44 search hits
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Crystalline-core micelles based on triblock terpolymers with polyethylene middle blocks
(2012)
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Joachim Schmelz
- This thesis is focused on the crystallization-induced structure formation of polyethylene containing triblock terpolymers in organic solvents to surface-compartmentalized worm-like crystalline-core micelles (wCCMs). Obtaining profound knowledge of the parameters controlling the self-assembly process allowed the production of a variety of complex one-dimensional micellar architectures with many potential applications, such as adaptive surfactants.
At first, the basic parameters that control the crystallization-induced self-assembly were explored using symmetric polystyrene-block-polyethylene-block-poly(methyl methacrylate) (PS-b-PE-b-PMMA) triblock terpolymers and a PS-b-PE-b-PS triblock copolymer. In good solvents for the PE block, e.g. THF and toluene, the selective formation of wCCMs was observed over a wide range of concentration, applied crystallization temperature and polymer composition. Whereas wCCMs produced by PS-b-PE-b-PS showed a homogeneous PS corona, a patch-like compartmentalization of the corona was observed if the micelles were formed by PS-b-PE-b-PMMA. As THF shows equal solvent quality for both corona blocks, wCCMs with almost alternating PS and PMMA compartments of about 15 nm were observed in this solvent. However, if structure formation was conducted in bad solvents for PE, such as dioxane or dimethylacetamide, spherical micelles with amorphous PE cores were formed already before crystallization. Hence, the subsequent crystallization of PE resulted in spherical CCMs with a patchy or a homogeneous corona depending on the used triblock. These findings allow the highly selective production of stable spherical or worm-like CCMs from the same polymer.
As the corona structure of the patchy micelles self-assembled from triblock terpolymers was mainly deduced from transmission electron microscopy (TEM) performed on dried samples, a small-angle neutron scattering (SANS) study was performed in order to elucidate the morphology in solution. Therefore a partly deuterated triblock terpolymer was synthesized and measured at different contrasts to allow the selective detection of the different corona compartments. The resulting SANS curves could be interpreted using a form factor model for core-shell cylinders with alternating PS and PMMA hemishells including interparticle interactions, thus validating the TEM observations. Notably, Janus-type and patchy cylinders can be clearly distinguished using the applied form factor model.
Moreover, the controlled formation of wCCMs with tunable corona composition and structure was achieved using the cocrystallization of different triblock copolymers. Via random cocrystallization of PS-b-PE-b-PMMA and PS-b-PE-b-PS the corona morphology could be tuned continuously from a mixed corona at low PMMA content over spherical PMMA patches of increasing number and size to alternating PS and PMMA patches. This approach allows to manufacture wCCMs with predefined corona structure omitting the need to synthesize a new tailor-made triblock terpolymer for every desired morphology.
By establishing the controlled crystallization-driven self-assembly of triblock terpolymers with PE middle blocks, it was further possible to prepare wCCMs with predefined average lengths up to 500 nm and length polydispersities as low as Lw/Ln = 1.1. Here, self-assembled spherical CCMs of PS-b-PE-b-PS were used as seeds for the controlled growth of PS-b-PE-b-PS unimers. Upon further addition of PS-b-PE-b-PMMA unimers these grew epitaxially onto the preexisting wCCMs, resulting in triblock co-micelles that consisted of middle blocks with a homogeneous PS corona and outer blocks with alternating PS/PMMA compartments. These structures represent not only the first block co-micelles including blocks with a patchy corona, but also the first ones produced from purely organic block copolymers.
In view of application, the ability of patchy wCCMs formed by PS-b-PE-b-PMMA to stabilize interfaces was investigated using pendant-drop tensiometry. The observed reduction of the interfacial tension at the toluene/water interface was significantly higher than that of comparable triblock terpolymer single chains and that of wCCMs with a homogeneous PS corona. Interestingly, the obtained equilibrium interfacial tension equaled that of Janus cylinders with similar dimensions. To explain this unexpected finding the corona chains were proposed to adapt to the interface via selective collapse and shielding of the incompatible part of the corona chains. Studying wCCMs formed by several triblock terpolymers with different compositions, the interfacial activity was found to increase with increasing overall length of the corona chains, and to a certain extent with the molar fraction of PS units in the corona.
