LAF1, a MYB transcription activator for phytochrome A signaling

The photoreceptor phytochrome (phy) A has a well-defined role in regulating gene expression in response to specific light signals. Here, we describe a new Arabidopsis mutant, laf1 (long after far-red light 1) that has an elongated hypocotyl specifically under far-red light. Gene expression studies showed that laf1 has reduced responsiveness to continuous far-red light but retains wild-type responses to other light wavelengths. As far-red light is only perceived by phyA, our results suggest that LAF1 is specifically involved in phyA signal transduction. Further analyses revealed that laf1 is affected in a subset of phyA-dependent responses and the phenotype is more severe at low far-red fluence rates. LAF1 encodes a nuclear protein with strong homology with the R2R3-MYB family of DNA-binding proteins. Experiments using yeast cells identified a transactivation domain in the C-terminal portion of the protein. LAF1 is constitutively targeted to the nucleus by signals in its N-terminal portion, and the full-length protein accumulates in distinct nuclear speckles. This accumulation in speckles is abolished by a point mutation in a lysine residue (K258R), which might serve as a modification site by a small ubiquitin-like protein (SUMO)

Tilted and crossing vortex chains in layered superconductors

In the presence of the Josephson vortex lattice in layered superconductors, a small c-axis magnetic field penetrates in the form of vortex chains. In general, the structure of a single chain is determined by the ratio of the London [$\lambda$] and Josephson [$\lambda_{J}$] lengths, $\alpha= \lambda/\lambda_{J}$. The chain is composed of tilted vortices at large $\alpha$'s (tilted chain) and at small $\alpha$'s it consists of a crossing array of Josephson vortices and pancake-vortex stacks (crossing chain). We study chain structures at intermediate $\alpha$'s and found two types of phase transitions. For $\alpha\lesssim 0.6$ the ground state is given by the crossing chain in a wide range of pancake separations $a\gtrsim [2-3]\lambda_J$. However, due to attractive coupling between deformed pancake stacks, the equilibrium separation can not exceed some maximum value depending on the in-plane field and $\alpha$. The first phase transition takes place with decreasing pancake-stack separation $a$ at $a=[1-2]\lambda_{J}$, and rather wide range of the ratio $\alpha$, $0.4 \lesssim \alpha\lesssim 0.65$. With decreasing $a$, the crossing chain goes through intermediate strongly-deformed configurations and smoothly transforms into a tilted chain via a second-order phase transition. Another phase transition occurs at very small densities of pancake vortices, $a\sim [20-30]\lambda_J$, and only when $\alpha$ exceeds a certain critical value $\sim 0.5$. In this case a small c-axis field penetrates in the form of kinks. However, at very small concentration of kinks, the kinked chains are replaced with strongly deformed crossing chains via a first-order phase transition. This transition is accompanied by a very large jump in the pancake density.Comment: Proceeding of the NATO ARW "Vortex dynamics in superconductors and other complex systems", Yalta, Crimea, Ukraine, 13-17 September 2004, To be published in the Journ. of Low Temp. Phys., 16 pages, 6 figure

Vortex wandering in a forest of splayed columnar defects

We investigate the scaling properties of single flux lines in a random pinning landscape consisting of splayed columnar defects. Such correlated defects can be injected into Type II superconductors by inducing nuclear fission or via direct heavy ion irradiation. The result is often very efficient pinning of the vortices which gives, e.g., a strongly enhanced critical current. The wandering exponent \zeta and the free energy exponent \omega of a single flux line in such a disordered environment are obtained analytically from scaling arguments combined with extreme-value statistics. In contrast to the case of point disorder, where these exponents are universal, we find a dependence of the exponents on details in the probability distribution of the low lying energies of the columnar defects. The analytical results show excellent agreement with numerical transfer matrix calculations in two and three dimensions.Comment: 11 pages, 9 figure

Thermodynamics of Mesoscopic Vortex Systems in 1+1 Dimensions

The thermodynamics of a disordered planar vortex array is studied numerically using a new polynomial algorithm which circumvents slow glassy dynamics. Close to the glass transition, the anomalous vortex displacement is found to agree well with the prediction of the renormalization-group theory. Interesting behaviors such as the universal statistics of magnetic susceptibility variations are observed in both the dense and dilute regimes of this mesoscopic vortex system.Comment: 4 pages, REVTEX, 6 figures included. Comments and suggestions can be sent to [email protected]

