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From Cucurbiturils to Amino Acids: Taking Advantage of Mild Catalysis for Reaction Rate Acceleration and Pharmaceutical Drug Syntheses
No full textCatalysis is a central theme of many current endeavors within synthetic organic chemistry. Within this thesis I describe how catalysis implementation has allowed three distinct contributions to the areas of reaction rate acceleration, site-selectivity, and more step-efficient synthesis of pharmaceutical drugs.
Site-selectivity is an emerging field within organic chemistry in which two or more of the same functional groups are differentiated on the same molecule. The tactic of site-selectivity holds the potential to free the synthetic chemist from protection/deprotection protocols during a natural product or drug synthesis for improved yield and step-efficiency. In particular, aldol site-selectivity for 4-substituted diketones with high chemo-, regio-, diastereo- and enantioselectivity has been shown. The aldol products there from have been converted to lactones (three stereogenic centers) and 1,3-diols (four stereogenic centers), and one lactone was successfully used to achieve the first enantioselective synthesis of an Alzheimer drug precursor in the highest overall yield to date.
Finally, cucurbituril (CB7) was used to catalyze Diels-Alder reaction of cyclopentadiene dimerization. I proved that using CB7 as a catalyst can accelerate the dimerization reaction up to 150 thousand fold in compare to the neat reaction. Cucurbituril ability in selectively catalyzing the dimerization of methylcyclopentadiene and co-dimerization of cyclopentadiene with methylcyclopentadiene was also noted
Impacts of Indonesian peatland degradation on the coastal ecosystems and the global carbon cycle
No full textIn recent years, there has been intense media attention concerning the outbreaks of devastating forest fires in Indonesia. These fires are fueled by forest wood and peat and emit large amounts of carbon to the atmosphere. Peatlands are a unique unbalanced ecosystem composed of organic-rich soils and are estimated to store approximately 600 Gt of carbon globally. Tropical peatlands are among the most space-efficient stores of carbon on Earth containing approximately 89 Gt C. Of this, 57 Gt (65%) are stored in Indonesian peatlands. Indonesian peatlands are one of the largest modern day near-surface reservoirs of terrestrial carbon, with accumulation that began as early as 22 thousand years ago and continued throughout the Pleistocene and Holocene. Despite the highly important and relevant carbon pool in peat swamp forests, they are largely neglected when modeling the past and present global carbon cycle. The forested tropical peatlands in Indonesia have been identified as a particularly crucial source of uncertainty in global carbon cycle models. In order to refine predictions of future and past climate change, this research will quantify the release of carbon from the Indonesian peatlands to better explain the effects that excess carbon has on the downstream marine ecosystems and the global carbon cycle. Currently, large-scale exploitation of land, including deforestation and drainage for the establishment of oil palm plantations, is changing the carbon balance of Indonesian peatlands, turning them from a previous sink to a source via outgassing of CO2 to the atmosphere and leakage of dissolved organic carbon (DOC) into the coastal ocean. The impacts of this perturbation to the coastal environment and the global climate are largely unknown. I use a biogeochemical box model in combination with novel observations and literature data to investigate the impact of different carbon emission scenarios on the combined ocean-atmosphere system
Application of Nonlinear Optical Techniques: Probing Ultrafast Dynamics in Ionic Liquids and Realization of an Ultrafast Toffoli Logic Gate
No full textNonlinear optical effects are known and investigated for several decades. Since the first observation of these phenomena, a great number of applications have been found for them in science and technology. The combination of nonlinear optical effects with ultra-short laser pulses has advanced the field of spectroscopy and now allows for studying and even controlling the elementary dynamics of molecular systems on a picosecond, femtosecond, and even attosecond time scale.
In the first part of this PhD thesis, femtosecond laser pulses are used to generate second-order nonlinear optical effects. By controlling the phase relation between these second order phenomena, an all-optical ultrafast Toffoli logic gate is implemented. The proposed simple technique is a proof of principle, which can be a step towards ultrafast switching and optical computation.
The second part of the thesis focuses on the application of the four-wave mixing (FWM) process, a third-order nonlinear effect, for the investigation of the vibrational dynamics of molecular systems. Femtosecond time-resolved coherent anti-Stokes Raman scattering (fs-CARS) is applied to probe the ultrafast coupling of vibrational modes in ionic liquids. Specifically, the effect of the alkyl chain length and anion substitution on the vibrational dynamics of fingerprint and C-H stretching modes in ionic liquids are investigated. This study provides a better insight into the intermolecular interactions in ionic liquids, which can be used to optimize the design of task-specific materials
The murine cytomegalovirus immunoevasin gp40 binds to MHC class I molecules to retain them in the early secretory pathway
No full textTo recognize the viral infection of a cell, the adaptive immune system depends on Major Histocompatibility Complex (MHC) class I molecules, which present viral peptides (antigens) at the surface of an infected cell to patrolling immune cells. MHC class I molecules are assembled and loaded with viral peptides in the endoplasmic reticulum (ER), and, after passing a thourough quality control, are transported to the cell surface.
