Meshing highly regular structures: The case of super carbon nanotubes of arbitrary order

Mesh generation is an important step inmany numerical methods.We present the “HierarchicalGraphMeshing” (HGM)method as a novel approach to mesh generation, based on algebraic graph theory.The HGM method can be used to systematically construct configurations exhibiting multiple hierarchies and complex symmetry characteristics. The hierarchical description of structures provided by the HGM method can be exploited to increase the efficiency of multiscale and multigrid methods. In this paper, the HGMmethod is employed for the systematic construction of super carbon nanotubes of arbitrary order, which present a pertinent example of structurally and geometrically complex, yet highly regular, structures. The HGMalgorithm is computationally efficient and exhibits good scaling characteristics. In particular, it scales linearly for super carbon nanotube structures and is working much faster than geometry-based methods employing neighborhood search algorithms. Its modular character makes it conducive to automatization. For the generation of a mesh, the information about the geometry of the structure in a given configuration is added in a way that relates geometric symmetries to structural symmetries. The intrinsically hierarchic description of the resulting mesh greatly reduces the effort of determining mesh hierarchies for multigrid and multiscale applications and helps to exploit symmetry-related methods in the mechanical analysis of complex structures.

Influence of the buffer environment on the Relative Biological Effectiveness of carbon ion radiation, investigated by Scanning Force Microscopy and gel electrophoresis

This work focuses on the analysis of the influence of environment on the relative biological effectiveness (RBE) of carbon ions on molecular level. Due to the high relevance of RBE for medical applications, such as tumor therapy, and radiation protection in space, DNA damages have been investigated in order to understand the biological efficiency of heavy ion radiation. The contribution of this study to the radiobiology research consists in the analysis of plasmid DNA damages induced by carbon ion radiation in biochemical buffer environments, as well as in the calculation of the RBE of carbon ions on DNA level by mean of scanning force microscopy (SFM). In order to study the DNA damages, besides the common electrophoresis method, a new approach has been developed by using SFM. The latter method allows direct visualisation and measurement of individual DNA fragments with an accuracy of several nanometres. In addition, comparison of the results obtained by SFM and agarose gel electrophoresis methods has been performed in the present study. Sparsely ionising radiation, such as X-rays, and densely ionising radiation, such as carbon ions, have been used to irradiate plasmid DNA in trishydroxymethylaminomethane (Tris buffer) and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES buffer) environments. These buffer environments exhibit different scavenging capacities for hydroxyl radical (HO0), which is produced by ionisation of water and plays the major role in the indirect DNA damage processes. Fragment distributions have been measured by SFM over a large length range, and as expected, a significantly higher degree of DNA damages was observed for increasing dose. Also a higher amount of double-strand breaks (DSBs) was observed after irradiation with carbon ions compared to X-ray irradiation. The results obtained from SFM measurements show that both types of radiation induce multiple fragmentation of the plasmid DNA in the dose range from D = 250 Gy to D = 1500 Gy. Using Tris environments at two different concentrations, a decrease of the relative biological effectiveness with the rise of Tris concentration was observed. This demonstrates the radioprotective behavior of the Tris buffer solution. In contrast, a lower scavenging capacity for all other free radicals and ions, produced by the ionisation of water, was registered in the case of HEPES buffer compared to Tris solution. This is reflected in the higher RBE values deduced from SFM and gel electrophoresis measurements after irradiation of the plasmid DNA in 20 mM HEPES environment compared to 92 mM Tris solution. These results show that HEPES and Tris environments play a major role on preventing the indirect DNA damages induced by ionising radiation and on the relative biological effectiveness of heavy ion radiation. In general, the RBE calculated from the SFM measurements presents higher values compared to gel electrophoresis data, for plasmids irradiated in all environments. Using a large set of data, obtained from the SFM measurements, it was possible to calculate the survive rate over a larger range, from 88% to 98%, while for gel electrophoresis measurements the survive rates have been calculated only for values between 96% and 99%. While the gel electrophoresis measurements provide information only about the percentage of plasmids DNA that suffered a single DSB, SFM can count the small plasmid fragments produced by multiple DSBs induced in a single plasmid. Consequently, SFM generates more detailed information regarding the amount of the induced DSBs compared to gel electrophoresis, and therefore, RBE can be calculated with more accuracy. Thus, SFM has been proven to be a more precise method to characterize on molecular level the DNA damage induced by ionizing radiations.