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Silent Sound Art: Performing the Unheard
(2012)
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Elen Flügge
- This article is a reflection on silent sound art, exemplified here by the works of Peter Ablinger and Akio Suzuki, in the context of a partially historical con-sideration of the participatory subject in Installation Art, with a primary focus on artistic movements and selected works from the late 1950s to the early 1970s by John Cage, George Brecht, and La Monte Young.
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Light Harvesting using Metal-Organic and Organic Sensitizers in Hybrid Solar Cells: Synthesis, Characterisation and Application
(2012)
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Katja Gräf
- This thesis addresses the question how to improve light harvesting with novel tailor-made metal-organic and organic sensitizers for solid-state hybrid solar cell applications. Two approaches are in the focus: 1) the design and synthesis of sensitizers featuring high extinction coefficients over a broad wavelength range and 2) modern device concepts to further enhance or extend the absorption by the combination of two sensitizers. In short: The primary goal was to broaden and boost the optical density of hybrid solar cells. To reach this, novel sensitizer with extended conjugated π-system providing excellent optical properties had to be designed and synthesised in complex multi-step reaction sequences. For ideal sensitizers, further aspects had to be taken into account such as structural demands, electronic properties, and the tendency towards aggregation.
The first part of this thesis deals with the synthesis, characterisation and application of a series of metal-organic ruthenium(II) donor-antenna complexes. In addition to the typically broad absorption of Ru(II)bis(bipyridyl)(NCS)2 complexes in the blue-green region arising from MLCT, these dyes feature much higher extinction coefficients in comparison to a commercially available reference dye lacking any donor-antenna groups. By the application of these Ru(II) complexes in solid-state dye-sensitized solar cells, we found a clear structure-property relationship. The performance - especially the photocurrent density - was significantly improved with increasing extension of the delocalized system of the donor-antenna groups.
To further boost the optical density in hybrid solar cells sensitized with a donor-antenna ruthenium dye (Ru-TPA-NCS), we developed an innovative and technically relevant concept for multichromophore sensitization involving a second sensitizer (TPD-dye). The latter absorbs in a region where Ru-TPA-NCS absorbs weakly. The solar cells were fabricated according to a novel method developed by us. However, the power conversion efficiencies of multichromophore hybrid blend solar cells were initially low due the weak interconnectivity of the TiO2 particles. This issue was addressed by an optimization of the TiO2:spiro-OMeTAD ratio and the addition of PCBM
A further concept dealing with the combination of two sensitizers in solid-state dye-sensitized solar cell was accomplished by co-sensitization of a triphenyldiamine-based dye (TPD-dye) absorbing in the blue region and squaraine dye (SQ-dye) mainly absorbing the red part of the visible spectrum. In this way, the optical response of the device was extended up to 700 nm. Under optimized conditions, a conversion efficiency of 2.41 % could be reached.
To accomplish the desired panchromaticity or even an extension of the absorption up to the NIR region with a single sensitizer, novel BODIPY dyes with excellent optical properties were designed and synthesised. We prepared BODIPYs with donor-groups to extend the delocalized system and integrated a meso-ethynyl bridge between the BODIPY core and the anchoring group to improve the electronic connection between them. For comparison, we synthesised the corresponding BODIPYs without donor-moieties and without ethynyl bridge. The multi-step synthetic routes were optimized, the mechanism of the donor-attachment was clarified and the introduction of the ethynylphenyl group in the meso-position was accomplished for the first time. The optical characterisation of the compounds disclosed an impressively broad and intensive spectral response, especially for a meso-ethynylphenyl BODIPY with donor-groups. This dye absorbs up to 1030 nm with high extinction coefficients. This makes suitable functionalised BODIPYs promising candidates for solar cell applications.
