Bayreuther Graduiertenschule für Mathematik und Naturwissenschaften (BayNAT)
Soil erosion and conservation potential of row crop farming in mountainous landscapes of South Korea
- Soils play an essential role for mankind because they provide fundamental ecosystem services required for human life, primarily for the production of food by providing the environment for plant growth. However, soils worldwide became highly threatened by human induced degradation, especially as a consequence of accelerated erosion by water during recent decades. In consideration of climate change and an increasing food demand of a rising population, there is an urgent need to conserve the soil resources by implementing effective erosion control measures for agricultural production. The effective implementation of those measures strongly depends on the specific conditions of particular regions and requires the analysis of the existing farming systems and their capability for erosion control.
Objective of this thesis is the analysis of the major agricultural practices applied for row crop cultivation in mountainous watersheds of South Korea with respect to water erosion and the identification of their conservation potential. Our first two studies analyze the subsurface flow processes, the runoff patterns, and the associated erosion rates of the widely applied plastic covered ridge-furrow system (plastic mulch), and our third study investigates the impact of herbicide applications on erosion associated with conventional and organic farming. To analyze the flow processes induced by the plastic mulch cultivation, we conducted four irrigation experiments on potato fields that represent a smooth surface, uncovered ridges, and plastic covered ridges with and without a developed crop canopy. With an automatic sprinkler, we irrigated small plots with a dye tracer solution of Brilliant Blue and potassium iodide, collected surface runoff, and excavated soil profiles to visualize the subsurface flow patterns, which were subsequently analyzed by image index functions. We found that the ridge-furrow system, especially when ridges are covered with plastic, decreased infiltration and generated high amounts of surface runoff, whereas a developed crop canopy increased infiltration due to interception and stem flow. The analyses of the subsurface flow patterns show that the plastic covered ridge-furrow system induces preferential infiltration in furrows and planting holes due to its topography and the impermeable covers, but that the impact on flow processes in the soils is relatively small compared to the impact on runoff generation. To identify the patterns of overland flow and the erosion rates associated with the plastic mulch system, we installed runoff collectors to monitor runoff and sediment transport of two potato fields with concave and convex topographies, and we applied the EROSION 3D model to compare the plastic covered ridge-furrow system to uncovered ridges and a smooth surface. We found that plastic mulch cultivation considerably increases soil erosion compared to uncovered ridges as a consequence of high amounts of surface runoff. Our results show that the ridge-furrow system concentrated overland flow on the concave field, resulting in severe gully erosion, but prevented flow accumulation and reduced erosion on the convex field, which demonstrates that the effect of this cultivation strategy is primarily controlled by the field topography and its orientation. To analyze the effects of conventional and organic farming on water erosion, we measured multiple vegetation parameters of crops and weeds of conventional and organic farms cultivating bean, potato, radish, and cabbage, and we simulated long-term soil loss rates with the Revised Universal Soil Loss Equation (RUSLE). We found that organic farming reduced erosion for radish, as a result of an increased weed biomass due to the absence of herbicides, but that it increased erosion for potato due to lower crop coverage, presumably as a consequence of crop-weed competition or herbivory associated with the absence of agricultural chemicals. Although we demonstrated that a developed weed cover in the furrows can potentially decrease the erosion risk for row crops, our results show that the average annual erosion rates of both farming systems exceed by far any tolerable soil loss.
In consideration of the generally high soil loss found in our studies, we conclude that the applied farming practices are not capable for effective erosion control and soil conservation in this region. However, based on our findings, we could identify possible modifications of those practices that can help to reduce the risk of erosion in the future. We recommend perforated plastic covers for ridges to reduce runoff generation, and the orientation of the ridge-furrow system along the contours or towards field edges to prevent flow accumulation and gully formation. Additionally, we suggest residue mulching of furrows to protect the soil surface from overland flow, and the cultivation of winter cover crops after harvest to maintain a better soil cover throughout the year.
Comparisons of N2O and CH4 fluxes as affected by land use systems and climate in small catchments in Korea
- In the course of global and climate change humankind has to face extreme weather events with increased intensity and frequency and it has to deal with feeding an increasing number of people which is accompanied by shortage of resources such as water. Since half of humankind directly depends on freshwater and other ecosystem services provided by mountainous areas, it is essential to study such complex terrains and how natural as well as agricultural systems react to climatic and other anthropogenic changes.
Emissions of greenhouse gases like Nitrous oxide (N2O) and Methane (CH4) are of global concern, too, because they are involved in global warming and therewith: climate change. Major sources of N2O are agriculturally managed soils, and very important sources of CH4 are rice paddies. Thus, it is of great importance to study intensively managed agricultural systems and the effects of the management practices on greenhouse gas emissions.
The major focus of this thesis is to quantify dry crop fields’ and forests’ N2O emissions as well as rice paddies’ N2O and CH4 emissions and to identify climatic as well as management related factors and underlying processes which are driving the N2O fluxes in a complex terrain.
