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Thermal radiation processes
(2008)
We discuss the different physical processes that are important to understand the thermal X-ray emission and absorption spectra of the diffuse gas in clusters of galaxies and the warm-hot intergalactic medium. The ionisation balance, line and continuum emission and absorption properties are reviewed and several practical examples are given that illustrate the most important diagnostic features in the X-ray spectra.
It has always been enigmatic which processes control the accretion of the North American terranes towards the Pacific plate and the landward migration of the San Andreas plate boundary. One of the theories suggests that the Pacific plate first cools and captures the uprising mantle in the slab window, and then it causes the accretion of the continental crustal blocks. The alternative theory attributes the accretion to the capture of Farallon plate fragments (microplates) stalled in the ceased Farallon-North America subduction zone. Quantitative judgement between these two end-member concepts requires a 3D thermomechanical numerical modeling. However, the software tool required for such modeling is not available at present in the geodynamic modeling community. The major aim of the presented work is comprised basically of two interconnected tasks. The first task is the development and testing of the research Finite Element code with sufficiently advanced facilities to perform the three-dimensional geological time scale simulations of lithospheric deformation. The second task consists in the application of the developed tool to the Neogene deformations of the crust and the mantle along the San Andreas Fault System in Central and northern California. The geological time scale modeling of lithospheric deformation poses numerous conceptual and implementation challenges for the software tools. Among them is the necessity to handle the brittle-ductile transition within the single computational domain, adequately represent the rock rheology in a broad range of temperatures and stresses, and resolve the extreme deformations of the free surface and internal boundaries. In the framework of this thesis the new Finite Element code (SLIM3D) has been successfully developed and tested. This code includes a coupled thermo-mechanical treatment of deformation processes and allows for an elasto-visco-plastic rheology with diffusion, dislocation and Peierls creep mechanisms and Mohr-Coulomb plasticity. The code incorporates an Arbitrary Lagrangian Eulerian formulation with free surface and Winkler boundary conditions. The modeling technique developed is used to study the aspects influencing the Neogene lithospheric deformation in central and northern California. The model setup is focused on the interaction between three major tectonic elements in the region: the North America plate, the Pacific plate and the Gorda plate, which join together near the Mendocino Triple Junction. Among the modeled effects is the influence of asthenosphere upwelling in the opening slab window on the overlying North American plate. The models also incorporate the captured microplate remnants in the fossil Farallon subduction zone, simplified subducting Gorda slab, and prominent crustal heterogeneity such as the Salinian block. The results show that heating of the mantle roots beneath the older fault zones and the transpression related to fault stepping, altogether, render cooling in the slab window alone incapable to explain eastward migration of the plate boundary. From the viewpoint of the thermomechanical modeling, the results confirm the geological concept, which assumes that a series of microplate capture events has been the primary reason of the inland migration of the San Andreas plate boundary over the recent 20 Ma. The remnants of the Farallon slab, stalled in the fossil subduction zone, create much stronger heterogeneity in the mantle than the cooling of the uprising asthenosphere, providing the more efficient and direct way for transferring the North American terranes to Pacific plate. The models demonstrate that a high effective friction coefficient on major faults fails to predict the distinct zones of strain localization in the brittle crust. The magnitude of friction coefficient inferred from the modeling is about 0.075, which is far less than typical values 0.6 – 0.8 obtained by variety of borehole stress measurements and laboratory data. Therefore, the model results presented in this thesis provide additional independent constrain which supports the “weak-fault” hypothesis in the long-term ongoing debate over the strength of major faults in the SAFS.
We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with increasing heterozygosity—a known phenomenon in the literature.
Using ESTs for phylogenomics
(2008)
Background
While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets.
Results
We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences.
Conclusion
These results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a major problem for phylogenetic analysis. The concern will be greatest for high-throughput phylogenomic analyses, in which Neighbor Joining is often the preferred method due to its computational efficiency. Both approaches can be used to increase the accuracy of phylogenetic inference from a gappy alignment. The choice between the two approaches will depend upon how robust the application is to the loss of sequences from the input set, with alignment masking generally giving a much greater improvement in accuracy but at the cost of discarding a larger number of the input sequences.