The next part took advantage of the excellent optical properties of BODIPYs and expanded the topic towards the concept of energy transfer. Here, an unattached energy donor dye provides additional adsorption and transfers the energy to a sensitizing acceptor dye. Indeed, for appropriate combinations an additional contribution to the external quantum efficiency was found in the absorption region of the energy donor dye.
Furthermore, a review chapter covering all aspects of dye-sensitized solar cells and the sensitizers is added as appendix.
In summary, this thesis presents the successful design, synthesis and characterisation of both metal-organic and organic sensitizers including ruthenium complexes, triphenyldiamine-based dyes, a squaraine sensitizer and BODIPY dyes. The sensitizers (either individually or in combination with complementary sensitizers) provide excellent optical properties for the application in solar cells. The applicability of these sensitizers was successfully demonstrated in standard solid-state dye-sensitized solar cells, in newly developed multichromophore hybrid blend solar cells, co-sensitized solar cells and in solid-state dye-sensitized solar cells taking advantage of energy transfer.
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Measurement of emotional reactions to television advertisements – A state of the art review
(2012)
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Christian Wolterink
- Human emotions and their measurement present a complex and intricate affair
which perpetuates an ongoing discourse in marketing research. Since emotions
play a pivotal role in the success of advertisements, the exploitation of tools for
their precise measurement is crucial to researchers and practitioners alike. Yet,
there is no single gold standard instrument existent that enables a comprehensive
detection of all emotion facets at once. This thesis therefore focuses on the theoretical
conceptualization of emotion, and afterwards presents a variety of measurement
methods that address different emotion components. Thereby, particular
emphasis is placed on their applicability as regards television commercials.
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The origins of olivine fabric transitions and their effects on seismic anisotropy in the upper mantle
(2012)
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Sushant Shekhar
- Convecting mantle plays a central role in the thermal and geochemical evolution of the Earth. It provides the principal force responsible for major geological features such as mountains and ocean basins. Plate tectonics and its violent consequences such as earthquakes and volcanoes are all manifestations of the dynamics of the convective mantle. Shearing forces generated by mantle convection leads to lattice preferred orientation (LPO) of the major upper mantle mineral phases. LPO that develops in this way is thought to be the principal cause behind seismic anisotropy in the upper mantle, which can consequently be used to chart convective flow of the mantle.
Strong changes in seismic anisotropy occur in the top 300 km of the upper mantle where olivine is the principal mineral. In this study a solid media high pressure deformation apparatus, called the deformation-DIA or D-DIA, has been used to deform aggregates of San Carlos olivine in simple shear geometry at pressures between 3 and 8.5 GPa and temperatures from 1300-1500°C. As part of this project a high pressure and temperature solid-media cubic assembly was developed to facilitate these experiment that employed alumina pistons cut at 45° to shear the sample but minimized cold deformation of the sample by employing initially porous alumina in the sample column. Once stable high pressures and temperature were reached the cubic assembly was deformed by compressing two vertically oriented anvils of the D-DIA, while the four horizontally oriented anvils were maintained at a constant loading force. This assembly shortening led to shearing of the olivine sample. Recovered samples were analyzed for fabric development employing electron backscattered diffraction (EBSD) and microstructure was observed using transmission electron microscopy (TEM).
Experiments were performed at each pressure and temperature as a function of strain rate and H2O content. In dry olivine deformation experiments performed at slower strain rates an A-type fabric dominated at all pressures and temperatures, implying deformation by dislocation glide through the (010)[100] slip system. At higher strain rates evidence for the B-type fabric was observed, suggesting increased activity of the (010)[001] slip system at higher stresses. Recrystallization grains size and dislocation densities were used to estimate stresses in the samples and a good correlation was observed between strain rate and estimated flow stresses. Dry experiments from 8.5 GPa and 1500°C exhibited no LPO, which may be an indication for deformation through diffusion accommodated grain boundary sliding at these conditions. No indication was found that pressure influences the dominant slip system in olivine, in contrast to previous studies. It is considered that previously reported incidences of pressure effects can in fact be attributed to the development of higher stresses in experiments performed at higher pressures.