A prolonged early summer drought in 2010 led to significant N2O consumption in soil of three different forest sites. The following above-average monsoon rainfall period indeed turned the N2O consumption into emission but could not turn the N2O balance of a forest on sandy-loam substrate from negative into a positive one, which means that for the first time a negative N2O balance was observed for a forest soil during the growing season. The N2O emissions of those forest sites were clearly driven by soil moisture and temperature and there appeared to be an effect of the substrate on N2O emissions as well, as it is increasingly often observed that sandy-loam soils show significant N2O consumption.
Plastic mulching – a worldwide used method in agriculture to increase crop production by enhancing soil temperature, creating more stable soil moisture conditions and restricting arable weed growth – turned out to have a mitigating effect on N2O emissions. DNDC (Denitrification and Decomposition) modeling results matched best with the measurement results when the maximum daily soil temperature and half of the daily precipitation was assumed to occur as dominating climate conditions underneath the impervious polyethylene (PE) film, suggesting that N2O production underneath the plastic cover was driven by soil moisture and temperature. N2O emissions from a non-fertilized soy bean field, which has Nitrogen fixation as an additional Nitrogen source, were similar to the N2O emissions from a radish field after application of an intermediate amount of N fertilizer of 200 kg ha-1.
Comparing N2O and CH4 emissions from rice paddies under different water management practices showed that intermittent irrigation (II) (no continuous flooding, no water logging)
had the least global warming potential (GWP) which was only 30% of the global warming potential (GWP) of a traditionally irrigated (TI) paddy (continuous flooding and water logging). Another practice of 2.5 months of continuous flooding, followed by midseason drainage and reflooding which created moist but non-water logged conditions (FDFM) lead to 66% of the traditionally irrigated paddies combined CH4 and N2O emissions. These results suggest that a trend towards less flooding has a great potential to mitigate greenhouse gas emissions from a sandy or sandy-loam substrate, respectively. Studying the three paddies’ subsoil conditions revealed that N2O production and consumption processes had mainly taken place between 25 and 50 cm soil depth judging by N2O concentrations and δ15N-N2O values along the soil profiles of all the investigated paddies as well as gene abundances of denitrifying and nitrifying bacteria of the FDFM paddy.
Apart from these important findings on N2O flux dynamics of three different land use systems, it is noticeable that the N2O emissions of the study region are in general very low which is very pleasing and implies that the area deals with global change challenges and associated intensive agriculture in a way that comparatively only small amounts of N2O degas. But this raises the question after the “why?” considering that large amounts of fertilizer are applied on the fields. This thesis does not have a final answer to that question but it discusses whether the sandy substrate may play a major role for the N dynamics of the whole area. There is evidence that NO3- - as the substrate for denitrification - leaches easily due to the soil conditions. To finally figure out why the N2O emissions are that low a more detailed investigation on the fate of NO3- would be desirable.
Impact of time and spatial averages on the energy balance closure
- Secondary circulations are large and relatively stationary eddies, which are caused by the surface heterogeneity and normally reside away from the ground. They are believed to be the cause of the energy balance closure problem at the earth's surface, because their contribution to the turbulent fluxes is missed by a fixed eddy-covariance tower measurement that has a typical averaging time of 30 minutes. In this thesis, data from the LITFASS-2003 experiment was used to investigate the impact of time and spatial averages on the energy balance closure. This data consisted of many observations over a large heterogeneous landscape that could generate secondary circulations; some of which might be still near the earth's surface.
For the time average analysis, the averaging time was extended to increase the possibility that secondary circulations were picked up by the sensor. Two approaches, which were the modified ogive analysis and the block ensemble average, were applied to analyze the data from ground-based measurements. The modified ogive analysis requiring a steady state condition, could extend the averaging time up to a few hours and suggested that an averaging time of 30 minutes was still overall sufficient for the eddy-covariance measurement over low vegetation. The block ensemble average, on the contrary, did not require a steady state condition, but could extend the averaging time to several days. However, this approach could only improve the energy balance closure for some sites during specific periods, when secondary circulations existed in the vicinity of the sensor. Based on this approach, it was found that the near-surface secondary circulations mainly transported sensible heat, which led to an alternative energy balance correction by the buoyancy flux ratio approach, in which the attribution of the residual depended on the relative contribution of the sensible heat flux to the buoyancy flux. The fraction of the residual attributed to the sensible heat flux by this energy balance correction was larger than in the energy balance correction that preserved the Bowen ratio.
In the spatial average analysis, two energy balance correction approaches, the buoyancy flux ratio and the Bowen ratio approaches, were applied to the area-averaged fluxes (composite fluxes) in order to include contribution from secondary circulations. These composite fluxes were aggregated from multiple ground-based measurements. The energy balance corrected fluxes were validated against the spatial average fluxes, which were measured by an aircraft and a large aperture scintillometer (LAS). In this validation, the backward Lagrangian footprint model was used to estimate the source area of the measurement. It was found that both energy balance correction approaches did improve the agreement between time and spatial averages fluxes. This suggested that the contribution from secondary circulations could be properly accounted by the energy balance correction.
