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  • Surface physics, nanoscale physics, low-dimensional systems  (6)
  • Professional Development
  • Nucleic acid structure, RNA characterisation and manipulation, Computational Methods
  • 2015-2019  (8)
  • 1
    Publication Date: 2016-06-15
    Description: In the yearly Internationally Genetically Engineered Machines (iGEM) competition, teams of Bachelor's and Master's students design and build an engineered biological system using DNA technologies. Advising an iGEM team poses unique challenges due to the inherent difficulties of mounting and completing a new biological project from scratch over the course of a single academic year; the challenges in obtaining financial and structural resources for a project that will likely not be fully realized; and conflicts between educational and competition-based goals. This article shares tips and best practices for iGEM team advisors, from two team advisors with very different experiences with the iGEM competition.
    Keywords: Professional Development
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 2
    Publication Date: 2015-06-27
    Description: Author(s): Bruno Schuler, Mats Persson, Sami Paavilainen, Niko Pavliček, Leo Gross, Gerhard Meyer, and Jascha Repp The formation of extended electron states in one-dimensional nanostructures is of key importance for the function of molecular electronics devices. In this paper, using a combination of atomic force microscopy, scanning tunneling spectroscopy, and tight-binding calculations the authors investigate the confinement of electronic states to controlled Cl vacancy pairs in a NaCl bilayer on Cu(111). They reveal that electron-phonon coupling has great influence on these quantities. [Phys. Rev. B 91, 235443] Published Wed Jun 24, 2015
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 3
    Publication Date: 2015-03-13
    Description: Author(s): Tatiana Krishtop, Manuel Houzet, and Julia S. Meyer We investigate theoretically the nonlocal conductance through a superconducting wire in tunnel contact with normal and ferromagnetic leads. In the presence of an in-plane magnetic field, the superconducting density of states is spin split, and the current injected from the normal lead is spin polari... [Phys. Rev. B 91, 121407] Published Thu Mar 12, 2015
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 4
    Publication Date: 2016-04-21
    Description: RNA–RNA interactions are fast emerging as a major functional component in many newly discovered non-coding RNAs. Basepairing is believed to be a major contributor to the stability of these intermolecular interactions, much like intramolecular basepairs formed in RNA secondary structure. As such, using algorithms similar to those for predicting RNA secondary structure, computational methods have been recently developed for the prediction of RNA–RNA interactions. We provide the first comprehensive comparison comprising 14 methods that predict general intermolecular basepairs. To evaluate these, we compile an extensive data set of 54 experimentally confirmed fungal snoRNA–rRNA interactions and 102 bacterial sRNA–mRNA interactions. We test the performance accuracy of all methods, evaluating the effects of tool settings, sequence length, and multiple sequence alignment usage and quality. Our results show that—unlike for RNA secondary structure prediction—the overall best performing tools are non-comparative energy-based tools utilizing accessibility information that predict short interactions on this data set. Furthermore, we find that maintaining high accuracy across biologically different data sets and increasing input lengths remains a huge challenge, causing implications for de novo transcriptome-wide searches. Finally, we make our interaction data set publicly available for future development and benchmarking efforts.
    Keywords: Nucleic acid structure, RNA characterisation and manipulation, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2018-05-01
    Description: Author(s): Ch. Zaum, K. M. Meyer-auf-der-Heide, and K. Morgenstern We follow the diffusion of CO molecules on Cu(111) by time-lapsed low-temperature scanning tunneling microscopy. The diffusivity of individual CO molecules oscillates with the distance to its nearest neighbor due to the long-range interaction mediated by the surface state electrons. The markedly dif... [Phys. Rev. B 97, 155437] Published Mon Apr 30, 2018
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 6
    Publication Date: 2016-09-07
    Description: Author(s): René Meyer, Alexander F. Zurhelle, Roger A. De Souza, Rainer Waser, and Felix Gunkel The electrical properties of donor-doped SrTi O 3 ( n -STO) are profoundly affected by an oxidation-induced metal-insulator transition (MIT). Here we employ dynamical numerical simulations to examine the high-temperature MIT of n -STO over a large range of time and length scales. The simulations are base… [Phys. Rev. B 94, 115408] Published Tue Sep 06, 2016
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 7
    Publication Date: 2015-07-25
    Description: Author(s): Fabrizio Dolcini, Manuel Houzet, and Julia S. Meyer We study the effect of a magnetic field on the current-phase relation of a topological Josephson junction formed by connecting two superconductors through the helical edge states of a quantum spin-Hall insulator. We predict that the Zeeman effect along the spin quantization axis of the helical edges… [Phys. Rev. B 92, 035428] Published Fri Jul 24, 2015
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 8
    Publication Date: 2017-02-15
    Description: Author(s): Erik Eriksson, Roman-Pascal Riwar, Manuel Houzet, Julia S. Meyer, and Yuli V. Nazarov The investigation of topological transitions in quantum systems is a thriving area of modern research. The authors recently predicted that multiterminal Josephson junctions realize a novel type of topological matter. Weyl singularities may appear in the Andreev bound-state spectrum of junctions with four superconducting terminals, giving rise to topological transitions as the superconducting phases are tuned. These transitions manifest themselves in a quantization of the transconductance between two voltage-biased terminals in fundamental units of 4 e 2 2/ h , where e is the electric charge and h is the Planck constant. The present work addresses the observability of this effect. The quantized transconductance is associated with adiabatic transport at fixed occupations of the Andreev states. On the other hand, a bias voltage leads to multiple Andreev reflections, where a quasiparticle is dissipatively transferred from the occupied states below the superconducting gap to the empty states above the superconducting gap. By computing the currents in the presence of weak inelastic relaxation, the authors establish the voltage threshold below which the equilibrium occupations of the Andreev states are restored, and the transconductances reach their quantized values. The results are an important step towards experimental verification of the topological properties of multiterminal Josephson junctions. [Phys. Rev. B 95, 075417] Published Tue Feb 14, 2017
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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