@phdthesis{Jozefczuk2009,
  author    = {J{\´o}zefczuk, Szymon},
  title     = {"Escherichia coli" stress response on the level of transcriptome and metabolome},
  pages     = {XV, 121 Bl. : graph. Darst.},
  year      = {2009},
  language  = {en}
}
@phdthesis{Fischer2008,
  author    = {Fischer, Anna},
  title     = {"Reactive hard templating" : from carbon nitrides to metal nitrides},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-19777},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {Nanostructured inorganic materials are routinely synthesized by the use of templates. Depending on the synthesis conditions of the product material, either "soft" or "hard" templates can be applied. For sol-gel processes, usually "soft" templating techniques are employed, while "hard" templates are used for high temperature synthesis pathways. In classical templating approaches, the template has the unique role of structure directing agent, in the sense that it is not participating to the chemical formation of the resulting material. This work investigates a new templating pathway to nanostructured materials, where the template is also a reagent in the formation of the final material. This concept is described as "reactive templating" and opens a synthetic path toward materials which cannot be synthesised on a nanometre scale by classical templating approaches. Metal nitrides are such kind of materials. They are usually produced by the conversion of metals or metal oxides in ammonia flow at high temperature (T > 1000°C), which make the application of classical templating techniques difficult. Graphitic carbon nitride, g-C3N4, despite its fundamental and theoretical importance, is probably one of the most promising materials to complement carbon in material science and many efforts are put in the synthesis of this material. A simple polyaddition/elimination reaction path at high temperature (T = 550°C) allows the polymerisation of cyanamide toward graphitic carbon nitride solids. By hard templating, using nanostructured silica or aluminium oxide as nanotemplates, a variety of nanostructured graphitic carbon nitrides such as nanorods, nanotubes, meso- and macroporous powders could be obtained by nanocasting or nanocoating. Due to the special semi-conducting properties of the graphitic carbon nitride matrix, the nanostructured graphitic carbon nitrides show unexpected catalytic activity for the activation of benzene in Friedel-Crafts type reactions, making this material an interesting metal free catalyst. Furthermore, due to the chemical composition of g-C3N4 and the fact that it is totally decomposed at temperatures between 600°C and 800°C even under inert atmosphere, g-C3N4 was shown to be a good nitrogen donor for the synthesis of early transition metal nitrides at high temperatures. Thus using the nanostructured carbon nitrides as "reactive templates" or "nanoreactors", various metal nitride nanostructures, such as nanoparticles and porous frameworks could be obtained at high temperature. In this approach the carbon nitride nanostructure played both the role of the nitrogen source and of the exotemplate, imprinting its size and shape to the resulting metal nitride nanostructure.},
  language  = {en}
}
@phdthesis{Schindler2021,
  author    = {Schindler, Eva Marie},
  title     = {"What we have done is just to put the people in form of a structure"},
  school      = {Universit{\"a}t Potsdam},
  pages     = {XIV, 288},
  year      = {2021},
  abstract  = {Participation has become an orthodoxy in the field of development, an essential element of projects and programmes. This book analyses participation in development interventions as an institutionalised expectation - a rationalized myth - and examines how organisations on different levels of government process it. At least two different objectives of participation are appropriate and legitimate for international organisations in the field: the empowerment of local beneficiaries and the achievement of programme goals. Both integrate participatory forums into the organisational logic of development interventions. Local administrations react to the institutionalised expectation with means-ends decoupling, where participatory forums are implemented superficially but de facto remain marginalised in local administrative processes and activities. The book furthermore provides a thick description of the organisationality of participation in development interventions. Participatory forums are shown to be a form of partial organisation. They establish an order in the relationship between administrations and citizens through the introduction of rules and the creation of a defined membership. At the same time, this order is found to be fragile and subject to criticism and negotiation.},
  language  = {en}
}
@phdthesis{Kneis2013,
  author    = {Kneis, Philipp},
  title     = {(S)aged by culture : Representations of old age in american indian literature and culture},
  publisher = {Peter Lang Edition},
  address   = {Frankfurt am Main, New York},
  isbn      = {978-3-631-63853-8},
  pages     = {298 S.},
  year      = {2013},
  language  = {en}
}
@phdthesis{Bendadani2015,
  author    = {Bendadani, Carolin},
  title     = {1-Methylpyren: Biotransformation und Gentoxizit{\"a}t},
  school      = {Universit{\"a}t Potsdam},
  pages     = {188},
  year      = {2015},
  language  = {en}
}
@phdthesis{Lontsi2016,
  author    = {Lontsi, Agostiny Marrios},
  title     = {1D shallow sedimentary subsurface imaging using ambient noise and active seismic data},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-103807},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xix, 119},