All findings in this thesis, therefore, depict that secondary circulations significantly transport energy in the atmospheric surface layer. The energy balance correction, accomplished by using either the Bowen ratio approach or the buoyancy flux ratio approach, is necessary to estimate the actual vertical transport of energy at the earth's surface.
Funktion und Einfluss der nicht-repetitiven, terminalen Domänen auf Speicherung und Assemblierung von Spinnenseidenproteinen
- Weibliche Radnetzspinnen sind in der Lage bis zu sechs verschiedene Spinnenseidenfasern mit unterschiedlichen mechanischen Eigenschaften herzustellen, die denen von syntheti-schen Hochleistungsfasern wie Kevlar oder Hochleistungsstahl zum Teil überlegen sind. Die am besten untersuchte Spinnenseide ist diejenige, die für die Speichen, den Rahmen sowie als Abseilfaden verwendet wird. Sie wird als dragline-Seide bezeichnet und ist hauptsächlich aus zwei Proteinklassen aufgebaut, die als MaSp1 und MaSp2(Major Ampullate Spidroin) bezeichnet werden. Die mehrere hundert Kilodalton großen Spidroine bestehen im Wesentlichen aus einer repetitiven, strukturell ungeordneten Kerndomäne, die von relativ kleinen, ca. 100-140 Aminosäuren langen nicht-repetitiven, globulären Domänen flankiert ist. Das Hauptunterscheidungsmerkmal zwischen MaSp1 und 2 ist der Prolingehalt der repetitiven Sequenzen wobei in MaSp2 viel (>10%) und MaSp1 (<0,4%) wenig Proline enthalten sind. In der dragline Seide der Gartenkreuzspinne Araneus diadematus sind zwei Spidroine, genannt ADF3 und 4, mit einem hohen Prolingehalt identifiziert wor-den, die beide deshalb zur Klasse der MaSp2-Proteine gehören. Die nicht-repetitiven terminalen Domänen sind globulär gefaltet und die Sequenzen sind über verschiedene Sei-denarten und Spezies stark konserviert.
Ziel dieser Arbeit war es den Einfluss der nicht-repetitiven amino- (NTD) und carboxyterminalen (CTD) Domänen auf das Lösungs- und Assemblierungsverhalten von rekombinanten Spinnenseidenproteinen auf Basis von ADF3 und 4 zu untersuchen. Der Fokus lag dabei zunächst auf der carboxyterminalen Domäne NR3 des Spinnenseidenproteins ADF3 aus A. diadematus. Die Struktur der Domäne wurde in Zusammenarbeit mit Dr. Franz Hagn (AG Kessler – TU München) mit Hilfe von NMR gelöst. Es bildet in Lösung ein parallel orientiertes, mittels Disulfidbrücke kovalent verknüpftes Dimer aus, zu dessen Struktur bisher keine Homologen bekannt sind. Es konnte gezeigt werden, dass die NR3-Domäne in Lösung die Bildung von sphärischen mizellartigen Assemblaten vermittelt, wie sie auch im natürlichen Spinntrakt beobachtet wurden. Eine weitere wichtige Rolle konnte bei der scherkraftinduzierten Assemblierung beobachtet werden, wo nur eADF3-Proteine mit der NR3-Domäne in der Lage sind ausgerichtete Faserbündel auszubilden.
In einem weiteren Projektteil wurde die Interaktion zwischen rekombinanten Varianten von ADF3 und 4 untersucht, da beide Proteine mit hoher Wahrscheinlichkeit auch in der Spinne in den gleichen Zellen produziert werden. Es konnte gezeigt werden, dass durch Co-Expression der entsprechenden Gene von eADF3-NR3 und eADF4-NR4 in E. coli ein NR3-NR4 vermitteltes Heterodimer entsteht. Dieses Heterodimer besitzt eine vergleichbare strukturelle Integrität wie die entsprechenden Homodimere. Das durch Phosphationen induzierte Assemblierungsverhalten des Heterodimers unterscheidet sich signifikant von dem der Homodimere. Während eADF3-NR3 sphärische Assemblate bildet und eADF4-NR4 mehrere hundert Nanometer lange Fibrillen, wie sie in ähnlicher Form in den natürlichen Fasern beobachtet wurden, lagert sich das Heterodimer zu einem Netzwerk aus im Vergleich dünneren und weniger langen Fibrillen zusammen. Diese Entdeckung ist unter Umständen wichtig für das Verständnis des natürlichen Spinnprozesses. Aus biotechnologischer Sicht stellt die quantitative Verknüpfung von Spinnenseidenproteinen mit unter-schiedlichen Eigenschaften über die carboxyterminalen Domänen einen interessanten Ansatz zur Generierung von neuen Materialien mit einstellbaren Eigenschaften dar.