Viruses have evolved mechanisms to impair the so-called antigen presentation, as this reduces viral dissemination. Herpesviruses, which usually chronically infect their host, dedicate a big part of their ample genome to manipulate the antigen presentation pathway at all possible levels.
In the presence of the murine cytomegalovirus (mCMV) gp40 (m152) protein, murine MHC class I molecules do not reach the cell surface but are retained in an early compartment of the secretory pathway by an unknown mechanism.
In this work, I found that gp40 does not hijack any known cellular factors to retain MHC class I molecules, but rather binds to them and most likely circulates with them in the early secretory pathway, which consists of the endoplasmic reticulum (ER), the ER-Golgi intermediate compartment (ERGIC), and the cis-Golgi.
A flexible sequence in the lumenal domain of gp40 appears to be responsible for the circulation, as destruction of this sequence releases both MHC class I molecules and gp40 from the early secretory pathway without impairing their interaction.
Furthermore, I could show that the expression of gp40 influences the transcription of genes of the antigen presenting machinery (APM) in some, but not in all, cell lines, and that factors that influence the folding and export speed of MHC class I molecules (protein sequence, β2m abundance) decide on the effectiveness of gp40 function
Structural and functional analysis of human voltage-dependent anion channel isoforms (hVDACs): Combining in-vitro and in-silico approaches
No full textThe most abundant porins occurring in the OMM are the voltage dependent anion selective channels (VDACs). Even if they had been previously studied they were not very well characterized until they were isolated from rat liver by Colombini in 1983. VDACs are a small family of conserved proteins located in the outer mitochondrial membrane. They conduct ions, metabolites and small molecules, among which the energetic nucleotides ATP, ADP and NADH. Three different VDAC isoforms have been characterized in higher eukaryotes, encoded by three separate nuclear genes. VDAC1 is the most abundant isoform in most cells, being ten and hundred times more prevalent than VDAC2 and VDAC3, respectively. It is thus not surprising that VDAC1 is the isoform most extensively characterized. Functionally, VDAC1 is anion selective and exhibits a single-channel conductance of ~3.5-4.0 nS in 1 M KCl at an applied voltage between -20 mV and +10 mV. The aim of the PhD project was to perform a comparative study on the human VDAC isoforms focusing on both the whole channels and the individuals N-terminal domains. In this sense, both experimental and computational techniques have been used pointing out their complementarity and contribute to the completeness of the study
Characterization of shape and functionality of optical components by gradient based transmission test
No full textGradient based measurement techniques for transmission testing of optical components represent a relatively small group in optical metrology. Nevertheless, some of them are already in wide spread use and others have the potential to be an all-around tool for the extensive characterization of optical components. This thesis will provide a thorough introduction into the theoretical background connected with these techniques. Furthermore, it will introduce several new methods to correctly determine two of the most relevant parameters of optical systems from gradient measurement with high accuracy. One of these is the effective focal length, whose correct determination still pose a problem for available measurement techniques, which deviate from its definition and provide the user with a result that suffers from aberrations effects. Especially for fast lenses with small diameter, these influences may generate errors that fairly excel common specified tolerances. Three numerical analysis methods are discussed and compared that evaluate the effective focal length from gradient measurement. This is done by simulations of a very strong spherical lens with an f/#‑number of 1. The advantage of using ray slopes over wavefront is not having to determine the exact position of the principle plane, since the slopes are invariant along the ray propagation in homogeneous media. Results from experiments demonstrated that these methods combined with a certain gradient method are able to retrieve a focal value with an error of only 0.063 %.
The second parameter of interest covered in this work is the modulation transfer function (MTF), which is a quantitative measure of image quality, describing the ability of an optical system to transfer different levels of detail from an object to an image. Its value is of high practical relevance and traditionally measured from imaging appropriate test target units. Several methods will be discussed that allow to generate the MTF from gradient measurement. One of these is also suitable for highly corrected optical systems, which are beyond the limits of other methods.