Fabrics in H2O bearing olivine deformed at similar conditions revealed the overriding dominance of the C-type fabric, developed through action of the (100)[001] slip system. Variations in pressure, temperature and strain rate had little influence on this fabric development. TEM observations confirmed the presence of dislocations with slip systems consistent with the development of the macroscopic fabrics. Viscoplastic self consistent modeling was employed to understand the development of fabric in the samples and to estimate the relative contributions of variations slip systems to the developed fabrics.
These results are used to construct an olivine fabric map which is found to be consistent with some previous studies at lower pressures. It is argued that the decrease in seismic anisotropy observed in the top 300 km of the upper mantle cannot originate from a pressure induced change in the dominant olivine deformation fabric. Instead it is argued that changes in the H2O content of olivine with depth cause a shift in the dominant fabric from A-type to C-type, with a possible excursion through the E-type fabric, dominant slip system (001)[100], which was, however, not observed in this study. Modeling is used to show that this variation in fabric with depth can cause the observed weakening the seismic anisotropy in the upper mantle if the olivine H2O content increases from below 100 ppm at 50 km to 250 ppm at 300 km. Rather than implying an increased in the H2O content of the mantle with depth, however, it is argued that this change in olivine H2O content can be caused by changes in the H2O olivine-pyroxene partition coefficients with depth, for a fixed bulk mantle H2O content of 200 ppm.
Similar deformation experiments performed on a peridotite assemblage at 8.5 GPa and 1300°C indicate identical olivine fabrics to those observed in monomineralic experiments at the same conditions. Fabrics for diopside and enstatite were found to be similar to those found in previously performed lower pressure experiments.
Experiments on a piezoelectric single crystal of GaPO4 were performed in the D-DIA and 6-ram MAVO press at high pressures in order to measure charge on the crystal developed through the application of deviatoric stresses. Electrical charges were measured through the use of an operational amplifier. Experiments performed at room temperature using a developed cubic assembly were successful in measuring quantifiable electrical charges resulting from the advancement of the deformation anvils by as little as 0.5 µm. Although the piezoelectric constant for this material is not yet calibrated at high pressures, stresses were estimated from the measured charges and measureable values were in the range 4-350 MPa.
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Synthesis and Combinatorial Optimization of Novel Star-Shaped Resist Materials for Lithographic Applications
(2012)
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Florian Wieberger
- Gordon Earle Moore predicted in the mid-1960s the cost-efficient doubling of transistors’ number on integrated circuits every two years – known as Moore’s Law. Leading companies orientates by the development of integrated circuits on this Moore’s Law and contributed to this prediction to come true up to the present. In so doing, the semiconductor industry drafts every two years aims to fulfill this prediction summarized in the so-called International Technology Roadmap for Semiconductors (ITRS). The ITRS lists guidelines for cost-effective progresses in performance of integrated circuits, e.g. design of integrated circuits, advancements of exposure tools and exposure techniques, and closely correlated resist materials. This thesis deals with the development of new resist materials and their combinatorial investigation concerning the performance in lithographic patterning.
The lithographic patterning procedure is a sequence of multiple processing steps and thus this procedure involves many processing variables interacting strongly with each other. For understanding and comprehensive investigation of such multi-variable dependent systems the development and implementation of combinatorial approaches were in the focus of this thesis. Furthermore this thesis is focused on the synthesis of new tailored resist materials for lithographic patterning. Star topology was the selected polymer architecture of this new resist material realized via the core-first atom transfer radical polymerization (ATRP) technique. The lithographic performance of electron beam lithography patterning was investigated for the resulting randomly distributed star terpolymers and star block copolymers by combinatorial libraries in view of features’ quality.
