TY - THES A1 - Pilz, Marco T1 - A comparison of proxies for seismic site conditions and amplification for the large urban area of Santiago de Chile T1 - Ein Vergleich seismischer Parameter für die Standort- und Verstärkungsabschätzung im Stadtgebiet von Santiago de Chile N2 - Situated in an active tectonic region, Santiago de Chile, the country´s capital with more than six million inhabitants, faces tremendous earthquake hazard. Macroseismic data for the 1985 Valparaiso and the 2010 Maule events show large variations in the distribution of damage to buildings within short distances indicating strong influence of local sediments and the shape of the sediment-bedrock interface on ground motion. Therefore, a temporary seismic network was installed in the urban area for recording earthquake activity, and a study was carried out aiming to estimate site amplification derived from earthquake data and ambient noise. The analysis of earthquake data shows significant dependence on the local geological structure with regards to amplitude and duration. Moreover, the analysis of noise spectral ratios shows that they can provide a lower bound in amplitude for site amplification and, since no variability in terms of time and amplitude is observed, that it is possible to map the fundamental resonance frequency of the soil for a 26 km x 12 km area in the northern part of the Santiago de Chile basin. By inverting the noise spectral rations, local shear wave velocity profiles could be derived under the constraint of the thickness of the sedimentary cover which had previously been determined by gravimetric measurements. The resulting 3D model was derived by interpolation between the single shear wave velocity profiles and shows locally good agreement with the few existing velocity profile data, but allows the entire area, as well as deeper parts of the basin, to be represented in greater detail. The wealth of available data allowed further to check if any correlation between the shear wave velocity in the uppermost 30 m (vs30) and the slope of topography, a new technique recently proposed by Wald and Allen (2007), exists on a local scale. While one lithology might provide a greater scatter in the velocity values for the investigated area, almost no correlation between topographic gradient and calculated vs30 exists, whereas a better link is found between vs30 and the local geology. When comparing the vs30 distribution with the MSK intensities for the 1985 Valparaiso event it becomes clear that high intensities are found where the expected vs30 values are low and over a thick sedimentary cover. Although this evidence cannot be generalized for all possible earthquakes, it indicates the influence of site effects modifying the ground motion when earthquakes occur well outside of the Santiago basin. Using the attained knowledge on the basin characteristics, simulations of strong ground motion within the Santiago Metropolitan area were carried out by means of the spectral element technique. The simulation of a regional event, which has also been recorded by a dense network installed in the city of Santiago for recording aftershock activity following the 27 February 2010 Maule earthquake, shows that the model is capable to realistically calculate ground motion in terms of amplitude, duration, and frequency and, moreover, that the surface topography and the shape of the sediment bedrock interface strongly modify ground motion in the Santiago basin. An examination on the dependency of ground motion on the hypocenter location for a hypothetical event occurring along the active San Ramón fault, which is crossing the eastern outskirts of the city, shows that the unfavorable interaction between fault rupture, radiation mechanism, and complex geological conditions in the near-field may give rise to large values of peak ground velocity and therefore considerably increase the level of seismic risk for Santiago de Chile. N2 - Aufgrund ihrer Lage in einem tektonisch aktiven Gebiet ist Santiago de Chile, die Hauptstadt des Landes mit mehr als sechs Millionen Einwohnern, einer großen Erdbebengefährdung ausgesetzt. Darüberhinaus zeigen makroseismische Daten für das 1985 Valparaiso- und das 2010 Maule-Erdbeben eine räumlich unterschiedliche