@phdthesis{Weikl2007,
  author    = {Weikl, Thomas R.},
  title     = {Transition states and loop-closure principles in protein folding},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-26975},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {Proteins are chain molecules built from amino acids. The precise sequence of the 20 different types of amino acids in a protein chain defines into which structure a protein folds, and the three-dimensional structure in turn specifies the biological function of the protein. The reliable folding of proteins is a prerequisite for their robust function. Misfolding can lead to protein aggregates that cause severe diseases, such as Alzheimer's, Parkinson's, or the variant Creutzfeldt-Jakob disease. Small single-domain proteins often fold without experimentally detectable metastable intermediate states. The folding dynamics of these proteins is thought to be governed by a single transition-state barrier between the unfolded and the folded state. The transition state is highly instable and cannot be observed directly. However, mutations in which a single amino acid of the protein is substituted by another one can provide indirect access. The mutations slightly change the transition-state barrier and, thus, the folding and unfolding times of the protein. The central question is how to reconstruct the transition state from the observed changes in folding times. In this habilitation thesis, a novel method to extract structural information on transition states from mutational data is presented. The method is based on (i) the cooperativity of structural elements such as alpha-helices and beta-hairpins, and (ii) on splitting up mutation-induced free-energy changes into components for these elements. By fitting few parameters, the method reveals the degree of structure formation of alpha-helices and beta-hairpins in the transition state. In addition, it is shown in this thesis that the folding routes of small single-domain proteins are dominated by loop-closure dependencies between the structural elements.},
  language  = {en}
}
@phdthesis{Green2007,
  author    = {Green, Antony Dubach},
  title     = {Phonology limited},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-939469-93-3},
  issn      = {1616-7392},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15512},
  school      = {Universit{\"a}t Potsdam},
  pages     = {x, 207},
  year      = {2007},
  abstract  = {Phonology Limited is a study of the areas of phonology where the application of optimality theory (OT) has previously been problematic. Evidence from a wide variety of phenomena in a wide variety of languages is presented to show that interactions involving more than just faithfulness and markedness are best analyzed as involving language-specific morphological constraints rather than universal phonological constraints. OT has proved to be a highly insightful and successful theory of linguistics in general and phonology in particular, focusing as it does on surface forms and treating the relationship between inputs and outputs as a form of conflict resolution. Yet there have also been a number of serious problems with the approach that have led some detractors to argue that OT has failed as a theory of generative grammar. The most serious of these problems is opacity, defined as a state of affairs where the grammatical output of a given input appears to violate more constraints than an ungrammatical competitor. It is argued that these problems disappear once language-specific morphological constraints are allowed to play a significant role in analysis. Specifically, a number of processes of Tiberian Hebrew traditionally considered opaque are reexamined and shown to be straightforwardly transparent, but crucially involving morphological constraints on form, such as a constraint requiring certain morphological forms to end with a syllabic trochee, or a constraint requiring paradigm uniformity with regard to the occurrence of fricative allophones of stop phonemes. Language-specific morphological constraints are also shown to play a role in allomorphy, where a lexeme is associated with more than one input; the constraint hierarchy then decides which input is grammatical in which context. For example, [ɨ]/[ə] and [u]/[ə] alternation found in some lexemes but not in others in Welsh is attributed to the presence of two inputs for the lexemes with the alternation. A novel analysis of the initial consonant mutations of the modern Celtic languages argues that mutated forms are separately listed inputs chosen in appropriate contexts by constraints on morphology and syntax, rather than being outputs that are phonologically unfaithful to their unmutated inputs. Finally, static irregularities and lexical exceptions are examined and shown to be attributable to language-specific morphological constraints. In American English, the distribution of tense and lax vowels is predictable in several contexts; however, in some contexts, the distributions of tense [ɔ] vs. lax [a] and of tense [{\ae}] vs. lax [{\ae}] are not as expected. It is shown that clusters of output-output faithfulness constraints create a pattern to which words are attracted, which however violates general phonological considerations. New words that enter the language first obey the general phonological considerations before being attracted into the language-specific exceptional pattern.},
  language  = {de}
}
@phdthesis{Wagner2007,
  author    = {Wagner, Dirk},
  title     = {Microbial perspectives of the methane cycle in permafrost ecosystems in the Eastern Siberian Arctic : implications for the global methane budget},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15434},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {The Arctic plays a key role in Earth's climate system as global warming is predicted to be most pronounced at high latitudes and because one third of the global carbon pool is stored in ecosystems of the northern latitudes. In order to improve our understanding of the present and future carbon dynamics in climate sensitive permafrost ecosystems, the present study concentrates on investigations of microbial controls of methane fluxes, on the activity and structure of the involved microbial communities, and on their response to changing environmental conditions. For this purpose an integrated research strategy was applied, which connects trace gas flux measurements to soil ecological characterisation of permafrost habitats and molecular ecological analyses of microbial