@phdthesis{Theves2013,
  author    = {Theves, Matthias},
  title     = {Bacterial motility and growth in open and confined environments},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70313},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {In the presence of a solid-liquid or liquid-air interface, bacteria can choose between a planktonic and a sessile lifestyle. Depending on environmental conditions, cells swimming in close proximity to the interface can irreversibly attach to the surface and grow into three-dimensional aggregates where the majority of cells is sessile and embedded in an extracellular polymer matrix (biofilm). We used microfluidic tools and time lapse microscopy to perform experiments with the polarly flagellated soil bacterium Pseudomonas putida (P. putida), a bacterial species that is able to form biofilms. We analyzed individual trajectories of swimming cells, both in the bulk fluid and in close proximity to a glass-liquid interface. Additionally, surface related growth during the early phase of biofilm formation was investigated. In the bulk fluid, P.putida shows a typical bacterial swimming pattern of alternating periods of persistent displacement along a line (runs) and fast reorientation events (turns) and cells swim with an average speed around 24 micrometer per second. We found that the distribution of turning angles is bimodal with a dominating peak around 180 degrees. In approximately six out of ten turning events, the cell reverses its swimming direction. In addition, our analysis revealed that upon a reversal, the cell systematically changes its swimming speed by a factor of two on average. Based on the experimentally observed values of mean runtime and rotational diffusion, we presented a model to describe the spreading of a population of cells by a run-reverse random walker with alternating speeds. We successfully recover the mean square displacement and, by an extended version of the model, also the negative dip in the directional autocorrelation function as observed in the experiments. The analytical solution of the model demonstrates that alternating speeds enhance a cells ability to explore its environment as compared to a bacterium moving at a constant intermediate speed. As compared to the bulk fluid, for cells swimming near a solid boundary we observed an increase in swimming speed at distances below d= 5 micrometer and an increase in average angular velocity at distances below d= 4 micrometer. While the average speed was maximal with an increase around 15\% at a distance of d= 3 micrometer, the angular velocity was highest in closest proximity to the boundary at d=1 micrometer with an increase around 90\% as compared to the bulk fluid. To investigate the swimming behavior in a confinement between two solid boundaries, we developed an experimental setup to acquire three-dimensional trajectories using a piezo driven objective mount coupled to a high speed camera. Results on speed and angular velocity were consistent with motility statistics in the presence of a single boundary. Additionally, an analysis of the probability density revealed that a majority of cells accumulated near the upper and lower boundaries of the microchannel. The increase in angular velocity is consistent with previous studies, where bacteria near a solid boundary were shown to swim on circular trajectories, an effect which can be attributed to a wall induced torque. The increase in speed at a distance of several times the size of the cell body, however, cannot be explained by existing theories which either consider the drag increase on cell body and flagellum near a boundary (resistive force theory) or model the swimming microorganism by a multipole expansion to account for the flow field interaction between cell and boundary. An accumulation of swimming bacteria near solid boundaries has been observed in similar experiments. Our results confirm that collisions with the surface play an important role and hydrodynamic interactions alone cannot explain the steady-state accumulation of cells near the channel walls. Furthermore, we monitored the number growth of cells in the microchannel under medium rich conditions. We observed that, after a lag time, initially isolated cells at the surface started to grow by division into colonies of increasing size, while coexisting with a comparable smaller number of swimming cells. After 5:50 hours, we observed a sudden jump in the number of swimming cells, which was accompanied by a breakup of bigger clusters on the surface. After approximately 30 minutes where planktonic cells dominated in the microchannel, individual swimming cells reattached to the surface. We interpret this process as an emigration and recolonization event. A number of complementary experiments were performed to investigate the influence of collective effects or a depletion of the growth medium on the transition. Similar to earlier observations on another bacterium from the same family we found that the release of cells to the swimming phase is most likely the result of an individual adaption process, where syntheses of proteins for flagellar motility are upregulated after a number of division cycles at the surface.},