Application of biogas slurries from energy crops to arable soils and their impact on carbon and nitrogen dynamics

The use of renewable primary products as co-substrate or single substrate for biogas production has increased consistently over the last few years. Maize silage is the preferential energy crop used for fermentation due to its high methane (CH4) yield per hectare. Equally, the by-product, namely biogas slurry (BS), is used with increasing frequency as organic fertilizer to return nutrients to the soil and to maintain or increase the organic matter stocks and soil fertility. Studies concerning the application of energy crop-derived BS on the carbon (C) and nitrogen (N) mineralization dynamics are scarce. Thus, this thesis focused on the following objectives: I) The determination of the effects caused by rainfall patterns on the C and N dynamics from two contrasting organic fertilizers, namely BS from maize silage and composted cattle manure (CM), by monitoring emissions of nitrous oxide (N2O), carbon dioxide (CO2) and CH4 as well as leaching losses of C and N. II) The investigation of the impact of differences in soil moisture content after the application of BS and temperature on gaseous emissions (CO2, N2O and CH4) and leaching of C and N compounds. III) A comparison of BS properties obtained from biogas plants with different substrate inputs and operating parameters and their effect on C and N dynamics after application to differently textured soils with varying application rates and water contents. For the objectives I) and II) two experiments (experiment I and II) using undisturbed soil cores of a Haplic Luvisol were carried out. Objective III) was studied on a third experiment (experiment III) with disturbed soil samples. During experiment I three rainfall patterns were implemented including constant irrigation, continuous irrigation with periodic heavy rainfall events, and partial drying with rewetting periods. Biogas slurry and CM were applied at a rate of 100 kg N ha-1. During experiment II constant irrigation and an irrigation pattern with partial drying with rewetting periods were carried out at 13.5°C and 23.5°C. The application of BS took place either directly before a rewetting period or one week after the rewetting period stopped. Experiment III included two soils of different texture which were mixed with ten BS’s originating from ten different biogas plants. Treatments included low, medium and high BS-N application rates and water contents ranging from 50% to 100% of water holding capacity (WHC). Experiment I and II showed that after the application of BS cumulative N2O emissions were 4 times (162 mg N2O-N m-2) higher compared to the application of CM caused by a higher content of mineral N (Nmin) in the form of ammonium (NH4+) in the BS. The cumulative emissions of CO2, however, were on the same level for both fertilizers indicating similar amounts of readily available C after composting and fermentation of organic material. Leaching losses occurred predominantly in the mineral form of nitrate (NO3-) and were higher in BS amended soils (9 mg NO3--N m-2) compared to CM amended soils (5 mg NO3--N m-2). The rainfall pattern in experiment I and II merely affected the temporal production of C and N emissions resulting in reduced CO2 and enhanced N2O emissions during stronger irrigation events, but showed no effect on the cumulative emissions. Overall, a significant increase of CH4 consumption under inconstant irrigation was found. The time of fertilization had no effect on the overall C and N dynamics. Increasing temperature from 13.5°C to 23.5°C enhanced the CO2 and N2O emissions by a factor of 1.7 and 3.7, respectively. Due to the increased microbial activity with increasing temperature soil respiration was enhanced. This led to decreasing oxygen (O2) contents which in turn promoted denitrification in soil due to the extension of anaerobic microsites. Leaching losses of NO3- were also significantly affected by increasing temperature whereas the consumption of CH4 was not affected. The third experiment showed that the input materials of biogas plants affected the properties of the resulting BS. In particular the contents of DM and NH4+ were determined by the amount of added plant biomass and excrement-based biomass, respectively. Correlations between BS properties and CO2 or N2O emissions were not detected. Solely the ammonia (NH3) emissions showed a positive correlation with NH4+ content in BS as well as a negative correlation with the total C (Ct) content. The BS-N application rates affected the relative CO2 emissions (% of C supplied with BS) when applied to silty soil as well as the relative N2O emissions (% of N supplied with BS) when applied to sandy soil. The impacts on the C and N dynamics induced by BS application were exceeded by the differences induced by soil texture. Presumably, due to the higher clay content in silty soils, organic matter was stabilized by organo-mineral interactions and NH4+ was adsorbed at the cation exchange sites. Different water contents induced highest CO2 emissions and therefore optimal conditions for microbial activity at 75% of WHC in both soils. Cumulative nitrification was also highest at 75% and 50% of WHC whereas the relative N2O emissions increased with water content and showed higher N2O losses in sandy soils. In summary it can be stated that the findings of the present thesis confirmed the high fertilizer value of BS’s, caused by high concentrations of NH4+ and labile organic compounds such as readily available carbon. These attributes of BS’s are to a great extent independent of the input materials of biogas plants. However, considerably gaseous and leaching losses of N may occur especially at high moisture contents. The emissions of N2O after field application corresponded with those of animal slurries.