Letztendlich wurden rekombinante eADF3 Spinnenseidenproteine, die sowohl amino- als auch carboxyterminale Domänen aufwiesen, näher charakterisiert. Die isolierte aminoterminale Domäne bildet bei Senkung des pH-Wertes von 7 auf 6 ein antiparalleles Dimer aus. Es konnte gezeigt werden, dass NTD-eADF3-Proteine, die nur die aminoterminale Domäne N1 enthielten, ebenfalls pH-abhängig Dimere bilden. Bei eADF3-Proteinen mit beiden terminalen Domänen, die per se als CTD-vermitteltes kovalentes Dimer vorliegen, ist die Ausbildung eines aminoterminal vermittelten intermolekularen Dimers-vom-Dimer hingegen nur schwach ausgebildet. Weitere Experimente deuten jedoch darauf hin, dass die NTD in einem intramolekularen Dimer vorliegen. Die Ergebnisse zeigen, dass die CTD einen starken Einfluss auf die Ausrichtung der repetitiven Kerndomäne hat und somit auch die NTD vermittelte intermolekulare Dimerisierung beeinflussen kann.
Die Erkenntnisse wurden verwendet um ein Modell über die molekularen Abläufe während des Spinnprozesses zu erstellen, dass sowohl die Speicherung der Proteine als auch die Assemblierung mit einschließt.
Iron in oxides, silicates and alloys under extreme pressure-temperature conditions
- (1) There is a general agreement, that magnesium silicate perovskite (Pv) comprises around 80 vol% of the Earth's lower-mantle, making it by volume the most abundant mineral in our planet, and and there is no doubt that Pv in the mantle contains Fe and Al. However, the exact concentrations are unknown, as well as the effect of pressure on physical properties of Pv at conditions of Earth lower mantle. In our study we investigate Pv with one of the less explored substitution Mg2+A+Si4+B→Fe3+A+Al3+B. Here we explore as a function of pressure and temperature the crystal structure of the material, the distribution of chemical elements between different crystallographic sites and the evolution the spin state of ferric iron, as one of crucial parameters determining electrical and radiative conductivity of the Earth's lower mantle. We perform single-crystal x-ray diffraction on magnesium silicate perovskite with the composition Mg0.63Fe0.37Si0.63Al0.37O3 (MgFeAlPv) using a combination of in-situ diamond anvil cell technique and laser heating in order to simulate the extreme conditions of the Earth's lower mantle. We provide a complete description of the behavior of MgFeAlPv in terms of crystal structure and ferric iron occupying its dodecahedral (A-)site. We observe no spin transition of ferric iron at A-site, confirming theoretical predictions and recent experimental observations. However, even upon heating MgFeAlPv samples to 1800 K at ~78 GPa we see no indication of a spin crossover or a pressure/temperature induced redistribution of ferric iron and aluminum between the different crystallographic sites as suggested previously. We combine these data with high pressure-high temperature measurements to obtain a thermal equation of state. (2) As a model Fe-O system, magnetite is a mixed valence iron oxide incorporating both ferric and ferrous iron. Being essential part of some sedimentary (banded iron formations) and igneous rocks, magnetite can be subjected to high pressure in natural systems, for instance, during subduction of oceanic crust, or during serpentinization (metamorphic reaction). In order to shed light on the complex physical properties of magnetite under compression we conducted a combined single crystal x-ray diffraction and Mössbauer spectroscopy at pressures below 25 GPa. We find no evidence for the transition from inverse to normal spinel in magnetite. Analyzing the collected Mössbauer data, we show that a high spin – intermediate spin transition cannot occur in magnetite in the pressure range of 10-20 GPa, and finally, based on a careful analysis of the data and results reported in the literature, we provide a model consistently describing the behavior of electronic and magnetic properties of magnetite in terms of a gradual charge delocalization induced by pressure. (3) Our study of wüstite (FexO) is focused on the high pressure – low temperature phase diagram of the Fe-end member in the (Mg,Fe)O system. We perform high resolution neutron diffraction experiments in order to investigate the low temperature phase diagram of Fe0.925O and Fe0.94O. We determine the critical temperatures of antiferromagnetic ordering (the Neél temperature TN) and structural transitions (TS) of the two compounds. We report divergence of TN and TS as a function of pressure. We argue that a modification of the defect structure in wüstite can be invoked explaining the drastically different response of Fe0.925O and Fe0.94O to compression. With that we show that although ferric iron is a minor structural component of wüstite, it is an essential component of defect structures and induces profound effects on the low temperature phase diagram of wüstite. (3) We investigate effect of pressure (P) on the elastic and electronic properties of Fe, Fe0.9Ni0.1 hcp phases below 70 GPa. After processing our experimental data, we report a gradual decrease in the ratio of the hcp lattice parameters c/a for Fe in the pressure range below 45-50 GPa, and a non-linear behavior of Mössbauer isomer shift for hcp phases of pure Fe and Fe0.9Ni0.1, suggesting an isostructural transition in these phases. We investigate paramagnetic hcp Fe under compression by employing state-of-art calculations (LDA+DMFT) and including many-body correlation effects. Based on the results of the calculations, we predict an electronic topological transition (ETT). After comparing data on materials with already known ETT with our observations and theoretical predictions, we conclude that results obtained from the independent experimental measurements can be explained in the framework of an ETT. (4) The development of a portable laser heating system was a necessary requirement for our work done on minerals at conditions of Earth’s lower mantle in general, and for the study of magnesium silicate perovskite containing iron and aluminum in particular. The main advantages of the system developed are compactness, versatility for different in-house and synchrotron based techniques, including high pressure measurements of resistivity, Raman spectroscopy, energy and time-resolved Mössbauer spectroscopy, powder and single crystal x-ray diffraction, nuclear inelastic x-ray scattering, and x-ray absorption. These advantages, the low times of assembly, stable and homogeneous conditions for heating, in-situ measurement of sample temperature, as well as the direct visual control over the heating area distinguish our system from similar, but bulkier devices.