  language  = {en}
}
@phdthesis{Schick2013,
  author    = {Schick, Daniel},
  title     = {Ultrafast lattice dynamics in photoexcited nanostructures : femtosecond X-ray diffraction with optimized evaluation schemes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-68827},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Within the course of this thesis, I have investigated the complex interplay between electron and lattice dynamics in nanostructures of perovskite oxides. Femtosecond hard X-ray pulses were utilized to probe the evolution of atomic rearrangement directly, which is driven by ultrafast optical excitation of electrons. The physics of complex materials with a large number of degrees of freedom can be interpreted once the exact fingerprint of ultrafast lattice dynamics in time-resolved X-ray diffraction experiments for a simple model system is well known. The motion of atoms in a crystal can be probed directly and in real-time by femtosecond pulses of hard X-ray radiation in a pump-probe scheme. In order to provide such ultrashort X-ray pulses, I have built up a laser-driven plasma X-ray source. The setup was extended by a stable goniometer, a two-dimensional X-ray detector and a cryogen-free cryostat. The data acquisition routines of the diffractometer for these ultrafast X-ray diffraction experiments were further improved in terms of signal-to-noise ratio and angular resolution. The implementation of a high-speed reciprocal-space mapping technique allowed for a two-dimensional structural analysis with femtosecond temporal resolution. I have studied the ultrafast lattice dynamics, namely the excitation and propagation of coherent phonons, in photoexcited thin films and superlattice structures of the metallic perovskite SrRuO3. Due to the quasi-instantaneous coupling of the lattice to the optically excited electrons in this material a spatially and temporally well-defined thermal stress profile is generated in SrRuO3. This enables understanding the effect of the resulting coherent lattice dynamics in time-resolved X-ray diffraction data in great detail, e.g. the appearance of a transient Bragg peak splitting in both thin films and superlattice structures of SrRuO3. In addition, a comprehensive simulation toolbox to calculate the ultrafast lattice dynamics and the resulting X-ray diffraction response in photoexcited one-dimensional crystalline structures was developed in this thesis work. With the powerful experimental and theoretical framework at hand, I have studied the excitation and propagation of coherent phonons in more complex material systems. In particular, I have revealed strongly localized charge carriers after above-bandgap femtosecond photoexcitation of the prototypical multiferroic BiFeO3, which are the origin of a quasi-instantaneous and spatially inhomogeneous stress that drives coherent phonons in a thin film of the multiferroic. In a structurally imperfect thin film of the ferroelectric Pb(Zr0.2Ti0.8)O3, the ultrafast reciprocal-space mapping technique was applied to follow a purely strain-induced change of mosaicity on a picosecond time scale. These results point to a strong coupling of in- and out-of-plane atomic motion exclusively mediated by structural defects.},
  language  = {en}
}
@phdthesis{Raetzel2013,
  author    = {R{\"a}tzel, Dennis},
  title     = {Tensorial spacetime geometries and background-independent quantum field theory},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-65731},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Famously, Einstein read off the geometry of spacetime from Maxwell's equations. Today, we take this geometry that serious that our fundamental theory of matter, the standard model of particle physics, is based on it. However, it seems that there is a gap in our understanding if it comes to the physics outside of the solar system. Independent surveys show that we need concepts like dark matter and dark energy to make our models fit with the observations. But these concepts do not fit in the standard model of particle physics. To overcome this problem, at least, we have to be open to matter fields with kinematics and dynamics beyond the standard