Nowadays, reactions on surfaces are attaining great scientific interest because of their diverse applications. Some well known examples are production of ammonia on metal surfaces for fertilizers and reduction of poisonous gases from automobiles using catalytic converters. More recently, also photoinduced reactions at surfaces, useful, \textit{e.g.}, for photocatalysis, were studied in detail. Often, very short laser pulses are used for this purpose. Some of these reactions are occurring on femtosecond (1 fs=$10^{-15}$ s) time scales since the motion of atoms (which leads to bond breaking and new bond formation) belongs to this time range. This thesis investigates the femtosecond laser induced associative photodesorption of hydrogen, H$_2$, and deuterium, D$_2$, from a ruthenium metal surface. Many interesting features of this reaction were explored by experimentalists: (i) a huge isotope effect in the desorption probability of H$_2$ and D$_2$, (ii) the desorption yield increases non-linearly with the applied visible (vis) laser fluence, and (iii) unequal energy partitioning to different degrees of freedom. These peculiarities are due to the fact that an ultrashort vis pulse creates hot electrons in the metal. These hot electrons then transfer energy to adsorbate vibrations which leads to desorption. In fact, adsorbate vibrations are strongly coupled to metal electrons, \textit{i.e.}, through non-adiabatic couplings. This means that, surfaces introduce additional channels for energy exchange which makes the control of surface reactions more difficult than the control of reactions in the gas phase. In fact, the quantum yield of surface photochemical reactions is often notoriously small. One of the goals of the present thesis is to suggest, on the basis of theoretical simulations, strategies to control/enhance the photodesorption yield of H$_2$ and D$_2$ from Ru(0001). For this purpose, we suggest a \textit{hybrid scheme} to control the reaction, where the adsorbate vibrations are initially excited by an infrared (IR) pulse, prior to the vis pulse. Both \textit{adiabatic} and \textit{non-adiabatic} representations for photoinduced desorption problems are employed here. The \textit{adiabatic} representation is realized within the classical picture using Molecular Dynamics (MD) with electronic frictions. In a quantum mechanical description, \textit{non-adiabatic} representations are employed within open-system density matrix theory. The time evolution of the desorption process is studied using a two-mode reduced dimensionality model with one vibrational coordinate and one translational coordinate of the adsorbate. The ground and excited electronic state potentials, and dipole function for the IR excitation are taken from first principles. The IR driven vibrational excitation of adsorbate modes with moderate efficiency is achieved by (modified) $\pi$-pulses or/and optimal control theory. The fluence dependence of the desorption reaction is computed by including the electronic temperature of the metal calculated from the two-temperature model. Here, our theoretical results show a good agreement with experimental and previous theoretical findings. We then employed the IR+vis strategy in both models. Here, we found that vibrational excitation indeed promotes the desorption of hydrogen and deuterium. To summarize, we conclude that photocontrol of this surface reaction can be achieved by our IR+vis scheme.
