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Energy Efficiency Investigations with a new Operator Training Simulator for Biorefineries
No full textBiorefineries are expected to significantly contribute to an environmentally sustainable future. However, a prerequisite for this goal is the resource conserving and energy efficient operation of these plants. This leads to great demands on plant operators and automation systems, since complex process dynamics have to be considered, which are supposed to have an important influence on resource- and energy efficiency.
In this contribution the influence of process control and automation strategies on the sustainable operation of a bioethanol plant is investigated, using a new operator training simulator (OTS). The investigated process consists of two linked bioreactors for the cultivation of the yeast S. cerevisiae, followed by a cross-flow filtration unit for cell separation and recycling and a rectification unit.
The OTS presented here is based on mechanistic and dynamic process models describing the unit operations and some additional equipment such as valves, pumps, etc.. The models were verified using pilot plant data and have been implemented in the control system and simulation software WinErs (Ingenieurbüro Schoop GmbH, Hamburg). WinErs was used to develop the automation and control structures as well as the graphical user interface of the simulator. Automation sequences for the full plant have been developed using Grafcet (a seqential function chart (IEC 60848, IEC 1131-3)).
Simulation experiments with the operator training simulator of the bioethanol production plant and the single unit operations clearly indicate the strong influence of control strategies on the resource efficiency and bioethanol yield of the process. The operational strategies for the bioethanol fermentation unit, the cross flow unit as well as the rectification unit and the overall process may lead to a variation of the energy demands for ethanol production by 48%.
This new type of simulator may be used for the investigation of the influence of control strategies on the resource efficiency of complete plants. Furthermore, it may be used for the effective training of plant operators with respect to their influence on a sustainable plant operation
Electronic transport through two-dimensional transition-metal chalcogenides
No full textThe electronic industry is rapidly approaching the limit of silicon-based technology. As a consequence, the development of new technology to replace silicon has become a very important topic in electronic and materials science. Layered transition-metal chalcogenides (TMCs), denoted as TX2 (T=Mo, Nb, W and X=Se, S, Te), have shown spectacular physical properties which make them intriguing candidates as a material for nanoelectronics.
We present the development of a flexible and generic method which can be used to calculate coherent electron transport based on the density functional based tight-binding (DFTB) method in combination with the non-equilibrium Green’s function (NEGF) technique and Landauer-Büttiker formula.
We have concentrated our efforts to understand the effect of intrinsic defects and mechanical deformations in electronic and transport properties of TX2 monolayers (MLs). We show that MoS2 MLs present spontaneous rippling which significantly alter their electronic properties e.g. band gap and electron conductivity. It is found that structural defects in MoS2 ML form scattering centers which can induce anisotropy in the electron conductivity. The results show that tensile strain modifies the direct band gap into an indirect one, and substantial strain even induces a semiconductor-metal transition without bond breaking. Furthermore, Raman signals of MLs depend linearly on the strain. In contrast to global deformations, the nanoindentation does not change significantly the electronic properties of the macroscopic MoS2 MLs. Our results show that noble TMCs demonstrate intriguing characteristics as they are subject to mechanical deformations and quantum confinement effects. As a result, the bilayers show metallic characteristics in contrast to semiconducting monolayers.
We believe that the knowledge obtained from this thesis can provide new perspectives for the application of TMCs in future nanoelectronic devices
Auditory Logistic Analysis : an exploratory approach
No full textThe accuracy of logistic performance becomes more and more a crucial factor for the competiveness of enterprises. Even small advantages decide on economic success or failure. Therefore, companies collect data at an increasing level of detail in order to gain more knowledge about in-depth manufacturing processes and their dynamics, serving as a basis for the adjustment of Production Planning and Control.