model. But these matter fields might then very well correspond to different spacetime geometries. This is the basis of this thesis: it studies the underlying spacetime geometries and ventures into the quantization of those matter fields independently of any background geometry. In the first part of this thesis, conditions are identified that a general tensorial geometry must fulfill to serve as a viable spacetime structure. Kinematics of massless and massive point particles on such geometries are introduced and the physical implications are investigated. Additionally, field equations for massive matter fields are constructed like for example a modified Dirac equation. In the second part, a background independent formulation of quantum field theory, the general boundary formulation, is reviewed. The general boundary formulation is then applied to the Unruh effect as a testing ground and first attempts are made to quantize massive matter fields on tensorial spacetimes.},
  language  = {en}
}
@phdthesis{Pingel2013,
  author    = {Pingel, Patrick},
  title     = {Morphology, charge transport properties, and molecular doping of thiophene-based organic semiconducting thin films},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-69805},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Organic semiconductors combine the benefits of organic materials, i.e., low-cost production, mechanical flexibility, lightweight, and robustness, with the fundamental semiconductor properties light absorption, emission, and electrical conductivity. This class of material has several advantages over conventional inorganic semiconductors that have led, for instance, to the commercialization of organic light-emitting diodes which can nowadays be found in the displays of TVs and smartphones. Moreover, organic semiconductors will possibly lead to new electronic applications which rely on the unique mechanical and electrical properties of these materials. In order to push the development and the success of organic semiconductors forward, it is essential to understand the fundamental processes in these materials. This thesis concentrates on understanding how the charge transport in thiophene-based semiconductor layers depends on the layer morphology and how the charge transport properties can be intentionally modified by doping these layers with a strong electron acceptor. By means of optical spectroscopy, the layer morphologies of poly(3-hexylthiophene), P3HT, P3HT-fullerene bulk heterojunction blends, and oligomeric polyquaterthiophene, oligo-PQT-12, are studied as a function of temperature, molecular weight, and processing conditions. The analyses rely on the decomposition of the absorption contributions from the ordered and the disordered parts of the layers. The ordered-phase spectra are analyzed using Spano's model. It is figured out that the fraction of aggregated chains and the interconnectivity of these domains is fundamental to a high charge carrier mobility. In P3HT layers, such structures can be grown with high-molecular weight, long P3HT chains. Low and medium molecular weight P3HT layers do also contain a significant amount of chain aggregates with high intragrain mobility; however, intergranular connectivity and, therefore, efficient macroscopic charge transport are absent. In P3HT-fullerene blend layers, a highly crystalline morphology that favors the hole transport and the solar cell efficiency can be induced by annealing procedures and the choice of a high-boiling point processing solvent. Based on scanning near-field and polarization optical microscopy, the morphology of oligo-PQT-12 layers is found to be highly crystalline which explains the rather high field-effect mobility in this material as compared to low molecular weight polythiophene fractions. On the other hand, crystalline dislocations and grain boundaries are identified which clearly limit the charge carrier mobility in oligo-PQT-12 layers. The charge transport properties of organic semiconductors can be widely tuned by molecular doping. Indeed, molecular doping is a key to highly efficient organic light-emitting diodes and solar cells. Despite this vital role, it is still not understood how mobile charge carriers are induced into the bulk semiconductor upon the doping process. This thesis contains a detailed study of the doping mechanism and the electrical properties of P3HT layers which have been p-doped by the strong molecular acceptor tetrafluorotetracyanoquinodimethane, F4TCNQ. The density of doping-induced mobile holes, their mobility, and the electrical conductivity are characterized in a broad range of acceptor concentrations. A long-standing debate on the nature of the charge transfer between P3HT and F4TCNQ is resolved by showing that almost every F4TCNQ acceptor undergoes a full-electron charge transfer with a P3HT site. However, only 5\% of these charge transfer pairs can dissociate and induce a mobile hole into P3HT which contributes electrical conduction. Moreover, it is shown that the left-behind F4TCNQ ions broaden the density-of-states distribution for the doping-induced mobile holes, which is due to the longrange Coulomb attraction in the low-permittivity organic semiconductors.},
