@phdthesis{Breuer2016,
  author    = {Breuer, David},
  title     = {The plant cytoskeleton as a transportation network},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93583},
  school      = {Universit{\"a}t Potsdam},
  pages     = {164},
  year      = {2016},
  abstract  = {The cytoskeleton is an essential component of living cells. It is composed of different types of protein filaments that form complex, dynamically rearranging, and interconnected networks. The cytoskeleton serves a multitude of cellular functions which further depend on the cell context. In animal cells, the cytoskeleton prominently shapes the cell's mechanical properties and movement. In plant cells, in contrast, the presence of a rigid cell wall as well as their larger sizes highlight the role of the cytoskeleton in long-distance intracellular transport. As it provides the basis for cell growth and biomass production, cytoskeletal transport in plant cells is of direct environmental and economical relevance. However, while knowledge about the molecular details of the cytoskeletal transport is growing rapidly, the organizational principles that shape these processes on a whole-cell level remain elusive. This thesis is devoted to the following question: How does the complex architecture of the plant cytoskeleton relate to its transport functionality? The answer requires a systems level perspective of plant cytoskeletal structure and transport. To this end, I combined state-of-the-art confocal microscopy, quantitative digital image analysis, and mathematically powerful, intuitively accessible graph-theoretical approaches. This thesis summarizes five of my publications that shed light on the plant cytoskeleton as a transportation network: (1) I developed network-based frameworks for accurate, automated quantification of cytoskeletal structures, applicable in, e.g., genetic or chemical screens; (2) I showed that the actin cytoskeleton displays properties of efficient transport networks, hinting at its biological design principles; (3) Using multi-objective optimization, I demonstrated that different plant cell types sustain cytoskeletal networks with cell-type specific and near-optimal organization; (4) By investigating actual transport of organelles through the cell, I showed that properties of the actin cytoskeleton are predictive of organelle flow and provided quantitative evidence for a coordination of transport at a cellular level; (5) I devised a robust, optimization-based method to identify individual cytoskeletal filaments from a given network representation, allowing the investigation of single filament properties in the network context. The developed methods were made publicly available as open-source software tools. Altogether, my findings and proposed frameworks provide quantitative, system-level insights into intracellular transport in living cells. Despite my focus on the plant cytoskeleton, the established combination of experimental and theoretical approaches is readily applicable to different organisms. Despite the necessity of detailed molecular studies, only a complementary, systemic perspective, as presented here, enables both understanding of cytoskeletal function in its evolutionary context as well as its future technological control and utilization.},
  language  = {en}
}
@phdthesis{Schroeder2016,
  author    = {Schr{\"o}der, Henning},
  title     = {Ultrafast electron dynamics in Fe(CO)5 and Cr(CO)6},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-94589},
  school      = {Universit{\"a}t Potsdam},
  pages     = {v, 87},
  year      = {2016},
  abstract  = {In this thesis, the two prototype catalysts Fe(CO)₅ and Cr(CO)₆ are investigated with time-resolved photoelectron spectroscopy at a high harmonic setup. In both of these metal carbonyls, a UV photon can induce the dissociation of one or more ligands of the complex. The mechanism of the dissociation has been debated over the last decades. The electronic dynamics of the first dissociation occur on the femtosecond timescale. For the experiment, an existing high harmonic setup was moved to a new location, was extended, and characterized. The modified setup can induce dynamics in gas phase samples with photon energies of 1.55eV, 3.10eV, and 4.65eV. The valence electronic structure of the samples can be probed with photon energies between 20eV and 40eV. The temporal resolution is 111fs to 262fs, depending on the combination of the two photon energies. The electronically excited intermediates of the two complexes, as well as of the reaction product Fe(CO)₄, could be observed with photoelectron spectroscopy in the gas phase for the first time. However, photoelectron spectroscopy gives access only to the final ionic states. Corresponding calculations to simulate these spectra are still in development. The peak energies and their evolution in time with respect to the initiation pump pulse have been determined, these peaks have been assigned based on literature data. The spectra of the two complexes show clear differences. The dynamics have been interpreted with the assumption that the motion of peaks in the spectra relates to the movement of the wave packet in the multidimensional energy landscape. The results largely confirm existing models for the reaction pathways. In both metal carbonyls, this pathway involves a direct excitation of the wave packet to a metal-to-ligand charge transfer state and the subsequent crossing to a dissociative ligand field state. The coupling of the electronic dynamics to the nuclear dynamics could explain the slower dissociation in Fe(CO)₅ as compared to Cr(CO)₆.},
  language  = {en}
}
@phdthesis{Rezanezhad2016,
  author    = {Rezanezhad, Vahid},