In traditional logistics, the application of conventional statistical methods for the analysis of manufacturing data has led to formidable improvements of the achievements of logistic objectives. In order to reduce complexity, these traditional approaches rely on greatly simplified models, mostly based on averaging. In order to evaluate data on a higher level of detail for further logistic improvements, actual analyses of manufacturing data more and more include advanced statistical methods, such as Knowledge Discovery in Databases (KDD) and Explorative Data Analysis (EDA).
The scientific discipline of Auditory Display has been successfully established in EDA as counterpart to graphical statistics. More specifically known as data sonification, an auditory display is particularly suitable to analyze chronological events, such as the workflow of a production.
In this fundamental research, Auditory Display has been applied to the analysis of manufacturing processes. A methodical transfer from logistic to sonic parameters has been developed in order to investigate the potential of sonifications for the identification of bottlenecks in a production workflow, also in regard to the impact of cross-system dynamics.
The developed method enables trained analysts to identify systematic order- and process-related bottlenecks, their temporal dynamic evolutions, and their overall impact on schedule adherence of a production workflow
Dipeptide mediated modulation of peptide binding to MHC class I molecules
No full textMHC (major histocompatibility complex) class I molecules are membrane proteins that play a central role in the mammalian immune response against pathogens and tumors by presenting the cellular proteome, in the form of peptides of 8-10 amino acids, at the cell surface for inspection by cytotoxic T lymphocytes. The decisive event for this system to function is the selection and stable binding of peptides to MHC class I molecules. In this research work, I investigated the peptide binding properties of MHC class I molecules and used small molecules to modulate the peptide binding process with the aim of improving our understanding of the MHC class I mediated immune defense and utilizing such small molecules for therapeutic applications.
Conventionally, in vitro folding of MHC class I requires full-length peptide for fold-ing and stabilization. I found that small molecules such as dipeptides can be used to fold and stabilize MHC class I molecules. The dipeptides keep the class I molecules in a peptide-receptive state that binds peptide faster than the empty state. Exogenously added dipeptides can accumulate and stabilize peptide receptive class I molecules at the cell surface. Intri-guingly, dipeptides also catalyze peptide exchange on human (HLA A*02:01) and murine (H 2Kb) class I molecules, both on recombinant and on cell surface class I molecules. They do this by increasing the dissociation rate of bound peptide, probably interacting with the F pocket area of the class I peptide binding groove, similar to the postulated mechanism for intracellular peptide editing by the chaperone protein tapasin that supports the selection of high affinity peptides for binding to class I. With our collaborators in Tübingen, I also show that dipeptide mediated peptide exchange allows for easy and efficient production of MHC class I tetramers for the detection of antigen specific T lymphocytes.
The findings from this project have widespread use in basic research as well as in di-agnostic and therapeutic applications. Dipeptides are efficient tools to generate empty class I molecules for the study of peptide dependent conformational changes, which could be utilized to understand the intracellular peptide selection mechanism. Dipeptide mediated peptide exchange provides an advance in class I multimer preparation that are used to counter viruses and tumors
Bioinformatic analyses of marine microorganisms from contrasting habitats
No full textDeep-sea hypersaline anoxic lakes (DHALs) are brine lakes found at the seafloor and harbor halophilic microorganisms that can withstand harsh physicochemical conditions. Various Eastern Mediterranean DHALs were investigated in the EU project MAMBA. It aimed at discovering extremophiles and their gene repertoires to elucidate the ecophysiological roles and enzymes with prospects in biotechnology. The interface-brine border of the DHAL Thetis was investigated and revealed a complex sulfur cycle.
Halorhabdus tiamatea from the sediment of the Shaban Deep, a DHAL in the Red Sea, was analyzed by comparative genomics. I characterized it as potential polysaccharide degrader which was supported by proteomics and glucosidase activity measurements. H. tiamatea might not belong to the autochthonous community in DHALs. Still, it revealed different niche adaptations toward its isolation source, such as heavy metal transporters and polysaccharide-degrading enzymes.