  language  = {en}
}
@phdthesis{Patra2013,
  author    = {Patra, Pintu},
  title     = {Population dynamics of bacterial persistence},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-69253},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {The life of microorganisms is characterized by two main tasks, rapid growth under conditions permitting growth and survival under stressful conditions. The environments, in which microorganisms dwell, vary in space and time. The microorganisms innovate diverse strategies to readily adapt to the regularly fluctuating environments. Phenotypic heterogeneity is one such strategy, where an isogenic population splits into subpopulations that respond differently under identical environments. Bacterial persistence is a prime example of such phenotypic heterogeneity, whereby a population survives under an antibiotic attack, by keeping a fraction of population in a drug tolerant state, the persister state. Specifically, persister cells grow more slowly than normal cells under growth conditions, but survive longer under stress conditions such as the antibiotic administrations. Bacterial persistence is identified experimentally by examining the population survival upon an antibiotic treatment and the population resuscitation in a growth medium. The underlying population dynamics is explained with a two state model for reversible phenotype switching in a cell within the population. We study this existing model with a new theoretical approach and present analytical expressions for the time scale observed in population growth and resuscitation, that can be easily used to extract underlying model parameters of bacterial persistence. In addition, we recapitulate previously known results on the evolution of such structured population under periodically fluctuating environment using our simple approximation method. Using our analysis, we determine model parameters for Staphylococcus aureus population under several antibiotics and interpret the outcome of cross-drug treatment. Next, we consider the expansion of a population exhibiting phenotype switching in a spatially structured environment consisting of two growth permitting patches separated by an antibiotic patch. The dynamic interplay of growth, death and migration of cells in different patches leads to distinct regimes in population propagation speed as a function of migration rate. We map out the region in parameter space of phenotype switching and migration rate to observe the condition under which persistence is beneficial. Furthermore, we present an extended model that allows mutation from the two phenotypic states to a resistant state. We find that the presence of persister cells may enhance the probability of resistant mutation in a population. Using this model, we explain the experimental results showing the emergence of antibiotic resistance in a Staphylococcus aureus population upon tobramycin treatment. In summary, we identify several roles of bacterial persistence, such as help in spatial expansion, development of multidrug tolerance and emergence of antibiotic resistance. Our study provides a theoretical perspective on the dynamics of bacterial persistence in different environmental conditions. These results can be utilized to design further experiments, and to develop novel strategies to eradicate persistent infections.},
  language  = {en}
}
@misc{LiBabuTurneretal.2013,
  author    = {Li, Hongguang and Babu, Sukumaran Santhosh and Turner, Sarah T. and Neher, Dieter and Hollamby, Martin J. and Seki, Tomohiro and Yagai, Shiki and Deguchi, Yonekazu and M{\"o}hwald, Helmuth and Nakanishi, Takashi},
  title     = {Alkylated-C60 based soft materials},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-95358},
  pages     = {1943 -- 1951},
  year      = {2013},