The first chapter deals with developed, adapted, and improved combinatorial techniques for thin film investigations in general and utilized for lithographic patterning investigations in particular. The lithographic patterning procedure of chemically amplified resist systems consists of various steps: film preparation, post apply bake (PAB) to remove residual solvent, exposure, post exposure bake (PEB) to activate the catalytic reaction, and development. For this rather complex process variable gradients were developed and adapted for each processing step to investigate and optimize the performance of especially new resist systems. For the film preparation a method was developed to prepare an internal material composition gradient. This was realized by a gradient extrudate prepared using two individual controllable syringe pumps and subsequent doctor-blading. The material composition gradient was verified by high performance liquid chromatography. The second (PAB) and also the fourth (PEB) processing step are both annealing processes of the resist film although they serve different purposes. For the investigation of such annealing processes temperature gradients were prepared adjustable in temperature range and temperature slope. This adjustability is ensured by the active heating and the active cooling source and also by the gap and the type of metal plate. For the third step exposure methods were developed to realize defined exposure dose gradients in very small areas of the resist film. Different exposure dose gradients were designed for photolithography as well as for electron beam lithography. For the latter case this dose gradient was programmed in the pattern design using the software which controls the electron beam during the exposure process. The dose gradient for photolithography investigations was realized by a special designed shadow mask. For the last processing step development a preliminary screening of the dissolubility conditions of the resist film was established utilizing quartz crystal microbalances. Based on this measured dissolubility behavior the time frame was set for development time gradients performed by a stepwise or continuously immersion of the resist films. Lastly two to three variable gradients were combined to binary or ternary combinatorial libraries, respectively. The ternary combinatorial libraries allow the investigation of three variables of the lithographic patterning process in one experiment. Thus it is possible to optimize a resist material system fast and efficiently in respect to resist performance.
In the second chapter a star-shaped teroligomer is reported as new high potential resist type for lithographic patterning purposes. The polymerization was carried out via the core-first ATRP route using a functionalized saccharose with eight initiating sites as core. Four star-shaped teroligomers were synthesized with varying target arm lengths. In addition a saccharose molecule was synthesized with an average number of 3.5 initiating sites and thus a star oligomer was realized with a reduced arm number but an identical core and similar arm length. As reference resist material a linear model oligomer was synthesized using ethyl 2-bromoisobutyrate as initiator. For all polymers narrow monomodal distributions were detected with polydispersity index values of lower than 1.1. Based on calibration polymerizations runs the monomer feed of the three used monomers was adapted to achieve targeted monomer incorporations for all teroligomers. The targeted monomer incorporation was copied from a currently industrially used linear teroligomer. One star oligomer was selected as proof of principle for the utilization of the star architecture for lithographic purposes. This new resist material was combinatorial investigated in a ternary library and thus optimized in one experiment concerning exposure dose, PEB temperature, and development time. The optimized patterns with a feature size of 100 nm and an excellent line edge roughness (LER) value of 3.1 nm were observed.
The last chapter of this thesis demonstrates the straight forward advancement of the star-shaped resist material reported in chapter two. The statistical monomer incorporation was exchanged by the introduction of the tailored star block copolymer architecture. This architecture was synthesized for the first time via the core-first ATRP route by full conversion of a first polar monomer and in-situ polymerization of additionally added nonpolar monomer. The successful syntheses were indicated by contact angle measurements showing increased hydrophobicity of star block copolymers in contrast to random star copolymers with the same monomer incorporation. The star block copolymers exhibited also enhanced dissolubility behavior characterized by quartz crystal microbalance measurements. Furthermore they demonstrated an up to eight times increased sensitivity at their lithographic application in contrast to the synthesized reference linear copolymer. The most promising star block copolymer was selected to investigate its lithographic performance. The optimization was performed in a ternary combinatorial library based on the gradient variables exposure dose and feature size, PEB temperature, and development time. The optimized pattern of clear lines and a feature size of 66 nm was observed with a LER value of 6 nm.