  year      = {2016},
  abstract  = {The Earth's shallow subsurface with sedimentary cover acts as a waveguide to any incoming wavefield. Within the framework of my thesis, I focused on the characterization of this shallow subsurface within tens to few hundreds of meters of sediment cover. I imaged the seismic 1D shear wave velocity (and possibly the 1D compressional wave velocity). This information is not only required for any seismic risk assessment, geotechnical engineering or microzonation activities, but also for exploration and global seismology where site effects are often neglected in seismic waveform modeling. First, the conventional frequency-wavenumber (f - k) technique is used to derive the dispersion characteristic of the propagating surface waves recorded using distinct arrays of seismometers in 1D and 2D configurations. Further, the cross-correlation technique is applied to seismic array data to estimate the Green's function between receivers pairs combination assuming one is the source and the other the receiver. With the consideration of a 1D media, the estimated cross-correlation Green's functions are sorted with interstation distance in a virtual 1D active seismic experiment. The f - k technique is then used to estimate the dispersion curves. This integrated analysis is important for the interpretation of a large bandwidth of the phase velocity dispersion curves and therefore improving the resolution of the estimated 1D Vs profile. Second, the new theoretical approach based on the Diffuse Field Assumption (DFA) is used for the interpretation of the observed microtremors H/V spectral ratio. The theory is further extended in this research work to include not only the interpretation of the H/V measured at the surface, but also the H/V measured at depths and in marine environments. A modeling and inversion of synthetic H/V spectral ratio curves on simple predefined geological structures shows an almost perfect recovery of the model parameters (mainly Vs and to a lesser extent Vp). These results are obtained after information from a receiver at depth has been considered in the inversion. Finally, the Rayleigh wave phase velocity information, estimated from array data, and the H/V(z, f) spectral ratio, estimated from a single station data, are combined and inverted for the velocity profile information. Obtained results indicate an improved depth resolution in comparison to estimations using the phase velocity dispersion curves only. The overall estimated sediment thickness is comparable to estimations obtained by inverting the full micortremor H/V spectral ratio.},
  language  = {en}
}
@phdthesis{Amour2013,
  author    = {Amour, Fr{\´e}d{\´e}ric},
  title     = {3-D modeling of shallow-water carbonate systems : a scale-dependent approach based on quantitative outcrop studies},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66621},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {The study of outcrop modeling is located at the interface between two fields of expertise, Sedimentology and Computing Geoscience, which respectively investigates and simulates geological heterogeneity observed in the sedimentary record. During the last past years, modeling tools and techniques were constantly improved. In parallel, the study of Phanerozoic carbonate deposits emphasized the common occurrence of a random facies distribution along single depositional domain. Although both fields of expertise are intrinsically linked during outcrop simulation, their respective advances have not been combined in literature to enhance carbonate modeling studies. The present study re-examines the modeling strategy adapted to the simulation of shallow-water carbonate systems, based on a close relationship between field sedimentology and modeling capabilities. In the present study, the evaluation of three commonly used algorithms Truncated Gaussian Simulation (TGSim), Sequential Indicator Simulation (SISim), and Indicator Kriging (IK), were performed for the first time using visual and quantitative comparisons on an ideally suited carbonate outcrop. The results show that the heterogeneity of carbonate rocks cannot be fully simulated using one single algorithm. The operating mode of each algorithm involves capabilities as well as drawbacks that are not capable to match all field observations carried out across the modeling area. Two end members in the spectrum of carbonate depositional settings, a low-angle Jurassic ramp (High Atlas, Morocco) and a Triassic isolated platform (Dolomites, Italy), were investigated to obtain a complete overview of the geological heterogeneity in shallow-water carbonate systems. Field sedimentology and statistical analysis performed on the type, morphology, distribution, and association of carbonate bodies and combined with palaeodepositional reconstructions, emphasize similar results. At the basin scale (x 1 km), facies association, composed of facies recording similar depositional conditions, displays linear and ordered transitions between depositional domains. Contrarily, at the bedding scale (x 0.1 km), individual lithofacies type shows a mosaic-like distribution consisting of an arrangement of spatially independent lithofacies bodies along the depositional profile. The increase of spatial disorder from the basin to bedding scale results from the influence of autocyclic factors on the transport and deposition of carbonate sediments. Scale-dependent types of carbonate heterogeneity are linked with the evaluation of algorithms in order to establish a modeling strategy that considers both the sedimentary characteristics of the outcrop and the