Tunneling Spectroscopy of Two-level Systems Inside Josephson Junction

We consider a two-level (TL) system with energy level separation Omega_0 inside a Josephson junction. The junction is shunted by a resistor R and is current I (or voltage V = RI) biased. If the TL system modulates the Josephson energy and/or is optically active, it is Rabi driven by the Josephson oscillations in the running phase regime near the resonance 2eV = Omega_0. The Rabi oscillations, in turn, translate into oscillations of current and voltage which can be detected in noise measurements. This effect provides an option to fully characterize the TL systems and to find the TL's contribution to the decoherence when the junction is used as a qubit.Comment: 4 page

Incommensurate Magnetism around Vortices and Impurities in High-TcT_c Superconductors

By solving self-consistently an effective Hamiltonian including interactions for both antiferromagnetic spin-density wave (SDW) and d-wave superconducting (DSC) orderings, a comparison study is made for the local magnetic structure around superconducting vortices and unitary impurities. To represent the optimally doped regime of cuprates, the parameter values are chosen such that the DSC is dominant while the SDW is vanishingly small. We show that when vortices are introduced into the superconductor, an oscillating SDW is induced around them. The oscillation period of the SDW is microscopically found, consistent with experiments, to be eight lattice constants ($8a_0$). The associated charge-density wave (CDW) oscillates with a period of one half ($4a_0$) of the SDW. In the case of unitary impurities, we find a SDW modulation with identical periodicity, however without an associated CDW. We propose neutron scattering experiments to test this prediction.Comment: 5 pages, 4 eps figures (color) included in the tex

Measurement of energy eigenstates by a slow detector

We propose a method for a weak continuous measurement of the energy eigenstates of a fast quantum system by means of a "slow" detector. Such a detector is only sensitive to slowly-changing variables, e. g. energy, while its back-action can be limited solely to decoherence of the eigenstate superpositions. We apply this scheme to the problem of detection of quantum jumps between energy eigenstates in a harmonic oscillator.Comment: 4 page

Characterization of InGaN and InAlN epilayers by microdiffraction X-Ray reciprocal space mapping

We report a study of InGaN and InAlN epilayers grown on GaN/Sapphire substrates by microfocused three-dimensional X-ray Reciprocal Space Mapping (RSM). The analysis of the full volume of reciprocal space, while probing samples on the microscale with a focused X-ray beam, allows us to gain uniquely valuable information about the microstructure of III-N alloy epilayers. It is found that “seed” InGaN mosaic nanocrystallites are twisted with respect to the ensemble average and strain free. This indicates that the growth of InGaN epilayers follows the Volmer-Weber mechanism with nucleation of “seeds” on strain fields generated by the a-type dislocations which are responsible for the twist of underlying GaN mosaic blocks. In the case of InAlN epilayer formation of composition gradient was observed at the beginning of the epitaxial growth

Evaluating Maintainability Prejudices with a Large-Scale Study of Open-Source Projects

Exaggeration or context changes can render maintainability experience into prejudice. For example, JavaScript is often seen as least elegant language and hence of lowest maintainability. Such prejudice should not guide decisions without prior empirical validation. We formulated 10 hypotheses about maintainability based on prejudices and test them in a large set of open-source projects (6,897 GitHub repositories, 402 million lines, 5 programming languages). We operationalize maintainability with five static analysis metrics. We found that JavaScript code is not worse than other code, Java code shows higher maintainability than C# code and C code has longer methods than other code. The quality of interface documentation is better in Java code than in other code. Code developed by teams is not of higher and large code bases not of lower maintainability. Projects with high maintainability are not more popular or more often forked. Overall, most hypotheses are not supported by open-source data.Comment: 20 page

4p states and X-Ray Spectroscopy

The 4p states in transition metals and their compounds usually play minor roles on their physical quantities. Recent development of resonant x-ray scattering (RXS) at the K-edge of transition metals, however, casts light on the 4p states, because the signals on orbital and magnetic superlattice spots are brought about by the modulation in the 4p states. The 4p states are extending in solids and thereby sensitive to electronic states at neighboring sites. This characteristic determines the mechanism of RXS that the intensity on the orbital superlattice spots are mainly generated by the lattice distortion and those on magnetic superlattice spots by the coupling of the 4p states with the orbital polarization in the 3d states at neighboring sites. Taking up typical examples for orbital and magnetic RXS, we demonstrate these mechanisms on the basis of the band structure calculation. Finally, we study the MCD spectra at the K-edge, demonstrating that the same mechanism as the magnetic RXS is working.Comment: 9 pages, 9 figures, submitted to Physica Scripta (comment

Stretching single polysaccharide molecules using AFM: A potential method for the investigation of the intermolecular uronate distribution of alginate?

Illustrative examples of the way in which the molecular force-extension behaviour of polysaccharides is governed by the nature of the linkage between their constituent pyranose rings are presented for a series of standard homopolymers. These results agree with previously proposed general hypotheses regarding the possibility of generating force-induced conformational transitions, and with the predictions of a model in which the inter-conversion of pyranose conformers is assumed to be an equilibrium process on the timescale of the molecular stretching. Subsequently, we investigate the potential of the technique in the characterisation of co-polymeric polysaccharides in which the nature of the glycan linkages is different between the two distinct residue types. Specifically, we explore the possibility that the ratio of mannuronic acid (M) to guluronic acid (G) in alginate chains will be reflected in their single molecule stretching behaviour, owing to their contrasting equatorial and axial linkages. Furthermore, as the technique described interrogates the sample one polymer at a time we outline the promise of, and the obstacles to, obtaining a new level of characterisation using this methodology where differences observed in the single molecule stretching curves obtained from single alginate samples reflectsomething of the real intermolecular distribution of the M / G ratio

Identification and correction of systematic error in high-throughput sequence data

A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisances to major problems affecting biological inferences. Recently developed “next-gen” sequencing technologies have greatly reduced the cost of sequencing, but have been shown to be more error prone than previous technologies. Both position specific (depending on the location in the read) and sequence specific (depending on the sequence in the read) errors have been identified in Illumina and Life Technology sequencing platforms. We describe a new type of _systematic_ error that manifests as statistically unlikely accumulations of errors at specific genome (or transcriptome) locations. We characterize and describe systematic errors using overlapping paired reads form high-coverage data. We show that such errors occur in approximately 1 in 1000 base pairs, and that quality scores at systematic error sites do not account for the extent of errors. We identify motifs that are frequent at systematic error sites, and describe a classifier that distinguishes heterozygous sites from systematic error. Our classifier is designed to accommodate data from experiments in which the allele frequencies at heterozygous sites are not necessarily 0.5 (such as in the case of RNA-Seq). Systematic errors can easily be mistaken for heterozygous sites in individuals, or for SNPs in population analyses. Systematic errors are particularly problematic in low coverage experiments, or in estimates of allele-specific expression from RNA-Seq data. Our characterization of systematic error has allowed us to develop a program, called SysCall, for identifying and correcting such errors. We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments