TY  - INPR
A1  - Schumacher, Jörg
A1  - Seehafer, Norbert
T1  - Bifurcation analysis of the plane sheet pinch
N2  - A numerical bifurcation analysis of the electrically driven plane sheet pinch is presented. The electrical conductivity varies across the sheet such as to allow instability of the quiescent basic state at some critical Hartmann number. The most unstable perturbation is the two-dimensional tearing mode. Restricting the whole problem to two spatial dimensions, this mode is followed up to a time-asymptotic steady state, which proves to be sensitive to three-dimensional perturbations even close to the point where the primary instability sets in. A comprehensive three-dimensional stability analysis of the two-dimensional steady tearing-mode state is performed by varying parameters of the sheet pinch. The instability with respect to three-dimensional perturbations is suppressed by a sufficiently strong magnetic field in the invariant direction of the equilibrium. For a special choice of the system parameters, the unstably perturbed state is followed up in its nonlinear evolution and is found to approach a three-dimensional steady state.
T3  - NLD Preprints - 56 
Y1  - 1999
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-14926
ER  - 
TY  - THES
A1  - Müller, Melanie J. I.
T1  - Bidirectional transport by molecular motors
T1  - Bidirektionaler Transport durch molekulare Motoren
N2  - In biological cells, the long-range intracellular traffic is powered by molecular motors which transport various cargos along microtubule filaments. The microtubules possess an intrinsic direction, having a 'plus' and a 'minus' end. Some molecular motors such as cytoplasmic dynein walk to the minus end, while others such as conventional kinesin walk to the plus end. Cells typically have an isopolar microtubule network. This is most pronounced in neuronal axons or fungal hyphae. In these long and thin tubular protrusions, the microtubules are arranged parallel to the tube axis with the minus ends pointing to the cell body and the plus ends pointing to the tip. In such a tubular compartment, transport by only one motor type leads to 'motor traffic jams'. Kinesin-driven cargos accumulate at the tip, while dynein-driven cargos accumulate near the cell body. We identify the relevant length scales and characterize the jamming behaviour in these tube geometries by using both Monte Carlo simulations and analytical calculations. A possible solution to this jamming problem is to transport cargos with a team of plus and a team of minus motors simultaneously, so that they can travel bidirectionally, as observed in cells. The presumably simplest mechanism for such bidirectional transport is provided by a 'tug-of-war' between the two motor teams which is governed by mechanical motor interactions only. We develop a stochastic tug-of-war model and study it with numerical and analytical calculations. We find a surprisingly complex cooperative motility behaviour. We compare our results to the available experimental data, which we reproduce qualitatively and quantitatively.
N2  - In biologischen Zellen transportieren molekulare Motoren verschiedenste Frachtteilchen entlang von Mikrotubuli-Filamenten. Die Mikrotubuli-Filamente besitzen eine intrinsische Richtung: sie haben ein "Plus-" und ein "Minus-"Ende. Einige molekulare Motoren wie Dynein laufen zum Minus-Ende, während andere wie Kinesin zum Plus-Ende laufen. Zellen haben typischerweise ein isopolares Mikrotubuli-Netzwerk. Dies ist besonders ausgeprägt in neuronalen Axonen oder Pilz-Hyphen. In diesen langen röhrenförmigen Ausstülpungen liegen die Mikrotubuli parallel zur Achse mit dem Minus-Ende zum Zellkörper und dem Plus-Ende zur Zellspitze gerichtet. In einer solchen Röhre führt Transport durch nur einen Motor-Typ zu "Motor-Staus". Kinesin-getriebene Frachten akkumulieren an der Spitze, während Dynein-getriebene Frachten am Zellkörper akkumulieren. Wir identifizieren die relevanten Längenskalen und charakterisieren das Stauverhalten in diesen Röhrengeometrien mit Hilfe von Monte-Carlo-Simulationen und analytischen Rechnungen. Eine mögliche Lösung für das Stauproblem ist der Transport mit einem Team von Plus- und einem Team von Minus-Motoren gleichzeitig, so dass die Fracht sich in beide Richtungen bewegen kann. Dies wird in Zellen tatsächlich beobachtet. Der einfachste Mechanismus für solchen bidirektionalen Transport ist ein "Tauziehen" zwischen den beiden Motor-Teams, das nur mit mechanischer Interaktion funktioniert. Wir entwickeln ein stochastisches Tauzieh-Modell, das wir mit numerischen und analytischen Rechnungen untersuchen. Es ergibt sich ein erstaunlich komplexes Motilitätsverhalten. Wir vergleichen unsere Resultate mit den vorhandenen experimentellen Daten, die wir qualitativ und quantitativ reproduzieren.
KW  - molekulare Motoren
KW  - bidirektionaler intrazellulärer Transport
KW  - Tauziehen
KW  - stochastische Prozesse
KW  - kooperative Phänomene
KW  - molecular motors
KW  - bidirectional intracellular transport
KW  - tug-of-war
KW  - stochastic processes
KW  - cooperative phenomena
Y1  - 2008
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-18715
ER  - 
TY  - JOUR
A1  - Hou, Ru
A1  - Cherstvy, Andrey G.
A1  - Metzler, Ralf
A1  - Akimoto, Takuma
T1  - Biased continuous-time random walks for ordinary and equilibrium cases
BT  - facilitation of diffusion, ergodicity breaking and ageing
JF  - Physical chemistry, chemical physics : a journal of European Chemical Societies
N2  - We examine renewal processes with power-law waiting time distributions (WTDs) and non-zero drift via computing analytically and by computer simulations their ensemble and time averaged spreading characteristics. All possible values of the scaling exponent alpha are considered for the WTD psi(t) similar to 1/t(1+alpha). We treat continuous-time random walks (CTRWs) with 0 < alpha < 1 for which the mean waiting time diverges, and investigate the behaviour of the process for both ordinary and equilibrium CTRWs for 1 < alpha < 2 and alpha > 2. We demonstrate that in the presence of a drift CTRWs with alpha < 1 are ageing and non-ergodic in the sense of the non-equivalence of their ensemble and time averaged displacement characteristics in the limit of lag times much shorter than the trajectory length. In the sense of the equivalence of ensemble and time averages, CTRW processes with 1 < alpha < 2 are ergodic for the equilibrium and non-ergodic for the ordinary situation. Lastly, CTRW renewal processes with alpha > 2-both for the equilibrium and ordinary situation-are always ergodic. For the situations 1 < alpha < 2 and alpha > 2 the variance of the diffusion process, however, depends on the initial ensemble. For biased CTRWs with alpha > 1 we also investigate the behaviour of the ergodicity breaking parameter. In addition, we demonstrate that for biased CTRWs the Einstein relation is valid on the level of the ensemble and time averaged displacements, in the entire range of the WTD exponent alpha.