Verteilung der an den Gebäuden festgestellten Schäden; dies weist auf einen starken Einfluss der unterliegenden Sedimentschichten und der Gestalt der Grenzfläche zwischen den Sedimenten und dem Festgestein auf die Bodenbewegung hin. Zu diesem Zweck wurde in der Stadt ein seismisches Netzwerk für die Aufzeichnung der Bodenbewegung installiert, um die auftretende Untergrundverstärkung mittels Erdbebendaten und seismischem Rauschen abzuschätzen. Dabei zeigt sich für die Erdbebendaten eine deutliche Abhängigkeit von der Struktur des Untergrunds hinsichtlich der Amplitude der Erschütterung und ihrer Dauer. Die Untersuchung der aus seismischem Rauschen gewonnenen horizontal-zu-vertikal-(H/V) Spektral-verhältnisse zeigt, dass diese Ergebnisse nur einen unteren Grenzwert für die Bodenverstärkung liefern können. Weil jedoch andererseits keine zeitliche Veränderung bei der Gestalt dieser Spektralverhältnisse festgestellt werden konnte, erlauben die Ergebnisse ferner, die Resonanzfrequenz des Untergrundes für ein 26 km x 12 km großes Gebiet im Nordteil der Stadt zu bestimmen. Unter Zuhilfenahme von Informationen über die Dicke der Sedimentschichten, welche im vorhinein schon durch gravimetrische Messungen bestimmt worden war, konnten nach Inversion der H/V-Spektralverhältnisse lokale Scherwellengeschwindigkeitsprofile und nach Interpolation zwischen den einzelnen Profilen ein dreidimensionales Modell berechnet werden. Darüberhinaus wurde mit den verfügbaren Daten untersucht, ob auf lokaler Ebene ein Zusammenhang zwischen der mittleren Scherwellengeschwindigkeit in den obersten 30 m (vs30) und dem Gefälle existiert, ein Verfahren, welches kürzlich von Wald und Allen (2007) vorgestellt wurde. Da für jede lithologische Einheit eine starke Streuung für die seismischen Geschwindigkeiten gefunden wurde, konnte kein Zusammenhang zwischen dem Gefälle und vs30 hergestellt werden; demgegenüber besteht zumindest ein tendenzieller Zusammenhang zwischen vs30 und der unterliegenden Geologie. Ein Vergleich der Verteilung von vs30 mit den MKS-Intensitäten für das 1985 Valparaiso-Erdbeben in Santiago zeigt, dass hohe Intensitätswerte vor allem in Bereichen geringer vs30-Werte und dicker Sedimentschichten auftraten. Weiterhin ermöglichte die Kenntnis über das Sedimentbeckens Simulationen der Bodenbewegung mittels eines spektralen-Elemente-Verfahrens. Die Simulation eines regionalen Erdbebens, welches auch von einem dichten seismischen Netzwerk aufgezeichnet wurde, das im Stadtgebiet von Santiago infolge des Maule-Erdbebens am 27. Februar 2010 installiert wurde, zeigt, dass das Modell des Sedimentbeckens realistische Berechnungen hinsichtlich Amplitude, Dauer und Frequenz erlaubt und die ausgeprägte Topographie in Verbindung mit der Form der Grenzfläche zwischen den Sedimenten und dem Festgestein starken Einfluss auf die Bodenbewegung haben. Weitere Untersuchungen zur Abhängigkeit der Bodenerschütterung von der Position des Hypozentrums für ein hypothetisches Erdbeben an der San Ramón-Verwerfung, welche die östlichen Vororte der Stadt kreuzt, zeigen, dass die ungünstige Wechselwirkung zwischen dem Verlauf des Bruchs, der Abstrahlung der Energie und der komplexen geologischen Gegebenheiten hohe Werte bei der maximalen Bodengeschwindigkeit erzeugen kann. Dies führt zu einer signifikanten Zunahme des seismischen Risikos für Santiago de Chile. KW - Standorteffekte KW - seismisches Rauschen KW - Sedimentbecken KW - Simulation KW - site effects KW - seismic noise KW - sedimentary basin KW - simulation Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-52961 ER - TY - JOUR A1 - Giese, Holger A1 - Henkler, Stefan A1 - Hirsch, Martin T1 - A multi-paradigm approach supporting the modular execution of reconfigurable hybrid systems JF - Simulation : transactions of the Society for Modeling and Simulation International N2 - Advanced mechatronic systems have to integrate existing technologies from mechanical, electrical and software engineering. They must be able to adapt their structure and behavior at runtime by reconfiguration to react flexibly to changes in the environment. Therefore, a tight integration of structural and behavioral models of the different domains is required. This integration results in complex reconfigurable hybrid