Depinning of disordered bosonic chains

We consider one-dimensional bosonic chains with a repulsive boson-boson interaction that decays exponentially on large length-scales. This model describes transport of Cooper-pairs in a Josepshon junction array, or transport of magnetic flux quanta in quantum-phase-slip ladders, i.e. arrays of superconducting wires in a ladder-configuration that allow for the coherent tunnelling of flux quanta. In the low-frequency, long wave-length regime these chains can be mapped to an effective model of a one-dimensional elastic field in a disordered potential. The onset of transport in these systems, when biased by external voltage, is described by the standard depinning theory of elastic media in disordered pinning potentials. We numerically study the regimes that are of relevance for quantum-phase-slip ladders. These are (i) very short chains and (ii) the regime of weak disorder. For chains shorter than the typical pinning length, i.e., the Larkin length, the chains reach a saturation regime where the depinning voltage does not depend on the decay length of the repulsive interaction. In the regime of weak disorder we find an emergent correlation length-scale that depends on the disorder strength. For arrays shorter than this length the onset of transport is similar to the clean arrays, i.e., is due to the penetration of solitons into the array. We discuss the depinning scenarios for longer arrays in this regime.Comment: 11 pages, 6 figure

Jump Rope Vortex in Liquid Metal Convection

Understanding large scale circulations (LSCs) in turbulent convective systems is important for the study of stars, planets and in many industrial applications. The canonical model of the LSC is quasi-planar with additional horizontal sloshing and torsional modes [Brown E, Ahlers G (2009) J. Fluid Mech. 638:383--400; Funfschilling D, Ahlers G (2004) Phys. Rev. Lett. 92(19):194502; Xi HD et al. (2009) Phys. Rev. Lett. 102(4):044503; Zhou Q et al. (2009) J. Fluid Mech. 630:367--390]. Using liquid gallium as the working fluid, we show via coupled laboratory-numerical experiments that the LSC in a tank with aspect ratios greater than unity takes instead the form of a "jump rope vortex", a strongly three-dimensional mode that periodically orbits around the tank following a motion much like a jump rope on a playground. Further experiments show that this jump rope flow also exists in more viscous fluids such as water, albeit with a far smaller signal. Thus, this new jump rope mode is an essential component of the turbulent convection that underlies our observations of natural systems

Icarus: Towards a Multistore Database System

The last years have seen a vast diversification on the database market. In contrast to the "one-size-fits-all" paradigm according to which systems have been designed in the past, today's database management systems (DBMSs) are tuned for particular workloads. This has led to DBMSs optimized for high performance, high throughput read/write workload in online transaction processing (OLTP) and systems optimized for complex analytical queries (OLAP). However, this approach reaches a limit when systems have to deal with mixed workloads that are neither pure OLAP nor pure OLTP workloads. In such cases, polystores are increasingly gaining popularity. Rather than supporting one single database paradigm and addressing one particular workload, polystores encompass several DBMSs that store data in different schemas and allow to route requests at a per-query-level to the most appropriate system. In this paper, we introduce the polystore Icarus. In our evaluation based on a workload that combines OLTP and OLAP elements, We show that Icarus is able to speed-up queries up to a factor of 3 by properly routing queries to the best underlying DBMS