Motional sidebands and direct measurement of the cooling rate in the resonance fluorescence of a single trapped ion

Resonance fluorescence of a single trapped ion is spectrally analyzed using a heterodyne technique. Motional sidebands due to the oscillation of the ion in the harmonic trap potential are observed in the fluorescence spectrum. From the width of the sidebands the cooling rate is obtained and found to be in agreement with the theoretical prediction.Comment: 4 pages, 4 figures. Final version after minor changes, 1 figure replaced; to be published in PRL, July 10, 200

Incommensuration Effects and Dynamics in Vortex Chains

We examine the motion of one-dimensional (1D) vortex matter embedded in a 2D vortex system with weak pinning using numerical simulations. We confirm the conjecture of Matsuda et al. [Science 294, 2136 (2001)] that the onset of the temperature induced motion of the chain is due to an incommensuration effect of the chain with the periodic potential created by the bulk vortices. In addition, under an applied driving force we find a two stage depinning transition, where the initial depinning of the vortex chain occurs through soliton like pulses. When an ac drive is added to the dc drive, we observe phase locking of the moving vortex chain.Comment: 4 pages, 4 postscript figure

Direct Repeat 6 from Human Herpesvirus-6B Encodes a Nuclear Protein that Forms a Complex with the Viral DNA Processivity Factor p41

The SalI-L fragment from human herpesvirus 6A (HHV-6A) encodes a protein DR7 that has been reported to produce fibrosarcomas when injected into nude mice, to transform NIH3T3 cells, and to interact with and inhibit the function of p53. The homologous gene in HHV-6B is dr6. Since p53 is deregulated in both HHV-6A and -6B, we characterized the expression of dr6 mRNA and the localization of the translated protein during HHV-6B infection of HCT116 cells. Expression of mRNA from dr6 was inhibited by cycloheximide and partly by phosphonoacetic acid, a known characteristic of herpesvirus early/late genes. DR6 could be detected as a nuclear protein at 24 hpi and accumulated to high levels at 48 and 72 hpi. DR6 located in dots resembling viral replication compartments. Furthermore, a novel interaction between DR6 and the viral DNA processivity factor, p41, could be detected by confocal microscopy and by co-immunoprecipitation analysis. In contrast, DR6 and p53 were found at distinct subcellular locations. Together, our data imply a novel function of DR6 during HHV-6B replication

Observation of Individual Josephson Vortices in YBCO Bicrystal Grain-boundary Junctions

The response of YBCO bicrystal grain-boundary junctions to small dc magnetic fields (0 - 10 Oe) has been probed with a low-power microwave (rf) signal of 4.4 GHz in a microwave-resonator setup. Peaks in the microwave loss at certain dc magnetic fields are observed that result from individual Josephson vortices penetrating into the grain-boundary junctions under study. The system is modeled as a long Josephson junction described by the sine-Gordon equation with the appropriate boundary conditions. Excellent quantitative agreement between the experimental data and the model has been obtained. Hysteresis effect of dc magnetic field is also studied and the results of measurement and calculation are compared.Comment: 11 pages, 4 figure

Workflow Engineering in Materials Design within the BATTERY 2030+Project

In recent years, modeling and simulation of materials have become indispensable to complement experiments in materials design. High-throughput simulations increasingly aid researchers in selecting the most promising materials for experimental studies or by providing insights inaccessible by experiment. However, this often requires multiple simulation tools to meet the modeling goal. As a result, methods and tools are needed to enable extensive-scale simulations with streamlined execution of all tasks within a complex simulation protocol, including the transfer and adaptation of data between calculations. These methods should allow rapid prototyping of new protocols and proper documentation of the process. Here an overview of the benefits and challenges of workflow engineering in virtual material design is presented. Furthermore, a selection of prominent scientific workflow frameworks used for the research in the BATTERY 2030+ project is presented. Their strengths and weaknesses as well as a selection of use cases in which workflow frameworks significantly contributed to the respective studies are discussed