Synthesis and Self-Assembly of Novel ABC Miktoarm Star Terpolymers
- A novel synthesis for ABC miktoarm star terpolymers and their self-assembly into complex superstructures in aqueous solution are described within this thesis. To this aim a modular route for such materials was developed, combining anionic polymerization and copper-catalyzed azide-alkyne cycloaddition. At the example of ABC miktoarm star terpolymers and an ABA’ miktoarm star copolymer containing a poly(N-methyl-2-vinypyridinium iodide) (P2VPq) segment, the counterion-mediated superstructure-formation of complex shaped aggregates was thoroughly investigated.
The key compound of the combinatorial synthesis is the newly synthesized 4-alkyne-substitued diphenylethylene derivative 1-[(4-(tert-butyldimethylsilyl)ethynyl)phenyl]-1-phenylethylene (“click-DPE”). This was applied in sequential anionic polymerization to prepare well-defined alkyne mid-functional diblock copolymers composed of polybutadiene (PB) as first and poly(tert-butyl methacrylate) (PtBMA), poly(2-vinylpyridine) (P2VP), or poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA) as second block. The alkyne-midfunctional diblock copolymers were afterwards conjugated with azido-functional polystyrenes (PS), poly(ethylene oxide) (PEO), PtBMA and PDMAEMA to successfully obtain different novel ABC miktoarm star terpolymers with narrow molecular weight distributions.
For an ABC miktoarm star terpolymer consisting of arms of PB, PtBMA and P2VP it was demonstrated that after quaternization with methyl iodide (yielding BVqT) and dialysis to water the nature of the counterion allows for manipulation of the obtained structures. The miktoarm star architecture together with iodide as counterion is essential for this directed self-assembly. Transformation of iodide to triiodide, via the addition of iodine before dialysis to water, decreases the hydrophilicity of the P2VPq corona and therefore induces the directed self-assembly of spherical micelles with a PB/PtBMA core, into cylinders, superstructures thereof and finally barrel-shaped aggregates of up to 1 µm with an internal lamellar fine structure. Based on their appearance in transmission electron micrographs these were termed “woodlouse” aggregates. The compact particles consist of alternating lamellae of a partially demixed PB/PtBMA phase and a swollen P2VPq phase.
The general applicability of this counterion-mediated hierarchical self-assembly was furthermore demonstrated by using two other miktoarm star systems. For three ABC miktoarm star terpolymers of different composition, consisting of PB, PS and P2VPq segments (BVqS), a dependence of the morphology on the fraction of the hydrophilic block was determined, in analogy to diblock copolymers. For long P2VPq blocks stacked lamellar/disk-like structures evolve from micellar building units. In contrast, a short P2VPq segment yields multilamellar vesicles via fusion of vesicular primary building blocks. The vesicle walls are supposed to consist of a lamellar structure with the PB phase in the centre, shielded from the P2VPq corona by thin PS layers. At the example of one BVqS miktoarm star terpolymer the successful formation of nanohybrids containing gold nanoparticles within the P2VPq phase is demonstrated.
In the second system the low-Tg PB segment was replaced by a second PS block of different length (SVqS’). Even though vesicles serve as initial building units, the triiodide-induced superstructure formation leads to anisotropic aggregation of deformed vesicles, rather than to the fusion into multilamellar vesicles. This is attributed to the two glassy PS core blocks which minimize the dynamics during self-assembly and allow only minor rearrangement of the aggregated structures. Similar to the “woodlouse” aggregates from BVqT, lamellar structured particles of elongated shape were obtained from SVqS’, despite vesicles serving as primary building units. Consequently, the presented triiodide-directed self-assembly into complex superstructures is not restricted to miktoarm star polymers containing a low-Tg segment, as the rearrangement processes take place during the dialysis process, where the organic co-solvent enables sufficient mobility of the core-forming blocks.
Besides the introduction of a novel synthetic approach for the construction of miktoarm star terpolymers and the synthetic advance of the alkyne-functionalized DPE, the presented triiodide-mediated superstructure formation represents an interesting concept for directed self-assembly processes.
Charge and excitation-energy transfer in time-dependent density functional theory
- Learning about and understanding the mechanisms and pathways of charge and excitation-energy transfer of natural molecular complexes is a promising approach for the tailored design of new artificial energy-converting materials. Therefore, next to extensive experimental investigations, a theoretical method that is able to reliably describe and predict these phenomena from first principles is of practical relevance. In principle, density functional theory (DFT) and time-dependent density functional theory (TDDFT) appear as natural choices to study the relevant sizable molecules on a first-principles scale at bearable computational cost. However, the application of standard local and semilocal density functional approximations suffers from well-known deficiencies, in particular, as far as the simulation of charge-transfer phenomena is concerned. The present thesis approaches charge and excitation-energy transfer with the objective of improving the predictive power and extending the range of applicability of (TD)DFT.
The deficiencies of standard density functional approximations have been related to self-interaction. Hence, one major aspect of this work is the extension of the self-interaction correction in Kohn-Sham DFT that is based on the generalized optimized effective potential to TDDFT using a real-time propagation approach. The multiplicative Kohn-Sham potential allows for a transparent analysis of the exchange-correlation potential during time evolution. It reveals frequency-dependent field-counteracting behavior and step structures that appear in dynamic charge-transfer situations. The latter are important for the proper description of charge transfer. Self-interaction correction allows to access many cases that are difficult for standard TDDFT ranging from chain-like systems over excitonic excitations in semiconductor nanoclusters to short- and long-range charge-transfer excitations. At the same time, it does not spoil the reasonable accuracy that already (semi)local functionals exhibit for local excitations. Moreover, the TDDFT perspective on self-interaction correction sheds new light also on the ground-state formalism. Complex degrees of freedom in the energy-minimizing transformation of the generalized optimized effective potential approach yield smoother orbital densities that appear more reasonable when inserted into approximate functionals in the self-interaction correction formalism. This work provides new insight into the use of different functional approximations. Last but not least, the influence of spin-symmetry breaking and step structures of the potential on the preference to transfer integer units of the elementary electric charge between largely separated donor and acceptor moieties is illustrated when static external electric fields are applied. This work has been reported in three publications and one submitted manuscript.
In the field of excitation-energy transfer, recent discoveries of quantum coherence effects shed new light on the mechanisms behind energy-transfer rates. The latter are affected by a number of different properties of the isolated molecules, but involve also effects due to the environment of the system. This thesis addresses excitation-energy transfer phenomena from two perspectives. First, I use real-time propagation TDDFT to investigate the intermolecular coupling strength and the coupling mechanism between single fragments of supermolecular setups. These investigations base on standard closed quantum system TDDFT and exploit the coherent oscillation of excitation energy between separated molecules after the initial excitation process. Second, I use open quantum system ideas in the framework of TDDFT to study the influence of the system’s environment on the energy-transfer time scales and pathways in a circular arrangement of molecules using an effective energy-dissipation mechanism. The first part of these results is published. The second part is presented in this thesis and includes work in progress.
Budget and fluxes of nitrogen in mountainous agroecosystems in a summer monsoonal climate under intensive land use
- A balanced nitrogen (N) cycle in intensively managed ecosystems is necessary as it underpins other ecosystem services. This study evaluated the agricultural practices in a typical mountainous catchment in South Korea in respect to N dynamics and their potential effect on water quality with the aim to develop options for a more sustainable catchment management.
In the 1st study, we used two approaches to calculate N budgets for the 5 key crops of the basin at the field scale. The gross and net N budgets for all crop types were found to be positive. Based on the small differences between the results of the two approaches we identified fertilizer N as well as soil Nmin as the dominant N input sources. As fertilizer N application was the major N input source (>50%), its reduction is the major scope of action for N savings at the field scale. A closely linked action is the synchronization of fertilizer N with soil Nmin. The large amount of fertilizer that is applied prior to planting (>60%) at the beginning of the monsoon season revealed that split applications could help reducing the fertilizer N additions and increase the low N use efficiencies (NUE). Based on the significant differences between gross and net N surplus for rice and bean fields, we identified the high amount of plant residues remaining after harvesting (>100 kg N ha-1) as a further factor for potential N savings. The 5 main crops accounted for over 80% of the total catchment N surplus (>400 Mg), even though their contribution to the area was only around 20%. A land use shift to perennial crops with lower N inputs was therefore found to be a possible but spatially limited chance to reduce N surpluses at the catchment scale. The comparison of catchment N surplus with stream N export revealed that 73-86% of the agricultural N surpluses were transported to water bodies in the catchment by either leaching or surface runoff.
