Decoherence spectroscopy with individual two-level tunneling defects

Recent progress with microfabricated quantum devices has revealed that an ubiquitous source of noise originates in tunneling material defects that give rise to a sparse bath of parasitic two-level systems (TLSs). For superconducting qubits, TLSs residing on electrode surfaces and in tunnel junctions account for a major part of decoherence and thus pose a serious roadblock to the realization of solid-state quantum processors. Here, we utilize a superconducting qubit to explore the quantum state evolution of coherently operated TLSs in order to shed new light on their individual properties and environmental interactions. We identify a frequency-dependence of TLS energy relaxation rates that can be explained by a coupling to phononic modes rather than by anticipated mutual TLS interactions. Most investigated TLSs are found to be free of pure dephasing at their energy degeneracy points, around which their Ramsey and spin-echo dephasing rates scale linearly and quadratically with asymmetry energy, respectively. We provide an explanation based on the standard tunneling model, and identify interaction with incoherent low-frequency (thermal) TLSs as the major mechanism of the pure dephasing in coherent high-frequency TLS.Comment: 6 pages, 3 figures, supplementary material availabl

Biocomputational prediction of non-coding RNAs in model cyanobacteria

<p>Abstract</p> <p>Background</p> <p>In bacteria, non-coding RNAs (ncRNA) are crucial regulators of gene expression, controlling various stress responses, virulence, and motility. Previous work revealed a relatively high number of ncRNAs in some marine cyanobacteria. However, for efficient genetic and biochemical analysis it would be desirable to identify a set of ncRNA candidate genes in model cyanobacteria that are easy to manipulate and for which extended mutant, transcriptomic and proteomic data sets are available.</p> <p>Results</p> <p>Here we have used comparative genome analysis for the biocomputational prediction of ncRNA genes and other sequence/structure-conserved elements in intergenic regions of the three unicellular model cyanobacteria <it>Synechocystis </it>PCC6803, <it>Synechococcus elongatus </it>PCC6301 and <it>Thermosynechococcus elongatus </it>BP1 plus the toxic <it>Microcystis aeruginosa </it>NIES843. The unfiltered numbers of predicted elements in these strains is 383, 168, 168, and 809, respectively, combined into 443 sequence clusters, whereas the numbers of individual elements with high support are 94, 56, 64, and 406, respectively. Removing also transposon-associated repeats, finally 78, 53, 42 and 168 sequences, respectively, are left belonging to 109 different clusters in the data set. Experimental analysis of selected ncRNA candidates in <it>Synechocystis </it>PCC6803 validated new ncRNAs originating from the <it>fabF-hoxH </it>and <it>apcC-prmA </it>intergenic spacers and three highly expressed ncRNAs belonging to the Yfr2 family of ncRNAs. Yfr2a promoter-<it>luxAB </it>fusions confirmed a very strong activity of this promoter and indicated a stimulation of expression if the cultures were exposed to elevated light intensities.</p> <p>Conclusion</p> <p>Comparison to entries in Rfam and experimental testing of selected ncRNA candidates in <it>Synechocystis </it>PCC6803 indicate a high reliability of the current prediction, despite some contamination by the high number of repetitive sequences in some of these species. In particular, we identified in the four species altogether 8 new ncRNA homologs belonging to the Yfr2 family of ncRNAs. Modelling of RNA secondary structures indicated two conserved single-stranded sequence motifs that might be involved in RNA-protein interactions or in the recognition of target RNAs. Since our analysis has been restricted to find ncRNA candidates with a reasonable high degree of conservation among these four cyanobacteria, there might be many more, requiring direct experimental approaches for their identification.</p