systems, the execution logic of which cannot be addressed directly with existing standard modeling, simulation, and code-generation techniques. We present in this paper how our component-based approach for reconfigurable mechatronic systems, MECHATRONIC UML, efficiently handles the complex interplay of discrete behavior and continuous behavior in a modular manner. In addition, its extension to even more flexible reconfiguration cases is presented. KW - code generation KW - hybrid systems KW - reconfigurable systems KW - simulation Y1 - 2011 U6 - https://doi.org/10.1177/0037549710366824 SN - 0037-5497 VL - 87 IS - 9 SP - 775 EP - 808 PB - Sage Publ. CY - London ER - TY - GEN A1 - Giese, Holger A1 - Henkler, Stefan A1 - Hirsch, Martin T1 - A multi-paradigm approach supporting the modular execution of reconfigurable hybrid systems N2 - Advanced mechatronic systems have to integrate existing technologies from mechanical, electrical and software engineering. They must be able to adapt their structure and behavior at runtime by reconfiguration to react flexibly to changes in the environment. Therefore, a tight integration of structural and behavioral models of the different domains is required. This integration results in complex reconfigurable hybrid systems, the execution logic of which cannot be addressed directly with existing standard modeling, simulation, and code-generation techniques. We present in this paper how our component-based approach for reconfigurable mechatronic systems, M ECHATRONIC UML, efficiently handles the complex interplay of discrete behavior and continuous behavior in a modular manner. In addition, its extension to even more flexible reconfiguration cases is presented. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 410 KW - code generation KW - hybrid systems KW - reconfigurable systems KW - simulation Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-402896 ER - TY - GEN A1 - Kuik, Friderike A1 - Lauer, Axel A1 - Churkina, Galina A1 - Denier Van der Gon, Hugo Anne Cornelis A1 - Fenner, Daniel A1 - Mar, Kathleen A. A1 - Butler, Tim M. T1 - Air quality modelling in the Berlin–Brandenburg region using WRF-Chem v3.7.1 BT - sensitivity to resolution of model grid and input data T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Air pollution is the number one environmental cause of premature deaths in Europe. Despite extensive regulations, air pollution remains a challenge, especially in urban areas. For studying summertime air quality in the Berlin-Brandenburg region of Germany, the Weather Research and Forecasting Model with Chemistry (WRF-Chem) is set up and evaluated against meteorological and air quality observations from monitoring stations as well as from a field campaign conducted in 2014. The objective is to assess which resolution and level of detail in the input data is needed for simulating urban background air pollutant concentrations and their spatial distribution in the Berlin-Brandenburg area. The model setup includes three nested domains with horizontal resolutions of 15, 3 and 1 km and anthropogenic emissions from the TNO-MACC III inventory. We use RADM2 chemistry and the MADE/SORGAM aerosol scheme. Three sensitivity simulations are conducted updating input parameters to the single-layer urban canopy model based on structural data for Berlin, specifying land use classes on a sub-grid scale (mosaic option) and downscaling the original emissions to a resolution of ca. 1 km x 1 km for Berlin based on proxy data including traffic density and population density. The results show that the model simulates meteorology well, though urban 2m temperature and urban wind speeds are biased high and nighttime mixing layer height is biased low in the base run with the settings described above. We show that the simulation of urban meteorology can be improved when specifying the input parameters to the urban model, and to a lesser extent when using the mosaic option. On average, ozone is simulated reasonably well, but maximum daily 8 h mean concentrations are underestimated, which is consistent with the results from previous modelling studies using the RADM2 chemical mechanism. Particulate matter is underestimated, which is partly due to an underestimation of secondary organic