Periodically-driven cold atoms: the role of the phase

Numerous theoretical and experimental studies have investigated the dynamics of cold atoms subjected to time periodic fields. Novel effects dependent on the amplitude and frequency of the driving field, such as Coherent Destruction of Tunneling have been identified and observed. However, in the last year or so, three distinct types of experiments have demonstrated for the first time, interesting behaviour associated with the driving phase: i.e. for systems experiencing a driving field of general form $V(x)\sin (\omega t + \phi)$, different types of large scale oscillations and directed motion were observed. We investigate and explain the phenomenon of Super-Bloch Oscillations (SBOs) in relation to the other experiments and address the role of initial phase in general. We analyse and compare the role of $\phi$ in systems with homogeneous forces ($V'(x)= const$), such as cold atoms in shaken or amplitude-modulated optical lattices, as well as non-homogeneous forces ($V'(x)\neq const$), such as the sloshing of atoms in driven traps, and clarify the physical origin of the different $\phi$-dependent effects.Comment: 10 pages, 1 figur

Züchtungsmethoden in der Diskussion - Brauchen wir Kohl aus Protoplastenfusion?

Bei Kohl aus ökologischem Anbau scheiden sich die Bio-Geister: Kohrabi-, Brokkoli- und Blumenkohlsorten aus Europa und den USA werden zunehmend mit Hilfe umstrittener Züchtungsmethoden wie der gentechnik-nahen Protoplastenfusion angebaut. Werte des Ökolandbaus wie der Erhalt der Artenvielfalt und der Schutz der natürlichen Reproduktionsfähigkeit von Pflanzen werden durch solche Techniken in Frage gestellt. Warum und mit welchem Nutzen sich diese Züchtungsmethode in den letzten Jahren im Gemüseanbau etabliert hat, wird von Fachleuten unterschiedlich beantwortet. Nur mit welchen Konsequenzen? Was sind die Alternativen für Anbau und Handel? Die Protoplastenfusion wird bei Kohl angewendet, um die erbliche Pollensterilität (cytoplasmatic male sterility = CMS) des Rettichs auf verschiedene Kohlarten zu übertragen. Sie erleichtert die Züchtung von Hybriden, die mittlerweile auch im Öko-Landbau weit verbreitet sind - unverdientermaßen, aber das wäre ein weiteres Diskussionsthema..

Ribosome selectivity and nascent chain context in modulating the incorporation of fluorescent non-canonical amino acid into proteins

Fluorescence reporter groups are important tools to study the structure and dynamics of proteins. Genetic code reprogramming allows for cotranslational incorporation of non‑canonical amino acids at any desired position. However, cotranslational incorporation of bulky fluorescence reporter groups is technically challenging and usually inefficient. Here we analyze the bottlenecks for the cotranslational incorporation of NBD‑, BodipyFL‑ and Atto520‑labeled Cys‑tRNACys into a model protein using a reconstituted in‑vitro translation system. We show that the modified Cys‑tRNACys can be rejected during decoding due to the reduced ribosome selectivity for the modified aa‑tRNA and the competition with native near‑cognate aminoacyl‑tRNAs. Accommodation of the modified Cys‑tRNACys in the A site of the ribosome is also impaired, but can be rescued by one or several Gly residues at the positions −1 to −4 upstream of the incorporation site. The incorporation yield depends on the steric properties of the downstream residue and decreases with the distance from the protein N‑terminus to the incorporation site. In addition to the full‑length translation product, we find protein fragments corresponding to the truncated N‑terminal peptide and the C‑terminal fragment starting with a fluorescence‑labeled Cys arising from a StopGo‑like event due to a defect in peptide bond formation. The results are important for understanding the reasons for inefficient cotranslational protein labeling with bulky reporter groups and for designing new approaches to improve the yield of fluorescence‑ labeled protein

Deducing the kinetics of protein synthesis in vivo from the transition rates measured in vitro