populations. Furthermore, methanogenic archaea isolated from Siberian permafrost have been used as potential keystone organisms for studying and assessing life under extreme living conditions. Long-term studies on methane fluxes were carried out since 1998. These studies revealed considerable seasonal and spatial variations of methane emissions for the different landscape units ranging from 0 to 362 mg m-2 d-1. For the overall balance of methane emissions from the entire delta, the first land cover classification based on Landsat images was performed and applied for an upscaling of the methane flux data sets. The regionally weighted mean daily methane emissions of the Lena Delta (10 mg m-2 d-1) are only one fifth of the values calculated for other Arctic tundra environments. The calculated annual methane emission of the Lena Delta amounts to about 0.03 Tg. The low methane emission rates obtained in this study are the result of the used remotely sensed high-resolution data basis, which provides a more realistic estimation of the real methane emissions on a regional scale. Soil temperature and near soil surface atmospheric turbulence were identified as the driving parameters of methane emissions. A flux model based on these variables explained variations of the methane budget corresponding to continuous processes of microbial methane production and oxidation, and gas diffusion through soil and plants reasonably well. The results show that the Lena Delta contributes significantly to the global methane balance because of its extensive wetland areas. The microbiological investigations showed that permafrost soils are colonized by high numbers of microorganisms. The total biomass is comparable to temperate soil ecosystems. Activities of methanogens and methanotrophs differed significantly in their rates and distribution patterns along both the vertical profiles and the different investigated soils. The methane production rates varied between 0.3 and 38.9 nmol h-1 g-1, while the methane oxidation ranged from 0.2 to 7.0 nmol h-1 g-1. Phylogenetic analyses of methanogenic communities revealed a distinct diversity of methanogens affiliated to Methanomicrobiaceae, Methanosarcinaceae and Methanosaetaceae, which partly form four specific permafrost clusters. The results demonstrate the close relationship between methane fluxes and the fundamental microbiological processes in permafrost soils. The microorganisms do not only survive in their extreme habitat but also can be metabolic active under in situ conditions. It was shown that a slight increase of the temperature can lead to a substantial increase in methanogenic activity within perennially frozen deposits. In case of degradation, this would lead to an extensive expansion of the methane deposits with their subsequent impacts on total methane budget. Further studies on the stress response of methanogenic archaea, especially Methanosarcina SMA-21, isolated from Siberian permafrost, revealed an unexpected resistance of the microorganisms against unfavourable living conditions. A better adaptation to environmental stress was observed at 4 °C compared to 28 °C. For the first time it could be demonstrated that methanogenic archaea from terrestrial permafrost even survived simulated Martian conditions. The results show that permafrost methanogens are more resistant than methanogens from non-permafrost environments under Mars-like climate conditions. Microorganisms comparable to methanogens from terrestrial permafrost can be seen as one of the most likely candidates for life on Mars due to their physiological potential and metabolic specificity.},
  language  = {en}
}
@phdthesis{Grenzer2007,
  author    = {Grenzer, Marina},
  title     = {Photoinduced material transport in amorphous azobenzene polymer films},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15771},
  school      = {Universit{\"a}t Potsdam},
  year      = {2007},
  abstract  = {The role played by azobenzene polymers in the modern photonic, electronic and opto-mechanical applications cannot be underestimated. These polymers are successfully used to produce alignment layers for liquid crystalline fluorescent polymers in the display and semiconductor technology, to build waveguides and waveguide couplers, as data storage media and as labels in quality product protection. A very hot topic in modern research are light-driven artificial muscles based on azobenzene elastomers. The incorporation of azobenzene chromophores into polymer systems via covalent bonding or even by blending gives rise to a number of unusual effects under visible (VIS) and ultraviolet light irradiation. The most amazing effect is the inscription of surface relief gratings (SRGs) onto thin azobenzene polymer films. At least seven models have been proposed to explain the origin of the inscribing force but none of them describes satisfactorily the light induced material transport on the molecular level. In most models, to explain the mass transport over micrometer distances during irradiation at room temperature, it is necessary to assume a considerable degree of photoinduced softening, at least comparable with that at the glass transition. Contrary to this assumption, we have gathered a convincing evidence that there is no considerable softening of the azobenzene layers under illumination. Presently we can surely say that light induced softening is a very weak accompanying effect rather than a necessary condition for the formation of SRGs. This means that the inscribing force should be above the yield point of the azobenzene polymer. Hence, an appropriate approach to describe the formation and relaxation of SRGs is a viscoplastic theory. It was used to reproduce pulse-like inscription of SRGs as measured by VIS light scattering. At longer inscription times the VIS scattering pattern exhibits some peculiarities which can be explained by the appearance of a density grating that will be shown to arise due to the final compressibility of the polymer film. As a logical consequence of the aforementioned research, a thermodynamic theory explaining the light-induced deformation of free standing films and the formation of SRGs is proposed. The basic idea of this theory is that under homogeneous illumination an initially isotropic sample should stretch itself along the polarization direction to compensate the entropy decrease produced by the photoinduced reorientation of azobenzene chromophores. Finally, some ideas about further development of this controversial topic will be discussed.},
  language  = {en}
}