with an aversive consequence. Once acquired, the fear response can be extinguished by repeatedly presenting the former neutral stimulus in the absence of the aversive consequence. Although most patients suffering from anxiety disorders cannot recall a specific conditioned association between a formerly neutral stimulus and the feeling of anxiety, the produced behavioral symptoms, such as avoidance or safety behavior to prevent the anticipated aversive consequence are commonly exhibited in all anxiety disorders. Moreover, there is considerable similarity between the neural structures involved in fear and extinction in the rodent and in the human. Translational research thus contributes to the understanding of neural circuitries involved in the development and maintenance of anxiety disorders, and further provides hypotheses for improvements in treatment strategies aiming at inhibiting the fear response.
Since the failure to appropriately inhibit or extinguish a fear response is a key feature of pathological anxiety, the present preclinical research focuses on the interplay between the amygdala and the medial prefrontal cortex (mPFC) during fear learning with particular regard to the prefrontal recruitment during fear extinction and its recall. By firstly demonstrating an increased mPFC activity over the time course of extinction learning with functional near-infrared spectroscopy, the main study of this dissertation focused on repetitive transcranial magnetic stimulation (rTMS) as brain stimulation technique suitable to enhance extinction learning. Since hypofrontality is assumed to underlie the maintenance of pathological anxiety, rTMS application revealed an increased mPFC activity, which resulted in a decreased fear response on the behavioral level both during extinction learning as well as during the recall of extinction 24 hours later and in the absence of another stimulation. The following attempt to improve the generalization of extinction with rTMS from an extinguished stimulus to a second stimulus which was reinforced but not extinguished was at least partially evidenced. By revealing an increased prefrontal activity to the non-extinguished stimulus, the active and the placebo rTMS condition, however, did not differ on behavioral parameters. These preclinical findings were discussed in the light of genetic and environmental risk factors with special regard to the combination of a risk variant of the neuropeptide S receptor 1 gene polymorphism (NPSR1 rs324981) and anxiety sensitivity. While the protective homozygous AA genotype group showed no correlation with anxiety sensitivity, the NPSR1 T genotype group exhibited an inverse correlation with anxiety sensitivity in the presence of emotionally negative stimuli. In light of other findings assuming a role of the NPSR1 T allele in panic disorder, the revealed hypofrontality was discussed to define a risk group of patients who might particularly benefit from an augmentation of exposure therapy with rTMS.
Taken together, the presented studies support the central role of the prefrontal cortex in fear extinction and suggest the usefulness of rTMS as an augmentation strategy to exposure therapy in order to decrease therapy relapse rates. The combination of rTMS and extinction has been herein evidenced to modulate fear processes in a preclinical approach thereby establishing important implications for the design of future clinical studies.
Aspergillus fumigatus is the most common cause for invasive fungal infections, a disease associated with high mortality in immune-compromised patients. CD1d-restricted invariant Natural Killer T (iNKT) cells compose a small subset of T cells known to impact the immune response towards various infectious pathogens. To investigate the role of human iNKT cells during A. fumigatus infection, we studied their activation as determined by CD69 expression and cytokine production in response to distinct fungal morphotypes in the presence of different CD1d⁺ antigen presenting cells using flow cytometry and multiplex ELISA. Among CD1d⁺ subpopulations, CD1d⁺CD1c⁺ mDCs showed the highest potential to activate iNKT cells on a per cell basis. The presence of A. fumigatus decreased this effect of CD1d⁺CD1c⁺ mDCs on iNKT cells and led to reduced secretion of TNF-α, G-CSF and RANTES. Production of other Th1 and Th2 cytokines was not affected by the fungus, suggesting an immune-modulating function for human iNKT cells during A. fumigatus infection.
In this work, Emilio de’ Cavalieri’s musical sources will serve as a platform in an attempt to overcome the lack of explicit original guidance and guidelines of performance practice of early basso continuo. It will offer a methodology that will allow the unraveling of implicit theory and practice hidden in the music sources themselves. The methodology of this work is based on the fact that Cavalieri’s Rappresentatione di Anima e di Corpo (Rome, 1600) is printed using a unique continuo notation, which is detailed, precise, and coherent—more so than any other contemporaneous printed source. Through thorough investigation of this continuo notation, it will be possible to enrich our practical as well as theoretical knowledge of the early basso continuo. A wide range of evidences will emerge, covering a wide spectrum, from general questions of instrumentation up to the very notes that should be played. Using a special notation for illustration, I will demonstrate how Cavalieri’s basso continuo figuration, when combined with the known rules of counterpoint, is at times equivalent to written-out realizations.