Y1  - 2018
U6  - https://doi.org/10.1039/c8cp01863d
SN  - 1463-9076
SN  - 1463-9084
VL  - 20
IS  - 32
SP  - 20827
EP  - 20848
PB  - Royal Society of Chemistry
CY  - Cambridge
ER  - 
TY  - THES
A1  - Streibel, Martin Albert Gerhard
T1  - Bestimmung  von Ozonabbauraten über der Arktis und Antarktis mittels Ozonsonden- und Satellitendaten
T1  - Determination of ozone loss rates over the Arctic and Antarctic using ozone sonde and satellite data
N2  - Diese Arbeit beschäftigt sich mit der chemischen Ozonzerstörung im arktischen und antarktischen stratosphärischen Polarwirbel. Diese wird durch Abbauprodukte von anthropogen emittierten Fluorchlorkohlenwasserstoffen und Halonen, Chlor- und Bromradikale, verursacht. Studien in denen der gemessene und modellierte Ozonabbau verglichen wird zeigen, dass die Prozeße bekannt sind, der quantitative Verlauf allerdings nicht vollständig verstanden ist.  Die Prozesse, die zur Ozonzerstörung führen sind in beiden Polarwirbeln ähnlich. Allerdings fällt als Konsequenz unterschiedlicher meteorologischer Bedingungen der chemische Ozonabbau im arktischen Polarwirbel weniger drastisch aus als über der Antarktis. Der arktische Polarwirbel ist im Mittel stärker dynamisch gestört als der antarktische und weist eine stärkere Jahr-zu-Jahr Variabilität auf. Das erschwert die Messung des chemischen Ozonabbaus. Zur Trennung des chemischen Ozonabbaus von der dynamischen Umverteilung des Ozons im arktischen Polarwirbel wurde die Matchmethode entwickelt. Bei dieser Methode werden Luftpakete innerhalb des Polarwirbels mehrfach beprobt, um den chemischen Anteil der Ozonänderung zu quantifizieren. Zur Identifizierung von doppelt beprobten Luftpaketen werden Trajektorien aus Windfeldern berechnet. Können zwei Messungen im Rahmen bestimmter Qualitätskriterien durch eine Trajektorie verbunden werden, kann die Ozondifferenz zwischen beiden Sondierungen berechnet und als chemischer Ozonabbau interpretiert werden. Eine solche Koinzidenz wird Match genannt. Der Matchmethode liegt ein statistischer Ansatz zugrunde, so dass eine Vielzahl solcher doppelt beprobter Luftmassen vorliegen muss, um gesicherte Aussagen über die Ozonzerstörung gewinnen zu können. So erhält man die Ozonzerstörung in einem bestimmten Zeitintervall, also Ozonabbauraten. Um die Anzahl an doppelt beprobten Luftpackten zu erhöhen wurde eine aktive Koordinierung der Ozonsondenaufstiege entwickelt.  Im Rahmen dieser Arbeit wurden Matchkampagnen während des arktischen Winters 2002/2003 und zum ersten Mal während eines antarktischen Winter (2003) durchgeführt. Aus den gewonnenen Daten wurden Ozonabbauraten in beiden Polarwirbeln bestimmt. Diese Abbauraten dienen zum einen der Evaluierung von Modellen, ermöglichen aber auch den direkten Vergleich von Ozonabbauraten in beiden Polarwirbeln.  Der Winter 2002/2003 war zu Beginn durch sehr tiefe Temperaturen in der mittleren und unteren Stratosphäre charakterisiert, so dass die Matchkampagne Ende November gestartet wurde. Ab Januar war der Polarwirbel zeitweise stark dynamisch gestört. Die Kampagne ging bis Mitte März. Für den Höhenbereich von 400 bis 550 K potentieller Temperatur (15-23 km) konnten Ozonabbauraten und der Verlust in der Gesamtsäule berechnet werden. Die Ozonabbauraten wurden in verschiedenen Tests auf ihre Stabilität überprüft.  Der antarktische Polarwirbel war vom Beginn des Winters bis Mitte Oktober 2003 sehr kalt und stellte Ende September kurzzeitig den Rekord für die größte bisher aufgetretene Ozonloch-Fläche ein. Es konnten für den Kampagnenzeitraum, Anfang Juni bis Anfang Oktober, Ozonabbauraten im Höhenbereich von 400 bis 550 K potentieller Temperatur ermittelt werden. Der zeitliche Verlauf des Ozonabbaus war dabei auf fast allen Höhenniveaus identisch. Die Zunahme des Sonnenlichtes im Polarwirbel mit der Zeit führt zu einem starken Anwachsen der Ozonabbauraten. Ab Mitte September gingen die Ozonabbauraten auf Null zurück, da bis zu diesem Zeitpunkt das gesamte Ozon zwischen ca. 14 und 21 km zerstört wurde.  Im letzten Teil der Arbeit wird ein neuer Algorithmus auf Basis der multivariaten Regression vorgestellt, mit dem Ozonabbauraten aus Ozonprofilen verschiedener Sensoren gleichzeitig berechnet werden können. Dabei können neben der Ozonabbaurate die systematischen Fehler zwischen den einzelnen Sensoren bestimmt werden. Dies wurde exemplarisch am antarktischen Winter 2003 für das 475 K potentielle Temperatur Niveau gezeigt. Neben den Ozonprofilen der Sonden wurden Daten von zwei Satellitenexperimenten verwendet. Die mit der multivariaten Matchtechnik berechneten Ozonabbauraten stimmen gut mit den Ozonabbauraten der Einzelsensor-Matchansätze überein.
