Evidence for symmetric chromosomal inversions around the replication origin in bacteria.

BackgroundWhole-genome comparisons can provide great insight into many aspects of biology. Until recently, however, comparisons were mainly possible only between distantly related species. Complete genome sequences are now becoming available from multiple sets of closely related strains or species.ResultsBy comparing the recently completed genome sequences of Vibrio cholerae, Streptococcus pneumoniae and Mycobacterium tuberculosis to those of closely related species - Escherichia coli, Streptococcus pyogenes and Mycobacterium leprae, respectively - we have identified an unusual and previously unobserved feature of bacterial genome structure. Scatterplots of the conserved sequences (both DNA and protein) between each pair of species produce a distinct X-shaped pattern, which we call an X-alignment. The key feature of these alignments is that they have symmetry around the replication origin and terminus; that is, the distance of a particular conserved feature (DNA or protein) from the replication origin (or terminus) is conserved between closely related pairs of species. Statistically significant X-alignments are also found within some genomes, indicating that there is symmetry about the replication origin for paralogous features as well.ConclusionsThe most likely mechanism of generation of X-alignments involves large chromosomal inversions that reverse the genomic sequence symmetrically around the origin of replication. The finding of these X-alignments between many pairs of species suggests that chromosomal inversions around the origin are a common feature of bacterial genome evolution

Efficient photon number detection with silicon avalanche photodiodes

We demonstrate an efficient photon number detector for visible wavelengths using a silicon avalanche photodiode. Under subnanosecond gating, the device is able to resolve up to four photons in an incident optical pulse. The detection efficiency at 600 nm is measured to be 73.8%, corresponding to an avalanche probability of 91.1% of the absorbed photons, with a dark count probability below 1.1x10^{-6} per gate. With this performance and operation close to room temperature, fast-gated silicon avalanche photodiodes are ideal for optical quantum information processing that requires single-shot photon number detection

Probing higher order correlations of the photon field with photon number resolving avalanche photodiodes

We demonstrate the use of two high speed avalanche photodiodes in exploring higher order photon correlations. By employing the photon number resolving capability of the photodiodes the response to higher order photon coincidences can be measured. As an example we show experimentally the sensitivity to higher order correlations for three types of photon sources with distinct photon statistics. This higher order correlation technique could be used as a low cost and compact tool for quantifying the degree of correlation of photon sources employed in quantum information science

A very brief introduction to quantum computing and quantum information theory for mathematicians

This is a very brief introduction to quantum computing and quantum information theory, primarily aimed at geometers. Beyond basic definitions and examples, I emphasize aspects of interest to geometers, especially connections with asymptotic representation theory. Proofs of most statements can be found in standard references

Shape-induced magnetic anisotropy in dilute magnetic alloys

We extend the theory of the surface-induced magnetic anisotropy to mesoscopic samples with arbitrary geometry. The shape-induced anisotropy of impurity spins in small brick-shaped grains of dilute magnetic alloys is studied in detail. The surface-induced blocking of a magnetic-impurity spin is shown to be very sensitive to geometric parameters of a grain. This implies that the apparent discrepancy between the experimental data of different groups on the size dependence of the Kondo resistivity can result from different microstructure of the used samples. In order to interpret recent experimental data on the anomalous Hall effect in thin polycrystalline Fe doped Au films, we analyse the magnetisation of impurity spins as a function of the impurity position and of the grain shape.Comment: 10 pages, 6 figures, E-mail addresses: [email protected], [email protected], [email protected]

Nanoimaging of Organic Charge Retention Effects: Implications for Nonvolatile Memory, Neuromorphic Computing, and High Dielectric Breakdown Devices

While a large variety of organic and molecular materials have been found to exhibit charge memory effects, the underlying mechanism is not well-understood, which hinders rational device design. Here, we study the charge retention mechanism of a nanoscale memory system, an organic monolayer on a silicon substrate, with Au nanoparticles on top serving as the electrical contact. Combining scanning probe imaging/manipulation and density functional simulations, we observe stable charge retention effects in the system and attributed it to polaron effects at the amine functional groups. Our findings can pave the way for applications in nonvolatile memory, neuromorphic computing, and high dielectric breakdown devices

Biological response to circulation driven by mean summertime winds off central Chile: A numerical model study

A coupled physical-biological model of the waters off central Chile is used to investigate the nitrogen-phytoplankton-zooplankton response to ocean circulation driven by mean summertime winds. The circulation drives the upwelling of middepth water onto the continental shelf and reaches a quasistable rate between days 40 and 60 of the simulation. High-nutrient, low-phytoplankton biomass water is upwelled at the coast, with nutrients being converted to phytoplankton within 3-10 days. A lagged response in zooplankton occurs after 6-30 days, by which time the water has been advected offshore. The magnitude and spatial distribution of phytoplankton biomass and export of organic matter off the continental shelf is sensitive to the zooplankton mortality term. For low zooplankton mortality, phytoplankton biomass on the continental shelf is limited by grazing pressure due to zooplankton, phytoplankton and zooplankton biomass remains low, and the nitrogen advected off the continental shelf in the surface waters is primarily dissolved inorganic nitrogen. When the mortality rate is increased fourfold, an approximately fourfold to fivefold increase is seen in the continental shelf phytoplankton biomass, phytoplankton productivity, and export of organic matter to the deep ocean. This dependence on zooplankton mortality illustrates the potential of top-down control of the shelf production and export of organic matter off the central Chile continental shelf. Copyright 2007 by the American Geophysical Union

The Drinfel'd twisted XYZ model

We construct a factorizing Drinfel'd twist for a face type model equivalent to the XYZ model. Completely symmetric expressions for the operators of the monodromy matrix are obtained.Comment: 15 pages, 4 figures, second preprint no. added, reference [14] added, typos correcte

Shearing Interferometer for Quantifying the Coherence of Hard X-Ray Beams

We report a quantitative measurement of the full transverse coherence function of the 14.4 keV x-ray radiation produced by an undulator at the Swiss Light Source. An x-ray grating interferometer consisting of a beam splitter phase grating and an analyzer amplitude grating has been used to measure the degree of coherence as a function of the beam separation out to 30 m. Importantly, the technique provides a model-free and spatially resolved measurement of the complex coherence function and is not restricted to high resolution detectors and small fields of view. The spatial characterization of the wave front has important applications in discovering localized defects in beam line optics

Looking back at superfluid helium

A few years after the discovery of Bose Einstein condensation in several gases, it is interesting to look back at some properties of superfluid helium. After a short historical review, I comment shortly on boiling and evaporation, then on the role of rotons and vortices in the existence of a critical velocity in superfluid helium. I finally discuss the existence of a condensate in a liquid with strong interactions, and the pressure variation of its superfluid transition temperature.Comment: Conference "Bose Einstein Condensation", Institut henri Poincare, Paris, 29 march 200