  abstract  = {Derivatization of fullerene (C60) with branched aliphatic chains softens C60-based materials and enables the formation of thermotropic liquid crystals and room temperature nonvolatile liquids. This work demonstrates that by carefully tuning parameters such as type, number and substituent position of the branched chains, liquid crystalline C60 materials with mesophase temperatures suited for photovoltaic cell fabrication and room temperature nonvolatile liquid fullerenes with tunable viscosity can be obtained. In particular, compound 1, with branched chains, exhibits a smectic liquid crystalline phase extending from 84 °C to room temperature. Analysis of bulk heterojunction (BHJ) organic solar cells with a ca. 100 nm active layer of compound 1 and poly(3-hexylthiophene) (P3HT) as an electron acceptor and an electron donor, respectively, reveals an improved performance (power conversion efficiency, PCE: 1.6 ± 0.1\%) in comparison with another compound, 10 (PCE: 0.5 ± 0.1\%). The latter, in contrast to 1, carries linear aliphatic chains and thus forms a highly ordered solid lamellar phase at room temperature. The solar cell performance of 1 blended with P3HT approaches that of PCBM/P3HT for the same active layer thickness. This indicates that C60 derivatives bearing branched tails are a promising class of electron acceptors in soft (flexible) photovoltaic devices.},
  language  = {en}
}
@misc{InalKoelschChiappisietal.2013,
  author    = {Inal, Sahika and K{\"o}lsch, Jonas D. and Chiappisi, Leonardo and Janietz, Dietmar and Gradzielski, Michael and Laschewsky, Andr{\´e} and Neher, Dieter},
  title     = {Structure-related differences in the temperature-regulated fluorescence response of LCST type polymers},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-95379},
  pages     = {6603 -- 6612},
  year      = {2013},
  abstract  = {We demonstrate new fluorophore-labelled materials based on acrylamide and on oligo(ethylene glycol) (OEG) bearing thermoresponsive polymers for sensing purposes and investigate their thermally induced solubility transitions. It is found that the emission properties of the polarity-sensitive (solvatochromic) naphthalimide derivative attached to three different thermoresponsive polymers are highly specific to the exact chemical structure of the macromolecule. While the dye emits very weakly below the LCST when incorporated into poly(N-isopropylacrylamide) (pNIPAm) or into a polyacrylate backbone bearing only short OEG side chains, it is strongly emissive in polymethacrylates with longer OEG side chains. Heating of the aqueous solutions above their cloud point provokes an abrupt increase of the fluorescence intensity of the labelled pNIPAm, whereas the emission properties of the dye are rather unaffected as OEG-based polyacrylates and methacrylates undergo phase transition. Correlated with laser light scattering studies, these findings are ascribed to the different degrees of pre-aggregation of the chains at low temperatures and to the extent of dehydration that the phase transition evokes. It is concluded that although the temperature-triggered changes in the macroscopic absorption characteristics, related to large-scale alterations of the polymer chain conformation and aggregation, are well detectable and similar for these LCST-type polymers, the micro-environment provided to the dye within each polymer network differs substantially. Considering sensing applications, this finding is of great importance since the temperature-regulated fluorescence response of the polymer depends more on the macromolecular architecture than the type of reporter fluorophore.},
  language  = {en}
}
@phdthesis{Inal2013,
  author    = {Inal, Sahika},
  title     = {Responsive polymers for optical sensing applications},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70806},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {LCST-type synthetic thermoresponsive polymers can reversibly respond to certain stimuli in aqueous media with a massive change of their physical state. When fluorophores, that are sensitive to such changes, are incorporated into the polymeric structure, the response can be translated into a fluorescence signal. Based on this idea, this thesis presents sensing schemes which transduce the stimuli-induced variations in the solubility of polymer chains with covalently-bound fluorophores into a well-detectable fluorescence output. Benefiting from the principles of different photophysical phenomena, i.e. of fluorescence resonance energy transfer and solvatochromism, such fluorescent copolymers enabled monitoring of stimuli such as the solution temperature and ionic strength, but also of association/disassociation mechanisms with other macromolecules or of biochemical binding events through remarkable changes in their fluorescence properties. For instance, an aqueous ratiometric dual sensor for temperature and salts was developed, relying on the delicate supramolecular assembly of a thermoresponsive copolymer with a thiophene-based conjugated