N2  - The subject of this thesis is the destruction of ozone in the stratospheric polar vortex of the Arctic and Antarctic. It is caused by decomposition products of anthropogenic emitted Chlorofluorocarbons and Halons, radicals of chlorine and bromine. Studies which are dealing with the comparison of measured and modelled ozone loss show that the processes are known but that the quantitative development is not fully understood yet.  The processes that lead to ozone destruction are similar in both polar vortices. But as a consequence of different meteorological conditions the chemical ozone loss in the arctic polar vortex is less dramatic than over the Antarctic. On average the Arctic polar vortex is stronger perturbed and exhibit a stronger annual variability. In order to distinguish between chemical ozone loss and the dynamical redistribution of ozone in the Arctic vortex the Match method was developed. Air parcels in the polar vortex are probed several times in order to quantify the chemical change in ozone. To identify those air parcels trajectories are calculated using wind fields. When it is possible to connect two measurements by a trajectory within certain quality criteria the difference in ozone can be calculated and is interpreted as chemical ozone loss. Such a coincidence is called a Match. The Match method is a statistical approach which needs many of those doubly probed air parcels in order to draw significant conclusions about the destruction of ozone. So the ozone destruction can be calculated for a certain period in time which gives ozone loss rates. In order to enhance the number of doubly probed air masses an active coordination was established.  Within the scope of the thesis Match campaigns were performed during the Arctic winter 2002/2003 and for the first time during the Antarctic winter 2003. The achieved data was used in order to determine ozone loss rates in both polar vortices. The loss rates serve for the evaluation of numerical models but allow as well the direct comparison of ozone loss rates of both polar vortices.  The beginning of the winter 2002/2003 is characterized by very low temperatures in the middle and lower stratosphere. Hence, the Match campaign started at the end of November. From January on the polar vortex was strongly dynamically disturbed at certain times. For the height region of 400 to 500 K potential temperature (15-23 km) ozone loss rates and the column loss were determined. The robustness of the ozone loss rates was checked with a variety of different tests.  From beginning of the winter until October 2003 the Antarctic polar vortex was very cold and the expansion of the ozone hole area reached record values in late September. From the beginning of June until the beginning of October ozone loss has been calculated in a height region from 400 to 550 K potential temperature. The development of the ozone loss was almost identical on the different height levels. The increase in sunlight led to an increase in ozone loss rates. From mid September the ozone loss rates decreased rapidly and the ozone was completely destroyed between approx. 14 and 21 km.  In the last part of the thesis a new algorithm is presented which is based on a multivariate regression in order to calculate ozone loss rates from ozone profiles made by different sensors. At the same time the systematic error between different sensors has to be considered. As an example the approach is shown for the Antarctic Winter 2003 on the 475 K potential temperature level. Beside the ozone profiles from the sondes, data from two satellites experiments have been used. The agreement between the ozone loss rates calculated by the multivariate regression method and those calculated by the single match approach is very good.
KW  - Ozon
KW  - Polarforschung
KW  - Polartief
KW  - Atmosphäre
KW  - Ozonzabbau
KW  - ozone
KW  - polar research
KW  - polar vortex
KW  - atmosphere
KW  - ozone loss
Y1  - 2005
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-6570
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  - Makarava, Natallia
T1  - Bayesian estimation of self-similarity exponent
T1  - Bayessche Schätzung des selbstählichen Exponenten
N2  - Estimation of the self-similarity exponent has attracted growing interest in recent decades and became a research subject in various fields and disciplines. Real-world data exhibiting self-similar behavior and/or parametrized by self-similarity exponent (in particular Hurst exponent) have been collected in different fields ranging from finance and human sciencies to hydrologic and traffic networks. Such rich classes of possible applications obligates researchers to investigate qualitatively new methods for estimation of the self-similarity exponent as well as identification of long-range dependencies (or long memory). In this thesis I present the Bayesian estimation of the Hurst exponent. In contrast to previous methods, the Bayesian approach allows the possibility to calculate the point estimator and confidence intervals at the same time, bringing significant advantages in data-analysis as discussed in this thesis. Moreover, it is also applicable to short data and unevenly sampled data, thus broadening the range of systems where the estimation of the Hurst exponent is possible. Taking into account that one of the substantial classes of great interest in modeling is the class of Gaussian self-similar processes, this thesis considers the realizations of the processes of fractional Brownian motion and fractional Gaussian noise. Additionally, applications to real-world data, such as the data of water level of the Nile River and fixational eye movements are also discussed.
N2  - Die Abschätzung des Selbstähnlichkeitsexponenten hat in den letzten Jahr-zehnten an Aufmerksamkeit gewonnen und ist in vielen wissenschaftlichen Gebieten und Disziplinen zu einem intensiven Forschungsthema geworden. Reelle Daten, die selbsähnliches Verhalten zeigen und/oder durch den Selbstähnlichkeitsexponenten (insbesondere durch den Hurst-Exponenten) parametrisiert werden, wurden in verschiedenen Gebieten gesammelt, die von Finanzwissenschaften über Humanwissenschaften bis zu Netzwerken in der Hydrologie und dem Verkehr reichen. Diese reiche Anzahl an möglichen Anwendungen verlangt von Forschern, neue Methoden zu entwickeln, um den Selbstähnlichkeitsexponenten abzuschätzen, sowie großskalige Abhängigkeiten zu erkennen. In dieser Arbeit stelle ich die Bayessche Schätzung des Hurst-Exponenten vor. Im Unterschied zu früheren Methoden, erlaubt die Bayessche Herangehensweise die Berechnung von Punktschätzungen zusammen mit Konfidenzintervallen, was von bedeutendem Vorteil in der Datenanalyse ist, wie in der Arbeit diskutiert wird. Zudem ist diese Methode anwendbar auf kurze und unregelmäßig verteilte Datensätze, wodurch die Auswahl der möglichen Anwendung, wo der Hurst-Exponent geschätzt werden soll, stark erweitert wird. Unter Berücksichtigung der Tatsache, dass der Gauß'sche selbstähnliche Prozess von bedeutender Interesse in der Modellierung ist, werden in dieser Arbeit Realisierungen der Prozesse der fraktionalen Brown'schen Bewegung und des fraktionalen Gauß'schen Rauschens untersucht. Zusätzlich werden Anwendungen auf reelle Daten, wie Wasserstände des Nil und fixierte Augenbewegungen, diskutiert.