Effects of grassland renovation on carbon concentrations and aggregate distribution in temperate grassland soils

The effects of continuous tillage on the distribution of soil organic matter (SOM) and aggregates have been well studied for arable soils. However, less is known about the effects of sporadic tillage on SOM and aggregate dynamics in grassland soils. The objectives of the present thesis were (I) to study the longer-term effects of sporadic tillage of grassland on organic carbon (Corg) stocks and the distribution of aggregates and SOM, (II) to investigate the combined effects of sporadic tillage and fertilization on carbon and nitrogen dynamics in grassland soils, and (III) to study the temporal dynamics of Corg stocks, aggregate distribution and microbial biomass in grassland soils. Soil samples were taken in three soil depths (0 – 10 cm; 10 – 25 cm; 25 – 40 cm) from a field trial with loamy sandy soils (Cambisols, Eutric Luvisols, Stagnosols, Anthrosols) north of Kiel, Germany. For Objective I we have sampled soil two and five years after one or two tillage operation(s). Treatments consisted of (i) permanent grassland, (ii) tillage of grassland followed by a re-establishment of grassland and (iii) tillage of grassland followed by a re-establishment of grassland with one season of winter wheat in between. The tillage in grassland led to a reduction in Corg stocks, large macroaggregates (>2000 µm) and SOM in the top 10 cm soil depth. These findings were still significant two years after tillage; however, five years after tillage no longer present. Regarding the soil profile (0 – 40 cm) no significant differences in the mentioned parameters between the tilled plots and the permanent grassland existed. A second tillage event and the insertion of one season of winter wheat did not lead to any further effects on Corg stocks as well as aggregate and SOM concentrations in comparison with a single tillage event in these grassland soils. Treatments adapted for Objective II included (i) long-term grassland and (ii) tillage of grassland followed by a re-establishment of grassland with one season of winter wheat in between. The plots were split and received either 240 kg N ha-1 year-1 in the form of cattle slurry or no cattle slurry application. The application of slurry within a period of four years had no effects on the Corg and total nitrogen stocks or the aggregate distribution, but led to a reduction of free and not physically protected SOM. However, the application of cattle slurry and the grassland renovation seems to change the plant species composition and therefore generalizations on the direct effects are not yet possible. For studying Objective III a further field trial was initiated in September 2010. Soil samples were taken six times within one year (from October 2010 to October 2011) (i) after the conversion from arable land into grassland, (ii) after the tillage of grassland followed by a re-establishment of grassland and (iii) in a permanent grassland. We found an increase in the microbial and fungal biomass after the conversion of arable land into grassland, but no effect on aggregate distribution and Corg stocks. A one-time tillage operation in grassland led to a reduction in large macroaggregates and Corg stocks in the top 10 cm soil depth with no effect on the sampled soil profile. However, we found large variations in the fungal biomass and aggregate distribution within one year in the permanent grassland, presumably caused by environmental factors. Overall, our results suggest that a single tillage operation in grassland soils markedly decreased the concentrations of Corg, larger aggregates and SOM. However, this does not result in long-lasting effects on the above mentioned parameters. The application of slurry cannot compensate the negative effects of a tillage event on aggregate concentrations or Corg stocks. However, while the Corg concentration is not subject to fluctuations within a year, there are large variations of the aggregate distribution even in a permanent grassland soil. Therefore conclusions of results from a single sampling time should be handled with care.