  title     = {Inversion of the 2004 M6.0 Parkfield Earthquake Coseismic Offsets by Partition Model},
  school      = {Universit{\"a}t Potsdam},
  pages     = {83},
  year      = {2016},
  language  = {en}
}
@phdthesis{Dionysopoulou2016,
  author    = {Dionysopoulou, Kyriaki},
  title     = {General-relativistic magnetohydrodynamics in compact objects},
  school      = {Universit{\"a}t Potsdam},
  pages     = {144},
  year      = {2016},
  language  = {en}
}
@phdthesis{Gomez2016,
  author    = {Gomez, David},
  title     = {Mechanisms of biochemical reactions within crowded environments},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-94593},
  school      = {Universit{\"a}t Potsdam},
  pages     = {vii, 112},
  year      = {2016},
  abstract  = {The cell interior is a highly packed environment in which biological macromolecules evolve and function. This crowded media has effects in many biological processes such as protein-protein binding, gene regulation, and protein folding. Thus, biochemical reactions that take place in such crowded conditions differ from diluted test tube conditions, and a considerable effort has been invested in order to understand such differences. In this work, we combine different computationally tools to disentangle the effects of molecular crowding on biochemical processes. First, we propose a lattice model to study the implications of molecular crowding on enzymatic reactions. We provide a detailed picture of how crowding affects binding and unbinding events and how the separate effects of crowding on binding equilibrium act together. Then, we implement a lattice model to study the effects of molecular crowding on facilitated diffusion. We find that obstacles on the DNA impair facilitated diffusion. However, the extent of this effect depends on how dynamic obstacles are on the DNA. For the scenario in which crowders are only present in the bulk solution, we find that at some conditions presence of crowding agents can enhance specific-DNA binding. Finally, we make use of structure-based techniques to look at the impact of the presence of crowders on the folding a protein. We find that polymeric crowders have stronger effects on protein stability than spherical crowders. The strength of this effect increases as the polymeric crowders become longer. The methods we propose here are general and can also be applied to more complicated systems.},
  language  = {en}
}
@phdthesis{Lehmann2016,
  author    = {Lehmann, Jascha In-su},
  title     = {Changes in extratropical storm track activity and their implications for extreme weather events},
  pages     = {221},
  year      = {2016},
  language  = {en}
}
@phdthesis{Kruesemann2016,
  author    = {Kr{\"u}semann, Henning},
  title     = {First passage phenomena and single-file motion in ageing continuous time random walks and quenched energy landscapes},
  school      = {Universit{\"a}t Potsdam},
  pages     = {122},
  year      = {2016},
  abstract  = {In der Physik gibt es viele Prozesse, die auf Grund ihrer Komplexit{\"a}t nicht durch physikalische Gleichungen beschrieben werden k{\"o}nnen, beispielsweise die Bewegung eines Staubkorns in der Luft. Durch die vielen St{\"o}ße mit Luftmolek{\"u}len f{\"u}hrt es eine Zufallsbewegung aus, die so genannte Diffusion. Auch Molek{\"u}le in biologischen Zellen diffundieren, jedoch befinden sich in einer solchen Zelle im selben Volumen viel mehr oder viel gr{\"o}ßere Molek{\"u}le. Das beobachtete Teilchen st{\"o}ßt dementsprechend {\"o}fter mit anderen zusammen und die Diffusion wird langsamer, sie wird subdiffusiv. Mit der Zeit kann sich die Charakteristik der Subdiffusion {\"a}ndern; dies wird als (mikroskopisches) Altern bezeichnet. Ich untersuche in der vorliegenden Arbeit zwei mathematische Modelle f{\"u}r eindimensionale Subdiffusion, einmal den continuous time random walk (CTRW) und einmal die Zufallsbewegung in einer eingefrorenen Energielandschaft (QEL=quenched energy landscape). Beide sind Sprungprozesse, das heißt, sie sind Abfolgen von r{\"a}umlichen Spr{\"u}ngen, die durch zufallsverteilte Wartezeiten getrennt sind. Die Wartezeiten in der QEL sind r{\"a}umlich korrelliert, w{\"a}hrend sie im CTRW unkorrelliert sind. Ich untersuche in der vorliegenden Arbeit verschiedene statistische Gr{\"o}ßen in beiden Modellen. Zun{\"a}chst untersuche ich den Einfluss des Alters und den Einfluss der Korrellationen einer QEL auf die Verteilung der Zeiten, die das diffundierendes Teilchen ben{\"o}tigt, um eine (r{\"a}umliche) Schwelle zu {\"u}berqueren. Ausserdem bestimme ich den Effekt des Alters auf Str{\"o}me von (sub)diffundierenden Partikeln, die sich auf eine absorbierende Barriere zubewegen. Zuletzt besch{\"a}ftige ich mich mit der Diffusion einer eindimensionalen Anordnung von Teilchen in einer QEL, in der diese als harte Kugeln miteinander wechselwirken. Dabei vergleiche ich die gemeinsame Bewegung in einer QEL und als individuelle CTRWs miteinander {\"u}ber die Standartabweichung von der Startposition, f{\"u}r die ich das Mittel {\"u}ber mehrere QELs untersuche. Meine Arbeit setzt sich zusammen aus theoretischen {\"U}berlegungen und Berechnungen sowie der Simulation der Zufallsprozesse. Die Ergebnisse der Simulation und, soweit vorhanden, experimentelle Daten werden mit der Theorie verglichen.},
  language  = {en}
}
@phdthesis{Berner2016,
  author    = {Berner, Nadine},
  title     = {Deciphering multiple changes in complex climate time series using Bayesian inference},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-100065},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xvi, 135},
  year      = {2016},