KW  - Hurst-Exponent
KW  - Bayessche Statistik
KW  - fraktionale Brown'schen Bewegung
KW  - fraktionales Gauß'sches Rauschen
KW  - fixierte Augenbewegungen
KW  - Hurst exponent
KW  - Bayesian inference
KW  - fractional Brownian motion
KW  - fractional Gaussian noise
KW  - fixational eye movements
Y1  - 2012
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-64099
ER  - 
TY  - JOUR
A1  - Seckler, Henrik
A1  - Metzler, Ralf
T1  - Bayesian deep learning for error estimation in the analysis of anomalous diffusion
JF  - Nature Communnications
N2  - Modern single-particle-tracking techniques produce extensive time-series of diffusive motion in a wide variety of systems, from single-molecule motion in living-cells to movement ecology. The quest is to decipher the physical mechanisms encoded in the data and thus to better understand the probed systems. We here augment recently proposed machine-learning techniques for decoding anomalous-diffusion data to include an uncertainty estimate in addition to the predicted output. To avoid the Black-Box-Problem a Bayesian-Deep-Learning technique named Stochastic-Weight-Averaging-Gaussian is used to train models for both the classification of the diffusionmodel and the regression of the anomalous diffusion exponent of single-particle-trajectories. Evaluating their performance, we find that these models can achieve a wellcalibrated error estimate while maintaining high prediction accuracies. In the analysis of the output uncertainty predictions we relate these to properties of the underlying diffusion models, thus providing insights into the learning process of the machine and the relevance of the output.
KW  - random-walk
KW  - models
Y1  - 2022
U6  - https://doi.org/10.1038/s41467-022-34305-6
SN  - 2041-1723
VL  - 13
PB  - Nature Publishing Group UK
CY  - London
ER  - 
TY  - JOUR
A1  - Seckler, Henrik
A1  - Metzler, Ralf
T1  - Bayesian deep learning for error estimation in the analysis of anomalous diffusion
JF  - Nature Communications
N2  - Modern single-particle-tracking techniques produce extensive time-series of diffusive motion in a wide variety of systems, from single-molecule motion in living-cells to movement ecology. The quest is to decipher the physical mechanisms encoded in the data and thus to better understand the probed systems. We here augment recently proposed machine-learning techniques for decoding anomalous-diffusion data to include an uncertainty estimate in addition to the predicted output. To avoid the Black-Box-Problem a Bayesian-Deep-Learning technique named Stochastic-Weight-Averaging-Gaussian is used to train models for both the classification of the diffusion model and the regression of the anomalous diffusion exponent of single-particle-trajectories. Evaluating their performance, we find that these models can achieve a well-calibrated error estimate while maintaining high prediction accuracies. In the analysis of the output uncertainty predictions we relate these to properties of the underlying diffusion models, thus providing insights into the learning process of the machine and the relevance of the output. <br /> Diffusive motions in complex environments such as living biological cells or soft matter systems can be analyzed with single-particle-tracking approaches, where accuracy of output may vary. The authors involve a machine-learning technique for decoding anomalous-diffusion data and provide an uncertainty estimate together with predicted output.
Y1  - 2022
U6  - https://doi.org/10.1038/s41467-022-34305-6
SN  - 2041-1723
VL  - 13
IS  - 1
PB  - Nature portfolio
CY  - Berlin
ER  - 
TY  - GEN
A1  - Seckler, Henrik
A1  - Metzler, Ralf
T1  - Bayesian deep learning for error estimation in the analysis of anomalous diffusion
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - Sprache
Englisch
Modern single-particle-tracking techniques produce extensive time-series of diffusive motion in a wide variety of systems, from single-molecule motion in living-cells to movement ecology. The quest is to decipher the physical mechanisms encoded in the data and thus to better understand the probed systems. We here augment recently proposed machine-learning techniques for decoding anomalous-diffusion data to include an uncertainty estimate in addition to the predicted output. To avoid the Black-Box-Problem a Bayesian-Deep-Learning technique named Stochastic-Weight-Averaging-Gaussian is used to train models for both the classification of the diffusionmodel and the regression of the anomalous diffusion exponent of single-particle-trajectories. Evaluating their performance, we find that these models can achieve a wellcalibrated error estimate while maintaining high prediction accuracies. In the analysis of the output uncertainty predictions we relate these to properties of the underlying diffusion models, thus providing insights into the learning process of the machine and the relevance of the output.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1314 
KW  - random-walk
KW  - models
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-586025
SN  - 1866-8372
IS  - 1314
ER  - 
TY  - JOUR
A1  - Thapa, Samudrajit
A1  - Lomholt, Michael Andersen
A1  - Krog, Jens
A1  - Cherstvy, Andrey G.
A1  - Metzler, Ralf
T1  - Bayesian analysis of single-particle tracking data using the nested-sampling algorithm: maximum-likelihood model selection applied to stochastic-diffusivity data
JF  - Physical chemistry, chemical physics : PCCP ; a journal of European Chemical Societies
N2  - We employ Bayesian statistics using the nested-sampling algorithm to compare and rank multiple models of ergodic diffusion (including anomalous diffusion) as well as to assess their optimal parameters for in silico-generated and real time-series. We focus on the recently-introduced model of Brownian motion with "diffusing diffusivity'-giving rise to widely-observed non-Gaussian displacement statistics-and its comparison to Brownian and fractional Brownian motion, also for the time-series with some measurement noise. We conduct this model-assessment analysis using Bayesian statistics and the nested-sampling algorithm on the level of individual particle trajectories. We evaluate relative model probabilities and compute best-parameter sets for each diffusion model, comparing the estimated parameters to the true ones. We test the performance of the nested-sampling algorithm and its predictive power both for computer-generated (idealised) trajectories as well as for real single-particle-tracking trajectories. Our approach delivers new important insight into the objective selection of the most suitable stochastic model for a given time-series. We also present first model-ranking results in application to experimental data of tracer diffusion in polymer-based hydrogels.