To conclude, different tailored star-shaped terpolymers were synthesized using the ATRP core-first route and successfully applied in the lithographic patterning process for the first time. In addition the combinatorial optimization offers the absolutely promising potential of utilizing these star shaped resist materials by the demonstrated brilliant LER values, the achieved extremely high sensitivity, and the fast and efficient development of clear 66 nm lines.
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Jahresbericht 2010-11 zum Förderprojekt 01879 Untersuchung der Veränderung der Konzentration von Luftbeimengungen und Treibhausgasen im hohen Fichtelgebirge 2007 – 2014
(2012)
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Thomas Foken
Lisa Dirks
- no abstract
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Polymer Melts Investigated by Field Cycling NMR Relaxometry: From Simple Liquid to Reptation Dynamics
(2012)
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Axel Herrmann
- The focus of this thesis is the investigation of linear polymer melts by applying Field Cycling Nuclear Magnetic Resonance (FC NMR) relaxometry. The objective is to understand their microscopic dynamics and its dependence on the molecular mass (M) of the polymer chains.
With the commercial availability of FC NMR relaxometers, the method gained attraction for studying dynamics of soft condensed matter due to its ability to detect both the structural or alpha-relaxation (identified with the segmental dynamics) and slower collective dynamics. In the case of polymer melts the latter is described most often by the Rouse model for non-entangled chains and the Doi/Edwards tube-reptation model for entangled polymers. Since 2004 a commercial relaxometer by Stelar has been operated in the Rössler group. Its capability to rapidly switch between different magnetic fields allows to measure the spin-lattice relaxation time in the proton frequency range from 10 kHz to 20 MHz. In previous works by the Rössler group the pioneering works by Kimmich and co-workers have been extended in order to combine the results of a broad temperature range: Frequency-temperature superposition is applied to construct master curves in the susceptibility representation. The key benefits are: the susceptibility is scaled by time constant of segmental dynamics and an "isofrictional" representation is achieved; the accessible frequency range is significantly increased; the time constants are provided and compared with those obtained by other techniques; the regimes of glassy and polymer dynamics can be easily distinguished; finally, the dipolar correlation function is obtained directly by Fourier transform.
In this thesis by employing the above approach, the dipolar correlation function of polybutadienes (PB) melts is presented and comprises - depending on M - glassy, Rouse and entanglement dynamics. The latter two relaxation regimes can be described by different power-laws, which are compared to the predictions of the tube-reptation model. A good agreement is found for the Rouse regime (I). For the constrained Rouse regime (II) at long times, a highly protracted crossover to completely established reptation dynamics is discovered. That is, the exponent depends on M and reaches 0.32 only at M=441000, which is in accord with Double Quantum (DQ) 1H NMR results by Saalwächter and co-workers and very close to 0.25 predicted for regime II of the tube-reptation model. This is only achieved by additional relaxation experiments in cooperation with the Fujara group at TU Darmstadt, since their home-built FC NMR relaxometer is equipped with an active stray field compensation, which allows to reach extremely low frequencies down to 200 Hz. Consequently, the frequency range is extended by two decades toward lower frequencies with respect to the commercial spectrometer and the obtained correlation function stretches over 10 decades in time and 8 in amplitude for molecular masses up to 220 Me. This establishes FC 1H NMR also at long times as competitive with DQ 1H NMR.