As part of this study, different models of contrapuntal phenomena will be analyzed, mainly in the context of cadences but also in the context of other progressions that deserve to be recognized as formulas. Their theoretical structure will be uncovered as well as their actual application in music and their manner of execution. The prevalence of each phenomenon will be examined in order to distinguish common and recurrent phenomena from rarely-used formulas. In order to do this, and due to problematic historical terminology, it will be necessary to create a set of new terms inspired by Cavalieri’s notation. Those terms will not be solely relevant to Cavalieri’s music; the models were made flexible so that they may prove useful for future discussions or studies of early continuo in general.
Out of the known early basso continuo sources, a “mini-compendium” of practical implications will be extracted in order to exhaust the practical knowledge implicit in them. This endeavor will be concluded with a list of rules and general advice drawn from the sources, but it will also reveal some problematic aspects of these sources.
This endeavor will make it possible to compare the “new” implicit practical information deduced in this study with the explicit known continuo sources, and assess to what extant Cavalieri’s continuo practices illuminate and complement the known knowledge from previously-studied yet opaque sources of basso continuo.
The focus of this dissertation is on Cavalieri’s music, but the findings proposed here will be traced so as to illuminate the broader realm of the early Baroque and the 17th century musical style at large. Finally, this new research about Cavalieri’s music and continuo, along reevaluating of its place among the common continuo sources, calls for redistribution of source materials on the traditional “shelf” of early basso continuo sources.
Summary (English)
I. Human induced global change threatens biodiversity and trophic interactions. Fragmentation is considered as one of the major threats to biodiversity and can cause reduced species richness, population declines, loss of genetic diversity and disruption of trophic interactions such as predation and parasitism. However forest fragmentation effects can be eclectic due to species specific traits. Specialist species with narrower niches or at higher trophic levels may be in danger of extinction whereas generalist species with less specific habitat requirements may even profit from fragmentation. In the tropics, known as “the” terrestrial biodiversity hotspots, even biodiversity inventories are often lacking, especially in forest canopies. Ongoing deforestation and resulting fragmentation in tropical regions are expected to heavily affect ecosystem functions by changes in biodiversity, community compositions and disruption of trophic interactions. It is even less unknown in what extent different global change drivers for example climate change and fragmentation interact. It is unlikely that deforestation will end, so that small secondary forest fragments will be important habitat elements that must be investigated to optimize their potential contribution to biodiversity conservation.
This dissertation aimed to disentangle the effects of forest fragmentation on trap-nesting bee and wasp communities in small secondary forest fragments addressing the following main questions:
1) Are there interactive effects between microclimate and fragmentation on the abundance of bees and wasps, their mortality - and parasitism rates (Chapter II)?
2) How does fragmentation affect bee biodiversity from canopy to the understory with considerations of single species patterns (Chapter III)?
3) How is fragmentation affecting diversity and community composition of different trophic levels between understory and canopy with emphasis on the host-antagonist relation? (Chapter IV).
II. A variety of global change drivers affect biodiversity and trophic interactions. The combined effects of habitat fragmentation and climate change are poorly understood and with ongoing deforestation and agricultural intensification secondary rainforest fragments might contribute to biodiversity conservation and mitigation of climate warming. This chapter investigated the interactive effects of habitat fragmentation and microclimate on the abundance and biotic interactions of trap-nesting bees and wasps in secondary forest fragments in the Northeastern lowlands of Costa Rica.
Habitat area did not affect hymenopteran abundance, parasitism and mortality rates, but tree location- from the forest border to the forest center- influenced all variables. Interactive effects were found such as in the higher mortality rates at interior locations in larger fragments. Mean temperature at edge and interior locations led to significant effects on all tested variables and interactive effects between temperature and tree locations were found. Abundances at interior locations were significantly higher with increasing temperatures. Mortality rates at interior location increased at lower mean temperatures, whereas higher temperatures at edges marginally increased mortality rates. Our results indicate, that edge effects, mediated by altered microclimatic conditions, significantly change biotic interactions of trap-nesting hymenopterans in small secondary fragments.
