SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

doi:10.1093/nar/gkn23

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank

The RCSB Protein Data Bank (RCSB PDB, www.pdb.org) is a key online resource for structural biology and related scientific disciplines. The website is used on average by 165 000 unique visitors per month, and more than 2000 other websites link to it. The amount and complexity of PDB data as well as the expectations on its usage are growing rapidly. Therefore, ensuring the reliability and robustness of the RCSB PDB query and distribution systems are crucially important and increasingly challenging. This article describes quality assurance for the RCSB PDB website at several distinct levels, including: (i) hardware redundancy and failover, (ii) testing protocols for weekly database updates, (iii) testing and release procedures for major software updates and (iv) miscellaneous monitoring and troubleshooting tools and practices. As such it provides suggestions for how other websites might be operated

Real time approach to tunneling in open quantum systems: decoherence and anomalous diffusion

Macroscopic quantum tunneling is described using the master equation for the reduced Wigner function of an open quantum system at zero temperature. Our model consists of a particle trapped in a cubic potential interacting with an environment characterized by dissipative and normal and anomalous diffusion coefficients. A representation based on the energy eigenfunctions of the isolated system, i.e. the system uncoupled to the environment, is used to write the reduced Wigner function, and the master equation becomes simpler in that representation. The energy eigenfunctions computed in a WKB approximation incorporate the tunneling effect of the isolated system and the effect of the environment is described by an equation that it is in many ways similar to a Fokker-Planck equation. Decoherence is easily identified from the master equation and we find that when the decoherence time is much shorter than the tunneling time the master equation can be approximated by a Kramers like equation describing thermal activation due to the zero point fluctuations of the quantum environment. The effect of anomalous diffusion can be dealt with perturbatively and its overall effect is to inhibit tunneling.Comment: 25 pages, 1 figur

Producing and Detecting Correlated atoms

We discuss experiments to produce and detect atom correlations in a degenerate or nearly degenerate gas of neutral atoms. First we treat the atomic analog of the celebrated Hanbury Brown Twiss experiment, in which atom correlations result simply from interference effects without any atom interactions.We have performed this experiment for both bosons and fermions. Next we show how atom interactions produce correlated atoms using the atomic analog of spontaneous four-wavemixing. Finally, we briefly mention experiments on a one dimensional gas on an atom chip in which correlation effects due to both interference and interactions have been observed.Comment: to appear in conference proceedings "Atomic Physics 20

Far-infrared observations of IRC + 10216

Broad-band photometric observations of IRC + 10216 in five wavelength intervals from 50 to 1000 μ are reported. The observed radiation is interpreted as thermal emission from dust in the extended molecular cloud heated by the compact 2-20 μ source as the core of the cloud. The shape of the 50-1000 μ spectrum suggests that the emissivity of the dust particles varies approximately as λ^(-1) over this spectral interval. The mass of dust inferred from the far-infrared emission is comparable with the mass of heavy molecules in the cloud

ValiDichro: a website for validating and quality control of protein circular dichroism spectra

Circular dichroism (CD) spectroscopy is widely used in structural biology as a technique for examining the structure, folding and conformational changes of proteins. A new server, ValiDichro, has been developed for checking the quality and validity of CD spectral data and metadata, both as an aid to data collection and processing and as a validation procedure for spectra to be included in publications. ValiDichro currently includes 25 tests for data completeness, consistency and quality. For each test that is done, not only is a validation report produced, but the user is also provided with suggestions for correcting or improving the data. The ValiDichro server is freely available at http://valispec.cryst.bbk.ac.uk/circularDichroism/ValiDichro/upload.html

Not Just Efficiency: Insolvency Law in the EU and Its Political Dimension

Certain insolvency law rules, like creditors’ priorities and set-off rights, have a distributive impact on creditors. Distributional rules reflect the hierarchies of values and interests in each jurisdiction and, as a result, have high political relevance and pose an obstacle to reforming the EU Insolvency Regulation. This paper will show the difficulty of reform by addressing two alternative options to regulate cross-border insolvencies in the European Union. The first one is the ‘choice model’, under which companies can select the insolvency law they prefer. Although such a model would allow distressed firms to select the most efficient insolvency law, it would also displace Member States’ power to protect local constituencies. The choice model therefore produces negative externalities and raises legitimacy concerns. The opposite solution is full harmonisation of insolvency law at EU level, including distributional rules. Full harmonisation would have the advantage of internalising all externalities produced by cross-border insolvencies. However, the EU legislative process, which is still based on negotiations between states, is not apt to decide on distributive insolvency rules; additionally, if harmonisation includes such rules, it will indirectly modify national social security strategies and equilibria. This debate shows that the choice regarding power allocation over bankruptcies in the EU depends on the progress of European integration and is mainly a matter of political legitimacy, not only of efficiency

Order alpha^3 ln(1/alpha) Corrections to Positronium Decays

The logarithmically enhanced alpha^3 ln(1/alpha) corrections to the para- and orthopositronium decay widths are calculated in the framework of dimensionally regularized nonrelativistic quantum electrodynamics.In the case of parapositronium, the correction is negative, approximately doubles the effect of the leading logarithmic alpha^3 ln^2(1/alpha) one, and is comparable to the nonlogarithmic O(alpha^2) one. As for orthopositronium, the correction is positive and almost cancels the alpha^3 ln^2(1/alpha) one. The uncertainties in the theoretical predictions for the decay widths are reduced.Comment: 10 pages (Latex); missing term added, corrected coefficient B_p used, numerical results insignificantly change

Oxygen impurities in NiAl: Relaxation effects

We have used a full-potential linear muffin-tin orbital method to calculate the effects of oxygen impurities on the electronic structure of NiAl. Using the supercell method with a 16-atom supercell we have investigated the cases where an oxygen atom is substitutionally placed at either a nickel or an aluminum site. Full relaxation of the atoms within the supercell was allowed. We found that oxygen prefers to occupy a nickel site over an aluminum site with a site selection energy of 138 mRy (21,370 K). An oxygen atom placed at an aluminum site is found to cause a substantial relaxation of its nickel neighbors away from it. In contrast, this steric repulsion is hardly present when the oxygen atom occupies the nickel site and is surrounded by aluminum neighbors. We comment on the possible relation of this effect to the pesting degradation phenomenon (essentially spontaneous disintegration in air) in nickel aluminides.Comment: To appear in Phys. Rev. B (Aug. 15, 2001