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.
Monsoonal affected dynamics of nitrate and dissolved organic carbon in a mountainous catchment under intensive land-use
- In recent decades, complex mountainous landscapes have been increasingly under pressure by deforestation and intensified highland agriculture. This trend not only compromises the quality of water in the highlands, but also impacts the availability of water resources downstream. Hence, an effective and sustainable management of these mountainous regions is essential and needed to mitigate this risk. Developing sustainable management principles to ensure the freshwater supply, however, requires a profound understanding of decisive factors and processes that control the water quality in mountainous landscapes. Amongst other substances, nitrate and dissolved organic carbon (DOC) play a critical role in the ecosystem health of water bodies. The major focus of this dissertation is on determining the nitrate and DOC mobilization processes and dynamics in the Haean Catchment, a mountainous watershed located in South Korea, which is agriculturally productive and strongly influenced by the prevailing East-Asian monsoon. The primary objective was to identify decisive factors that control the nitrate and DOC mobilization processes and dynamics in such catchments.
To these ends, we conducted stream water quality and discharge measurements during a range of conditions, from monsoonal rainfall events to dry, baseflow conditions. Assessments were completed along the topographic elevation gradient of the catchment, from an upland deciduous forest, over areas intensively used for agriculture, down to the catchment outlet. In order to gain a better understanding of nutrient fate within the Haean Catchment, we investigated river-aquifer exchange fluxes. In addition to hydraulic gradient monitoring, we used heat as tracer. To resolve the river-aquifer exchange fluxes, we set up a two-dimensional flow and heat transport model using the numerical code HydroGeoSphere (HGS). Potential effects of river-aquifer exchange dynamics on local water quality were investigated by collecting both, river and groundwater samples. Furthermore, we determined the impact of the ridge and furrow cultivation that is commonly applied in South Korean dryland agriculture, on nitrate leaching and evaluated fertilizer best management practices (FBMPs) using a three-dimensional flow and solute transport model (HGS).
Our results show that DOC and nitrate sources as well as their mobilization differ between the forest and agricultural river sites. In the forest, elevated in-stream DOC concentrations during rainfalls were due to hydrologic flushing of soluble organic matter in upper soil horizons with a strong dependency on pre-storm wetness conditions. Nitrate contributions to the stream occurred predominantly along interflow transport pathways.
At the agricultural sites, in-stream DOC concentrations were considerably higher and supplied from adjacent rice paddies. The highest in-stream nitrate concentrations occurred in the lower agricultural part of the catchment. Through hydraulic gradient monitoring, we identified in this part of the catchment a distinct connection between the river and aquifer, and nitrate-rich groundwater inputs to the river elevated the in-stream nitrate concentration. In the mid-elevation portion of the catchment, however, a limited connectivity between the river and aquifer was identified and river water quality was consequently unaffected in these areas.
The results of our HGS modeling study show a high temporal and spatial variability in river-aquifer exchange fluxes with frequent flow reversals during the monsoon season. Our results also suggest that these flow reversals may enhance the natural attenuation of nitrate in the shallow groundwater below the stream. The simulation results on evaluating FBMPs demonstrate that applying a combination of several FBMPs such as an adapted placement and timing is recommended to minimize the risk of groundwater nitrate contamination.
Overall, this dissertation demonstrates that the hydrologic pathways resulting from the monsoon climate drive the in-stream DOC dynamics in the forested catchment, whereas sources and mobilization of DOC in downstream agricultural areas are mainly controlled by the specific land-use type. In particular, the widely used rice paddy “plot-to-plot” irrigation system in Korean highlands was shown to control in-stream DOC concentrations. Nitrate dynamics in streams and aquifers in the agricultural areas of the catchment reflect the combined effects of land-use type and monsoonal hydrology. Particularly, the highly variable river-aquifer exchange fluxes with frequent flow reversals, which may enhance the nitrate attenuation, are driven by monsoonal extreme precipitation events. Since it has been forecasted that global warming will increase the frequency and the intensity of extreme precipitation events also in other regions of the world, our results will become increasingly important in future water quality assessments and research.
Development of an artificial silk protein on the basis of a lacewing egg stalk protein
- Silks are widely used in textile industry as clothing and furnishings due to their tensile strength, smoothness, soft texture, lustre, and drape. Most commonly silk of the mulberry silkworm Bombyx mori (B. mori) is used in such applications, however, silks evolved independently in many different arthropods for various purposes.1 During evolution the different silks were optimised for their task-specific uses over millions of years, e.g. adopting different mechanical properties. The mechanical properties mainly derive from the protein secondary structure and its higher order arrangement in silk fibres. Spider silk, for example, is known for its tensile properties surpassing nylon, Kevlar®, silkworm silk, and high-tensile steel.2-5 Beyond their mechanical properties, some silks are also reported to be biocompatible and non-immunogenic.6 One beneficial feature of silk proteins is the possibility to process them into various morphologies.7, 8
Several of these silk features make them interesting for material scientists, intending to produce silks with tuneable properties depending on the desired application, ranging from technical ones such as high performance fibres to medical ones such as drug delivery.
This thesis deals with the characterisation and reproduction of a less explored silk, the lacewing egg stalk silk. Mechanical testing revealed a strong dependence on the relative humidity. In the dry state at 30% relative humidity, the stalks are quite rigid and break at an elongation of 2% whereas at 70% and 100% relative humidity they elongate up to 434%. This extension is accompanied by a secondary structure change from cross-ß to parallel-ß. The cross-ß structure in unstretched stalks provides bending stiffness and rigidity to the stalk, and this bending stiffness gets lost when the stalks are stretched. In this thesis a model is proposed which explains these differences at various relative humidity on the molecular level, wherein changes in the strength of hydrogen bonds upon exposure to water (a hydrogen bond donor/acceptor) in combination with multiple disulphide cross-links (which are not affected by water) act together and are responsible for this behaviour.
Based on consensus sequences of published sequence data (derived from MalXB2 an egg stalk protein of Mallada signata (M. signata)),9 an engineered egg stalk protein named N[AS]8C was recombinantly produced.
To produce an artificial stalk, a droplet of a solution of purified N[AS]8C was placed on a substrate, and tweezers were used to pull out a fibre. After drying, and post treatment, the properties of the artificial stalks were investigated in comparison to the natural ones. Mechanical testing revealed similar behaviour at 30% relative humidity, but at 70% and 100% relative humidity the artificial stalks were not as extensible as the natural ones. This corresponds to the fact, that no cross-ß structure was formed, and, therefore, no rearrangement into parallel-ß structure was possible.
Subsequently, N[AS]8C was processed into non-fibrous morphologies. It was possible to produce capsules, hydrogels, foams, and films. The foams show an interesting micro and nano structure which differs from that of recombinant spider silk. The cavities are filled with a mesh of nano fibres building a 3D scaffold.
Films are a morphology with potential for application in cell culture. Fibroblast attachment on N[AS]8C films is quite poor. Therefore, we tried to induce guided fibroblast growth on patterned protein films. A first layer of the films was cast from ntagCysC16-c(RGDfK), an engineered spider silk protein coupled with the integrin recognition motif RGD to provide a protein layer to which fibroblasts attached well. The second protein layer was produced using a PDMS (polydimethylsiloxane) template and N[AS]8C. Fibroblasts grown on these films adhere only to the RGD modified spider silk and not to the N[AS]8C areas. A second feature of such films is to orient the fibroblasts on films with alternating lines of the two proteins. Such films might be useful for tissue engineering to control cell adhesion and get a structured cell pattern. This is essential for many tissues such as bones, muscles, and epithelia tissue. The low cell adhesion properties of N[AS]8C films might be interesting for coatings for applications where cell adhesion is not desired such as stents or catheters.
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.
Partikel und Kapseln auf Basis des rekombinanten Spinnenseidenproteins eADF4(C16)
- Natürliche Spinnenseide als Biomaterial wird aufgrund seiner einzigartigen mechanischen Eigenschaften und seiner guten Biokompatibilität schon seit Jahrhunderten vom Menschen genutzt. Hierbei sind insbesondere die Proteine des Abseilfadens der Gartenkreuzspinne A. diadematus von Interesse. Der Abseilfaden setzt sich aus mehreren Proteinkomponenten zusammen, eine dieser Komponenten ist das Protein ADF4, diesem nachempfunden ist das rekombinant hergestellte Protein eADF4. ADF4 besteht aus bis zu 100 Wiederholungen einer repetitiven Kernsequenz, welche von nicht-repetitiven terminalen Regionen flankiert wird. eADF4 besteht aus dieser, jedoch für E. coli optimierten, Kernsequenz (C-Modul). In dieser Arbeit lag das Hauptaugenmerk auf eADF4(C16). Dieses besteht aus 16 Wiederholungen des C-Moduls, das daraus resultierende Protein hat ein Molekulargewicht von ca. 47 kDa.
Die kontrollierte und gezielte Freisetzung von Wirkstoffen oder Enzymen (controlled drug delivery) ist ein wichtiges Forschungsgebiet sowohl in der Pharmazie als auch in der Medizin. Mittels controlled drug delivery sollen Probleme der herkömmlichen Medikamentation behoben werden. Hierzu zählen beispielsweise Nebenwirkungen die aufgrund einer sehr hohen lokalen Wirkstoffkonzentration nach Injektion des Wirkstoffs oder nach Auflösen einer Tablette am Wirkort auftreten können. Um dies zu minimieren, sollen Depotsysteme Medikamente kontrolliert über einen längeren Zeitraum am gewünschten Wirkort abgeben. Hierfür eignen sich insbesondere mobile Systeme, wie Partikel und Kapseln.
Bei Partikeln aus eADF4(C16) handelt es sich um Vollkugeln, welche durch Aussalzprozesse aus wässriger Lösung hergestellt werden. Sie eignen sich insbesondere für den Transport von wasserlöslichen Stoffen, was am Beispiel Rhodamin B gezeigt wurde. Die Beladung der Partikel erfolgt hierbei auf zwei verschiedene Arten. Zum einen durch Eindiffundieren der Wirkstoffe in die fertig ausgebildeten Partikel, zum anderen durch co-Präzipitation des Wirkstoffs zusammen mit dem Protein. Es konnte gezeigt werden, dass die Beladung der Partikel mit Wirkstoffen durch co-Präzipitation im Vergleich zu Diffusionsprozessen deutlich erhöht werden konnte. Zusätzlich sollte durch Vernetzungsprozesse (crosslinking) Einfluss auf die Wirkstofffreisetzung genommen werden. Dies konnte jedoch nicht in vollem Umfang erzielt werden. Es konnte jedoch gezeigt werden, dass chemisches Vernetzen einen deutlichen Einfluss auf die chemische Stabilität der Partikel hat und dass sowohl chemisches als auch physikalisches Vernetzen die Mechanik der Partikel stark beeinflusst. Zusätzlich konnte das Quellverhalten der Partikel analysiert werden, was einen entscheidenden Einfluss auf ihre Lagerstabilität aufweist. Sowohl die Mechanik als auch die Oberflächeneigenschaften der Partikel sind wichtige Parameter in Bezug auf weitere Anwendungsmöglichkeiten. Insbesondere im Bereich der Kompositmaterialien sind die Partikel vielseitig einsetzbar. Durch Inkorporation von eADF4 Partikeln in eine Matrix können die mechanischen Eigenschaften des Matrixmaterials möglicherweise stark verbessert werden und durch die Bioabbaubarkeit der Partikel ergeben sich weitere Möglichkeiten im Bereich von Knochenersatzmaterialien.
Bei Kapseln handelt es sich um flüssigkeitsgefüllte Systeme, die von einem dünnen, aber stabilen Seidenfilm umhüllt sind. Die Kapselherstellung erfolgt mittels Grenzflächenpolymerisation an der Grenzfläche zwischen Öl und Wasser. Das bisher etablierte System basiert auf der Verwendung von Toluol, welches in Hinblick auf eine medizintechnische Anwendung bedenklich ist. Kapseln als Transportsystem eignen sich sowohl für schlechtlösliche als auch für gut-wasserlösliche Wirkstoffe mit einem Molekulargewicht größer als 30 kDa. Durch die Herstellung von Kapseln mittels Silikonöl anstatt Toluol, konnte ihre Verwendung als Transportsystem für Enzyme erfolgreich gezeigt werden. Dies erfolgte mittels -Galaktosidase als Modellenzym. Die Substrate können, aufgrund der semi-permeablen Kapselhülle, in die Kapseln eindiffundieren, bestimmte Proteasen mit entsprechend großem Molekulargewicht werden jedoch abgehalten. Ein Vorteil der Spinnenseidenkapseln gegenüber anderen Systemen ist, dass auch inaktive Enzyme verkapselt und am Wirkort durch Zugabe des Aktivators gezielt aktiviert werden können. Um eine möglichst homogene Größenverteilung der Kapseln zu erzielen, wurde eine Herstellung mittels Mikrofluidik erprobt.
Um die Anwendbarkeit von eADF4 Proteinen im medizinischen oder pharmazeutischen Bereich sicherstellen zu können ist die Sterilität der Proteine ein entscheidendes Kriterium. Rekombinante Proteine, speziell solche, die in Bakterien produziert wurden, sind in der Regel auch nach Aufreinigung unsteril. Aus diesem Grund wurden in meiner Arbeit verschiedene Sterilisationsmethoden getestet und ihre Auswirkungen auf die rekombinanten Spinnenseidenproteine analysiert.
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.