Such adaptations were also shown by the flavobacterium Formosa agariphila. Members of its genus were abundant during a phytoplankton bloom in the North Sea in 2009. The genome of F. agariphila was sequenced and analyzed with a focus on CAZymes. It revealed thirteen polysaccharide utilization loci, which show its capability to degrade polysaccharides from green, red and brown algae.
The two major epibionts of the gill of the deep-sea shrimp Rimicaris exoculata were analyzed by metagenomics. They belong to the genera Sulfurovum and Leucothrix and deal with fluctuating conditions at hydrothermal vents. They share similar core metabolisms and might evade competition by niche-differentiation.
The gene repertoire of extremophiles is widely unexploited. Despite the advances of NGS technologies, a large resource of enzyme candidates is untapped. I developed the software tool madeira which recognizes key motifs of protein sequences and allows a rapid screening of enzyme classes which constitute promising targets for biotechnology
Structural, Electronic and Mechanical Properties of One- and Two-Dimensional Transition Metal Dichalcogenide Materials
No full textThe successful isolation of single sheet of graphene and the considerable progress in miniaturizing electronic devices have prompted researchers to explore alternative materials other than silicon, particularly two-dimensional (2D) materials. This has led to the renaissance of layered Transition-Metal diChalchogenide (TMC) materials, which have recently received special considerations due to their fundamentally and technologically intriguing properties. In fact, bulk layered TMC compounds have been studied for many years and have mainly been exploited as lubricants and intercalation materials. Recent development in the exfoliation and synthesis techniques offered the opportunity of exploring their properties at low dimensions, in particular 1D and 2D. Consequently, many applications of low dimension TMCs have been developed and proposed for the next generation of nanoelectronic devices, including field-effect transistors, photodetectors, sensors, light-emitting diodes, solar cell and so on.
In this Ph.D. dissertation, the physical properties of one- and two-dimension semiconducting TMC materials have been studied via first-principles approach based on density functional theory. The main focus is about the electronic structure of nanotubular, monoand few-layer TMC systems. The role of quantum confinement and the effect of spin-orbit coupling are examined. The results show the thickness dependence of the electronic properties, when the bulk systems are thinned down to the monolayer level. A giant spin-orbit splitting is revealed in the monolayered systems due to the inversion symmetry breaking. The electronic properties of TMC nanotubes are also investigated and compared to that of the layered counterparts. Moreover, the response of these TMC materials to external factors, in particular tensile strain and electric field, is explored. The electronic band structures, band gaps and charge carrier mobilities with respect to the applied tensile strain or the electric field are strongly affected. This shows the possibility of controlling and tuning the properties of TMC materials, which may provide new functionalities and hence eminent applications in nanoelectronics, optoelectronics and flexible devices
Uni- and bimanual control across the adult lifespan - age and expertise, behavior and neurophysiological correlates
No full textAge-related differences in fine motor control are characterized by general slowing and higher variability. Little is known about the early stages of the deterioration of fine motor control. The main research question of my dissertation was how age and expertise influence fine motor control during the middle-aged lifespan with particular attention to possible effects of task characteristics, i.e. uni- or bimanual tasks, required various target profiles, speeds, and force levels.
Three series of experiments have been conducted using uni- and bimanual tasks in different age groups (young, early middle-aged, and late middle-aged adults) and practice levels (novices and experts) collecting kinetic (force control and coordination) and neurophysiological (EEG) data.
Performance deteriorated with increasing age. Age-related differences were higher in bi- than in unimanual tasks and in tasks requiring comparably high force production per time. Reduced attention allocation with increasing age was a decisive factor - deficits occurred during innervating both hands at the same time, integrating different coordination patterns of both hands, and integrating visual feedback. Additionally, middle-aged compared to younger adults initiated corrective movements more slowly. Experts outperformed novices in all tasks. This indicates positive plasticity. Fine motor control of experts was more efficient on a behavioral as well as a neurophysiological level.