polyelectrolyte. Alternatively, by taking advantage of the sensitivity of solvatochromic fluorophores, an increase in solution temperature or the presence of analytes was signaled as an enhancement of the fluorescence intensity. A simultaneous use of the sensitivity of chains towards the temperature and a specific antibody allowed monitoring of more complex phenomena such as competitive binding of analytes. The use of different thermoresponsive polymers, namely poly(N-isopropylacrylamide) and poly(meth)acrylates bearing oligo(ethylene glycol) side chains, revealed that the responsive polymers differed widely in their ability to perform a particular sensing function. In order to address questions regarding the impact of the chemical structure of the host polymer on the sensing performance, the macromolecular assembly behavior below and above the phase transition temperature was evaluated by a combination of fluorescence and light scattering methods. It was found that although the temperature-triggered changes in the macroscopic absorption characteristics were similar for these polymers, properties such as the degree of hydration or the extent of interchain aggregations differed substantially. Therefore, in addition to the demonstration of strategies for fluorescence-based sensing with thermoresponsive polymers, this work highlights the role of the chemical structure of the two popular thermoresponsive polymers on the fluorescence response. The results are fundamentally important for the rational choice of polymeric materials for a specific sensing strategy.},
  language  = {en}
}
@phdthesis{Garz2013,
  author    = {Garz, Andreas},
  title     = {Nichtlineare Mikroskopie und Bilddatenverarbeitung zur biochemischen Analyse synchronisierter Chlamydomonas-Zellen},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66904},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {Unter geeigneten Wachstumsbedingungen weisen Algenkulturen oft eine gr{\"o}ßere Produktivit{\"a}t der Zellen auf, als sie bei h{\"o}heren Pflanzen zu beobachten ist. Chlamydomonas reinhardtii-Zellen sind vergleichsweise klein. So betr{\"a}gt das Zellvolumen w{\"a}hrend des vegetativen Zellzyklus etwa 50-3500 µm³. Im Vergleich zu h{\"o}heren Pflanzen ist in einer Algensuspension die Konzentration der Biomasse allerdings gering. So enth{\"a}lt beispielsweise 1 ml einer {\"u}blichen Konzentration zwischen 10E6 und 10E7 Algenzellen. Quantifizierungen von Metaboliten oder Makromolek{\"u}len, die zur Modellierung von zellul{\"a}ren Prozessen genutzt werden, werden meist im Zellensemble vorgenommen. Tats{\"a}chlich unterliegt jedoch jede Algenzelle einer individuellen Entwicklung, die die Identifizierung charakteristischer allgemeing{\"u}ltiger Systemparameter erschwert. Ziel dieser Arbeit war es, biochemisch relevante Messgr{\"o}ßen in-vivo und in-vitro mit Hilfe optischer Verfahren zu identifizieren und zu quantifizieren. Im ersten Teil der Arbeit wurde ein Puls-Amplituden-Modulation(PAM)-Fluorimetriemessplatz zur Messung der durch {\"a}ußere Einfl{\"u}sse bedingten ver{\"a}nderlichen Chlorophyllfluoreszenz an einzelnen Zellen vorgestellt. Die Verwendung eines kommerziellen Mikroskops, die Implementierung empfindlicher Nachweiselektronik und einer geeignete Immobilisierungsmethode erm{\"o}glichten es, ein Signal-zu-Rauschverh{\"a}ltnis zu erreichen, mit dem Fluoreszenzsignale einzelner lebender Chlamydomonas-Zellen gemessen werden konnten. Insbesondere wurden das Zellvolumen und der als Maß f{\"u}r die Effizienz des Photosyntheseapparats bzw. die Zellfitness geltende Chlorophyllfluoreszenzparameter Fv/Fm ermittelt und ein hohes Maß an Heterogenit{\"a}t dieser zellul{\"a}ren Parameter in verschiedenen Entwicklungsstadien der synchronisierten Chlamydomonas-Zellen festgestellt. Im zweiten Teil der Arbeit wurden die bildgebende Laser-Scanning-Mikroskopie und anschließende Bilddatenanalyse zur quantitativen Erfassung der wachstumsabh{\"a}ngigen zellul{\"a}ren Parameter angewandt. Ein kommerzielles konfokales Mikroskop wurde um die M{\"o}glichkeit der nichtlinearen Mikroskopie erweitert. Diese hat den Vorteil einer lokalisierten Anregung, damit verbunden einer h{\"o}heren Ortsaufl{\"o}sung und insgesamt geringeren Probenbelastung. Weiterhin besteht neben der Signalgewinnung durch Fluoreszenzanregung die M{\"o}glichkeit der Erzeugung der Zweiten Harmonischen (SHG) an biophotonischen Strukturen, wie der zellul{\"a}ren St{\"a}rke. Anhand der Verteilungsfunktionen war es m{\"o}glich mit Hilfe von modelltheoretischen Ans{\"a}tzen zellul{\"a}re Parameter zu ermitteln, die messtechnisch nicht unmittelbar zug{\"a}nglich sind. Die morphologischen Informationen der Bilddaten erm{\"o}glichten die Bestimmung