Y1  - 2018
U6  - https://doi.org/10.1039/c8cp04043e
SN  - 1463-9076
SN  - 1463-9084
VL  - 20
IS  - 46
SP  - 29018
EP  - 29037
PB  - Royal Society of Chemistry
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Perdigón-Toro, Lorena
A1  - Zhang, Huotian
A1  - Markina, Anastaa si
A1  - Yuan, Jun
A1  - Hosseini, Seyed Mehrdad
A1  - Wolff, Christian Michael
A1  - Zuo, Guangzheng
A1  - Stolterfoht, Martin
A1  - Zou, Yingping
A1  - Gao, Feng
A1  - Andrienko, Denis
A1  - Shoaee, Safa
A1  - Neher, Dieter
T1  - Barrierless free charge generation in the high-performance PM6:Y6 bulk heterojunction non-fullerene solar cell
JF  - Advanced materials
N2  - Organic solar cells are currently experiencing a second golden age thanks to the development of novel non-fullerene acceptors (NFAs). Surprisingly, some of these blends exhibit high efficiencies despite a low energy offset at the heterojunction. Herein, free charge generation in the high-performance blend of the donor polymer PM6 with the NFA Y6 is thoroughly investigated as a function of internal field, temperature and excitation energy. Results show that photocurrent generation is essentially barrierless with near-unity efficiency, regardless of excitation energy. Efficient charge separation is maintained over a wide temperature range, down to 100 K, despite the small driving force for charge generation. Studies on a blend with a low concentration of the NFA, measurements of the energetic disorder, and theoretical modeling suggest that CT state dissociation is assisted by the electrostatic interfacial field which for Y6 is large enough to compensate the Coulomb dissociation barrier.
KW  - driving force
KW  - non-fullerene acceptors
KW  - organic solar cells
KW  - photocurrent generation
Y1  - 2020
U6  - https://doi.org/10.1002/adma.201906763
SN  - 0935-9648
SN  - 1521-4095
VL  - 32
IS  - 9
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - THES
A1  - Theves, Matthias
T1  - Bacterial motility and growth in open and confined environments
T1  - Bacterial motility and growth in open and confined environments
N2  - In the presence of a solid-liquid or liquid-air interface, bacteria can choose between a planktonic and a sessile lifestyle. Depending on environmental conditions, cells swimming in close proximity to the interface can irreversibly attach to the surface and grow into three-dimensional aggregates where the majority of cells is sessile and embedded in an extracellular polymer matrix (biofilm). We used microfluidic tools and time lapse microscopy to perform experiments with the polarly flagellated soil bacterium Pseudomonas putida (P. putida), a bacterial species that is able to form biofilms. We analyzed individual trajectories of swimming cells, both in the bulk fluid and in close proximity to a glass-liquid interface. Additionally, surface related growth during the early phase of biofilm formation was investigated. In the bulk fluid, P.putida shows a typical bacterial swimming pattern of alternating periods of persistent displacement along a line (runs) and fast reorientation events (turns) and cells swim with an average speed around 24 micrometer per second. We found that the distribution of turning angles is bimodal with a dominating peak around 180 degrees. In approximately six out of ten turning events, the cell reverses its swimming direction. In addition, our analysis revealed that upon a reversal, the cell systematically changes its swimming speed by a factor of two on average. Based on the experimentally observed values of mean runtime and rotational diffusion, we presented a model to describe the spreading of a population of cells by a run-reverse random walker with alternating speeds. We successfully recover the mean square displacement and, by an extended version of the model, also the negative dip in the directional autocorrelation function as observed in the experiments. The analytical solution of the model demonstrates that alternating speeds enhance a cells ability to explore its environment as compared to a bacterium moving at a constant intermediate speed. As compared to the bulk fluid, for cells swimming near a solid boundary we observed an increase in swimming speed at distances below d= 5 micrometer and an increase in average angular velocity at distances below d= 4 micrometer. While the average speed was maximal with an increase around 15% at a distance of d= 3 micrometer, the angular velocity was highest in closest proximity to the boundary at d=1 micrometer with an increase around 90% as compared to the bulk fluid. To investigate the swimming behavior in a confinement between two solid boundaries, we developed an experimental setup to acquire three-dimensional trajectories using a piezo driven objective mount coupled to a high speed camera. Results on speed and angular velocity were consistent with motility statistics in the presence of a single boundary. Additionally, an analysis of the probability density revealed that a majority of cells accumulated near the upper and lower boundaries of the microchannel. The increase in angular velocity is consistent with previous studies, where bacteria near a solid boundary were shown to swim on circular trajectories, an effect which can be attributed to a wall induced torque. The increase in speed at a distance of several times the size of the cell body, however, cannot be explained by existing theories which either consider the drag increase on cell body and flagellum near a boundary (resistive force theory) or model the swimming microorganism by a multipole expansion to account for the flow field interaction between cell and boundary. An accumulation of swimming bacteria near solid boundaries has been observed in similar experiments. Our results confirm that collisions with the surface play an important role and hydrodynamic interactions alone cannot explain the steady-state accumulation of cells near the channel walls. Furthermore, we monitored the number growth of cells in the microchannel under medium rich conditions. We observed that, after a lag time, initially isolated cells at the surface started to grow by division into colonies of increasing size, while coexisting with a comparable smaller number of swimming cells. After 5:50 hours, we observed a sudden jump in the number of swimming cells, which was accompanied by a breakup of bigger clusters on the surface. After approximately 30 minutes where planktonic cells dominated in the microchannel, individual swimming cells reattached to the surface. We interpret this process as an emigration and recolonization event. A number of complementary experiments were performed to investigate the influence of collective effects or a depletion of the growth medium on the transition. Similar to earlier observations on another bacterium from the same family we found that the release of cells to the swimming phase is most likely the result of an individual adaption process, where syntheses of proteins for flagellar motility are upregulated after a number of division cycles at the surface.