Workplace-related anxieties and workplace phobia : a concept of domain-specific mental disorders
(2008)
Background: Anxiety in the workplace is a special problem as workplaces are especially prone to provoke anxiety: There are social hierarchies, rivalries between colleagues, sanctioning through superiors, danger of accidents, failure, and worries of job security. Workplace phobia is a phobic anxiety reaction with symptoms of panic occurring when thinking of or approaching the workplace, and with clear tendency of avoidance. Objectives: What characterizes workplace-related anxieties and workplace phobia as domain-specific mental disorders in contrast to conventional anxiety disorders? Method: 230 patients from an inpatient psychosomatic rehabilitation center were interviewed with the (semi-)structured Mini-Work-Anxiety-Interview and the Mini International Neuropsychiatric Interview, concerning workplace-related anxieties and conventional mental disorders. Additionally, the patients filled in the self-rating questionnaires Job-Anxiety-Scale (JAS) and the Symptom Checklist (SCL-90-R)measuring job-related and general psychosomatic symptom load. Results: Workplace-related anxieties occurred together with conventional anxiety disorders in 35% of the patients, but also alone in others (23%). Workplace phobia could be found in 17% of the interviewed, any diagnosis of workplace-related anxiety was stated in 58%. Workplace phobic patients had significantly higher scores in job-anxiety than patients without workplace phobia. Patients with workplace phobia were significantly longer on sick leave in the past 12 months (23,5 weeks) than patients without workplace phobia (13,4 weeks). Different qualities of workplace-related anxieties lead with different frequencies to work participation disorders. Conclusion: Workplace phobia cannot be described by only assessing the general level of psychosomatic symptom load and conventional mental disorders. Workplace-related anxieties and workplace phobia have an own clinical value which is mainly defined by specific workplace-related symptom load and work-participation disorders. They require special therapeutic attention and treatment instead of a “sick leave” certification by the general health physician. Workplace phobia should be named with a proper diagnosis according to ICD-10 chapter V, F 40.8: “workplace phobia”.
Stellar magnetic fields, as a crucial component of star formation and evolution, evade direct observation at least with current and near future instruments. However investigating whether magnetic fields are generated by a dynamo process or represent relics from the formation process, or whether they show a behavior similar to the sun or something very different, it is essential to investigate their structure and temporal evolution. Fortunately nature provides us with the possibility to indirectly observe surface topologies on distant stars by means of Doppler shift and polarization of light, though not without its challenges. Based on the mentioned effects, the so called Zeeman-Doppler Imaging technique is a powerful method to retrieve magnetic fields from rapid rotating stars based on measurements of spectropolarimetric observations in terms of Stokes profiles. In recent years, a large number of stellar magnetic field distributions could be reconstructed by Zeeman-Doppler Imaging (ZDI). However, the implementation of this method often relies on many approximations because, as an inversion method, it entails enormous computational requirements. The aim of this thesis is to develop methods for a ZDI, designed to invert time-resolved spectropolarimetric data of active late type stars, and to account for the expected complex and small scale magnetic fields on these stars. In order to reliably reconstruct the detailed field orientation and strength, the inversion method is employed to be able to use of all four Stokes components. Furthermore it is based on fully polarized radiative transfer calculations to account for the intricate interplay between temperature and magnetic field. Finally, the application of a newly developed ZDI code to Stokes I and V observations of II Pegasi (short: II Peg) was supposed to deliver the first magnetic surface maps for this highly active star. To accomplish the high computational burden of a radiative transfer based ZDI, we developed a novel approximation method to speed up the inversion process. It is based on Principal Component Analysis and Artificial Neural Networks. The latter approximate the functional mapping between atmospheric parameters and the corresponding local Stokes profiles. Inverse problems, as we are dealing with, are potentially ill-posed and require a regularization method. We propose a new regularization scheme, which implements a local entropy function that accounts for the peculiarities of the reconstruction of localized magnetic fields. To deal with the relatively large noise that is always present in polarimetric data, we developed a multi-line denoising technique based on Principal Component Analysis. In contrast to other multi-line techniques that extract from a large number of spectral lines a sort of mean profile, this method allows to extract individual spectral lines and thus allows for an inversion on the basis of specific lines. All these methods are incorporated in our newly developed ZDI code iMap, which is based on a conjugated gradient method. An in depth validation of our new synthesis method demonstrates the reliability and accuracy of this approach as well as a gain in computation time by almost three orders of magnitude relative to the conventional radiative transfer calculations. We investigated the influence of the different Stokes components (IV / IVQU) on the ability to reconstruct a known synthetic field configuration. In doing so we validate the capability of our inversion code, and we also assess limitations of magnetic field inversions in general. In a first application to II Peg, a K2 IV subgiant, we derived temperature and magnetic field surface distributions from spectropolarimetric data obtained in 2004 and 2007. It gives for the first time simultaneously the temporal evolution of the surface temperature and magnetic field distribution on II Peg.