Assessing trends in land use change in the Borana rangeland Ethiopia as one cause of greenhouse gas emissions and carbon sequestration variations

Landnutzungsänderungen sind eine wesentliche Ursache von Treibhausgasemissionen. Die Umwandlung von Ökosystemen mit permanenter natürlicher Vegetation hin zu Ackerbau mit zeitweise vegetationslosem Boden (z.B. nach der Bodenbearbeitung vor der Aussaat) führt häufig zu gesteigerten Treibhausgasemissionen und verminderter Kohlenstoffbindung. Weltweit dehnt sich Ackerbau sowohl in kleinbäuerlichen als auch in agro-industriellen Systemen aus, häufig in benachbarte semiaride bis subhumide Rangeland Ökosysteme. Die vorliegende Arbeit untersucht Trends der Landnutzungsänderung im Borana Rangeland Südäthiopiens. Bevölkerungswachstum, Landprivatisierung und damit einhergehende Einzäunung, veränderte Landnutzungspolitik und zunehmende Klimavariabilität führen zu raschen Veränderungen der traditionell auf Tierhaltung basierten, pastoralen Systeme. Mittels einer Literaturanalyse von Fallstudien in ostafrikanischen Rangelands wurde im Rahmen dieser Studie ein schematisches Modell der Zusammenhänge von Landnutzung, Treibhausgasemissionen und Kohlenstofffixierung entwickelt. Anhand von Satellitendaten und Daten aus Haushaltsbefragungen wurden Art und Umfang von Landnutzungsänderungen und Vegetationsveränderungen an fünf Untersuchungsstandorten (Darito/Yabelo Distrikt, Soda, Samaro, Haralo, Did Mega/alle Dire Distrikt) zwischen 1985 und 2011 analysiert. In Darito dehnte sich die Ackerbaufläche um 12% aus, überwiegend auf Kosten von Buschland. An den übrigen Standorten blieb die Ackerbaufläche relativ konstant, jedoch nahm Graslandvegetation um zwischen 16 und 28% zu, während Buschland um zwischen 23 und 31% abnahm. Lediglich am Standort Haralo nahm auch „bare land“, vegetationslose Flächen, um 13% zu. Faktoren, die zur Ausdehnung des Ackerbaus führen, wurden am Standort Darito detaillierter untersucht. GPS Daten und anbaugeschichtlichen Daten von 108 Feldern auf 54 Betrieben wurden in einem Geographischen Informationssystem (GIS) mit thematischen Boden-, Niederschlags-, und Hangneigungskarten sowie einem Digitales Höhenmodell überlagert. Multiple lineare Regression ermittelte Hangneigung und geographische Höhe als signifikante Erklärungsvariablen für die Ausdehnung von Ackerbau in niedrigere Lagen. Bodenart, Entfernung zum saisonalen Flusslauf und Niederschlag waren hingegen nicht signifikant. Das niedrige Bestimmtheitsmaß (R²=0,154) weist darauf hin, dass es weitere, hier nicht erfasste Erklärungsvariablen für die Richtung der räumlichen Ausweitung von Ackerland gibt. Streudiagramme zu Ackergröße und Anbaujahren in Relation zu geographischer Höhe zeigen seit dem Jahr 2000 eine Ausdehnung des Ackerbaus in Lagen unter 1620 müNN und eine Zunahme der Schlaggröße (>3ha). Die Analyse der phänologischen Entwicklung von Feldfrüchten im Jahresverlauf in Kombination mit Niederschlagsdaten und normalized difference vegetation index (NDVI) Zeitreihendaten dienten dazu, Zeitpunkte besonders hoher (Begrünung vor der Ernte) oder niedriger (nach der Bodenbearbeitung) Pflanzenbiomasse auf Ackerland zu identifizieren, um Ackerland und seine Ausdehnung von anderen Vegetationsformen fernerkundlich unterscheiden zu können. Anhand der NDVI Spektralprofile konnte Ackerland gut Wald, jedoch weniger gut von Gras- und Buschland unterschieden werden. Die geringe Auflösung (250m) der Moderate Resolution Imaging Spectroradiometer (MODIS) NDVI Daten führte zu einem Mixed Pixel Effect, d.h. die Fläche eines Pixels beinhaltete häufig verschiedene Vegetationsformen in unterschiedlichen Anteilen, was deren Unterscheidung beeinträchtigte. Für die Entwicklung eines Echtzeit Monitoring Systems für die Ausdehnung des Ackerbaus wären höher auflösende NDVI Daten (z.B. Multispektralband, Hyperion EO-1 Sensor) notwendig, um kleinräumig eine bessere Differenzierung von Ackerland und natürlicher Rangeland-Vegetation zu erhalten. Die Entwicklung und der Einsatz solcher Methoden als Entscheidungshilfen für Land- und Ressourcennutzungsplanung könnte dazu beitragen, Produktions- und Entwicklungsziele der Borana Landnutzer mit nationalen Anstrengungen zur Eindämmung des Klimawandels durch Steigerung der Kohlenstofffixierung in Rangelands in Einklang zu bringen.