Age affects fine motor control already in middle-aged adults. The amount of remarkable age-related loss depends on task characteristics. Extensive and dexterous use of hands leads to maintenance or even improvement of fine motor control. Our results contribute to a better understanding of the underlying mechanisms of age- and expertise-related differences in fine motor control and they provide useful starting points to future research on bimanual coordination, learning, and neurophysiological correlates over the lifespan
Antibiotic Permeation Through Bacterial Membrane Porins
No full textBacterial cell envelope acts as a first line of defense against various antibacterial compounds. Antibacterial compounds such as antibiotics and antimicrobial peptides need to penetrate the outer membrane barrier of the cell envelope to reach their target site. Hydrophilic antibiotics such as penicillins and carbapenems are known to utilize water-filled protein channels in the outer-membrane to diffuse inside the cell periplasm. Down-regulation in expression of channel proteins and mutations in important amino acid residues of the proteins channels are often induced to limit the permeation of penetrating antibiotics.
This thesis highlights an interdisciplinary approach to comprehend the mechanisms of antibiotics translocation through the bacterial cell envelope. In vitro single channel electrophysiology experiments, in vivo biological assays and molecular dynamics simulation studies are combined together to obtain an atomistic and molecular detail of antibiotic permeation through the outer membrane protein channels. Antibiotics interaction with the outer-membrane proteins channels from Gram-negative bacteria such as Escherichia coli and Enterobacter aerogenes and Gram-positive bacteria Nocardia farcinica have been characterized in detail.
Here, we present two fascinating aspects that could alter the interaction of antibiotic with the protein channels. First, the biophysical characteristics of membrane proteins play a significant role in determining the translocation of antibiotics. For example, we have shown how the negatively charged N. farcinica porin allow the permeation of positively charged antibiotics; however neutralizing the negatively charged residues of the pore showed a depleted interaction of positively charged antibiotics. Second, the external conditions can also drastically change the kinetics of antibiotic interaction with the channel protein. For instance, we have shown that the presence of magnesium ion in the solution can modulate the kinetics of enrofloxacin interaction with the E. coli OmpF porin. Similarly, changing the external electrolyte solution from potassium chloride to bulky ionic liquid solution can drastically slow down the kinetics of antibiotic with the channel protein.
Overall, we have explored various aspects involved in understanding the permeation of hydrophilic antibiotics through the outer-membrane protein channels
Stereophotography in Marine Biology: Development, Application and Evaluation
No full textStereophotography has been well known since the 1840s and has been continuously applied as a tool in the aquatic sciences since the early sixties. Stereophotography enables reference-free and non-invasive measurements of object coordinates in the three-dimensional domain of the underwater world. Underwater stereophotography is only seldom used by the scientific community because of the apparently complex set-up of the camera system and the complicate post process of the stereo images. The first goal of this study was to provide a practical, reliable a sufficiently precise procedure to assess dimensions by stereo photographic evaluation for ecological in situ studies. The second main goal of this study was to evaluate the possibilities, as well as the technical limitations, of the non-invasive method stereophotography in both the laboratory and in two different in situ applications. The results show that the camera system in combination with the calibration software Camera Calibration Toolbox and StereoMarker works well with an accuracy of -1.5 % and a CV of 10.7 %. In an in Situ test with Ctenolabrus rupestris around Helgoland, the system revealed, significantly differences in the height-length relationship between the two sites Sathurnbrunn and Margate. The system presented furthermore its ability to produce a reliable set of data in the length- and height assessment of benthic associated fish but has to prove this ability in the observation of pelagic fish, especially in turbid waters. In combination with DISTA, a professional software for stereo calibration and analyse developed by the institute i3-Mainz, the camera works with a high accuracy and precision in a simulation of benthos observation down to sizes of 1 mm. In conclusion, this study and the obtained results provide a solid basis in the building of a stereo-system and the use of stereophotography in marine biology. Furthermore, it indicates the limitations but gives also suggestions for improvements. With the here gained knowledge further studies in fish or benthos observation could be performed in shorter time periods and in high quality
Identification and characterization of channel-forming proteins in the cell wall of Corynebacterium jeikeium and Corynebacterium urealyticum
No full textIt was commonly believed that the cell walls of Gram-positive bacteria do not represent any permeability barrier and do not contain pore-forming proteins. Members of the phylum: Actinobacteria within the order: Corynebacteriales and the family: Corynebacteriaceae as recently defined form a noticeable exception within this rule. These organisms contain in addition to the peptidoglycan layer, large amounts of lipids in their cell wall. Major constituents of their lipid layers are the mycolic acids.