N2  - Bakterien sind einzellige Mikroorganismen, die sich in flüssigem Medium mit Hilfe von rotierenden Flagellen, länglichen Fasern aus Proteinen, schwimmend fortbewegen. In Gegenwart einer Grenzfläche und unter günstigen Umweltbedingungen siedeln sich Bakterien an der Oberfläche an und gehen in eine sesshafte Wachstumsphase über. Die Wachstumsphase an der Oberfläche ist gekennzeichnet durch das Absondern von klebrigen, nährstoffreichen extrazellulären Substanzen, welche die Verbindung der Bakterien untereinander und mit der Oberfläche verstärken. Die entstehenden Aggregate aus extrazellulärer Matrix und Bakterien werden als Biofilm bezeichnet. In der vorliegenden Arbeit untersuchten wir ein Bodenbakterium, Pseudomonas putida (P. putida), welches in wässriger Umgebung an festen Oberflächen Biofilme ausbildet. Wir benutzten photolithographisch hergestellte Mikrokanäle und Hochgeschwindigkeits-Videomikroskopie um die Bewegung schwimmender Zellen in verschiedenen Abständen zu einer Glasoberfläche aufzunehmen. Zusätzlich wurden Daten über das parallel stattfindende Wachstum der sesshaften Zellen an der Oberfläche aufgezeichnet. Die Analyse von Trajektorien frei schwimmender Zellen zeigte, dass sich Liniensegmente, entlang derer sich die Zellen in eine konstante Richtung bewegen, mit scharfen Kehrtwendungen mit einem Winkel von 180 Grad abwechseln. Dabei änderte sich die Schwimmgeschwindigket von einem zum nächsten Segment im Mittel um einen Faktor von 2. Unsere experimentellen Daten waren die Grundlage für ein mathematisches Modell zur Beschreibung der Zellbewegung mit alternierender Geschwindigkeit. Die analytische Lösung des Modells zeigt elegant, dass eine Population von Bakterien, welche zwischen zwei Geschwindigkeiten wechseln, signifikant schneller expandiert als eine Referenzpopulation mit Bakterien konstanter Schwimmgeschwindkeit. Im Vergleich zu frei schwimmenden Bakterien beobachteten wir in der Nähe der Oberfläche eine um 15% erhöhte Schwimmgeschwindigkeit der Zellen und eine um 90 % erhöhte Winkel-geschwindigkeit. Außerdem wurde eine signifikant höhere Zelldichte in der Nähe der Grenzfläche gemessen. Während sich der Anstieg in der Winkelgeschwindigkeit durch ein Drehmoment erklären lässt, welches in Oberflächennähe auf den rotierenden Zellkörper und die rotierenden Flagellen wirkt, kann die Beschleunigung und Akkumulation der Zellen bei dem beobachteten Abstand nicht durch existierende Theorien erklärt werden. Unsere Ergebnisse lassen vermuten, dass neben hydrodynamischen Effekten auch Kollisionen mit der Oberfläche eine wichtige Rolle spielen und sich die Rotationsgeschwindigkeit der Flagellenmotoren in der Nähe einer festen Oberfläche grundsätzlich verändert. Unsere Experimente zum Zellwachstum an Oberflächen zeigten, dass sich etwa sechs Stunden nach Beginn des Experiments größere Kolonien an der Kanaloberfläche auflösen und Zellen für ca. 30 Minuten zurück in die schwimmende Phase wechseln. Ergebnisse von mehreren Vergleichsexperimenten deuten darauf hin, dass dieser Übergang nach einer festen Anzahl von Zellteilungen an der Oberfläche erfolgt und nicht durch den Verbrauch des Wachstumsmediums bedingt wird.
KW  - Pseudomonas putida
KW  - Motilität
KW  - Flagellenbewegung
KW  - Random-Walk-Theorie
KW  - Schwimmende Mikroorganismen
KW  - pseudomonas putida
KW  - motility
KW  - flagellar filaments
KW  - random walk
KW  - cell tracking
Y1  - 2013
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-70313
ER  - 
TY  - GEN
A1  - Pavlenko, Elena S.
A1  - Sander, Mathias
A1  - Mitzscherling, Steffen
A1  - Pudell, Jan-Etienne
A1  - Zamponi, Flavio
A1  - Rössle, Matthias
A1  - Bojahr, Andre
A1  - Bargheer, Matias
T1  - Azobenzene – functionalized polyelectrolyte nanolayers as ultrafast optoacoustic transducers
N2  - We introduce azobenzene-functionalized polyelectrolyte multilayers as efficient, inexpensive optoacoustic transducers for hyper-sound strain waves in the GHz range. By picosecond transient reflectivity measurements we study the creation of nanoscale strain waves, their reflection from interfaces, damping by scattering from nanoparticles and propagation in soft and hard adjacent materials like polymer layers, quartz and mica. The amplitude of the generated strain ε ∼ 5 × 10−4 is calibrated by ultrafast X-ray diffraction.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 297 
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-101996
VL  - 8
SP  - 13297
EP  - 13302
ER  - 
TY  - JOUR
A1  - Stojkoski, Viktor
A1  - Sandev, Trifce
A1  - Kocarev, Ljupco
A1  - Pal, Arnab
T1  - Autocorrelation functions and ergodicity in diffusion with stochastic resetting
JF  - Journal of physics : A, Mathematical and theoretical
N2  - Diffusion with stochastic resetting is a paradigm of resetting processes. Standard renewal or master equation approach are typically used to study steady state and other transport properties such as average, mean squared displacement etc. 
What remains less explored is the two time point correlation functions whose evaluation is often daunting since it requires the implementation of the exact time dependent probability density functions of the resetting processes which are unknown for most of the problems. 

We adopt a different approach that allows us to write a stochastic solution for a single trajectory undergoing resetting. 
Moments and the autocorrelation functions between any two times along the trajectory can then be computed directly using the laws of total expectation. Estimation of autocorrelation functions turns out to be pivotal for investigating the ergodic properties of various observables for this canonical model. 
In particular, we investigate two observables (i) sample mean which is widely used in economics and (ii) time-averaged-mean-squared-displacement (TAMSD) which is of acute interest in physics. 

We find that both diffusion and drift-diffusion processes with resetting are ergodic at the mean level unlike their reset-free counterparts. In contrast, resetting renders ergodicity breaking in the TAMSD while both the stochastic processes are ergodic when resetting is absent. We quantify these behaviors with detailed analytical study and corroborate with extensive numerical simulations. 

Our results can be verified in experimental set-ups that can track single particle trajectories and thus have strong implications in understanding the physics of resetting.
KW  - autocorrelations
KW  - ergodicity
KW  - diffusion
KW  - stochastic resetting
Y1  - 2022
U6  - https://doi.org/10.1088/1751-8121/ac4ce9
SN  - 1751-8113
SN  - 1751-8121
VL  - 55
IS  - 10
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - JOUR
A1  - Gerlach, Marius
A1  - Preitschopf, Tobias
A1  - Karaev, Emil
A1  - Quitian-Lara, Heidy Mayerly
A1  - Mayer, Dennis
A1  - Bozek, John
A1  - Fischer, Ingo
A1  - Fink, Reinhold F.
T1  - Auger electron spectroscopy of fulminic acid, HCNO
BT  - an experimental and theoretical study
JF  - Physical chemistry, chemical physics : a journal of European Chemical Societies
N2  - HCNO is a molecule of considerable astrochemical interest as a precursor to prebiotic molecules. It is synthesized by preparative pyrolysis and is unstable at room temperature. Here, we investigate its spectroscopy in the soft X-ray regime at the C 1s, N 1s and O 1s edges. All 1s ionization energies are reported and X-ray absorption spectra reveal the transitions from the 1s to the pi* state. Resonant and normal Auger electron spectra for the decay of the core hole states are recorded in a hemispherical analyzer. An assignment of the experimental spectra is provided with the aid of theoretical counterparts. The latter are using a valence configuration interaction representation of the intermediate and final state energies and wavefunctions, the one-center approximation for transition rates and band shapes according to the moment theory. The computed spectra are in very good agreement with the experimental data and most of the relevant bands are assigned. Additionally, we present a simple approach to estimate relative Auger transition rates on the basis of a minimal basis representation of the molecular orbitals. We demonstrate that this provides a qualitatively good and reliable estimate for several signals in the normal and resonant Auger electron spectra which have significantly different intensities in the decay of the three core holes.
Y1  - 2022
U6  - https://doi.org/10.1039/d2cp02104h
SN  - 1463-9076
SN  - 1463-9084
VL  - 24
IS  - 25
SP  - 15217
EP  - 15229
PB  - Royal Society of Chemistry
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Zacharias, Michael
A1  - Chen, Xuhui
A1  - Wagner, Stefan
T1  - Attenuation of TeV gamma-rays by the starlight photon field of the host galaxy
JF  - Monthly notices of the Royal Astronomical Society
N2  - The absorption of TeV gamma-ray photons produced in relativistic jets by surrounding soft photon fields is a long-standing problem of jet physics. In some cases, the most likely emission site close to the central black hole is ruled out because of the high opacity caused by strong optical and infrared photon sources, such as the broad-line region. Mostly neglected for jet modelling is the absorption of gamma-rays in the starlight photon field of the host galaxy. Analysing the absorption for arbitrary locations and observation angles of the gamma-ray emission site within the host galaxy, we find that the distance to the galaxy centre, the observation angle, and the distribution of starlight in the galaxy are crucial for the amount of absorption. We derive the absorption value for a sample of 20 TeV-detected blazars with a redshift z(r) < 0.2. The absorption value of the gamma-ray emission located in the galaxy centre may be as high as 20 per cent, with an average value of 6 per cent. This is important in order to determine the intrinsic blazar parameters. We see no significant trends in our sample between the degree of absorption and host properties, such as starlight emissivity, galactic size, half-light radius, and redshift. While the uncertainty of the spectral properties of the extragalactic background light exceeds the effect of absorption by stellar light from the host galaxy in distant objects, the latter is a dominant effect in nearby sources. It may also be revealed in a differential comparison of sources with similar redshifts.
KW  - opacity
KW  - radiation mechanisms: non-thermal
KW  - galaxies: active
KW  - gamma-rays: galaxies
Y1  - 2016
U6  - https://doi.org/10.1093/mnras/stw3032
SN  - 0035-8711
SN  - 1365-2966
VL  - 465
IS  - 3
SP  - 3767
EP  - 3774
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Merchel, Silke
A1  - Gärtner, Andreas
A1  - Beutner, Sabrina
A1  - Bookhagen, Bodo
A1  - Chabilan, Amelie
T1  - Attempts to understand potential deficiencies in chemical procedures for AMS: Cleaning and dissolving quartz for Be-10 and Al-26 analysis
JF  - Nuclear instruments & methods in physics research : a journal on accelerators, instrumentation and techniques applied to research in nuclear and atomic physics, materials science and related fields in physics, Section B, Beam interactions with materials and atoms
N2  - The purity of the analysed samples (e.g. quartz) with respect to chemical composition and radionuclide contamination is essential for geomorphologic applications using so-called terrestrial cosmogenic nuclides (TCNs). To guarantee this, numerous cleaning and dissolution procedures have been developed. At the DREsden Accelerator Mass Spectrometry (DREAMS) facility, we also work on enhancing the chemical quartz-enrichment methodology from bulk rock and dissolution of quartz. Repeated exposure of the bulk material to acid mixtures (HCl/H2SiF6) at room temperature for cleaning and its monitoring by optical microscopy works for most quartz-rich samples. The quartz dissolution in HF under rather mild conditions (at room temperature on a shaker-table) has the advantage to leave difficult-to-dissolve minerals (e.g., tourmaline, zircon, rutile, sillimanite, kyanite, chromite, corundum), not separated by other physical methods before, as residue. Our comparison with a high-temperature dissolution method (in a microwave) indicates an additional amount of interfering elements, such as in average about 3 mg of Ti, more than 7 mg of Al, and about 22 mu g of Be (for 50 g SiO2), is added to the sample, hence showing the superiority of our mild method. This way, we reduce problems for chemistry and AMS, but also ensure better comparability to production rates of cleaner stoichiometric quartz from calibration sites.