aerosols. NOx (NO + NO2) concentrations are simulated reasonably well on average, but nighttime concentrations are overestimated due to the model's underestimation of the mixing layer height, and urban daytime concentrations are underestimated. The daytime underestimation is improved when using downscaled, and thus locally higher emissions, suggesting that part of this bias is due to deficiencies in the emission input data and their resolution. The results further demonstrate that a horizontal resolution of 3 km improves the results and spatial representativeness of the model compared to a horizontal resolution of 15 km. With the input data (land use classes, emissions) at the level of detail of the base run of this study, we find that a horizontal resolution of 1 km does not improve the results compared to a resolution of 3 km. However, our results suggest that a 1 km horizontal model resolution could enable a detailed simulation of local pollution patterns in the Berlin-Brandenburg region if the urban land use classes, together with the respective input parameters to the urban canopy model, are specified with a higher level of detail and if urban emissions of higher spatial resolution are used. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 531 KW - urban canopy model KW - aqmeii phase-2 KW - Mexico-City KW - Heat-Island KW - ozone KW - performance KW - transport KW - chemistry KW - meteorology KW - simulation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-410131 SN - 1866-8372 IS - 531 ER - TY - JOUR A1 - Schröder, Boris A1 - Seppelt, Ralf T1 - Analysis of pattern-process interactions based on landscape models - Overview, general concepts, and methodological issues JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Pattern-process analysis is one of the main threads in landscape ecological research. It aims at understanding the complex relationships between ecological processes and landscape patterns, identifying the underlying mechanisms and deriving valid predictions for scenarios of landscape change and its consequences. Today, various studies cope with these tasks through so called "landscape modelling" approaches. They integrate different aspects of heterogeneous and dynamic landscapes and model different driving forces, often using both statistical and process-oriented techniques. We identify two main approaches to deal with the analysis of pattern-process interactions: the first starts with pattern detection, pattern description and pattern analysis, the second with process description, simulation and pattern generation. Focussing on the interplay between these two approaches, landscape analysis and landscape modelling will improve our understanding of pattern-process interactions. The comparison of simulated and observed pattern is a prerequisite for both approaches. Therefore, we identify a set of quantitative, robust, and reproducible methods for the analysis of spatiotemporal patterns that is a starting point for a standard toolbox for ecologists as major future challenge and suggest necessary further methodological developments. (c) 2006 Elsevier B.V. All rights reserved. KW - pattern-process interrelationship KW - landscape analysis KW - landscape modelling KW - simulation KW - inverse modelling KW - pattern description KW - wavelet analysis Y1 - 2006 U6 - https://doi.org/10.1016/j.ecolmodel.2006.05.036 SN - 0304-3800 VL - 199 IS - 4 SP - 505 EP - 516 PB - Elsevier CY - Amsterdam ER - TY - BOOK A1 - Dyck, Johannes A1 - Giese, Holger A1 - Lambers, Leen T1 - Automatic verification of behavior preservation at the transformation level for relational model transformation N2 - The correctness of model transformations is a crucial element for model-driven engineering of high quality software. In particular, behavior preservation is the most important correctness property avoiding the introduction of semantic errors during the model-driven engineering process. Behavior preservation verification techniques either show that specific properties are preserved, or more generally and complex, they show some kind of behavioral equivalence or refinement between source and target model of the transformation. Both kinds of behavior preservation verification goals have been presented