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Multi-criteria flexibility allocation for electric distribution networks
No full textGermany’s national climate protection policy, the German Energy Transition, is oriented towards the reduction of energy-related greenhouse gas emissions by rapidly expanding the share of renewable energy systems. New challenges arise regarding technical and energy economical integration as installed wind and photovoltaic power capacities increase continuously. This thesis contributes to the topic by introducing a framework for online multi-criteria flexibility allocation in electrical distribution networks with transport capacity limitations. It considers technical aspects and market participant interests that may contradict each other. Local master data is preprocessed using geospatial information of buildings, photovoltaic systems, wind turbines, and the human population within a spatial domain of interest. By combining weather forecast data, this establishes the foundation for predicting power flow in the electrical distribution network and generating grid-beneficial criteria utilizing the smart grid traffic light concept. Furthermore, master data of the German wind and photovoltaic power plant portfolio is combined with weather forecast data to predict ationwide wind and photovoltaic power feed-in and to generate ecological- and market-beneficial criteria. In addition, metamodels are created and employed to forecast balancing group management data, i.e., EPEX SPOT Day-Ahead electricity prices in the bidding zone of Germany and Luxembourg, and imbalance energy demand of difference balancing groups. At last, non-scalarized schedule solutions are estimated to reach a multi-criteria flexibility allocation. The framework applicability is demonstrated by defined scenarios. Results show that publicly available data allows modelling, calibrating, and operating the introduced multi-criteria flexibility allocation framework in a real-world setting
Continuous Downstream Bioprocessing of Proteins Employing Fluidised Bed Adsorption Technology
No full textIn this work capacity constraints during downstream processing of biologics are addressed by development of novel platform for continuous and direct purification of target protein from unclarified feed (e.g. fermentation broth or cell culture). The work is focused on addressing hinderances observed in related work on truly continuous moving expanded or fluidized bed systems by establishing a novel platform referred as Fluidized Bed Riser Adsorption System (FBRAS) that is based on two distinct components: a) a co-current column where the feedstock and the adsorbent beads are contacted permitting simultaneous product capture and biomass removal. Within this section, the fluid velocity is considerably lower than the terminal settling velocity of the adsorbent particles, thus leading to increased residence time and increased contact time. b) A series of counter-current baffle-modified contactors/columns in series, allowing adsorbent washing, and efficient product elution and bead regeneration/re-equilibration due to restricted settling of adsorbent. The second part of this work is aimed to support the overall technology development with construction of novel resin materials suitable for continuous processing by exploiting double network (DN) strategy for co-polymerisation of agarose via hydrogen bonding induced by freeze-thaw (FT) method. The FBRAS was validated for continuous capture and concentration of lysozyme followed by implementation to an existing DSP routine for production of antifungal peptide in collaboration with Protera SAS
Application of Enhanced Sampling Approaches to the Translocation of Antibiotics through Porins
No full textAntibiotics enter the bacterial cells through the outer membrane diffusion channels called porins. The antibiotic permeation process through porins is of immediate interest and the understanding is expected to aid the development of antibacterial drugs with improved efficacy. The accurate estimation of free energy for translocation is a prerequisite for obtaining quantitative estimates from simulations which would enable a meaningful comparison of different antibiotic permeation mechanisms. This goal, however, has proved to be a significant challenge in the studies on bulky antibiotics, presumably due to a number of slow modes that govern the permeation process. Umbrella sampling and well-tempered metadynamics, that have been extensively used in the field, are limited in the number of degrees of freedom that can be simultaneously biased. In recent years, several methods have been developed that allow biasing simultaneously more degrees of freedom. The
primary objective of the present thesis is to examine a few temperature acceleration-based sampling schemes for the enhanced exploration of antibiotic permeation pathways. Subsequently, the temperature accelerated sliced sampling method has been applied to the study of permeation pathways for a few antibiotics. The method, in combination with applied field simulations, is used to uncover the mechanistic aspects of L3 conformational dynamics in antibiotic permeation and voltage gating. The findings provide a strong rationale for the fast permeation of positive and zwitterionic antibiotics reported in experiments. Finally, the combination of a Brownian dynamics scheme with the temperature accelerated molecular dynamics method has been used for the fast and approximate
estimation of antibiotic permeability constants
Numerical mixing across density surfaces in ocean modelling
No full textSeveral oceanic processes depend delicately on mixing of fluid parcels, particularly across density surfaces because of its extremely small magnitude. Even a fractional deviation in its representation can therefore cause large errors in various other ocean modelling aspects like circulation or tracer distribution. Moreover, since this mixing is also vital in maintaining the global energy balance, its accurate representation is highly desirable. This thesis thus deals with the issue of spurious mixing (artificial mixing of numerical or non-physical origin) across density surfaces in general circulation ocean models. It explores ways to properly identify it and also to potentially mitigate it.