From the gradient techniques, experimental ray tracing was demonstrated to be capable of retrieving the shape of an aspherical lens from transmission test, provided that certain assumptions apply. The performance of the retrieval is bound to the utilized model function of the aspherical surface. In this case, traditional surface descriptions of aspheres are inefficient and numerical unstable when it comes to modeling surface feature in the mid-spatial regime. With Forbes' Q-polynomials, two sets of orthogonal polynomials were found, that are superior to the standard equation and promise to be a suitable replacement. Their positive properties solely result from their orthogonality. Recurrence relations will be demonstrated that enable the evaluation of the polynomials to arbitrary high orders on the base of lower order terms. In gradient techniques, the lateral resolution is commonly limited. In these cases, the Q-polynomials, defined in the continuous sense, will lose their positive properties. Within this work, a process will be proposed that retains the properties of this polynomials in case of discrete data sets by discrete orthonormalization. Orthogonal polynomials play a vital role in various parts of this work and therefore, will be discussed in more detail
Uncertainty Estimation and Visualization in Segmenting Uni- and Multi-modal Medical Imaging Data
No full textUncertainty is widespread when interpreting medical imaging data sets due to different sources of artifacts such as signal measurement errors or noise and partial volume effects in the acquisition process. The effectiveness of visualization methods for supporting decision making and diagnostic exploration is limited by the lack of suitable uncertainty estimation and visualization tools. A striking example of uncertainty visualization importance is given in neurosurgery, where errors in the range of a millimeter can have dramatic effects.
Image segmentation plays an essential role in a broad range of computer vision and image processing applications such as pattern recognition, geographical imaging, geology, remote sensing, and medical imaging. In image segmentation, images are partitioned into disjoint regions of homogeneous
properties.
This study is concerned with deriving estimates of uncertainty associated with the segmentation result of single- and multi-modal medical imaging data, developing methods to visualize these estimates intuitively, and using these estimation in both evaluating and improving image segmentation results and the analysis of these results. As domain of applications, we use synthetic images that simulate the main brain structures in magnetic resonance imaging (MRI) data, simulated MRI data from BrainWeb, and Real MRI data as well.
The main objectives of our study are to distinguish the certain and uncertain areas in the segmentation result, and to categorize the uncertain areas according to their level of uncertainty. By uncertain area, we basically understand the area that is affected by one or more sources of artifacts.
Note: (see the complete abstract in the thesis
Solution processed post-transition metal oxide thin film transistors: understanding fabrication challenges and transport mechanism
No full textThis thesis investigates sol-gel precursor based solution processed metal oxide mixture, iXsenic® S, provided by Evonik Industries AG. This work tries to identify the challenges associated with the fabrication of iXsenic® S based thin film transistors in bottom gate top contact architecture currently popular in amorphous silicon technology. This architecture would allow cost effective solution of retrofitting existing amorphous silicon plants.
The post-transition metal oxide semiconductors are known to degrade under negative bias illumination stress which is touted as their biggest weakness. The surface of these semiconductors is widely accepted as the source of this degradation. The surface is prone to defects, particularly in the form of oxygen vacancies. Passivation and post deposition annealing have been used to combat this challenge. The oxidation of the transistor top contacts due to oxygen out-diffusion from the semiconductor bulk during the post deposition annealing step has been identified as a major fabrication challenge in this work. The solution to this challenge is offered as an optimization of post deposition annealing and its subsequent passivation process. The quality of the solution processed passivation layer is found to be very important to ensure long term device stability. This is because the passivation binds to the defects at the semiconductor surface to heal the degradation sources. Passivation quality control is found to be critical in mixed oxides than in binary oxides.
After the fabrication challenges are addressed and possible solutions proposed, the transport mechanism of the resulting thin film transistor is studied. Despite their high mobility operation, temperature activated hopping like transport similar to other disordered semiconductor systems is observed.
