Inferring mixed-layer depth variability from Argo observations in the western Indian Ocean

The seasonal and spatial variability of mixed layer depth (MLD) was examined in the Western Indian Ocean (WIO) (30E – 80E and 10S – 30N) for three consecutive years starting from June 2002 – May 2005 using Argo temperature and salinity (T/S) profiles. These were compared with MLD estimates from World Ocean Atlas 2001 (WOA01) T/S data. Temporal and spatial variability of MLD estimated from Argo T/S profiles were found to correspond well with the MLD obtained from WOA01 T/S data. However, slight deviations in the form of months of occurrence of minima and maxima MLDs were observed. MLD from WOA01 climatology is underestimated compared to MLD from Argo for almost the entire three years of study. It is also observed that MLD variability features as brought out by both the data sets followed the dynamics that govern the mixed layer variability in this region

Electric Dipole Moments and Polarizability in the Quark-Diquark Model of the Neutron

For a bound state internal wave function respecting parity symmetry, it can be rigorously argued that the mean electric dipole moment must be strictly zero. Thus, both the neutron, viewed as a bound state of three quarks, and the water molecule, viewed as a bound state of ten electrons two protons and an oxygen nucleus, both have zero mean electric dipole moments. Yet, the water molecule is said to have a nonzero dipole moment strength $d=e\Lambda$ with $\Lambda_{H_2O} \approx 0.385\ \dot{A}$. The neutron may also be said to have an electric dipole moment strength with $\Lambda_{neutron} \approx 0.612\ fm$. The neutron analysis can be made experimentally consistent, if one employs a quark-diquark model of neutron structure.Comment: four pages, two figure

Rate-dependent phase transformations in nanoindented germanium

There is considerable controversy over the deformation behavior of germanium(Ge) under nanoindentation using a sharp diamond tip, with a diverse range of observations that suggest competing mechanisms. Here we show the deformation mechanism of Ge can be controlled by the rate of applied load. Loading rate is varied over three orders of magnitude using depth-sensing nanoindentation. At slow loading rates, shear-induced plasticity is observed. At rapid loading rates (>100 mN s¯¹), pressure-induced phase transformations are detected by ex situ micro-Raman spectroscopy and transmission electron microscopy. This switch in the deformation mechanism is due to the differing rate sensitivities of the respective deformation modes, shear-induced plasticity or pressure-induced phase transformation

Asymptotic Infrared Fractal Structure of the Propagator for a Charged Fermion

It is well known that the long-range nature of the Coulomb interaction makes the definition of asymptotic ``in'' and ``out'' states of charged particles problematic in quantum field theory. In particular, the notion of a simple particle pole in the vacuum charged particle propagator is untenable and should be replaced by a more complicated branch cut structure describing an electron interacting with a possibly infinite number of soft photons. Previous work suggests a Dirac propagator raised to a fractional power dependent upon the fine structure constant, however the exponent has not been calculated in a unique gauge invariant manner. It has even been suggested that the fractal ``anomalous dimension'' can be removed by a gauge transformation. Here, a gauge invariant non-perturbative calculation will be discussed yielding an unambiguous fractional exponent. The closely analogous case of soft graviton exponents is also briefly explored.Comment: Updated with a corrected sign error, longer discussion of fractal dimension, and more reference

Enhancing Acceleration Radiation from Ground-State Atoms via Cavity Quantum Electrodynamics

When ground state atoms are accelerated through a high Q microwave cavity, radiation is produced with an intensity which can exceed the intensity of Unruh acceleration radiation in free space by many orders of magnitude. The cavity field at steady state is described by a thermal density matrix under most conditions. However, under some conditions gain is possible, and when the atoms are injected in a regular fashion, the radiation can be produced in a squeezed state

Water in HD 209458b's atmosphere from 3.6 - 8 microns IRAC photometric observations in primary transit

The hot Jupiter HD 209458b was observed during primary transit at 3.6, 4.5, 5.8 and 8.0 microns using the Infrared Array Camera (IRAC) on the Spitzer Space Telescope. We detail here the procedures we adopted to correct for the systematic trends present in the IRAC data. The light curves were fitted including limb darkening effects and fitted using Markov Chain Monte Carlo and prayer-bead Monte Carlo techniques, finding almost identical results. The final depth measurements obtained by a combined Markov Chain Monte Carlo fit are at 3.6 microns, 1.469 +- 0.013 % and 1.448 +- 0.013 %; at 4.5 microns, 1.478 +- 0.017 % ; at 5.8 microns, 1.549 +- 0.015 % and at 8.0 microns 1.535 +- 0.011 %. Our results clearly indicate the presence of water in the planetary atmosphere. Our broad band photometric measurements with IRAC prevent us from determining the additional presence of other other molecules such as CO, CO2 and methane for which spectroscopy is needed. While water vapour with a mixing ratio of 10^-4-10^-3 combined with thermal profiles retrieved from the day-side may provide a very good fit to our observations, this data set alone is unable to resolve completely the degeneracy between water abundance and atmospheric thermal profile.Comment: 14 pages, 6 tables, 10 figures, Accepted for publication in MNRA

Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

Most recent initiatives to sequence and assemble new species’ genomes de-novo fail to achieve the ultimate endpoint to produce a series of contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of sub-chromosomal sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, scaffold verification by PCR and physical mapping to chromosomes. Multi genome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffold loci to chromosomes on all avian genomes. As proof of principle we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome level comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food and/or environmental reasons. Pigeon has a typical avian karyotype (2n=80) while falcon (2n=50) is highly rearranged compared to the avian ancestor. Using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved non-coding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts”. This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species while the overall strategy for scaffold assembly and mapping provides the basis for an approach that could be applied to any animal genome

Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors

Nonlinear control techniques by means of a software sensor that are commonly used in chemical engineering could be also applied to genetic regulation processes. We provide here a realistic formulation of this procedure by introducing an additive white Gaussian noise, which is usually found in experimental data. Besides, we include model errors, meaning that we assume we do not know the nonlinear regulation function of the process. In order to illustrate this procedure, we employ the Goodwin dynamics of the concentrations [B.C. Goodwin, Temporal Oscillations in Cells, (Academic Press, New York, 1963)] in the simple form recently applied to single gene systems and some operon cases [H. De Jong, J. Comp. Biol. 9, 67 (2002)], which involves the dynamics of the mRNA, given protein, and metabolite concentrations. Further, we present results for a three gene case in co-regulated sets of transcription units as they occur in prokaryotes. However, instead of considering their full dynamics, we use only the data of the metabolites and a designed software sensor. We also show, more generally, that it is possible to rebuild the complete set of nonmeasured concentrations despite the uncertainties in the regulation function or, even more, in the case of not knowing the mRNA dynamics. In addition, the rebuilding of concentrations is not affected by the perturbation due to the additive white Gaussian noise and also we managed to filter the noisy output of the biological systemComment: 21 pages, 7 figures; also selected in vjbio of August 2005; this version corrects a misorder in the last three references of the published versio