The thesis predominantly evolves around Finite volumE Sea Ice-Ocean Model (FESOM2). It develops a split-explicit external model solver together with an asynchronous time-stepping procedure that supports Arbitrary Largangian Eulerian (ALE) coordinates. It also implements a few such ALE coordinates known to reduce spurious mixing across density surfaces. The thesis then further develops a diagnostic technique that provides semi-local in space and time estimates for such spurious mixing on any grid without operator splitting. The work shows the novel solver to be less dissipative and scale better at any given workload without the need for additional temporal-filtering subcycles. It also shows the novel diagnostic technique to provide a local decomposition of various spurious mixing components. It reports levels of spurious mixing across density surfaces for different cases and how it can be much larger than the physical mixing. Finally, it provides discussion on the future possibilities and objectives
Transition of soluble membrane pore forming proteins from solution into the membrane: hsPEX5 and LaTXs.
No full textProteins are usually classified as water-soluble proteins or membrane proteins based on their cellular localization. In the course of their biogenesis, there is a significant number of initially water-soluble proteins and, after crossing into the membrane, develop their actual function as pore-forming or receptor proteins. Although the passage of the water-soluble proteins into the membrane and the associated refolding of the proteins are essential steps for the formation of the protein functions, only a few high-resolution methods exist to investigate these individual steps of the protein-membrane binding and the simultaneous development of the final active conformation in the membrane. In this study the transition of some proteins from the aqueous phase into the functional integral membrane form is examined for two cases, the human peroxisomal targeting signal 1 (PTS1) receptor hsPEX5 and the presynaptic pore-forming neu-rotoxins (LaTXs) found in the venom of Latrodectus spiders, namely α-LCT, δ-LIT and α-LTX. A vertical and horizontal artificial bilayer setup was used, enabling simultaneous and sequential high-resolution electrical and fluorescent measurements at the single-molecule level. It is presented that hsPEX5 alone harbors the ability to interact with the artificial mem-brane and generate a conductive membrane-pore. The electrophysiological results revealed for the LaTXs the essential role of calcium in stabilizing the oligomerized pore and moreover the significance of the latrotoxin-channels in cellular calcium homeostasis
Modelling the atmosphere-ocean interface with improved energetic consistency
No full textOur unintentional large-scale geoengineering project, characterized
by a rapid in- crease in greenhouse gas concentrations, poses significant challenges in predicting and mitigating global and regional consequences. Climate researchers worldwide are constructing and refining climate models to understand and navigate the complex Earth system state and evolution. This thesis focuses on my contributions to this endeavor, specifically the construction, evaluation, and application of the AWI-CM3 coupled climate model.
Additionally, I address the importance of improving the energetic consistency across the critical interface between the atmosphere and ocean. This research was conducted as part of the DFG collaborative Research Center Transregio (TRR) 181 ”Energy Transfers in Atmosphere and Ocean”, which aims to develop mathematically rigorous tools for climate analysis and modelling. By focusing on the interactions between the atmosphere and ocean, I strive to enhance our under- standing of the exchange of heat, momentum, and mass, while incorporating model components for sea ice and river runoff.
I review the selection and method of computation for physical interface fluxes, introduce of stochastic remapping to conserve information across the coupling interface, and adapt vertical ocean mixing parameterizations to enhance the realism of the AWI-CM3 model. Through these efforts, I aim to contribute to the development of a comprehensive Earth System Model and advance our understanding of climate change and its societal implications
The Role of Drug Repurposing in Containment of Emerging Viral Disease Caused by SARS‐CoV‐2
No full textThis thesis focuses on the role of drug repurposing in containment of an emerging disease, taking SARSCoV‐2 as a case study. The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) emerged in2019 causing a deadly respiratory disease: COVID‐19. The increasing knowledge about SARS‐CoV‐2allowed the expansion of multiple approaches to contain the spread of infection. Eventually the rapid development of anti‐SARS‐CoV‐2 vaccines allowed a control of the pandemic. Effective antiviral pharmacological treatments are still rare and viral evolution allowed a fast adaptation and escape from available containment methods. Since the beginning of the SARS‐CoV‐2 pandemic drug repurposing was considered as a valuable source for identification of new antivirals, due to the advantage of available clinical safety data and activity profiles. To interfere with SARS‐CoV‐2 infection and to identify new antiviral compounds, key steps of the virus replication cycle and their corresponding targets were selected for assay development. The screening approaches not only identified new molecules, that can act as starting points to develop new antiviral therapies, but also revealed critical steps and pitfalls in developing assays, that will help to optimize the translation of compound effects from biochemical to cell‐based state. The study also adresses the misconception that repurposed drug cannot interfere with assay, by showing examples of compound‐reactivity through generation of reactive oxygen species, and readout interference. In addition, a drug‐combination approach for entry‐inhibitors aiming at a synergistic response is shown as an option to overcome difficulties in reaching necessary intracellular target‐doses without increasing cytotoxicity. In conclusion, this research highlights the potential of drug repurposing in antiviral drug discovery. The generated results contribute to the publicly available data on drug repurposing against SARS‐CoV‐2, which may be used for research
An Investigation of Nearly Geostrophic Flows in Bounded Domains
No full textThis thesis investigates the use and behavior of balance relations for studying the nearly-geostrophic flow in a bounded domain. The goal is to derive simple, fully nonlinear models for the large scale flow in the vicinity of basin boundaries and investigate their asymptotic behavior. This will help improve our conceptual understanding and provide benchmarks for the calibration of larger numerical ocean models.
