@article{ChipperfieldDythamHovestadt2011,
  author    = {Chipperfield, Joseph D. and Dytham, Calvin and Hovestadt, Thomas},
  title     = {An Updated Algorithm for the Generation of Neutral Landscapes by Spectral Synthesis},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-68938},
  year      = {2011},
  abstract  = {Background: Patterns that arise from an ecological process can be driven as much from the landscape over which the process is run as it is by some intrinsic properties of the process itself. The disentanglement of these effects is aided if it possible to run models of the process over artificial landscapes with controllable spatial properties. A number of different methods for the generation of so-called 'neutral landscapes' have been developed to provide just such a tool. Of these methods, a particular class that simulate fractional Brownian motion have shown particular promise. The existing methods of simulating fractional Brownian motion suffer from a number of problems however: they are often not easily generalisable to an arbitrary number of dimensions and produce outputs that can exhibit some undesirable artefacts. Methodology: We describe here an updated algorithm for the generation of neutral landscapes by fractional Brownian motion that do not display such undesirable properties. Using Monte Carlo simulation we assess the anisotropic properties of landscapes generated using the new algorithm described in this paper and compare it against a popular benchmark algorithm. Conclusion/Significance: The results show that the existing algorithm creates landscapes with values strongly correlated in the diagonal direction and that the new algorithm presented here corrects this artefact. A number of extensions of the algorithm described here are also highlighted: we describe how the algorithm can be employed to generate landscapes that display different properties in different dimensions and how they can be combined with an environmental gradient to produce landscapes that combine environmental variation at the local and macro scales.},
  subject      = {Landschaft},
  language  = {en}
}
@phdthesis{Hartel2013,
  author    = {Hartel, Andreas J. W.},
  title     = {Die laterale Diffusion des variablen Oberfl{\"a}chenglykoproteins in Trypanosomen und in artifiziellen Membranen},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-90997},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {Die Diffusion von Membranproteinen spielt bei einer Vielzahl von zellbiologischen Prozessen eine zentrale Rolle. So hat die Beweglichkeit von Glykosyl-Phosphatidyl-Inositol-(GPI-) verankerten Proteinen zum Beispiel eine tragende Funktion bei der Alzheimer Krankheit, der Creutzfeldt-Jacob Krankheit und der Afrikanischen Schlafkrankheit. Der Erreger der Afrikanischen Schlafkrankheit, Trypanosoma brucei spec., pr{\"a}sentiert auf seiner Zelloberfl{\"a}che einen dichten Mantel aus identischen GPI-verankerten Proteinen. Diese sogenannten Variant Surface Glycoproteins (VSGs) stellen den zentralen Pathogenit{\"a}tsfaktor der Trypanosomen im Blutstrom des Wirtes dar und erm{\"o}glichen dem Parasiten die Antigene Variation. W{\"a}hrend der Antigenen Variation wird der VSGMantel durch einen immunologisch distinkten Mantel ersetzt. Hierf{\"u}r ist die Diffusion der VSG essentiell. In der vorliegenden Arbeit wird die Diffusion des VSG in lebenden Trypanosomen und in artifiziellen Membranen systematisch untersucht. Auf diese Weise werden der Einfluss der lateralen Proteindichte, der N-Glykosylierung und der Proteingr{\"o}ße auf die Diffusion der GPI-verankerten Proteine charakterisiert. Die Mobilit{\"a}t des VSG auf lebenden Trypanosomen ist an der Grenze zu einem Diffusionsschwellenwert, dieser wird allerdings nicht {\"u}berschritten. Die Mobilit{\"a}t des VSG in der N{\"a}he des Diffusionsschwellenwertes wird durch die N-Glykosylierung der VSG erm{\"o}glicht. Außerdem kann gezeigt werden, dass die Gr{\"o}ße der Proteine einen entscheidenden Einfluss auf den Diffusionskoeffizienten der GPI-verankerten Proteine aus{\"u}bt. Zusammengefasst zeigen die Ergebnisse der vorliegenden Arbeit deutlich, dass der VSG-Mantel der Trypanosomen ein, an seine Anforderungen, hoch-adaptiertes System darstellt. W{\"u}rde entweder die laterale Dichte, die N-Glykosylierung oder die Gr{\"o}ße der Proteine beeintr{\"a}chtigt werden, so w{\"a}re die Funktion der Antigenen Variation gest{\"o}rt und die Pathogenit{\"a}t des Parasiten gef{\"a}hrdet. Da die lokale Verteilung von GPI-verankerten Proteinen in biologischen Membranen ein wichtiges funktionelles Konzept darstellt, ist der Einfluss der untersuchten Faktoren nicht nur f{\"u}r den VSG-Mantel relevant, sondern kann auch f{\"u}r das generelle Verst{\"a}ndnis der Dynamik von Proteinen in zellul{\"a}ren Membranen dienen.},
  subject      = {Trypanosomen},
  language  = {de}
}
@phdthesis{Meiser2023,
  author    = {Meiser, Elisabeth},
  title     = {Single-molecule dynamics at a bottleneck: a systematic study of the narrow escape problem in a disc},
  doi       = {10.25972/OPUS-31965},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-319650},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Diffusion facilitates numerous reactions within the biological context of a cell. It is remarkable how the cost-efficient random process of Brownian motion promotes fast reactions. From the narrow escape theory, it is possible to determine the mean first passage time of such processes based on their reaction space and diffusion coefficient. The narrow escape theory of Brownian particles is characterized by a confining domain with reflective boundaries and a small reaction site. In this thesis, the mean first passage time was systematically tested in a disc as a function of the escape opening size in vitro and in silico. For the in vitro experiments, a model system of patterned supported-lipid bilayers (SLB) was established. Such a model is prepared by a combined colloid metalization approach, where a gold scaffold on glass facilitates assembly of SLB patches of distinct sizes through vesicle fusion. The model setup was evaluated and found to match all necessary requirements to test the nar- row escape problem in vitro. In particular, the reflectivity of the boundaries, the unhindered, free diffusion of the tracer lipids, and the distinct area were assessed. Observed results of the mean first passage time agreed with the theory of the narrow escape problem. There was excellent agreement in both absolute values and across a range of small escape opening sizes. Additionally, I developed a straightforward method, a correction factor, to calculate the mean first passage time from incomplete experimental traces. By re-scaling the mean first passage time to the fraction of particles that escaped, I was able to overcome the lifetime limitations of fluorescent probes. Previously inaccessible measurements of the mean first passage time relying on fluorescent probes will be made possible through this approach. The in vitro experiments were complemented with various in silico experiments. The latter were based on random walk simulations in discs, mimicking the in vitro situation with its uncertainties. The lifetime of single particles was either set sufficiently long to allow all particles to escape, or was adjusted to meet the lifetime limitations observed in the in vitro experiments. A comparison of the mean first passage time from lifetime-unlimited particles to the corrected, lifetime-limited particles did support the use of the correction factor. In agreement with the narrow escape theory, it was experimentally found that the mean first passage time is independent of the start point of the particle within the domain. This is when the particle adheres to a minimum distance to the escape site. In general, the presented random walk simulations do accurately represent the in vitro experiments in this study. The required hardware for the establishment of an astigmatism-based 3D system was installed in the existing microscope. The first attempts to analyze the obtained 3D imaging data gave insight into the potential of the method to investigate molecule dynamics in living trypanosome cells. The full functionality will be realized with the ongoing improvement of image analysis outside of this thesis.},
  subject      = {Freies Molek{\"u}l},
  language  = {en}
}