Conductance of the Single Electron Transistor for Arbitrary Tunneling Strength

We study the temperature and gate voltage dependence of the conductance of the single electron transistor focusing on highly conducting devices. Electron tunneling is treated nonperturbatively by means of path integral Monte Carlo techniques and the conductance is determined from the Kubo formula. A regularized singular value decomposition scheme is employed to calculate the conductance from imaginary time simulation data. Our findings are shown to bridge between available analytical results in the semiclassical and perturbative limits and are found to explain recent experimental results in a regime not accessible by earlier methods.Comment: 4 pages, 2 figure

Iodine Biofortification of Apples and Pears in an Orchard Using Foliar Sprays of Different Composition

Many people across the world suffer from iodine (I) deficiency and related diseases. The I content in plant-based foods is particularly low, but can be enhanced by agronomic biofortification. Therefore, in this study two field experiments were conducted under orchard conditions to assess the potential of I biofortification of apples and pears by foliar fertilization. Fruit trees were sprayed at various times during the growing season with solutions containing I in different concentrations and forms. In addition, tests were carried out to establish whether the effect of I sprays can be improved by co-application of potassium nitrate (KNO3) and sodium selenate (Na2SeO4). Iodine accumulation in apple and pear fruits was dose-dependent, with a stronger response to potassium iodide (KI) than potassium iodate (KIO3). In freshly harvested apple and pear fruits, 51% and 75% of the biofortified iodine was localized in the fruit peel, respectively. The remaining I was translocated into the fruit flesh, with a maximum of 3% reaching the core. Washing apples and pears with running deionized water reduced their I content by 14%. To achieve the targeted accumulation level of 50-100 μg I per 100 g fresh mass in washed and unpeeled fruits, foliar fertilization of 1.5 kg I per hectare and meter canopy height was required when KIO3 was applied. The addition of KNO3 and Na2SeO4 to I-containing spray solutions did not affect the I content in fruits. However, the application of KNO3 increased the total soluble solids content of the fruits by up to 1.0 °Brix compared to the control, and Na2SeO4 in the spray solution increased the fruit selenium (Se) content. Iodine sprays caused leaf necrosis, but without affecting the development and marketing quality of the fruits. Even after three months of cold storage, no adverse effects of I fertilization on general fruit characteristics were observed, however, I content of apples decreased by 20%

Iron Deprivation in Synechocystis : Inference of Pathways, Non-coding RNAs, and Regulatory Elements from Comprehensive Expression Profiling

Iron is an essential cofactor in many metabolic reactions. Mechanisms controlling iron homeostasis need to respond rapidly to changes in extracellular conditions, but they must also keep the concentration of intracellular iron under strict control to avoid the generation of damaging reactive oxygen species. Due to its role as a redox carrier in photosynthesis, the iron quota in cyanobacteria is about 10 times higher than in model enterobacteria. The molecular details of how such a high quota is regulated are obscure. Here we present experiments that shed light on the iron regulatory system in cyanobacteria. We measured time-resolved changes in gene expression after iron depletion in the cyanobacterium Synechocystis sp. PCC 6803 using a comprehensive microarray platform, monitoring both protein-coding and non-coding transcripts. In total, less than a fifth of all protein-coding genes were differentially expressed during the first 72 hr. Many of these proteins are associated with iron transport, photosynthesis, or ATP synthesis. Comparing our data with three previous studies, we identified a core set of 28 genes involved in iron stress response. Among them were genes important for assimilation of inorganic carbon, suggesting a link between the carbon and iron regulatory networks. Nine of the 28 genes have unknown functions and constitute key targets for further functional analysis. Statistical and clustering analyses identified 10 small RNAs, 62 antisense RNAs, four 59UTRs, and seven intragenic elements as potential novel components of the iron regulatory network in Synechocystis. Hence, our genome-wide expression profiling indicates an unprecedented complexity in the iron regulatory network of cyanobacteria.Portuguese Fundacao para a Ciencia e a Tecnologia (FCT) [PTDC/BIA-MIC/101036/2008]; Deutsche Forschungsgemeinschaft (DFG) Focus program "Sensory and regulatory RNAs in Prokaryotes [SPP1258]; FCT [PEst-OE/EQB/LA0023/2011]info:eu-repo/semantics/publishedVersio