III. This chapter focusses on the vertical distribution of bees, their parasitism and mortality rates as well as single species patterns in relation to fragment size and edge effects in secondary rainforest remnants.
No size effects on bee abundance, bee diversity and on parasitism- and mortality rates were found. Bees were least abundant at the intermediate height and were most abundant in the understory; whereas the highest diversity was found in the canopy. Tree location had no effect on bee abundance, but on bee diversity since most species were found in the forest interior. The cuckoo bees Aglaomelissa duckei and Coelioxys sp. 1 only partly followed the patterns of their hosts, two Centris species.
Edge effects greatly influenced the bee community, so that the amount of edge habitat in secondary forest fragments will influence the conservation value for bees.
IV. In this section the effects of habitat fragmentation on biodiversity, on community structure of hosts and natural enemies as well as the relation of hosts and antagonists were investigated from the understory to the canopy. The results stress the importance to monitor biodiversity, community composition and trophic interactions from the understory to the canopy. The higher trophic level of the antagonists was found to be more sensitive to fragment size compared to their hosts. Again edge effects were found to be the dominant driver since both host and antagonist richness, as well as community compositions were strongly affected. Ongoing fragmentation and increased amount of edge habitat could favor few abundant disturbance-adapted species over the rare and more diverse forest-adapted species. A positive-density dependent parasitism rate was demonstrated, as well as an increase of the parasitism rate not only with antagonist abundance but also diversity.
Small secondary forest fragments surely can contribute to the conservation of biodiversity and trophic interactions, but increase of edge habitat will have negative consequences on above-ground nesting Hymenoptera, so that important interactions such as pollination, predation and parasitism could be disrupted. Therefore small forest fragments could contribute to biodiversity conservation but will not be able to compensate for the loss of large areas of primary forests.
V. This dissertation contributes to the understanding of habitat area - and edge effects as well as the interaction of those with microclimatic conditions in small secondary rainforest fragments. As study system trap nests inhabited by solitary above-ground nesting bees, wasps and their natural enemies were chosen because they allow to study trophic interactions along their whole vertical distribution from the understory to the canopy. The effect of fragment size was rather weak, however, larger sizes affected the diversity of natural enemies positively, proofing the hypothesis that higher trophic levels react more sensitive to habitat loss. Edge effects heavily affected the abundance, diversity and community composition of hosts and their natural enemies as well as parasitism and mortality rates. Increased edge conditions resulting from ongoing fragmentation and deforestation will therefore negatively affect bees, wasps and their trophic interactions with natural enemies. Those changes affect important processes such as pollination, predation and parasitism, which could result in changes of ecosystem functioning. This study showed the importance to include all strata in biodiversity monitoring since height did matter for the trap-nesting communities. Diversity was shown to be higher in the canopy and community composition did change significantly. To conclude we could show that secondary forest fragments can sustain a trap-nesting bee and wasp community, but the amount of interior habitat is highly important for the conservation of forest-adapted species. Probably the conservation of large primary forest in combination with a high habitat connectivity, for example with small secondary forest fragments, will help to sustain biodiversity and ecosystem functioning better than the mere presence of small forest fragments.
Merocyanine Dyes as Organic Semiconductors for Vacuum-processed Solar Cell and Transistor Devices
(2015)
The present thesis comprises the synthesis of new functional merocyanine dyes, the study of their electro-optical properties as well as solid state packing and their application as p-type semiconductor materials in transistor and solar cell devices. The absorption properties of the obtained compounds could be modified by variation of the donor unit, the introduction of electron-withdrawing substituents in the acceptor unit or elongation of the polymethine chain. For a particular dye, the absorption band could be shifted by more than 160 nm by increasing the solvent polarity due to a conformational switch between a merocyanine-like and a cyanine-like structure. Single crystal analyses revealed that the studied dyes tend to pack either in an antiparallel fashion forming dimers with no overall dipole moment or in a staircase-like pattern where the dipole moments point to the same direction and are only balanced by another staircase oriented in the opposite direction (stair dimer). With respect to application as semiconductor materials, the latter packing arrangement resulted most favorable for charge carrier mobility. We concluded that this packing motif is preserved in the solar cell devices, where the selenium-containing dye afforded the highest performance of this series for an optimized planar-mixed heterojunction solar cell (6.2 %).