with automatic tool support for the instance level, i.e. for a given source and target model specified by the model transformation. However, up until now there is no automatic verification approach available at the transformation level, i.e. for all source and target models specified by the model transformation. In this report, we extend our results presented in [27] and outline a new sophisticated approach for the automatic verification of behavior preservation captured by bisimulation resp. simulation for model transformations specified by triple graph grammars and semantic definitions given by graph transformation rules. In particular, we show that the behavior preservation problem can be reduced to invariant checking for graph transformation and that the resulting checking problem can be addressed by our own invariant checker even for a complex example where a sequence chart is transformed into communicating automata. We further discuss today's limitations of invariant checking for graph transformation and motivate further lines of future work in this direction. N2 - Die Korrektheit von Modelltransformationen ist von zentraler Wichtigkeit bei der Anwendung modellgetriebener Softwareentwicklung für die Entwicklung hochqualitativer Software. Insbesondere verhindert Verhaltensbewahrung als wichtigste Korrektheitseigenschaft die Entstehung semantischer Fehler während des modellgetriebenen Entwicklungsprozesses. Techniken zur Verifikation von Verhaltensbewahrung zeigen, dass bestimmte spezifische Eigenschaften bewahrt bleiben oder, im allgemeineren und komplexeren Fall, dass eine Form von Verhaltensäquivalenz oder Verhaltensverfeinerung zwischen Quell- und Zielmodell der Transformation besteht. Für beide Ansätze existieren automatisierte Werkzeuge für die Verifikation auf der Instanzebene, also zur Überprüfung konkreter Paare aus Quell- und Zielmodellen der Transformation. Allerdings existiert kein automatischer Verifikationsansatz, der auf der Transformationsebene arbeitet, also Aussagen zu allen Quell- und Zielmodellen einer Modelltransformation treffen kann. Dieser Bericht erweitert unsere Vorarbeit und Ergebnisse aus [27] und stellt einen neuen Ansatz zur automatischen Verifikation von Verhaltensbewahrung vor, der auf Bisimulation bzw. Simulation basiert. Dabei werden Modelltransformationen durch Triple-Graph-Grammatiken und Verhaltensdefinitionen mittels Graphtransformationsregeln beschrieben. Insbesondere weisen wir nach, dass das Problem der Verhaltensbewahrung durch Bisimulation auf Invariant-Checking für Graphtransformationssysteme reduziert werden kann und dass das entstehende Invariant-Checking-Problem für ein komplexes Beispiel durch unser Werkzeug zur Verifikation induktiver Invarianten gelöst werden kann. Das Beispiel beschreibt die Transformation von Sequenzdiagrammen in Systeme kommunizierender Automaten. Darüber hinaus diskutieren wir bestehende Einschränkungen von Invariant-Checking für Graphtransformationssysteme und Ansätze für zukünftige Arbeiten in diesem Bereich. T3 - Technische Berichte des Hasso-Plattner-Instituts für Digital Engineering an der Universität Potsdam - 112 KW - model transformation KW - behavior preservation KW - semantics preservation KW - relational model transformation KW - bisimulation KW - simulation KW - invariant checking KW - transformation level KW - behavioral equivalenc KW - behavioral refinement KW - behavioral abstraction KW - graph transformation systems KW - graph constraints KW - triple graph grammars KW - Modelltransformationen KW - Verhaltensbewahrung KW - relationale Modelltransformationen KW - Bisimulation KW - Simulation KW - Invariant-Checking KW - Transformationsebene KW - Verhaltensäquivalenz KW - Verhaltensverfeinerung KW - Verhaltensabstraktion KW - Graphtransformationssysteme KW - Graph-Constraints KW - Triple-Graph-Grammatiken Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-100279 SN - 978-3-86956-391-6 SN - 1613-5652 SN - 2191-1665 IS - 112 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - THES A1 - Codutti, Agnese T1 - Behavior of magnetic microswimmers T1 - Verhalten magnetischer Microschwimmer BT - simulations for natural swimmers and synthetic propellers BT - Simulationen von natürlichen Schwimmern und synthetischen Propellern