Order N photonic band structures for metals and other dispersive materials

We show, for the first time, how to calculate photonic band structures for metals and other dispersive systems using an efficient Order N scheme. The method is applied to two simple periodic metallic systems where it gives results in close agreement with calculations made with other techniques. Further, the approach demonstrates excellent numerical stablity within the limits we give. Our new method opens the way for efficient calculations on complex structures containing a whole new class of material.Comment: Four pages, plus seven postscript figures. Submitted to Physical Review Letter

Three-Dimensional FDTD Simulation of Biomaterial Exposure to Electromagnetic Nanopulses

Ultra-wideband (UWB) electromagnetic pulses of nanosecond duration, or nanopulses, have been recently approved by the Federal Communications Commission for a number of various applications. They are also being explored for applications in biotechnology and medicine. The simulation of the propagation of a nanopulse through biological matter, previously performed using a two-dimensional finite difference-time domain method (FDTD), has been extended here into a full three-dimensional computation. To account for the UWB frequency range, a geometrical resolution of the exposed sample was $0.25 mm$, and the dielectric properties of biological matter were accurately described in terms of the Debye model. The results obtained from three-dimensional computation support the previously obtained results: the electromagnetic field inside a biological tissue depends on the incident pulse rise time and width, with increased importance of the rise time as the conductivity increases; no thermal effects are possible for the low pulse repetition rates, supported by recent experiments. New results show that the dielectric sample exposed to nanopulses behaves as a dielectric resonator. For a sample in a cuvette, we obtained the dominant resonant frequency and the $Q$-factor of the resonator.Comment: 15 pages, 8 figure

First radial velocity results from the MINiature Exoplanet Radial Velocity Array (MINERVA)

The MINiature Exoplanet Radial Velocity Array (MINERVA) is a dedicated observatory of four 0.7m robotic telescopes fiber-fed to a KiwiSpec spectrograph. The MINERVA mission is to discover super-Earths in the habitable zones of nearby stars. This can be accomplished with MINERVA's unique combination of high precision and high cadence over long time periods. In this work, we detail changes to the MINERVA facility that have occurred since our previous paper. We then describe MINERVA's robotic control software, the process by which we perform 1D spectral extraction, and our forward modeling Doppler pipeline. In the process of improving our forward modeling procedure, we found that our spectrograph's intrinsic instrumental profile is stable for at least nine months. Because of that, we characterized our instrumental profile with a time-independent, cubic spline function based on the profile in the cross dispersion direction, with which we achieved a radial velocity precision similar to using a conventional "sum-of-Gaussians" instrumental profile: 1.8 m s$^{-1}$ over 1.5 months on the RV standard star HD 122064. Therefore, we conclude that the instrumental profile need not be perfectly accurate as long as it is stable. In addition, we observed 51 Peg and our results are consistent with the literature, confirming our spectrograph and Doppler pipeline are producing accurate and precise radial velocities.Comment: 22 pages, 9 figures, submitted to PASP, Peer-Reviewed and Accepte

Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers

Small molecule splicing modifiers have been previously described that target the general splicing machinery and thus have low specificity for individual genes. Several potent molecules correcting the splicing deficit of the SMN2 (survival of motor neuron 2) gene have been identified and these molecules are moving towards a potential therapy for spinal muscular atrophy (SMA). Here by using a combination of RNA splicing, transcription, and protein chemistry techniques, we show that these molecules directly bind to two distinct sites of the SMN2 pre-mRNA, thereby stabilizing a yet unidentified ribonucleoprotein (RNP) complex that is critical to the specificity of these small molecules for SMN2 over other genes. In addition to the therapeutic potential of these molecules for treatment of SMA, our work has wide-ranging implications in understanding how small molecules can interact with specific quaternary RNA structures

Electro-thermal modelling for plasmonic structures in the TLM Method

This paper presents a coupled electromagnetic-thermal model for modelling temperature evolution in nano-size plasmonic heat sources. Both electromagnetic and thermal models are based on the Transmission Line Modelling (TLM) method and are coupled through a nonlinear and dispersive plasma material model. The stability and accuracy of the coupled EM-thermal model is analysed in the context of a nano-tip plasmonic heat source example

Rigorous analysis of numerical methods: a comparative study

For any photonic device simulation, the accuracy of the numerical solution not only depends on the methods being used but also on the discretization parameters used in that numerical method. In this work, Finite Element Method and Finite Difference Time Domain Method based on Maxwell’s equations were used to simulate optical waveguides and directional couplers. As the solution accuracy may also depend on the index contrast used in such photonic devices, the characteristics of low-index contrast Germanium doped Silica and high-index contrast Silicon Nanowire Waveguides were analyzed, evaluated and benchmarked. Numerical results to benchmark Directional Couplers are also reported in this paper