modeling capabilities. A surface-based modeling approach was used to model depositional sequences. Facies associations were populated using TGSim to preserve ordered trends between depositional domains. At the lithofacies scale, a fully stochastic approach with SISim was applied to simulate a mosaic-like lithofacies distribution. This new workflow is designed to improve the simulation of carbonate rocks, based on the modeling of each scale of heterogeneity individually. Contrarily to simulation methods applied in literature, the present study considers that the use of one single simulation technique is unlikely to correctly model the natural patterns and variability of carbonate rocks. The implementation of different techniques customized for each level of the stratigraphic hierarchy provides the essential computing flexibility to model carbonate systems. Closer feedback between advances carried out in the field of Sedimentology and Computing Geoscience should be promoted during future outcrop simulations for the enhancement of 3-D geological models.},
  language  = {en}
}
@phdthesis{Ehrig2017,
  author    = {Ehrig, Sebastian},
  title     = {3D curvature and its role on tissue organization},
  school      = {Universit{\"a}t Potsdam},
  pages     = {132},
  year      = {2017},
  abstract  = {Shape change is a fundamental process occurring in biological tissues during embryonic development and regeneration of tissues and organs. This process is regulated by cells that are constrained within a complex environment of biochemical and physical cues. The spatial constraint due to geometry has a determining role on tissue mechanics and the spatial distribution of force patterns that, in turn, influences the organization of the tissue structure. An understanding of the underlying principles of tissue organization may have wide consequences for the understanding of healing processes and the development of organs and, as such, is of fundamental interest for the tissue engineering community. This thesis aims to further our understanding of how the collective behaviour of cells is influenced by the 3D geometry of the environment. Previous research studying the role of geometry on tissue growth has mainly focused either on flat surfaces or on substrates where at least one of the principal curvatures is zero. In the present work, tissue growth from MC3T3-E1 pre-osteoblasts was investigated on surfaces of controlled mean curvature. One key aspect of this thesis was the development of substrates of controlled mean curvature and their visualization in 3D. It was demonstrated that substrates of controlled mean curvature suitable for cell culture can be fabricated using liquid polymers and surface tension effects. Using these substrates, it was shown that the mean surface curvature has a strong impact on the rate of tissue growth and on the organization of the tissue structure. It was thereby not only demonstrated that the amount of tissue produced (i.e. growth rates) by the cells depends on the mean curvature of the substrate but also that the tissue surface behaves like a viscous fluid with an equilibrium shape governed by the Laplace-Young-law. It was observed that more tissue was formed on highly concave surfaces compared to flat or convex surfaces. Motivated by these observations, an analytical model was developed, where the rate of tissue growth is a function of the mean curvature, which could successfully describe the growth kinetics. This model was also able to reproduce the growth kinetics of previous experiments where tissues have been cultured in straight-sided prismatic pores. A second part of this thesis focuses on the tissue structure, which influences the mechanical properties of the mature bone tissue. Since the extracellular matrix is produced by the cells, the cell orientation has a strong impact on the direction of the tissue fibres. In addition, it was recently shown that some cell types exhibit collective alignment similar to liquid crystals. Based on this observation, a computational model of self-propelled active particles was developed to explore in an abstract manner how the collective behaviour of cells is influenced by 3D curvature. It was demonstrated that the 3D curvature has a strong impact on the self-organization of active particles and gives, therefore, first insights into the principles of self-organization of cells on curved surfaces.},
  language  = {en}
}
@phdthesis{Holz2013,
  author    = {Holz, Christian},
  title     = {3D from 2D touch},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-67796},
  school      = {Universit{\"a}t Potsdam},
  year      = {2013},
  abstract  = {While interaction with computers used to be dominated by mice and keyboards, new types of sensors now allow users to interact through touch, speech, or using their whole body in 3D space. These new interaction modalities are often referred to as "natural user interfaces" or "NUIs." While 2D NUIs have experienced major success on billions of mobile touch devices sold, 3D NUI systems have so far been unable to deliver a mobile form factor, mainly due to their use of cameras. The fact that cameras require a certain distance from the capture volume has prevented 3D NUI systems from reaching the flat form factor mobile users expect. In this dissertation, we address this issue by sensing 3D input using flat 2D sensors. The systems we present observe the input from 3D objects as 2D imprints upon physical contact. By sampling these imprints at very high resolutions, we obtain the objects' textures. In some cases, a texture uniquely identifies a biometric feature, such as the user's fingerprint. In