In this work, Emilio de’ Cavalieri’s musical sources will serve as a platform in an attempt to overcome the lack of explicit original guidance and guidelines of performance practice of early basso continuo. It will offer a methodology that will allow the unraveling of implicit theory and practice hidden in the music sources themselves. The methodology of this work is based on the fact that Cavalieri’s Rappresentatione di Anima e di Corpo (Rome, 1600) is printed using a unique continuo notation, which is detailed, precise, and coherent—more so than any other contemporaneous printed source. Through thorough investigation of this continuo notation, it will be possible to enrich our practical as well as theoretical knowledge of the early basso continuo. A wide range of evidences will emerge, covering a wide spectrum, from general questions of instrumentation up to the very notes that should be played. Using a special notation for illustration, I will demonstrate how Cavalieri’s basso continuo figuration, when combined with the known rules of counterpoint, is at times equivalent to written-out realizations.
As part of this study, different models of contrapuntal phenomena will be analyzed, mainly in the context of cadences but also in the context of other progressions that deserve to be recognized as formulas. Their theoretical structure will be uncovered as well as their actual application in music and their manner of execution. The prevalence of each phenomenon will be examined in order to distinguish common and recurrent phenomena from rarely-used formulas. In order to do this, and due to problematic historical terminology, it will be necessary to create a set of new terms inspired by Cavalieri’s notation. Those terms will not be solely relevant to Cavalieri’s music; the models were made flexible so that they may prove useful for future discussions or studies of early continuo in general.
Out of the known early basso continuo sources, a “mini-compendium” of practical implications will be extracted in order to exhaust the practical knowledge implicit in them. This endeavor will be concluded with a list of rules and general advice drawn from the sources, but it will also reveal some problematic aspects of these sources.
This endeavor will make it possible to compare the “new” implicit practical information deduced in this study with the explicit known continuo sources, and assess to what extant Cavalieri’s continuo practices illuminate and complement the known knowledge from previously-studied yet opaque sources of basso continuo.
The focus of this dissertation is on Cavalieri’s music, but the findings proposed here will be traced so as to illuminate the broader realm of the early Baroque and the 17th century musical style at large. Finally, this new research about Cavalieri’s music and continuo, along reevaluating of its place among the common continuo sources, calls for redistribution of source materials on the traditional “shelf” of early basso continuo sources.
The thesis focuses on the valuation of firms in a system context where cross-holdings of the firms in liabilities and equities are allowed and, therefore, systemic risk can be modeled on a structural level. A main property of such models is that for the determination of the firm values a pricing equilibrium has to be found. While there exists a small but growing amount of research on the existence and the uniqueness of such price equilibria, the literature is still somewhat inconsistent. An example for this fact is that different authors define the underlying financial system on differing ways. Moreover, only few articles pay intense attention on procedures to find the pricing equilibria. In the existing publications, the provided algorithms mainly reflect the individual authors' particular approach to the problem. Additionally, all existing methods do have the drawback of potentially infinite runtime.
For these reasons, the objects of this thesis are as follows. First, a definition of a financial system is introduced in its most general form in Chapter 2. It is shown that under a fairly mild regularity condition the financial system has a unique existing payment equilibrium. In Chapter 3, some extensions and differing definitions of financial systems that exist in literature are presented and it is shown how these models can be embedded into the general model from the proceeding chapter. Second, an overview of existing valuation algorithms to find the equilibrium is given in Chapter 4, where the existing methods are generalized and their corresponding mathematical properties are highlighted. Third, a complete new class of valuation algorithms is developed in Chapter 4 that includes the additional information whether a firm is in default or solvent under a current payment vector. This results in procedures that are able find the solution of the system in a finite number of iteration steps. In Chapter 5, the developed concepts of Chapter 4 are applied to more general financial systems where more than one seniority level of debt is present. Chapter 6 develops optimal starting vectors for non-finite algorithms and Chapter 7 compares the existing and the new developed algorithms concerning their efficiency in an extensive simulation study covering a wide range of possible settings for financial systems.