In the 2nd study, we followed the fate of fertilizer N in a ridge and furrow (R/F) cultivation with polyethylene (PE) mulch by using 15N tracer. N leaching was simulated with Hydrus 2D. The comparison of 4 N fertilization levels (0, 150, 250 and 350 kg N ha-1) revealed that already 150 kg N ha-1 is sufficient to reach the maximal yield of radishes. Based on the low results of fertilizer N use efficiency (FNUE), we recommend two applications during the first 25 days of growth and a further application around day 50. These split applications adjusted to the plants’ needs increase the FNUE of the radish and decrease the fertilizer N losses during the growing season. However, split applications might be impractical in plastic covered R/F cultivations because mechanical equipment to apply fertilizer under the PE mulch is required. Based on the finding that 15N retention in soil and nitrate concentration in seepage water decreased similarly for ridges and furrows during the entire growing season, we conclude that the PE mulch had no significant effect on 15N retention in soil and on nitrate concentration in seepage water and did therefore not effectively protect the fertilizer in the ridges from percolation. Based on the simulation results, we found that the ridges and furrows contributed approximately an equal amount of leached N to the total amount. We therefore conclude that the PE mulch provided little protection for the fertilizer N in the ridges during heavy rainfall. N leaching amounts were further found to increase linearly with an increase in N addition rate as it is well known for R/F cultivations without PE mulch. The PE mulch did therefore not prevent the linear increase in leaching with an increase in fertilizer N addition. We summarize that without the use of additional measures such as split applications of fertilizer, the application of PE mulch in a summer monsoon climate with heavy rainfall events does not positively influence the N leaching rates.
In the 3rd study, we monitored soil water dynamics in the field and used this data set to simulate the influence of PE mulch on water fluxes with Hydrus 2D. We simulated soil water dynamics in 1) conventional flat tillage (CT); 2) R/F cultivation without PE mulched ridges (RT); and 3) R/F cultivation with PE mulched ridges (RTpm). The comparison of the simulated pressure heads during dry and wet periods revealed that the PE mulch induced significant soil moisture patterns only during the dry periods. During monsoon events, the effect of the PE mulch was dependent on the soil texture and the hydraulic conductivity. Summarizing the advantages and disadvantages of the R/F cultivation with PE mulch on sloped fields, the practice was observed to have the lowest amount of drainage water, the lowest evaporation rates but also the highest surface runoff rates. Hence, PE mulching might be assessed as a tool to reduce percolating water, but it concurrently increases water contribution to the river network by surface runoff.
Foamy Virus RNase H - Aktivität, Struktur und Funktion
Das für die Replikation des RNA-Genoms von Foamy Viren (FV) notwendige Enzym, die Protease-Reverse Transkriptase (PR-RT), beinhaltet die Protease-, die Polymerase- und RNase H-Domäne. Letztere ist für den Abbau der RNA im entstehenden RNA/DNA Hybrid verantwortlich. Während die FV PR-RT als Monomer vorliegt, besteht die HIV-1 RT aus einem p66/p51-Heterodimer. Erstaunlicherweise ist die isolierte HIV-1 RNase H im Vergleich zur z.B. E. coli oder separaten MoMLV RNase H nicht aktiv. Aus den Sequenzvergleichen verschiedener RNase H-Domänen ergibt sich, dass die Prototyp FV (PFV) RNase H im Gegensatz zur HIV-1 RNase H einen Sekundärstrukturbereich aufweist, bei dem es sich um die sogenannte C-Helix mit einer sich anschließenden basischen Schleife (basic protrusion) handelt. Da zu Beginn der Arbeit keine 3D-Struktur einer retroviralen RNase H mit basic protrusion bekannt war, sollte in dieser Arbeit die Struktur der PFV RNase H und die Funktion der basic protrusion bei der Substratbindung geklärt werden.
Die Tertiärstruktur der PFV RNase H-Domäne konnte mit NMR-Spektroskopie gelöst werden. Somit war es möglich, die basic protrusion einschließlich der C-Helix zu identifizieren. Die isolierte RNase H-Domäne zeigte in fluoreszenzbasierten Tests sowie in qualitativen RNase H-Versuchen mit radioaktiv markiertem Substrat Aktivität. Um die Funktion der C-Helix und der sich anschließenden basischen Schleife bei der Substratbindung zu analysieren, wurden NMR-Titrationsexperimente durchgeführt. Dafür wurde die PFV RNase H-Domäne zunächst durch den Austausch der zwei katalytisch wichtigen Reste Aspartat 599 und Histidin 724 zu Asparagin inaktiviert (RNase H-(D599N-H724N)), um den Abbau des Substrates während der Messungen zu vermeiden. Die Auswertung von [15N, 1H]-HSQC- und [1H, 15N, 1H]-NOESY-HSQC-Spektren erbrachte eine Übereinstimmung der Tertiärstrukturen der RNase H-(D599N-H724N) mit der wt RNase H.