The molecular machinery of life relies on complex multistep processes that involve numerous individual transitions, such as molecular association and dissociation steps, chemical reactions, and mechanical movements. The corresponding transition rates can be typically measured in vitro but not in vivo. Here, we develop a general method to deduce the in-vivo rates from their in-vitro values. The method has two basic components. First, we introduce the kinetic distance, a new concept by which we can quantitatively compare the kinetics of a multistep process in different environments. The kinetic distance depends logarithmically on the transition rates and can be interpreted in terms of the underlying free energy barriers. Second, we minimize the kinetic distance between the in-vitro and the in-vivo process, imposing the constraint that the deduced rates reproduce a known global property such as the overall in-vivo speed. In order to demonstrate the predictive power of our method, we apply it to protein synthesis by ribosomes, a key process of gene expression. We describe the latter process by a codon-specific Markov model with three reaction pathways, corresponding to the initial binding of cognate, near-cognate, and non-cognate tRNA, for which we determine all individual transition rates in vitro. We then predict the in-vivo rates by the constrained minimization procedure and validate these rates by three independent sets of in-vivo data, obtained for codon-dependent translation speeds, codon-specific translation dynamics, and missense error frequencies. In all cases, we find good agreement between theory and experiment without adjusting any fit parameter. The deduced in-vivo rates lead to smaller error frequencies than the known in-vitro rates, primarily by an improved initial selection of tRNA. The method introduced here is relatively simple from a computational point of view and can be applied to any biomolecular process, for which we have detailed information about the in-vitro kinetics

Atomic motion in tilted optical lattices

This paper presents a formalism describing the dynamics of a quantum particle in a one-dimensional, time-dependent, tilted lattice. The formalism uses the Wannier-Stark states, which are localized in each site of the lattice, and provides a simple framework allowing fully-analytical developments. Analytic solutions describing the particle motion are explicit derived, and the resulting dynamics is studied.Comment: 6 pages, 2 figs, submitted to EPJD, Springer Verlag styl

Different levels of context-specificity of teacher self-efficacy and their relations with teaching quality

On the basis of Bandura’s social cognitive theory, researchers often assume that a teachers’ self-efficacy (TSE) will have a positive effect on teaching quality. However, the available empirical evidence is mixed. Building on previous research into TSE, we examined whether assessing class-/task-specific TSE gives a more accurate indication of the associations between TSE assessments and student-rated teaching quality. The analyses were based on the English sample of the Teaching and Learning International Survey (TALIS) Video Study. Mathematics teachers (N = 86) rated their self-efficacy beliefs using generalized task-specific TSE items and class-/task-specific TSE items. Their students (N = 1,930) rated the quality of teaching in their math class. Multilevel regression analyses revealed stronger associations between student-rated teaching quality and class-/task-specific TSE than generalized task-specific TSE. We discuss possible reasons for these results and outline the potential benefits of using class-specific assessments for future TSE research

Classical chaos with Bose-Einstein condensates in tilted optical lattices

A widely accepted definition of ``quantum chaos'' is ``the behavior of a quantum system whose \emph{classical} \emph{limit is chaotic}''. The dynamics of quantum-chaotic systems is nevertheless very different from that of their classical counterparts. A fundamental reason for that is the linearity of Schr{\"o}dinger equation. In this paper, we study the quantum dynamics of an ultra-cold quantum degenerate gas in a tilted optical lattice and show that it displays features very close to \emph{classical} chaos. We show that its phase space is organized according to the Kolmogorov-Arnold-Moser theorem.Comment: 4 pages, 3 figure

Synonymous codons direct cotranslational folding toward different protein conformations.

In all genomes, most amino acids are encoded by more than one codon. Synonymous codons can modulate protein production and folding, but the mechanism connecting codon usage to protein homeostasis is not known. Here we show that synonymous codon variants in the gene encoding gamma-B crystallin, a mammalian eye-lens protein, modulate the rates of translation and cotranslational folding of protein domains monitored in real time by Forster resonance energy transfer and fluorescence-intensity changes. Gamma-B crystallins produced from mRNAs with changed codon bias have the same amino acid sequence but attain different conformations, as indicated by altered invivo stability and invitro protease resistance. 2D NMR spectroscopic data suggest that structural differences are associated with different cysteine oxidation states of the purified proteins, providing a link between translation, folding, and the structures of isolated proteins. Thus, synonymous codons provide a secondary code for protein folding in the cell

Wavepacket reconstruction via local dynamics in a parabolic lattice

We study the dynamics of a wavepacket in a potential formed by the sum of a periodic lattice and of a parabolic potential. The dynamics of the wavepacket is essentially a superposition of ``local Bloch oscillations'', whose frequency is proportional to the local slope of the parabolic potential. We show that the amplitude and the phase of the Fourier transform of a signal characterizing this dynamics contains information about the amplitude and the phase of the wavepacket at a given lattice site. Hence, {\em complete} reconstruction of the the wavepacket in the real space can be performed from the study of the dynamics of the system.Comment: 4 pages, 3 figures, RevTex