N2 - Microswimmers, i.e. swimmers of micron size experiencing low Reynolds numbers, have received a great deal of attention in the last years, since many applications are envisioned in medicine and bioremediation. A promising field is the one of magnetic swimmers, since magnetism is biocom-patible and could be used to direct or actuate the swimmers. This thesis studies two examples of magnetic microswimmers from a physics point of view. The first system to be studied are magnetic cells, which can be magnetic biohybrids (a swimming cell coupled with a magnetic synthetic component) or magnetotactic bacteria (naturally occurring bacteria that produce an intracellular chain of magnetic crystals). A magnetic cell can passively interact with external magnetic fields, which can be used for direction. The aim of the thesis is to understand how magnetic cells couple this magnetic interaction to their swimming strategies, mainly how they combine it with chemotaxis (the ability to sense external gradient of chemical species and to bias their walk on these gradients). In particular, one open question addresses the advantage given by these magnetic interactions for the magnetotactic bacteria in a natural environment, such as porous sediments. In the thesis, a modified Active Brownian Particle model is used to perform simulations and to reproduce experimental data for different systems such as bacteria swimming in the bulk, in a capillary or in confined geometries. I will show that magnetic fields speed up chemotaxis under special conditions, depending on parameters such as their swimming strategy (run-and-tumble or run-and-reverse), aerotactic strategy (axial or polar), and magnetic fields (intensities and orientations), but it can also hinder bacterial chemotaxis depending on the system. The second example of magnetic microswimmer are rigid magnetic propellers such as helices or random-shaped propellers. These propellers are actuated and directed by an external rotating magnetic field. One open question is how shape and magnetic properties influence the propeller behavior; the goal of this research field is to design the best propeller for a given situation. The aim of the thesis is to propose a simulation method to reproduce the behavior of experimentally-realized propellers and to determine their magnetic properties. The hydrodynamic simulations are based on the use of the mobility matrix. As main result, I propose a method to match the experimental data, while showing that not only shape but also the magnetic properties influence the propellers swimming characteristics. N2 - Die Forschung an Mikroschwimmern oder genauer gesagt an aktiv schwimmenden Mikroorganismen oder Objekten mit niedrigen Reynolds Zahlen, hat in den letzten Jahren wegen ihrer vielfältigen Anwendungen in der Medizin und Bioremediation stark an Bedeutung gewonnen. Besonders vielversprechend ist die Arbeit mit magnetischen Mikroschwimmern, da deren biokompatibler Magnetismus genutzt werden kann um die Schwimmer gezielt zu steuern. In dieser Arbeit werden zwei Beispiele von magnetischen Mikroschwimmern aus physikalischer Sicht untersucht. Das erste Modellsystem hierfür sind magnetische Zellen. Diese können entweder magnetische Biohybride (eine schwimm-Zelle gekoppelt mit einer synthetischen magnetischen Komponente) oder magnetotaktische Bakterien (natürlich vorkommende Bakterien die eine intrazelluläre Kette von magnetischen Kristallen produzieren) sein. Die passive Wechselwirkung der magnetischen Zelle mit einem externen Magnetfeld kann zu deren Steuerung genutzt werden. Das Ziel dieser Arbeit ist es zu verstehen wie magnetische Zellen die magnetische Wechselwirkung mit ihre Schwimmstrategie verknüpfen, oder genauer gesagt, wie sie sie zur Chemotaxis (die Fähigkeit externe chemische Gradienten wahrzunehmen und die Fortbewegungsrichtung daran anzupassen) zu nutzen. Es ist immer noch nicht restlos geklärt worin in der natürlichen Umgebung der magnetischen Bakterien, wie beispielsweise in porösem Sediment, der Vorteil der Wechselwirkung mit dem externen magnetischen Feld liegt. In dieser Arbeit wurde ein modifiziertes „Active Brownian Particle model“ verwendet um mittels Computersimulationen experimentelle Ergebnisse an Bakterien zu