  abstract  = {Change points in time series are perceived as heterogeneities in the statistical or dynamical characteristics of the observations. Unraveling such transitions yields essential information for the understanding of the observed system's intrinsic evolution and potential external influences. A precise detection of multiple changes is therefore of great importance for various research disciplines, such as environmental sciences, bioinformatics and economics. The primary purpose of the detection approach introduced in this thesis is the investigation of transitions underlying direct or indirect climate observations. In order to develop a diagnostic approach capable to capture such a variety of natural processes, the generic statistical features in terms of central tendency and dispersion are employed in the light of Bayesian inversion. In contrast to established Bayesian approaches to multiple changes, the generic approach proposed in this thesis is not formulated in the framework of specialized partition models of high dimensionality requiring prior specification, but as a robust kernel-based approach of low dimensionality employing least informative prior distributions. First of all, a local Bayesian inversion approach is developed to robustly infer on the location and the generic patterns of a single transition. The analysis of synthetic time series comprising changes of different observational evidence, data loss and outliers validates the performance, consistency and sensitivity of the inference algorithm. To systematically investigate time series for multiple changes, the Bayesian inversion is extended to a kernel-based inference approach. By introducing basic kernel measures, the weighted kernel inference results are composed into a proxy probability to a posterior distribution of multiple transitions. The detection approach is applied to environmental time series from the Nile river in Aswan and the weather station Tuscaloosa, Alabama comprising documented changes. The method's performance confirms the approach as a powerful diagnostic tool to decipher multiple changes underlying direct climate observations. Finally, the kernel-based Bayesian inference approach is used to investigate a set of complex terrigenous dust records interpreted as climate indicators of the African region of the Plio-Pleistocene period. A detailed inference unravels multiple transitions underlying the indirect climate observations, that are interpreted as conjoint changes. The identified conjoint changes coincide with established global climate events. In particular, the two-step transition associated to the establishment of the modern Walker-Circulation contributes to the current discussion about the influence of paleoclimate changes on the environmental conditions in tropical and subtropical Africa at around two million years ago.},
  language  = {en}
}
@phdthesis{Soriano2016,
  author    = {Soriano, Manuel Flores},
  title     = {Short-term evolution and coexistence of photospheric and chromospheric activity on LQ Hydrae},
  school      = {Universit{\"a}t Potsdam},
  pages     = {90},
  year      = {2016},
  language  = {en}
}
@phdthesis{Daschewski2016,
  author    = {Daschewski, Maxim},
  title     = {Thermophony in real gases},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-98866},
  school      = {Universit{\"a}t Potsdam},
  pages     = {79},
  year      = {2016},
  abstract  = {A thermophone is an electrical device for sound generation. The advantages of thermophones over conventional sound transducers such as electromagnetic, electrostatic or piezoelectric transducers are their operational principle which does not require any moving parts, their resonance-free behavior, their simple construction and their low production costs. In this PhD thesis, a novel theoretical model of thermophonic sound generation in real gases has been developed. The model is experimentally validated in a frequency range from 2 kHz to 1 MHz by testing more then fifty thermophones of different materials, including Carbon nano-wires, Titanium, Indium-Tin-Oxide, different sizes and shapes for sound generation in gases such as air, argon, helium, oxygen, nitrogen and sulfur hexafluoride. Unlike previous approaches, the presented model can be applied to different kinds of thermophones and various gases, taking into account the thermodynamic properties of thermophone materials and of adjacent gases, degrees of freedom and the volume occupied by the gas atoms and molecules, as well as sound attenuation effects, the shape and size of the thermophone surface and the reduction of the generated acoustic power due to photonic emission. As a result, the model features better prediction accuracy than the existing models by a factor up to 100. Moreover, the new model explains previous experimental findings on thermophones which can not be explained with the existing models. The acoustic properties of the thermophones have been tested in several gases using unique, highly precise experimental setups comprising a Laser-Doppler-Vibrometer combined with a thin polyethylene film which acts as a broadband and resonance-free sound-pressure detector. Several outstanding properties of the thermophones have been demonstrated for the first time, including the ability to generate arbitrarily shaped acoustic signals, a greater acoustic efficiency compared to conventional piezoelectric and electrostatic airborne ultrasound transducers, and applicability as powerful and tunable sound sources with a bandwidth up to the megahertz range and beyond. Additionally, new applications of thermophones such as the study of physical properties of gases, the thermo-acoustic gas spectroscopy, broad-band characterization of transfer functions of sound and ultrasound detection systems, and applications in non-destructive materials testing are discussed and experimentally demonstrated.},
  language  = {en}
}