der Zellvolumina und die Volumina subzellularer Strukturen, wie Nuclei, extranucle{\"a}re DNA oder St{\"a}rkegranula. Weiterhin konnte die Anzahl subzellul{\"a}rer Strukturen innerhalb einer Zelle bzw. eines Zellverbunds ermittelt werden. Die Analyse der in den Bilddaten enthaltenen Signalintensit{\"a}ten war Grundlage einer relativen Konzentrationsbestimmung von zellul{\"a}ren Komponenten, wie DNA bzw. St{\"a}rke. Mit dem hier vorgestellten Verfahren der nichtlinearen Mikroskopie und nachfolgender Bilddatenanalyse konnte erstmalig die Verteilung des zellul{\"a}ren St{\"a}rkegehalts in einer Chlamydomonas-Population w{\"a}hrend des Wachstums bzw. nach induziertem St{\"a}rkeabbau verfolgt werden. Im weiteren Verlauf wurde diese Methode auch auf Gefrierschnitte h{\"o}herer Pflanzen, wie Arabidopsis thaliana, angewendet. Im Ergebnis wurde gezeigt, dass viele zellul{\"a}re Parameter, wie das Volumen, der zellul{\"a}re DNA- und St{\"a}rkegehalt bzw. die Anzahl der St{\"a}rkegranula durch eine Lognormalverteilung, mit wachstumsabh{\"a}ngiger Parametrisierung, beschrieben werden. Zellul{\"a}re Parameter, wie Stoffkonzentration und zellul{\"a}res Volumen, zeigen keine signifikanten Korrelationen zueinander, woraus geschlussfolgert werden muss, dass es ein hohes Maß an Heterogenit{\"a}t der zellul{\"a}ren Parameter innerhalb der synchronisierten Chlamydomonas-Populationen gibt. Diese Aussage gilt sowohl f{\"u}r die als homogenste Form geltenden Synchronkulturen von Chlamydomonas reinhardtii als auch f{\"u}r die gemessenen zellul{\"a}ren Parameter im intakten Zellverbund h{\"o}herer Pflanzen. Dieses Ergebnis ist insbesondere f{\"u}r modelltheoretische Betrachtungen von Relevanz, die sich auf empirische Daten bzw. zellul{\"a}re Parameter st{\"u}tzen welche im Zellensemble gemessen wurden und somit nicht notwendigerweise den zellul{\"a}ren Status einer einzelnen Zelle repr{\"a}sentieren.},
  language  = {de}
}
@phdthesis{Boedecker2013,
  author    = {Boedecker, Geesche},
  title     = {Resonance Fluorescence in a Photonic Crystal},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-69591},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {The problem under consideration in the thesis is a two level atom in a photonic crystal and a pumping laser. The photonic crystal provides an environment for the atom, that modifies the decay of the exited state, especially if the atom frequency is close to the band gap. The population inversion is investigated als well as the emission spectrum. The dynamics is analysed in the context of open quantum systems. Due to the multiple reflections in the photonic crystal, the system has a finite memory that inhibits the Markovian approximation. In the Heisenberg picture the equations of motion for the system variables form a infinite hierarchy of integro-differential equations. To get a closed system, approximations like a weak coupling approximation are needed. The thesis starts with a simple photonic crystal that is amenable to analytic calculations: a one-dimensional photonic crystal, that consists of alternating layers. The Bloch modes inside and the vacuum modes outside a finite crystal are linked with a transformation matrix that is interpreted as a transfer matrix. Formulas for the band structure, the reflection from a semi-infinite crystal, and the local density of states in absorbing crystals are found; defect modes and negative refraction are discussed. The quantum optics section of the work starts with the discussion of three problems, that are related to the full resonance fluorescence problem: a pure dephasing model, the driven atom and resonance fluorescence in free space. In the lowest order of the system-environment coupling, the one-time expectation values for the full problem are calculated analytically and the stationary states are discussed for certain cases. For the calculation of the two time correlation functions and spectra, the additional problem of correlations between the two times appears. In the Markovian case, the quantum regression theorem is valid. In the general case, the fluctuation dissipation theorem can be used instead. The two-time correlation functions are calculated by the two different methods. Within the chosen approximations, both methods deliver the same result. Several plots show the dependence of the spectrum on the parameters. Some examples for squeezing spectra are shown with different approximations. A projection operator method is used to establish two kinds of Markovian expansion with and without time convolution. The lowest order is identical with the lowest order of system environment coupling, but higher orders give different results.},
  language  = {en}
}