reproduzieren, die sich frei, in einer Glaskapillare, oder in anders begrenzten Geometrien bewegen. Ich werde zeigen, dass abhängig von der Schwimmstrategie („run-and-tumble“ oder „runand-reverse“), aerotaktische Strategie (axial oder polar), und der Feldintensität und Orientierung, das magnetische Feld Chemotaxis beschleunigen kann. Abhängig von dem gewählten Modellsystem kann es jedoch auch zu einer Behinderung der Chemotaxis kommen. Das zweite Beispiel für magnetische Mikroschwimmer sind starre (z.B. Helices) oder zufällig geformte magnetische Propeller. Sie werden durch ein externes magnetisches Feld angetrieben und gelenkt. Hierbei stellt sich die Frage wie die Form der Propeller deren Verhalten beeinflusst und wie sie für eine bestimmte Anwendung optimiert werden können. Daher ist es das Ziel dieser Arbeit Simulationsmethoden vorzuschlagen um das experimentell beobachtete Verhalten zu reproduzieren und die magnetischen Eigenschaften der Propeller zu beschreiben. Hierfür wird die Mobilitätsmatrix verwendet um die hydrodynamischen Simulationen zu realisieren. Ein Hauptresultat meiner Arbeit ist eine neue Methode, welche die Simulationen in Einklang mit den experimentellen Resultaten bringt. Hierbei zeigt sich, dass nicht nur die Form sondern insbesondere auch die magnetischen Eigenschaften die Schwimmcharakteristik der Propeller entscheidend beeinflussen. KW - microswimmers KW - magnetism KW - bacteria KW - propellers KW - simulation KW - Microschwimmer KW - Magnetismus KW - Bakterien KW - Propeller KW - Simulationen Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-422976 ER - TY - THES A1 - Moreira, André Guérin T1 - Charged systems in bulk and at interfaces N2 - Eine der Faustregeln der Kolloid- und Oberflächenphysik ist, dass die meisten Oberflächen geladen sind, wenn sie mit einem Lösungsmittel, normalerweise Wasser, in Kontakt treten. Dies ist zum Beispiel bei ladungsstabilisierten Kolloidalen Suspensionen der Fall, bei denen die Oberfläche der Kolloidteilchen geladen ist (gewöhnlich mit einer Ladung von mehreren Hunderttausend Elementarladungen), oder bei Monoschichten ionischer Tenside, die auf einer Luft-Wasser Grenzfläche sitzen (wobei die wasserliebenden Kopfgruppen durch die Freisetzung von Gegenionen geladen werden), sowie bei Doppelschichten, die geladene phospholipide enthalten (wie Zellmembranen). In dieser Arbeit betrachten wir einige Modellsysteme, die zwar eine vereinfachte Fassung der Realität darstellen, von denen wir aber dennoch erwarten koennen, dass wir mit ihrer Hilfe einige physikalische Eigenschaften realer geladener Systeme (Kolloide und Elektrolyte) einfangen können. N2 - One of the rules-of-thumb of colloid and surface physics is that most surfaces are charged when in contact with a solvent, usually water. This is the case, for instance, in charge-stabilized colloidal suspensions, where the surface of the colloidal particles are charged (usually with a charge of hundreds to thousands of e, the elementary charge), monolayers of ionic surfactants sitting at an air-water interface (where the water-loving head groups become charged by releasing counterions), or bilayers containing charged phospholipids (as cell membranes). In this work, we look at some model-systems that, although being a simplified version of reality, are expected to capture some of the physical properties of real charged systems (colloids and electrolytes). We initially study the simple double layer, composed by a charged wall in the presence of its counterions. The charges at the wall are smeared out and the dielectric constant is the same everywhere. The Poisson-Boltzmann (PB) approach gives asymptotically exact counterion density profiles around charged objects in the weak-coupling limit of systems with low-valent counterions, surfaces with low charge density and high temperature (or small Bjerrum length). Using Monte Carlo simulations, we obtain the profiles around the charged wall and compare it with both Poisson-Boltzmann (in the low coupling limit) and the novel strong coupling (SC) theory in the opposite limit of high couplings. In the latter limit, the simulations show that the SC leads in fact to asymptotically correct density profiles. We also compare the Monte Carlo data with previously calculated