Atypical activation of the G protein Gα by the oncogenic mutation Q209P

The causative role of G protein-coupled receptor (GPCR) pathway mutations in uveal melanoma (UM) has been well-established. Nearly all UMs bear an activating mutation in a GPCR pathway mediated by G proteins of the G family, driving tumor initiation and possibly metastatic progression. Thus, targeting this pathway holds therapeutic promise for managing UM. However, direct targeting of oncogenic Gα mutants, present in ∼90% of UMs, is complicated by the belief that these mutants structurally resemble active Gα WT. This notion is solidly founded on previous studies characterizing Gα mutants in which a conserved catalytic glutamine (Gln-209 in Gα) is replaced by leucine, which leads to GTPase function deficiency and constitutive activation. Whereas Q209L accounts for approximately half of GNAQ mutations in UM, Q209P is as frequent as Q209L and also promotes oncogenesis, but has not been characterized at the molecular level. Here, we characterized the biochemical and signaling properties of Gα Q209P and found that it is also GTPase-deficient and activates downstream signaling as efficiently as Gα Q209L. However, Gα Q209P had distinct molecular and functional features, including in the switch II region of Gα Q209P, which adopted a conformation different from that of Gα Q209L or active WT Gα, resulting in altered binding to effectors, Gβγ, and regulators of G-protein signaling (RGS) proteins. Our findings reveal that the molecular properties of Gα Q209P are fundamentally different from those in other active Gα proteins and could be leveraged as a specific vulnerability for the ∼20% of UMs bearing this mutation

A functional variant in the Stearoyl-CoA desaturase gene promoter enhances fatty acid desaturation in pork

There is growing public concern about reducing saturated fat intake. Stearoyl-CoA desaturase (SCD) is the lipogenic enzyme responsible for the biosynthesis of oleic acid (18:1) by desaturating stearic acid (18:0). Here we describe a total of 18 mutations in the promoter and 3′ non-coding region of the pig SCD gene and provide evidence that allele T at AY487830:g.2228T>C in the promoter region enhances fat desaturation (the ratio 18:1/18:0 in muscle increases from 3.78 to 4.43 in opposite homozygotes) without affecting fat content (18:0+18:1, intramuscular fat content, and backfat thickness). No mutations that could affect the functionality of the protein were found in the coding region. First, we proved in a purebred Duroc line that the C-T-A haplotype of the 3 single nucleotide polymorphisms (SNPs) (g.2108C>T; g.2228T>C; g.2281A>G) of the promoter region was additively associated to enhanced 18:1/18:0 both in muscle and subcutaneous fat, but not in liver. We show that this association was consistent over a 10-year period of overlapping generations and, in line with these results, that the C-T-A haplotype displayed greater SCD mRNA expression in muscle. The effect of this haplotype was validated both internally, by comparing opposite homozygote siblings, and externally, by using experimental Duroc-based crossbreds. Second, the g.2281A>G and the g.2108C>T SNPs were excluded as causative mutations using new and previously published data, restricting the causality to g.2228T>C SNP, the last source of genetic variation within the haplotype. This mutation is positioned in the core sequence of several putative transcription factor binding sites, so that there are several plausible mechanisms by which allele T enhances 18:1/18:0 and, consequently, the proportion of monounsaturated to saturated fat.This research was supported by grants from the Spanish Ministry of Science and Innovation (AGL2009-09779 and AGL2012-33529). RRF is recipient of a PhD scholarship from the Spanish Ministry of Science and Innovation (BES-2010-034607). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of manuscript

Toward Rational Design of Metal-Organic Frameworks for Sensing Applications: Efficient Calculation of Adsorption Characteristics in Zero Loading Regime

The Henry’s constant of adsorption, differential enthalpy of adsorption, free energy barriers between various compartments of the porous space, and selectivity are important characteristics of a porous material. These characteristics are directly related to the performance of the porous material in a sensing application and can be used as preliminary criteria for computational screening of the candidate porous materials. All these properties are linked to each other through well-established statistical–mechanical relations. In this article we demonstrate that the finely discretized representation of the simulation cell offers a particularly convenient way to exploit these relations, and, for rigid molecules in rigid porous materials, the majority of these characteristics can be calculated from a single simulation run. We apply the methodology to calculate the Henry’s constants and other characteristics for several small organic and aromatic molecules in two metal–organic frameworks, IRMOF-1 and MIL-47(V). We further provide predictions for TNT adsorption in these structures and discuss the implications of our findings in the context of sensing applications