A path to an all-solution processed thin film transistor based on metal oxide semiconductor system is paved by the knowledge obtained from this work
Workplace Flexibility and the Aging Workforce: How Two Contemporary Workplace Trends Shape the Work/Nonwork Interface
No full textThe present dissertation investigates how workplace flexibility and the aging workforce shape the work/nonwork interface, i.e., the intersection of work and nonwork lives. Based on three independent samples relying on cross-sectional and experience sampling data, significant contributions to the work/family literature emerge from three empirical chapters. Results demonstrate that workplace flexibility and age impact workers’ work-nonwork boundaries, affective well-being, and work-life balance. Overall, the findings suggest that workplace flexibility regarding start, end, and break times, if used in moderation, helps workers to maintain strong boundaries. Strong boundaries, in turn, were consistently related to better well-being and favorable interactions between work and nonwork lives. Goal completion, individual preferences for boundary strength, and boundary management strategies strengthened workers’ boundaries at work and at home, whereas the need to be available for the employer during nonwork time weakened the boundary at home. Further, older as compared to younger workers seem to be more successful in reconciling competing work and nonwork demands, over and above age-related changes in life contexts. A reason for this seems to be their active boundary management strategy use, which emerged as a mediator in the link of age with boundary strength. Finally, the present research highlights the dynamic nature of the work/nonwork interface and shows the importance of considering both day- and person-level associations when analyzing processes at the work/nonwork interface: Whereas occasional flexibility use positively related to nonwork goal completion and boundary strength, its enduring use constitutes a resource-depleting demand that undermines work goal completion. The dissertation adds to the development of an analytical framework of the work/nonwork interface with implications for research and practice.Die Dissertation untersucht, wie Arbeitsplatzflexibilität und alternde Belegschaften die Schnittstelle von Arbeits- und Privatleben prägen. Basierend auf drei unabhängigen Stichproben mit Querschnitts- und Tagebuchdaten trägt die Dissertation zur Forschung in Hinblick auf Arbeits- und Privatleben bei. Ergebnisse legen dar, wie Arbeitsplatzflexibilität und Alter die Grenzen zwischen Lebensbereichen sowie das affektives Wohlbefinden und Work-Life Balance der Beschäftigten beeinflussen. Die Befunde zeigen, dass in Maßen genutzte Flexibilität (Start-, End- und Pausenzeiten) Beschäftigten hilft, Grenzen zwischen den Lebensbereichen aufrecht zu erhalten. Diese wiederum hingen durchweg mit höherem Wohlbefinden und vorteilhaften Interaktionen zwischen Lebensbereichen zusammen. Zielerreichung, individuelle Präferenzen für Stärke der Grenzen und Strategien des Grenzmanagements unterstützten die Trennung von Arbeits- und Privatleben, während Erreichbarkeit außerhalb regulärer Arbeitszeit die Grenzen um das Privatleben schwächte. Zudem scheinen ältere im Vergleich zu jüngeren Beschäftigten, unabhängig von altersbedingten Änderungen in Lebensumständen, konkurrierende Anforderungen aus Arbeits- und Privatleben erfolgreicher zu vereinbaren. Ein Grund hierfür liegt scheinbar im aktiven Grenzmanagement, welches den Zusammenhang zwischen Alter und Stärke der Grenzen zwischen Lebensbereichen mediierte. Die Dissertation betont den dynamischen Charakter der Schnittstelle von Lebensbereichen sowie die Wichtigkeit, Zusammenhänge sowohl auf Tages- als auch auf Personenebene zu analysieren: Während die gelegentliche Nutzung von Flexibilität positiv mit dem Erreichen von privaten Zielen und Grenzstärke zusammenhängt, stellt die dauerhafte Nutzung eine an Ressourcen zehrende Belastung dar, die das Erreichen von Arbeitszielen untergräbt. Die Dissertation trägt zur Entwicklung eines Analyserasters der Schnittstelle von Arbeits- und Privatleben bei mit Implikationen für Forschung und Praxis
Understanding the Impact of Network Infrastructure Changes using Large-Scale Measurement Platforms
No full textA number of large-scale network measurement platforms have emerged in the last few years. These platforms have deployed thousands of measurement probes at strategic locations within access and backbone networks and at residential gateways. The primary goal of these efforts is typically to measure the performance of broadband access networks and to help regulators sketch better policy decisions. In this dissertation we expand the goal further by using large-scale measurement platforms to understand the impact of network infrastructure changes. We utilise probes deployed at the edge of the network to measure IPv6 and access network performance. This dissertation largely provides three main contributions: a) Survey on Internet Performance Measurement Platforms: For each performance measurement platform, we present its coverage, scale, lifetime, deployed metrics and measurement tools, architecture and overall research impact. Furthermore, we discuss standardization efforts that are currently being pursued in this space. b) Measuring IPv6 Performance: We present metrics, measurement tools, measurement insights and experience from studying geographically varied IPv6 networks. We provide a comparison of how content delivery over IPv6 compares to that of IPv4. We identify glitches in this content delivery that can help improve user experience over IPv6. Our observations also identify areas of improvements in the standards work within the IETF. c) Measuring Access Network Performance: We perform a characterization of last-mile latency by time of day, by subscriber location, by broadband product subscription and by access technology used by the DSL modem. We show that DSL deployments not only tend to enable interleaving on the last-mile, but also employ multiple depth levels that change over time. Our characterization of last-mile latency can be used by simulation studies to model DSL, cable and fibre access links in the future