corrections to the Poisson-Boltzmann theory. We also discuss in detail the methods used to perform the computer simulations. After studying the simple double layer in detail, we introduce a dielectric jump at the charged wall and investigate its effect on the counterion density distribution. As we will show, the Poisson-Boltzmann description of the double layer remains a good approximation at low coupling values, while the strong coupling theory is shown to lead to the correct density profiles close to the wall (and at all couplings). For very large couplings, only systems where the difference between the dielectric constants of the wall and of the solvent is small are shown to be well described by SC. Another experimentally relevant modification to the simple double layer is to make the charges at the plane discrete. The counterions are still assumed to be point-like, but we constraint the distance of approach between ions in the plane and counterions to a minimum distance D. The ratio between D and the distance between neighboring ions in the plane is, as we will see, one of the important quantities in determining the influence of the discrete nature of the charges at the wall over the density profiles. Another parameter that plays an important role, as in the previous case, is the coupling as we will demonstrate, systems with higher coupling are more subject to discretization effects than systems with low coupling parameter. After studying the isolated double layer, we look at the interaction between two double layers. The system is composed by two equally charged walls at distance d, with the counterions confined between them. The charge at the walls is smeared out and the dielectric constant is the same everywhere. Using Monte-Carlo simulations we obtain the inter-plate pressure in the global parameter space, and the pressure is shown to be negative (attraction) at certain conditions. The simulations also show that the equilibrium plate separation (where the pressure changes from attractive to repulsive) exhibits a novel unbinding transition. We compare the Monte Carlo results with the strong-coupling theory, which is shown to describe well the bound states of systems with moderate and high couplings. The regime where the two walls are very close to each other is also shown to be well described by the SC theory. Finally, Using a field-theoretic approach, we derive the exact low-density ("virial") expansion of a binary mixture of positively and negatively charged hard spheres (two-component hard-core plasma, TCPHC). The free energy obtained is valid for systems where the diameters d_+ and d_- and the charge valences q_+ and q_- of positive and negative ions are unconstrained, i.e., the same expression can be used to treat dilute salt solutions (where typically d_+ ~ d_- and q_+ ~ q_-) as well as colloidal suspensions (where the difference in size and valence between macroions and counterions can be very large). We also discuss some applications of our results. KW - geladene Systeme KW - elektrische Doppelschicht KW - Elektrolyte KW - Theorie KW - Simulation KW - charged systems KW - electric double layer KW - electrolytes KW - theory KW - simulation Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-0000677 ER - TY - JOUR A1 - Banerjee, Pallavi A1 - Lipowsky, Reinhard A1 - Santer, Mark T1 - Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein JF - Journal of Chemical Theory and Computation N2 - Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models. KW - Martini force-field KW - osmotic-pressure KW - potential-functions KW - aqueous-solution KW - dynamics KW - coefficient KW - simulation KW - trypanosoma KW - transition KW - parameters Y1 - 2020 U6 - https://doi.org/10.1021/acs.jctc.0c00056 SN - 1549-9626 SN - 1549-9618 VL - 16 IS - 6 PB - ACS Publications CY - Washington DC ER - TY - GEN A1 - Banerjee, Pallavi A1 - Lipowsky, Reinhard A1 - Santer, Mark T1 - Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1216 KW - Martini force-field KW - osmotic-pressure KW - potential-functions KW - aqueous-solution KW - dynamics KW - coefficient KW - simulation KW - trypanosoma KW - transition KW - parameters Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523742 SN - 1866-8372 IS - 6 ER -