The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

Scalar dissipation rate transport in the corrugated flamelets and thin reaction zones regime for turbulent premixed flames

The characteristics of the scalar dissipation rate transport in the corrugated flamelets and the thin reaction zones regimes are studied based on two three-dimensional Direct Numerical Simulation (DNS) databases for freely propagating statistically planar turbulent premixed flames. The turbulent flame parameters are so chosen that the database which represents the corrugated flamelets regime has a global Damköhler number Da>1 whereas the database representing the thin reaction zones regime has Da <1. It is demonstrated that the terms originating from the correlation between fluctuating velocity and scalar gradient T1 shows strong Da dependence. The terms originating from dilatation T2, the scalar inner product of gradients of velocity and scalar fields T3 and the correlation between reaction rate and scalar gradients T4 and the dissipation term D2 remain important for both the flames. However, T3 dissipates scalar dissipation rate in the Da > 1 flame while it produces scalar dissipation rate in the Da < 1 flame. This difference is because of the change in the alignment between scalar and velocity gradients

A priori assessment of algebraic flame surface density models in the context of large eddy simulation for nonunity lewis number flames in the thin reaction zones regime

The performance of algebraic flame surface density (FSD) models has been assessed for flames with nonunity Lewis number (Le) in the thin reaction zones regime, using a direct numerical simulation (DNS) database of freely propagating turbulent premixed flames with Le ranging from 0.34 to 1.2. The focus is on algebraic FSD models based on a power-law approach, and the effects of Lewis number on the fractal dimension D and inner cut-off scale η i have been studied in detail. It has been found that D is strongly affected by Lewis number and increases significantly with decreasing Le. By contrast, η i remains close to the laminar flame thermal thickness for all values of Le considered here. A parameterisation of D is proposed such that the effects of Lewis number are explicitly accounted for. The new parameterisation is used to propose a new algebraic model for FSD. The performance of the new model is assessed with respect to results for the generalised FSD obtained from explicitly LES-filtered DNS data. It has been found that the performance of the most existing models deteriorates with decreasing Lewis number, while the newly proposed model is found to perform as well or better than the most existing algebraic models for FSD. © 2012 Mohit Katragadda et al.

Effects of turbulent reynolds number on the performance of algebraic flame surface density models for large eddy simulation in the thin reaction zones regime: A direct numerical simulation analysis

A direct numerical simulation (DNS) database of freely propagating statistically planar turbulent premixed flames with a range of different turbulent Reynolds numbers has been used to assess the performance of algebraic flame surface density (FSD) models based on a fractal representation of the flame wrinkling factor. The turbulent Reynolds number Ret has been varied by modifying the Karlovitz number Ka and the Damköhler number Da independently of each other in such a way that the flames remain within the thin reaction zones regime. It has been found that the turbulent Reynolds number and the Karlovitz number both have a significant influence on the fractal dimension, which is found to increase with increasing Ret and Ka before reaching an asymptotic value for large values of Ret and Ka. A parameterisation of the fractal dimension is presented in which the effects of the Reynolds and the Karlovitz numbers are explicitly taken into account. By contrast, the inner cut-off scale normalised by the Zel'dovich flame thickness ηi/δz does not exhibit any significant dependence on Ret for the cases considered here. The performance of several algebraic FSD models has been assessed based on various criteria. Most of the algebraic models show a deterioration in performance with increasing the LES filter width. © 2012 Mohit Katragadda et al.

Near-field characterization of chemical vapor deposition graphene in the microwave regime

Near-field measurements were performed at X-band frequencies for graphene on copper microstrip transmission lines. An improvement in radiation of 0.88 dB at 10.2 GHz is exhibited from the monolayer graphene antenna which has dc sheet resistivity of 985 Ω/sq. Emission characteristics were validated via ab initio simulations and compared to empirical findings of geometrically comparable copper patches. This study contributes to the current knowledge of the electronic properties of graphene. © 2013 AIP Publishing LLC.

The breakdown of the viscous regime in riblets

We investigate the mechanisms involved in the breakdown of the viscous regime in riblets, with a view to determining the point of optimum performance, where drag reduction ceases to be proportional to the riblet size. This occurs empirically for a groove cross-section $A_g^+ \approx 120^+$. To study the interaction of the riblets with the overlaying turbulent flow, we systematically conduct DNSes in a ribbed turbulent channel with increasing riblet size. The conditionally averaged crossflow above and within the grooves reveals a mean recirculation bubble that exists up to the point of viscous breakdown, isolating the groove floor from the overlying crossflow, and preventing the high momentum fluid from entering the grooves. We do not find evidence of outside vortices lodging within the grooves until $A_g^+ \approx 400$, which is well past the drag minimum, and already into the drag increasing regime. Interestingly, as the bubble breaks down, we observe that quasi-two-dimensional spanwise structures form just above the riblets, similar to those observed above porous surfaces and plant canopies, which appear to be involved in the performance degradation.

Instability of the steady-state regime of generation in laser diodes with a broad gain spectrum

The laser-diode parameters at which the steady-state regime of generation becomes unstable are analyzed within the framework of the mode-locking model. The crucial role of the transverse inhomogeneity of the field, pumping intensity, and spectrum width in developing the instabilities of the steady-state regime of generation is demonstrated. The calculated values of the instability threshold are shown to be consistent with the experimental results. © 2008 Springer Science+Business Media, Inc.

Locally oxidized silicon surface-plasmon Schottky detector for telecom regime.

We experimentally demonstrate an on-chip nanoscale silicon surface-plasmon Schottky photodetector based on internal photoemission process and operating at telecom wavelengths. The device is fabricated using a self-aligned approach of local-oxidation of silicon (LOCOS) on silicon on insulator substrate, which provides compatibility with standard complementary metal-oxide semiconductor technology and enables the realization of the photodetector and low-loss bus photonic waveguide at the same fabrication step. Additionally, LOCOS technique allows avoiding lateral misalignment between the silicon surface and the metal layer to form a nanoscale Schottky contact. The fabricated devices showed enhanced detection capability for shorter wavelengths that is attributed to increased probability of the internal photoemission process. We found the responsivity of the nanodetector to be 0.25 and 13.3 mA/W for incident optical wavelengths of 1.55 and 1.31 μm, respectively. The presented device can be integrated with other nanophotonic and nanoplasmonic structures for the realization of monolithic opto-electronic circuitry on-chip.

Plasmonic graded-index planar lens based on subwavelength features in the effective index regime

We experimentally demonstrate the planar focusing of Surface Plasmon Polaritons using space variant PMMA subwavelength features on top of a metallic film. Focusing is obtained by creating an effective graded refractive index profile. © 2012 OSA.