\textbf{Molecular Determinants of Drug-Target Residence Times of Bacterial Enoyl-ACP Reductases.} Whereas optimization processes of early drug discovery campaigns are often affinity-driven, the drug-target residence time $t_R$ should also be considered due to an often strong correlation with \textit{in vivo} efficacy of compounds. However, rational optimization of $t_R$ is not straightforward and generally hampered by the lack of structural information about the transition states of ligand association and dissociation. The enoyl-ACP reductase FabI of the fatty acid synthesis (FAS) type II is an important drug-target in antibiotic research. InhA is the FabI enzyme of \textit{Mycobacterium tuberculosis}, which is known to be inhibited by various compound classes. Slow-onset inhibition of InhA is assumed to be associated with the ordering of the most flexible protein region, the substrate binding loop (SBL). Diphenylethers are one class of InhA inhibitors that can promote such SBL ordering, resulting in long drug-target residence times. Although these inhibitors are energetically and kinetically well characterized, it is still unclear how the structural features of a ligand affect $t_R$.
Using classical molecular dynamics (MD) simulations, recurring conformational families of InhA protein-ligand complexes were detected and structural determinants of drug-target residence time of diphenyl\-ethers with different kinetic profiles were described. This information was used to deduce guidelines for efficacy improvement of InhA inhibitors, including 5'-substitution on the diphenylether B-ring. The validity of this suggestion was then analyzed by means of MD simulations.
Moreover, Steered MD (SMD) simulations were employed to analyze ligand dissociation of diphenylethers from the FabI enzyme of \textit{Staphylococcus aureus}. This approach resulted in a very accurate and quantitative linear regression model of the experimental $ln(t_R)$ of these inhibitors as a function of the calculated maximum free energy change of induced ligand extraction. This model can be used to predict the residence times of new potential inhibitors from crystal structures or valid docking poses.
Since correct structural characterization of the intermediate enzyme-inhibitor state (EI) and the final state (EI*) of two-step slow-onset inhibition is crucial for rational residence time optimization, the current view of the EI and EI* states of InhA was revisited by means of crystal structure analysis, MD and SMD simulations. Overall, the analyses affirmed that the EI* state is a conformation resembling the 2X23 crystal structure (with slow-onset inhibitor \textbf{PT70}), whereas a twist of residues Ile202 and Val203 with a further opened helix $\alpha 6$ corresponds to the EI state. Furthermore, MD simulations emphasized the influence of close contacts to symmetry mates in the SBL region on SBL stability, underlined by the observation that an MD simulation of \textbf{PT155} chain A with chain B' of a symmetry mate in close proximity of the SBL region showed significantly more stable loops, than a simulation of the tetrameric assembly. Closing Part I, SMD simulations were employed which allow the delimitation of slow-onset InhA inhibitors from rapid reversible ligands.
\textbf{Prediction of \textit{Mycobacterium tuberculosis} Cell Wall Permeability.} The cell wall of \textit{M. tuberculosis} hampers antimycobacterial drug design due to its unique composition, providing intrinsic antibiotic resistance against lipophilic and hydrophilic compounds. To assess the druggability space of this pathogen, a large-scale data mining endeavor was conducted, based on multivariate statistical analysis of differences in the physico-chemical composition of a normally distributed drug-like chemical space and a database of antimycobacterial--and thus very likely permeable--compounds. The approach resulted in the logistic regression model MycPermCheck, which is able to predict the permeability probability of small organic molecules based on their physico-chemical properties. Evaluation of MycPermCheck suggests a high predictive power. The model was implemented as a freely accessible online service and as a local stand-alone command-line version.
Methodologies and findings from both parts of this thesis were combined to conduct a virtual screening for antimycobacterial substances. MycPermCheck was employed to screen the chemical permeability space of \textit{M. tuberculosis} from the entire ZINC12 drug-like database. After subsequent filtering steps regarding ADMET properties, InhA was chosen as an exemplary target. Docking to InhA led to a principal hit compound, which was further optimized. The quality of the interaction of selected derivatives with InhA was subsequently evaluated using MD and SMD simulations in terms of protein and ligand stability, as well as maximum free energy change of induced ligand egress. The results of the presented computational experiments suggest that compounds with an indole-3-acethydrazide scaffold might constitute a novel class of InhA inhibitors, worthwhile of further investigation.