Many species within this diverse group of mycolic acid containing bacteria are known either because of their medical or biotechnological relevance. The emergence of drug resistance in the clinical environment has been a constant threat over the past decades. Therefore, design of new antibiotics based on the knowledge of porin properties could be helpful to control pathogenic microorganisms that have a natural resistance against certain antibiotics such as C. jeikeium, a resident of human skin, often associated with multidrug resistant nosocomial infections in immunodepressed patients. C. urealyticum, another pathogenic memberof the mycolata, is known as causative agent of urinary tract infections although it is also a bacterium of the skin flora. These two pathogenic bacteria share with the mycolata the property of having an unusual cell envelope composition and architecture.
The work presented in this dissertation describes detailed biochemical and biophysical investigations of recombinant proteins of both pathogenic bacteria.
The first project focuses on cell wall channels of C. jeikeium. Of interest is also the genetic engineering of the channel with the goal to alter the permeability properties of the cell wall channels by applying site-directed mutagenesis.
A gene coding for a 40 amino acid long polypeptide responsible for the pore-forming activity was identified in the known genome of C. jeikeium by its similar chromosomal localization to known porH and porA genes of other Corynebacterium strains. The gene jk0268 was expressed in a porin deficient C. glutamicum or porin deficient BL21 DE3 Omp8 E. coli strains. After purification with a temporary C-terminal histidine-tag or a GST-tag at the N-terminus, the homogeneous protein caused channel-forming activity in lipid bilayers with an average conductance of 1.25 nS in 1M KCl identical to the channels formed by the detergent extracts of the whole cell wall of C. jeikeium. Zero-current membrane potential measurements performed with the voltage dependent channel implied selectivity for anions, and we demonstrate that the anion selectivity was caused by a strategically located positive charge (K24) in the channel lumen.
In the second part of the presented thesis, based on partial sequencing of the protein responsible for the channel formation derived from C. glutamicum, we investigated the homology of PorA and PorH of C. glutamicum and related bacteria to PorACur of C. urealyticum by its similar chromosomal localization to known porH and porA genes of other Corynebacterium strains. The results suggested that a corresponding gene cur_1714 within the known genome sequence of C. urealyticum codes for the cell wall channel. The gene responsible for coding of PorACur in C. urealyticum was cloned into the plasmids pXmj19, pXHis and pGEX-2T for its expression in C. glutamicum ΔporAΔporH and in porin deficient BL21 DE3 Omp8 E. coli strains. Biophysical characterization of the purified protein (PorACur) suggested that cur_1714 is the gene coding for the pore-forming protein in C. urealyticum.
The cell wall porin of C. urealyticum was purified to homogeneity using different biochemical methods and had an apparent molecular mass of about 4 kDa on tricine-containing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The 4 kDa protein formed ion-permeable channels in lipid bilayer membranes with a single-channel conductance of 1.5 nS ± 0.25 in 1 M KCl. The channel-forming proteins were present in detergent treated cell walls and in extracts of whole cells using organic solvents.
Zero-current membrane potential measurements with different salt solutions suggested that PorACur is slightly cation selective because of negative charges localized at the channel mouth. The study is the first report of a cell wall channel in the pathogenic C. urealyticum