The balance models are those in which the Coriolis force balances the pressure gradient force in the limit of small Rossby number. These models are derived using a Lagrangian-based variational approach. The idea was first proposed by Salmon (1983), in which the author derived the approximate model for nearly geostrophic flow for the rotating shallow water equations. He applied the approximations on the Lagrangian of the parent fluid model and then took variations to get the Euler-Lagrangian equations, which he named as L1 balance model. Oliver (2006) generalized this idea and started with the arbitrary change in coordinates to the canonical coordinates, and then consistently truncated the transformation and the Lagrangian to a desired order. This approach gives the one-parameter generalized family of large-scale models (GLSG), among which Salmon’s L1 model is observed to be numerically well-behaved, as noted by Dritschel et al. (2017).
In the current study, we employ the approach detailed in Oliver (2006) and derived the variational L1 balance model for the shallow water equations with constant Coriolis force in the vicinity of the boundaries. At the boundary, zero-flux is assumed in the normal direction and the variational derivation of the model suggests the geostrophic balance up to O(ε) in the tangential direction. We numerically investigated how well the balance dynamics capture the shallow water equations under specified boundary conditions. For this, we initialized the full shallow water equations with the balanced state and allowed it to advect until time T. We then compared the fields using their root mean square (r.m.s.) differences and observed their asymptotic behaviour. Furthermore, Eulerian time scales are also determined at which both the models can be compared. Notably, we observed that the physical boundary interactions result in a slowdown of the time scales when compared to the time scales in the case of periodic boundaries
Application of Machine Learning and Optimization to Problems in Supply Network Management
No full textThe field of logistics and supply chain management deals with various supply network problems on multiple levels starting from strategic years-long decisions regarding network topology, down to operational weekly-based decisions. Moreover, due to the interaction of customers and random accidents, the system becomes stochastic and difficult to control based only on logistic experience. To help with the problem of supply chain design and management, scientists try to approach the field with existing instruments including network science, mathematical modeling, control theory, machine learning, etc. In this thesis, a complex approach that addresses different aspects of supply network management is demonstrated. First, an automatization scheme for the daily management of logistic requirements is proposed. Second, an in-depth investigation of non-conventional usage of natural language processing and machine learning algorithms is presented. The developed approach can be used to enhance the process of requirement management by extracting additional knowledge about the supply network operation. Third, the strategic problem of designing robust supply networks is addressed by developing a minimalistic model of a supply network. The model is designed to simulate a scenario of supply-demand imbalance and generate networks that satisfy the imbalance in a robust way. The overall outcome of the work is a better understanding of separate supply network aspects and an attempt to holistically improve the way how supply networks are managed
Surface-Enhanced Raman Scattering – New Insights into Its Basic Mechanisms and Possible Applications Using the Kretschmann Arrangement
No full textThe contribution of the chemical enhancement mechanism to the SERS process has been studied using a Kretschmann configuration (KC) with a thin silver layer attached to the totally reflecting surface for reproducibility of the results. After studying fundamental properties, additionally, the KC was applied for specific applications.
The basic KC setup has been optimized and the observed enhancement was investigated in detail. SERS studies have been performed on a monolayer of Nile blue, Crystal Violet, and 4-Nitrobenzenethiol. Under resonance conditions for the coupling of the light to the surface plasmons, a decay of the Raman line intensities has been observed over time, converging to constant signal levels. By analyzing this time-dependent intensity variation for the single vibrational modes, we found a mode-dependent Raman deactivation rate. This process has also been investigated for different angles of incidence of the beam (varying the resonance condition), and a clear dependence on the strength of the coupling to the plasmons for the behavior of the different Raman lines has been found. Although, a uniform enhancement of the electromagnetic fields of exciting and scattered light can be assumed for a given angle of incidence when considering the electromagnetic enhancement (EME) mechanism, which usually dominates the SERS process, the relative enhancements were found to be strongly mode-dependent, which is a clear indication of an electronic effect. Obviously, the KC allows for the observation of a dominating chemical enhancement (CE) in these single-layer SERS experiments.
Knowing that only chemisorbed molecules should contribute to the CE, we switched this mechanism off by introducing an isolating interim layer such as Octadecanethiol, 4- Nitrobenzenethiol, or MoO2 between the metal substrate and the molecules (Nile Blue). The intensity ratio between the signals taken under resonance and off-resonance conditions was significantly reduced even when these interim layers were only few nanometers thick where EME should not be considerably affected. This was supporting the assumption that CE is the major contribution in the KC SERS experiment.
Due to the domination of the CE, which only involves chemisorbed molecules, the KC SERS arrangement appears to be attractive for applications where thin layers of molecules have to be studied. As an example, we have demonstrated the detection and quantization of a low concentration (100 nM) of Moxifloxacin (Moxi)