The analyses of the dipolar correlation function appear to support the applicability of the tube-reptation model. However, intramolecular and intermolecular relaxation contributions have to be discriminated and up to now the dominance of the first has been assumed implicitly. Therefore, isotopic blends of high-M protonated and deuterated PB are investigated, which allows to decompose the 1H master curves into intramolecular and intermolecular relaxation contributions. They reflect reorientational and translational dynamics, respectively. It is demonstrated that at long times or low frequencies the intermolecular contribution dominates. Consequently, the reorientational correlation function obtained from the intramolecular part exhibits a faster decay with the long-time exponent 0.49. This is ascertained by the FC 2H NMR relaxation of completely deuterated PB, which detects reorientational dynamics only. The observed exponent is significantly larger than 0.25 of regime II of the tube reptation model. Concomitantly, the segmental mean square displacement is attained from the intermolecular part following an approach by Kimmich and Fatkullin. The predicted power-laws of the tube-reptation model for the Rouse and constrained Rouse regimes are identified for the first time by FC NMR: a transition between the power-laws t^ 0.49 and t^0.19 is revealed, respectively. Thus, NMR relaxometry is designated as a method comparable to neutron scattering to study subdiffusion in polymer melts. In conclusion, the power-law predictions of the tube-reptation model are disclosed by the segmental mean square displacement, yet not by the reorientational correlation function. Thus, the simple tube-reptation model does not completely describe the microscopic dynamics of polymer melts.
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Impact of extreme hydrological conditions on belowground carbon cycling and redox dynamics in peat soils from a northern temperate fen
(2012)
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Cristian Estop Aragonés
- Peatlands have an important role in the global carbon cycle and constitute the largest pool of carbon stored in terrestrial ecosystems due to their disproportionally high areal soil carbon density. This globally relevant carbon stock is the result of a process mostly initiated after the last glaciation period. A key factor for this long term carbon accumulation is the relative low decomposition of organic matter in these predominantly water logged ecosystems. Hydrological conditions play thus a fundamental role in peatlands and the feedback of carbon cycling in these ecosystems in response to climate change is under debate. Peatlands are important CO2 sinks but also constitute global sources of CH4. The atmospheric exchange and production rates of these greenhouse gases are strongly influenced by the hydrological regime. An increased frequency of extreme meteorological conditions resulting in drying and flooding events is predicted to occur in the future.
The major issue regarding the climate change debate at the global scale is how rapid these greenhouse gases are being released to the atmosphere. Despite the general consensus regarding the broad effects of drying and flooding on CO2 and CH4 exchange, belowground processes producing such greenhouse gases and their response to water table dynamics is underrepresented and usually simplified or overgeneralized. Temperature, moisture, oxygen content and nutrient content are among the major environmental controls for organic matter decomposition rates in peat soils. Another important and intrinsic control is peat quality or humification degree of organic matter. The interrelation and relevance of all these factors vary among sites and with hydrological condition in a temporal and spatial scale.
This work presents investigations focusing on belowground redox processes aiming to witness the dynamic interrelation of soil physical and chemical (soil gas and pore water chemistry) variables, and evaluates the relevance of some controls of organic matter decomposition during a wide range of hydrological conditions. Most of this work shows information under in situ conditions and complementary laboratory experiments were performed minding the in situ observations. The findings contribute to general knowledge by providing raw data in fen peats under fluctuating and contrasting water table conditions in a relatively high spatiotemporal resolved scale. Dryings led to increased air filled porosity, O2 intrusion, CO2 degassing, inhibition of methanogenesis and renewal of electron acceptors. The opposite trend occurred upon rewetting with pulses of iron and sulphate reduction and delayed methane production to a variable extent. Upon flooding, continued anaerobic conditions stimulated the accumulation of reduced products, methanogenic precursors (acetate and hydrogen) and CH4.
The general assumption that the water table directly controls the oxygen content in peat was relativized. This work shows that such relation is greatly influenced by peat physical properties, which partially control the changes in moisture. Based on these findings, the mineral content and the degree of compaction in organic soils can be implemented to more accurately represent the dynamics of aeration in peats upon water table changes. Another general assumption is that drying events, i.e. temporary decline of water table below mean position, lead to increased CO2 production and emission from peat soils to the atmosphere. Such statement was also relativized and must account for the depth distribution of respiration rates in relation to the mean water table of the peat deposit. Based on these findings, the high relative contribution of upper peat layers already exposed above the water table mask the effects of increased CO2 production in deeper peat upon water table drop. Additionally, the role of moisture was shown to be little for aerobic respiration. This work also evaluates the importance of drought severity by accounting for the post drought effects on methane production. More intense and prolonged drying events led to a greater regeneration of electron acceptors in peat soil, which broadly suppressed or limited methane production upon rewetting. This relation was not simple and several factors such as water table position, post drought water table fluctuations, temperature and organic matter content contributed to the recovery of methane production after drying. The provision of substrates by fermentation processes limited peat respiration during shallow water table and drying. In contrast, accumulation of acetate and hydrogen was observed during flooding indicating a decoupling of fermentation from terminal metabolism and favouring the co-occurrence of iron reduction, sulphate reduction and methanogenesis.