High Temperature Conductance of the Single Electron Transistor

The linear conductance of the single electron transistor is determined in the high temperature limit. Electron tunneling is treated nonperturbatively by means of a path integral formulation and the conductance is obtained from Kubo's formula. The theoretical predictions are valid for arbitrary conductance and found to explain recent experimental data.Comment: 4 pages, 2 figure

Charge Fluctuations in the Single Electron Box

Quantum fluctuations of the charge in the single electron box are investigated. Based on a diagrammatic expansion we calculate the average island charge number and the effective charging energy in third order in the tunneling conductance. Near the degeneracy point where the energy of two charge states coincides, the perturbative approach fails, and we explicitly resum the leading logarithmic divergencies to all orders. The predictions for zero temperature are compared with Monte Carlo data and with recent renormalization group results. While good agreement between the third order result and numerical data justifies the perturbative approach in most of the parameter regime relevant experimentally, near the degeneracy point and at zero temperature the resummation is shown to be insufficient to describe strong tunneling effects quantitatively. We also determine the charge noise spectrum employing a projection operator technique. Former perturbative and semiclassical results are extended by the approach.Comment: 20 pages, 15 figure

Decoherence spectroscopy with individual two-level tunneling defects

Recent progress with microfabricated quantum devices has revealed that an ubiquitous source of noise originates in tunneling material defects that give rise to a sparse bath of parasitic two-level systems (TLSs). For superconducting qubits, TLSs residing on electrode surfaces and in tunnel junctions account for a major part of decoherence and thus pose a serious roadblock to the realization of solid-state quantum processors. Here, we utilize a superconducting qubit to explore the quantum state evolution of coherently operated TLSs in order to shed new light on their individual properties and environmental interactions. We identify a frequency-dependence of TLS energy relaxation rates that can be explained by a coupling to phononic modes rather than by anticipated mutual TLS interactions. Most investigated TLSs are found to be free of pure dephasing at their energy degeneracy points, around which their Ramsey and spin-echo dephasing rates scale linearly and quadratically with asymmetry energy, respectively. We provide an explanation based on the standard tunneling model, and identify interaction with incoherent low-frequency (thermal) TLSs as the major mechanism of the pure dephasing in coherent high-frequency TLS

Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1

Oxygenic photosynthesis crucially depends on proteins that possess Fe (2+) or Fe/S complexes as co-factors or prosthetic groups. Here, we show that the small regulatory RNA (sRNA) IsaR1 (Iron-Stress-Activated RNA 1) plays a pivotal role in acclimation to low-iron conditions. The IsaR1 regulon consists of more than 15 direct targets, including Fe (2+)-containing proteins involved in photosynthetic electron transfer, detoxification of anion radicals, citrate cycle, and tetrapyrrole biogenesis. IsaR1 is essential for maintaining physiological levels of Fe/S cluster biogenesis proteins during iron deprivation. Consequently, IsaR1 affects the acclimation of the photosynthetic apparatus to iron starvation at three levels: (1) directly, via posttranscriptional repression of gene expression; (2) indirectly, via suppression of pigment; and (3) Fe/S cluster biosynthesis. Homologs of IsaR1 are widely conserved throughout the cyanobacterial phylum. We conclude that IsaR1 is a critically important riboregulator. These findings provide a new perspective for understanding the regulation of iron homeostasis in photosynthetic organisms.German Federal Ministry of Education and Research [0316165]DFG [HE 2544/9-1]Academy of Finland [253269, 271832, 273870]Portuguese Fundacao para a Ciencia e a Tecnologia [IF/00881/2013, UID/Multi/04326/2013-CCMAR]European Commission FP7 Marie Curie Initial Training Network "Photo.COMM'' [317184]info:eu-repo/semantics/publishedVersio