other cases, an imprint stems from the user's clothing, such as when walking on multitouch floors. By analyzing from which part of the 3D object the 2D imprint results, we reconstruct the object's pose in 3D space. While our main contribution is a general approach to sensing 3D input on 2D sensors upon physical contact, we also demonstrate three applications of our approach. (1) We present high-accuracy touch devices that allow users to reliably touch targets that are a third of the size of those on current touch devices. We show that different users and 3D finger poses systematically affect touch sensing, which current devices perceive as random input noise. We introduce a model for touch that compensates for this systematic effect by deriving the 3D finger pose and the user's identity from each touch imprint. We then investigate this systematic effect in detail and explore how users conceptually touch targets. Our findings indicate that users aim by aligning visual features of their fingers with the target. We present a visual model for touch input that eliminates virtually all systematic effects on touch accuracy. (2) From each touch, we identify users biometrically by analyzing their fingerprints. Our prototype Fiberio integrates fingerprint scanning and a display into the same flat surface, solving a long-standing problem in human-computer interaction: secure authentication on touchscreens. Sensing 3D input and authenticating users upon touch allows Fiberio to implement a variety of applications that traditionally require the bulky setups of current 3D NUI systems. (3) To demonstrate the versatility of 3D reconstruction on larger touch surfaces, we present a high-resolution pressure-sensitive floor that resolves the texture of objects upon touch. Using the same principles as before, our system GravitySpace analyzes all imprints and identifies users based on their shoe soles, detects furniture, and enables accurate touch input using feet. By classifying all imprints, GravitySpace detects the users' body parts that are in contact with the floor and then reconstructs their 3D body poses using inverse kinematics. GravitySpace thus enables a range of applications for future 3D NUI systems based on a flat sensor, such as smart rooms in future homes. We conclude this dissertation by projecting into the future of mobile devices. Focusing on the mobility aspect of our work, we explore how NUI devices may one day augment users directly in the form of implanted devices.},
  language  = {en}
}
@phdthesis{Vranic2019,
  author    = {Vranic, Marija},
  title     = {3D Structure of the biomarker hepcidin-25 in its native state},
  doi       = {10.25932/publishup-45929},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-459295},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xii, 135},
  year      = {2019},
  abstract  = {Hepcidin-25 (Hep-25) plays a crucial role in the control of iron homeostasis. Since the dysfunction of the hepcidin pathway leads to multiple diseases as a result of iron imbalance, hepcidin represents a potential target for the diagnosis and treatment of disorders of iron metabolism. Despite intense research in the last decade targeted at developing a selective immunoassay for iron disorder diagnosis and treatment and better understanding the ferroportin-hepcidin interaction, questions remain. The key to resolving these underlying questions is acquiring exact knowledge of the 3D structure of native Hep-25. Since it was determined that the N-terminus, which is responsible for the bioactivity of Hep-25, contains a small Cu(II)-binding site known as the ATCUN motif, it was assumed that the Hep-25-Cu(II) complex is the native, bioactive form of the hepcidin. This structure has thus far not been elucidated in detail. Owing to the lack of structural information on metal-bound Hep-25, little is known about its possible biological role in iron metabolism. Therefore, this work is focused on structurally characterizing the metal-bound Hep-25 by NMR spectroscopy and molecular dynamics simulations. For the present work, a protocol was developed to prepare and purify properly folded Hep-25 in high quantities. In order to overcome the low solubility of Hep-25 at neutral pH, we introduced the C-terminal DEDEDE solubility tag. The metal binding was investigated through a series of NMR spectroscopic experiments to identify the most affected amino acids that mediate metal coordination. Based on the obtained NMR data, a structural calculation was performed in order to generate a model structure of the Hep-25-Ni(II) complex. The DEDEDE tag was excluded from the structural calculation due to a lack of NMR restraints. The dynamic nature and fast exchange of some of the amide protons with solvent reduced the overall number of NMR restraints needed for a high-quality structure. The NMR data revealed that the 20 Cterminal Hep-25 amino acids experienced no significant conformational changes, compared to published results, as a result of a pH change from pH 3 to pH 7 and metal binding. A 3D model of the Hep-25-Ni(II) complex was constructed from NMR data recorded for the hexapeptideNi(II) complex and Hep-25-DEDEDE-Ni(II) complex in combination with the fixed conformation of 19 C-terminal amino acids. The NMR data of the Hep-25-DEDEDE-Ni(II) complex indicates that the ATCUN motif moves independently from the rest of the structure. The 3D model structure of the metal-bound Hep-25 allows for future works to elucidate hepcidin's interaction with its receptor ferroportin and should serve as a starting point for the development of antibodies with improved selectivity.},
  language  = {en}
}