KW  - Accelerator mass spectrometry
KW  - In-situ
KW  - Terrestrial cosmogenic nuclide
KW  - Residue
KW  - Quartz
Y1  - 2019
U6  - https://doi.org/10.1016/j.nimb.2019.02.007
SN  - 0168-583X
SN  - 1872-9584
VL  - 455
SP  - 293
EP  - 299
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Janowski, Marcin Andrzej
A1  - Zoschke, Reimo
A1  - Scharff, Lars B.
A1  - Jaime, Silvia Martinez
A1  - Ferrari, Camilla
A1  - Proost, Sebastian
A1  - Xiong, Jonathan Ng Wei
A1  - Omranian, Nooshin
A1  - Musialak-Lange, Magdalena
A1  - Nikoloski, Zoran
A1  - Graf, Alexander
A1  - Schoettler, Mark Aurel
A1  - Sampathkumar, Arun
A1  - Vaid, Neha
A1  - Mutwil, Marek
T1  - AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome
JF  - The plant journal
N2  - Plastid ribosomes are very similar in structure and function to the ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favorable under biological conditions it requires the activity of many assembly factors. Here we have characterized a homolog of bacterial RsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous, chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were increased, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signaling pathways. To conclude, this study reveals a chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function. Significance Statement AtRsgA is an assembly factor necessary for maturation of the small subunit of the chloroplast ribosome. Depletion of AtRsgA leads to dwarfed, chlorotic plants, a decrease of mature 16S rRNA and smaller, but more numerous, chloroplasts. Large-scale transcriptomic and proteomic analysis revealed that chloroplast-encoded and -targeted proteins were less abundant, while the corresponding transcripts were increased in the mutant. We analyze the transcriptional responses of several retrograde signaling pathways to suggest the mechanism underlying this compensatory response.
KW  - ribosome assembly
KW  - chloroplast ribosome
KW  - assembly factor
KW  - 30S subunit
KW  - RsgA
KW  - Arabidopsis thaliana
Y1  - 2018
U6  - https://doi.org/10.1111/tpj.14040
SN  - 0960-7412
SN  - 1365-313X
VL  - 96
IS  - 2
SP  - 404
EP  - 420
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - GEN
A1  - Henkel, Carsten
A1  - Courtois, Jean-Yves
A1  - Aspect, Alain
T1  - Atomic diffraction by a thin phase grating
N2  - We present a semiclassical perturbation method for the description of atomic diffraction by a weakly modulated potential. It proceeds in a way similar to the treatment of light diffraction by a thin phase grating, and consists in calculating the atomic wavefunction by means of action integrals along the classical trajectories of the atoms in the absence of the modulated part of the potential. The capabilities and the validity condition of the method are illustrated on the well-known case of atomic diffraction by a Gaussian standing wave. We prove that in this situation the perturbation method is equivalent to the Raman-Nath approximation, and we point out that the usually-considered Raman-Nath validity condition can lead to inaccuracies in the evaluation of the phases of the diffraction amplitudes. The method is also applied to the case of an evanescent wave reflection grating, and an analytical expression for the diffraction pattern at any incidence angle is obtained for the first time. Finally, the application of the method to other situations is briefly discussed.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 101 
Y1  - 1994
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-42269
ER  - 
TY  - THES
A1  - Keles, Engin
T1  - Atmospheric properties and dynamics of gaseous exoplanets inferred from high-resolution alkali line transmission spectroscopy
N2  - The characterization of exoplanets applying high-resolution transmission spectroscopy ini- tiated a new era making it possible to trace atmospheric signature at high altitudes in exoplanet atmospheres and to determine atmospheric properties which enrich our under- standing of the formation and evolution of the solar system. In contrast to what is observed in our solar system, where gaseous planets orbit at wide orbits, Jupiter type exoplanets were detected in foreign stellar systems surrounding their host stars within few days, in close orbits, the so called hot- and ultra-hot Jupiters. The most well studied ones are HD209458b and HD189733b, which are the first exoplanets where absorption is detected in their atmospheres, namely from the alkali line sodium. For hot Jupiters, the resonant alkali lines are the atmospheric species with one of the strongest absorption signatures, due to their large absorption cross-section. However, al- though the alkali lines sodium and potassium were detected in low-resolution observations for various giant exoplanets, potassium was absent in different high-resolution investiga- tions in contrast to sodium. The reason for this is quite puzzling, since both alkalis have very similar physical and chemical properties (e.g. condensation and ionization proper- ties). Obtaining high-resolution transit observations of HD189733b and HD209458b, we were able to detect potassium on HD189733b (Manuscript 1), which was the first high-resolution detection of potassium on an exoplanet. The absence of potassium on HD209458b could be reasoned by depletion processes, such as condensation or photo-ionization or high-altitude clouds. In a further study (Manuscript II), we resolved the potassium line and compared this to a previously detected sodium absorption on this planet. The comparison showed, that the potassium lines are either tracing different altitudes and temperatures compared to the sodium lines, or are depleted so that the planetary Na/K- ratio is way larger than the stellar one. A comparison of the alkali lines with synthetic line profiles showed that the sodium lines were much broader than the potassium lines, probably being induced by winds. To investigate this, the effect of zonal streaming winds on the sodium lines on Jupiter-type planets is investigated in a further study (Manuscript III), showing that such winds can significantly broaden the Na- lines and that high-resolution observations can trace such winds with different properties. Furthermore, investigating the Na-line observations for different exoplanets, I showed that the Na-line broadening follows a trend with cooler planets showing stronger line broadening and so hinting on stronger winds, matching well into theoretical predictions. Each presented manuscript depends on the re- sults published within the previous manuscript, yielding a unitary study of the exoplanet HD189733b. The investigation of the potassium absorption required to account for different effects: The telluric lines removal and the effect of center-to-limb variation (see Manuscript I), the residual Rossiter-Mc-Laughlin effect (see Manuscript II) and the broadening of spectral lines on a translucent atmospheric ring by zonal jet streams (see Manuscript III). This thesis shows that high-resolution transmission spectroscopy is a powerful tool to probe sharp alkali line absorption on giant exoplanet atmospheres and to investigate on the properties and dynamics of hot Jupiter type atmospheres.
KW  - planets and satellites: atmospheres
KW  - planets and satellites: composition
KW  - planets and satellites: gaseous planets
KW  - exoplanets
Y1  - 2021
ER  -