Die NMR-Titrationsexperimente zeigten, dass die C-Helix in der PFV RNase H wie ein Lineal agiert, das die sich anschließende basische Schleife zum Substrat orientiert. Darüber hinaus besitzt die basic protrusion zusätzlich eine Reihe an positiv geladenen Resten, die gut lösungsmittelzugänglich sind und dadurch erste Kontakte mit dem Substrat ermöglichen. Damit bietet die basic protrusion eine Art Plattform für die Substratbindung. Der HIV-1 RNase H fehlt nicht nur die C-Helix, zusätzlich ist die sich anschließende Schleife vermutlich zu kurz, um das Substrat zu binden. Da diese Schleife außerdem nur über einen basischen Rest verfügt, ist wahrscheinlich auch die Gesamtaffinität dieses Bereichs für die Substratbindung zu gering. Strukturvergleiche der PFV RNase H mit der HIV-1 RT zeigen, dass die fehlende basic protrusion der HIV-1 RNase H durch eine Schleife aus der Verbindungs-Subdomäne der p66-Untereinheit kompensiert wird. Dieser Bereich könnte somit ein neuer Angriffspunkt für Inhibitoren in der antiretroviralen Therapie bei HIV 1 sein.
Um zukünftig weitere Strukturanalysen mit der PR-RT bzw. mit einzelnen Domänen durchführen zu können, wurden in einem weiteren Projekt verschiedene N- und C-terminale Deletionsvarianten der PR-RT des Simian Foamy Virus hergestellt. Durch Aktivitätstests mit diesen Deletionsvarianten konnten die Abgrenzungen für die PR-, die Polymerase-, die RNase H-Domäne und die Verbindungs-Subdomäne in der PR-RT identifiziert werden. Dabei zeigte sich, dass die Region H107-N143 C-terminal von der PR wichtig für die Funktion der Polymerase ist. Die Deletion der RNase H-Domäne und Verbindungs-Subdomäne führte zu einer drastischen Abnahme der Substrataffinität, Integrität und Polymerisationsfähigkeit des Enzyms. Trotzdem konnte eine minimale Polymerase-Domäne bestimmt werden (RT(107 454)), die ohne PR- und RNase H-Domäne sowie ohne die Verbindungs-Subdomäne in der Lage ist, zu polymerisieren. Für die Dimerisierung und damit Aktivierung der PR, die durch Bindung von zwei PR-RTs an das sog. PARM-Element (engl. protease activating RNA motif) auf der genomischen RNA geschieht, sind jedoch die RNase H-Domäne und die Verbindungs-Subdomäne unverzichtbar. Dadurch ist die RNase H nicht nur für die reverse Transkription essenziell; in FV stellt sie auch ein Regulationselement für die PR-Aktivierung dar und ist somit indirekt an der Prozessierung von Gag (Strukturproteine) und Pol (virale Enzyme) beteiligt.
Structural and electronic properties of transition metal nanoalloys and magnetic compounds
- In transition metal clusters, potentially profitable technological applications and fascinating fundamental questions are closely connected. Bimetallic nanoalloys, e.g., have become increasingly popular as their performance in catalysis is often superior to their pure counterparts. Exemplary for this are gold-platinum (Au-Pt) nanoalloys that have been used as highly potent catalysts in electrocatalysis and in a variety of oxidation reactions. However, the mere existence of Au-Pt nanoalloys is astonishing, as Au and Pt cannot be mixed in bulk over a wide range of compositions. Furthermore, how a combination of Au and Pt in nanoalloys results in their special properties has not yet been determined conclusively.
It has been shown in empirical simulations and first-principles density functional theory (DFT) calculations that Au-Pt nanoalloys preferably arrange in a core-shell mixing pattern with Au forming a shell around a Pt core. This is in contradiction to many experimental studies that report the formation of solid solutions of Au and Pt. In the present work, this seeming discrepancy is addressed by simulating x-ray diffraction patterns that are experimentally used to characterize nanoalloys. It is shown that the interpretation of the diffraction patterns relies on questionable assumptions and therefore does not suffice as a definite characterization tool for Au-Pt nanoalloys.
To shed light on the special catalytic properties of Au-Pt nanoalloys under rather different experimental conditions, a thorough investigation of their electronic and structural properties has been carried out. It is found that features favorable for catalysis in Au-Pt nanoalloys emerge as a consequence of combining two fundamental properties: Pt contributes a high density of states close to the Fermi level, which promotes chemical activity. Au increases the structural flexibility of the Au-Pt system, which might be beneficial for the formation of active and element-specific binding sites as well as regeneration of the catalyst after the reaction.
Although DFT offers an attractive compromise between computational effort and accuracy for a theoretical description of Au-Pt nanoalloys, other transition metal compounds severely challenge existing DFT approximations. Manganese (Mn) doped silicon (Si) clusters represent an ideal model system to study the interaction of a single magnetic impurity with a semiconducting host both experimentally and theoretically. The transition from exohedral (lowly coordinated) to endohedral (highly coordinated) doping that occurs for Si clusters with more than ten atoms, is accompanied by complete quenching of the magnetic moment of Mn. We show that MnSi11+, the smallest endohedral cluster found in experiment, suffers strongly from a well-known general problem of most DFT approximations: the self-interaction error. Finally, a universal correlation between magnetic moment and the coordination of the Mn dopant is established that can be generalized to extended systems and suggests a route to stabilize the magnetic moment of bulk Mn-Si compounds.