DNA elimination in the ciliate Tetrahymena

Während der sexuellen Fortpflanzung finden im neu entstehenden Makronukleus von Tetrahymena weitreichende Umgestaltungen des Genoms statt, bei denen mehr als 30 % des Genoms eliminiert werden. Dieser Prozess beinhaltet die spezifische Erkennung interner eliminierter Sequenzen durch einen Argonaut-scanRNA Komplex und die darauf folgende Heterochromatinbildung. Diese führt zur Akkumulierung der methylierten Lysine 9 und 27 des Histons H3 woraufhin das Chromodomänen Protein Pdd1p rekrutiert wird. Im Anschluss daran bilden sich sichtbar abgegrenzte Heterochromatinkörperchen von denen man davon ausgeht, dass in ihnen die DNS Eliminierung stattfindet. In meiner Doktorarbeit konnte ich zeigen, dass die piggyBac-ähnliche Transposase Tpb2p in diese Heterochromatinkörperchen rekrutiert wird und dass sie für die DNS Eliminierung unerlässlich ist. Zudem erkennt und schneidet das rekombinant in Bakterien hergestellte Tpb2p die Grenzen verschiedener interner eliminierter Sequenzen in vitro, wenn diese in der Mitte einer künstlich ausgearbeiteten und synthetisierten oligo DNS vorhanden sind. Daher führt Tpb2p wahrscheinlich auch den initialen Doppelstrangbruch während des Ausschneidens der internen eliminierten Sequenzen aus. Um einen Einblick zu erhalten wie die Präzission während des Ausschneidens erreicht wird, habe ich die Nuklease Aktivität des rekombinanten Tpb2p genauer untersucht. Dafür verwendete ich synthetisierte oligo DNS in der jede Position der linken Grenze des gut untersuchten R-Elements (Sequenz AGTGAT) individuell mutiert wurde. Ich konnte zeigen, dass die Positionen drei und vier wichtig für ein effektives Schneiden der Sequenz durch Tpb2p sind. Des Weiteren konnte ich veranschaulichen, dass diese Positionen auch für die präzise Eliminierung des R-Elements wichtig sind. Daher trägt die Präferenz von Tpb2p für bestimmte DNS Sequenzen sicherlich zur genauen Eliminierung der internen eliminierten Sequenzen bei. Andererseits lokalisiert Tpb2p in den Heterochromatinkörperchen und ist für deren Ausbildung essentiell. Daher ist es auch möglich, dass Tpb2p direkt mit dem Heterochromatin interagiert, und dass diese Interaktion die präzise Eliminierung ermöglicht. Tpb2p hat eine Endonuklease Domäne und eine Zink Finger Domäne. Ich habe herausgefunden, dass die Zink Finger Domäne, allerdings nicht die Endonuklease Domäne essentiell für die Ausbildung der Heterochromatinkörperchen ist. Außerdem konnte ich zeigen, dass die Zink Finger Domäne in vitro an Peptide des Histons H3 bindet, wenn diese an Lysin 9 oder 27 tri-methyliert sind. Dies lässt die Schlussfolgerung zu, dass diese Modifikationen, die spezifisch sind für interne eliminierte Sequenzen – zusammen mit der Sequenz Präferenz von Tpb2p – das präzise Ausschneiden der internen eliminierten Sequenzen vermittelt.During sexual reproduction the new developing macronucleus of Tetrahymena undergoes massive programmed DNA rearrangement, where over 30 % of the genome is eliminated. This process involves the sequence specific recognition of internal eliminated sequences by an Argonaute-scan RNA complex followed by heterochromatin formation including the accumulations of methylated histone H3 at lysine 9 and lysine 27 and the chromodomain protein Pdd1p. This heterochromatin formation eventually leads to the formation of distinct heterochromatin bodies in which DNA elimination is believed to occur. In my thesis I demonstrated that the piggyBac-like transposase Tpb2p is recruited to the heterochromatin bodies and that it is essential for DNA elimination. Furthermore, the recombinantly expressed Tpb2p from bacteria can recognize and cut boundaries of different internal eliminated sequences in vitro when they are placed in the middle of an artificially designed and synthesized oligo. Thus Tpb2p probably introduces the initial double strand break during DNA excision. To get insight into how the precision of excision is achieved, I first analyzed the nuclease activity of recombinant Tpb2p in more detail. Using synthesized oligo DNAs where every position of the reported left boundary of the well studied R element (sequence AGTGAT) was individually mutated, I found that the third and fourth positions in the boundary sequence are important for efficient cleavage by Tpb2p. Furthermore, an in vivo study confirmed that these two positions were crucial for the precise elimination of the R IES element. Therefore, some DNA sequence preference of Tpb2p clearly contributes to the precise elimination of internal eliminated sequences. On the other hand, because Tpb2p is a component of heterochromatin and is required for heterochromatin body formation, heterochromatin interaction with Tpb2p might also be involved in the precise DNA elimination. Tpb2p has an endonuclease domain and a zinc finger domain. I found that the zinc finger domain, but not the endonuclease domain, was essential for heterochromatin body formation. I could show in vitro that the zinc finger domain binds to histone H3 peptides that are tri-methylated at lysines 9 or 27 suggesting that these modifications specific to internal eliminated sequences are - together with the sequence preference of Tpb2p- specifying the precise IES excision

De-pinning of disordered bosonic chains

We consider onset of transport (de-pinning) in one-dimensional bosonic chains with a repulsive boson?boson interaction that decays exponentially on large length-scales. Our study is relevant for (i) de-pinning of Cooper-pairs in Josephson junction arrays; (ii) de-pinning of magnetic flux quanta in quantum-phase-slip ladders, i.e. arrays of superconducting wires in a ladder-configuration that allow for the coherent tunneling of flux quanta. In the low-frequency, long wave-length regime these chains can be mapped onto an effective model of a one-dimensional elastic field in a disordered potential. The standard de-pinning theories address infinitely long systems in two limiting cases: (a) of uncorrelated disorder (zero correlation length); (b) of long range power-law correlated disorder (infinite correlation length). In this paper we study numerically chains of finite length in the intermediate case of long but finite disorder correlation length. This regime is of relevance for, e.g., the experimental systems mentioned above. We study the interplay of three length scales: the system length, the interaction range, the correlation length of disorder. In particular, we observe the crossover between the solitonic onset of transport in arrays shorter than the disorder correlation length to onset of transport by de-pinning for longer arrays

Chronos: The Swiss Army Knife for Database Evaluations

Systems evaluations are an important part of empirical research in computer science. Such evaluations encompass the systematic assessment of the run-time characteristics of systems based on one or several parameters. Considering all possible parameter settings is often a very tedious and time-consuming task with many manual activities, or at least the manual creation of evaluation scripts. Ideally, the thorough evaluation of a complete evaluation space can be fully automated. This includes the set-up of the evaluation, its execution, and the subsequent analysis of the results. In this paper, we introduce Chronos, a system for the automation of the entire evaluation workflow. While Chronos has originally been built for database systems evaluations, its generic approach also allows its usage in other domains. We show how Chronos can be deployed for a concrete database evaluation, the comparative performance analysis of different storage engines in MongoDB

Establishment of a Cre/loxP recombination system for N-terminal epitope tagging of genes in Tetrahymena

<p>Abstract</p> <p>Background</p> <p>Epitope tagging is a powerful strategy to study the function of proteins. Although tools for C-terminal protein tagging in the ciliated protozoan <it>Tetrahymena thermophila </it>have been developed, N-terminal protein tagging in this organism is still technically demanding.</p> <p>Results</p> <p>In this study, we have established a Cre/loxP recombination system in <it>Tetrahymena </it>and have applied this system for the N-terminal epitope tagging of <it>Tetrahymena </it>genes. Cre can be expressed in <it>Tetrahymena </it>and localizes to the macronucleus where it induces precise recombination at two loxP sequences in direct orientation in the <it>Tetrahymena </it>macronuclear chromosome. This Cre/loxP recombination can be used to remove a loxP-flanked drug-resistance marker from an N-terminal tagging construct after it is integrated into the macronucleus.</p> <p>Conclusions</p> <p>The system established in this study allows us to express an N-terminal epitope tagged gene from its own endogenous promoter in <it>Tetrahymena</it>.</p