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Monte Carlo Simulation Methods for Studying the Thermodynamics of Ligand Binding & Transfer Processes in Biomolecules
(2012)
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R. Thomas Ullmann
- The binding and transfer of ligands is of central
importance for the function of many biomolecular
systems. The main topic of this thesis is the
development and application of Monte Carlo (MC)
simulation methods for studying complex ligand
binding equilibria which can also involve
conformational changes. The simulated systems
were described by microstates within a continuum
electrostatics/molecular mechanics (CE/MM) model
of the receptor-ligand system. The CE/MM modeling
methodology was improved. The improvements led to
more detailed molecular models that enable a more
realistic reproduction of system properties and
environmental conditions. The developed simulation
methods were applied to biomolecular systems whose
function involves aspects that are important for
the understanding of bioenergetic energy
transduction. The results of this thesis are
presented in five articles that are published in
peer reviewed scientific journals.
Manuscript A presents the Monte Carlo simulation
software GMCT which was largely developed in this
thesis. The software offers a variety of different
simulation methods that allow the user to harness
the full potential of CE/MM models in the simulation
of complex receptor systems.
Manuscript B presents a novel theoretical framework
for free energy calculations with the free energy
perturbation method. The novel framework is more
broadly applicable and can lead to more efficient
simulations than previous formulations. The
derivation of the formalism also led to interesting
insights into general statistical mechanics. The
formalism was implemented in GMCT and could already
be used fruitfully for the free energy calculations
presented in Manuscripts C and D.
Manuscript C demonstrates the application of free
energy measures of cooperativity to study the
coupling of protonation, reduction and conformational
change in azurin from Pseudomonas aeruginosa (PaAz).
Such a coupling is prototypic for bioenergetic systems
because it forms the thermodynamic basis of their
energy transducing function. PaAz is an experimentally
well characterized, small electron transport protein.
For this reason, PaAz was used here as model system
to demonstrate the usefulness of cooperativity free
energies in detecting and quantifying thermodynamic
coupling between events in complex biomolecular
systems. The results of this study led to new insight
that could help to determine the still enigmatic
physiological role of PaAz.
In Manuscript D, free energy calculations were
applied to study the thermodynamics of transport
through the ammonium transporter Amt-1 from
Archaeoglobus fulgidus (AfAmt-1). Ammonium is the most
directly utilizable nitrogen source for plants and
microorganisms. AfAmt-1 and its homologues facilitate
the transport of ammonia/ammonium across biological
membranes in living beings from all domains of life.
It is intensely debated how these proteins perform
their function and whether ammonia or its protonated
form ammonium is actually transported. The study
extended upon previous theoretical studies by
including the effects of substrate concentration,
electrochemical transmembrane gradients,
proton-coupled binding equilibria and competitive
binding of different ligand species. It was found
that the transported species is most likely the
ammonium ion. An ammonia/proton symport mechanism
that involves a pair of coplanar histidine residues
at the center of the transmembrane pore as transient
proton acceptor is made plausible by the high
genetic conservation of these residues.
Manuscript E presents a first application of the
microstate description within a CE/MM model to the
simulation of the non-equilibrium dynamics of a
molecular system. We simulated the re-reduction
kinetics of the primary electron donor in the
photocycle of the bacterial photosynthetic reaction
center from Blastochloris viridis. The simulation
results are in very good agreement with
experimentally measured data.
