Archimedean spiral cavity ring resonators in silicon as ultra-compact optical comb filters

We present an ultra-compact comb filter using an add-drop ring resonator with an Archimedean spiral cavity. The cavity consists of two interleaved spiral branches which are connected in the center using arcs of circle of a radius that causes minimum bend loss. We describe the design procedure and examine the physical parameters governing the resonator performance. As an example, we demonstrate experimentally a comb filter with a 25 GHz channel spacing made of silicon photonic wires and only occupies an area of 80 × 90 µm2, approximately a 70 fold size reduction compared to a racetrack resonator. The filter transmission is free of spurious reflections, attesting to the smooth transition between different sections of the resonator cavity. Over a 40 channel wavelength span, the filter exhibits a quality factor Q > 35,000, extinction ratios > 10 dB, and an excellent power uniformity with variations < 0.5 dB for both the through and drop ports

Folded cavity SOI microring sensors for high sensitivity and real time measurement of biomolecular binding.

We demonstrate folded waveguide ring resonators for biomolecular sensing. We show that extending the ring cavity length increases the resonator quality factor, and thereby enhances the sensor resolution and minimum level of detection, while at the same time relaxing the tolerance on the coupling conditions to provide stable and large resonance contrast. The folded spiral path geometry allows a 1.2 mm long ring waveguide to be enclosed in a 150 microm diameter sensor area. The spiral cavity resonator is used to monitor the streptavidin protein binding with a detection limit of approximately 3 pg/mm(2), or a total mass of approximately 5 fg. The real time measurements are used to analyze the kinetics of biotin-streptavidin binding

Real-time cancellation of temperature induced resonance shifts in SOI wire waveguide ring resonator label-free biosensor arrays.

A comprehensive investigation of real-time temperature-induced resonance shift cancellation for silicon wire based biosensor arrays is reported for the first time. A reference resonator, protected by either a SU8 or SiO(2) cladding layer, is used to track temperature changes. The temperature dependence of resonators in aqueous solutions, pertinent to biosensing applications, is measured under steady-state conditions and the operating parameters influencing these properties are discussed. Real-time measurements show that the reference resonator resonances reflect the temperature changes without noticeable time delay, enabling effective cancellation of temperature-induced shifts. Binding between complementary IgG protein pairs is monitored over 4 orders of magnitude dynamic range down to a concentration of 20 pM, demonstrating a resolvable mass of 40 attograms. Reactions are measured over time periods as long as 3 hours with high stability, showing a scatter corresponding to a fluid refractive index fluctuation of ± 4 × 10(-6) in the baseline data. Sensor arrays with a SU8 protective cladding are easy to fabricate, while oxide cladding is found to provide superior stability for measurements involving long time scales

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

BACKGROUND: Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts. RESULTS: We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively. CONCLUSIONS: Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly

Low levels of nucleotide diversity in Crocodylus moreletii and evidence of hybridization with C. acutus

Examinations of both population genetic structure and the processes that lead to such structure in crocodilians have been initiated in several species in response to a call by the IUCN Crocodile Specialist Group. A recent study used microsatellite markers to characterize Morelet\u27s crocodile (Crocodylus moreletii) populations in north-central Belize and presented evidence for isolation by distance. To further investigate this hypothesis, we sequenced a portion of the mitochondrial control region for representative animals after including samples from additional locales in Belize, Guatemala and Mexico. While there is limited evidence of subdivision involving other locales, we found that most of the differentiation among populations of C. moreletii can be attributed to animals collected from a single locale in Belize, Banana Bank Lagoon. Furthermore, mitochondrial DNA sequence analysis showed that animals from this and certain other locales display a haplotype characteristic of the American crocodile, C. acutus, rather than C. moreletii. We interpret this as evidence of hybridization between the two species and comment on how these new data have influenced our interpretation of previous findings. We also find very low levels of nucleotide diversity in C. moreletii haplotypes and provide evidence for a low rate of substitution in the crocodilian mitochondrial control region. Finally, the conservation implications of these findings are discussed

NFIRAOS adaptive optics for the Thirty Meter Telescope

NFIRAOS (Narrow-Field InfraRed Adaptive Optics System) will be the first-light multi-conjugate adaptive optics system for the Thirty Meter Telescope (TMT). NFIRAOS houses all of its opto-mechanical sub-systems within an optics enclosure cooled to precisely -30°C in order to improve sensitivity in the near-infrared. It supports up to three client science instruments, including the first-light InfraRed Imaging Spectrograph (IRIS). Powering NFIRAOS is a Real Time Controller that will process the signals from six laser wavefront sensors, one natural guide star pyramid WFS, up to three low-order on-instrument WFS and up to four guide windows on the client instrument’s science detector in order to correct for atmospheric turbulence, windshake, optical errors and plate-scale distortion. NFIRAOS is currently preparing for its final design review in late June 2018 at NRC Herzberg in Victoria, British Columbia in partnership with Canadian industry and TMT

Diversidade e estrutura genética em populações naturais de Hancornia speciosa var. speciosa Gomes no nordeste do Brasil

Hancornia speciosa Gomes is a fruit tree native from Brazil that belongs to Apocinaceae family, and is popularly known as Mangabeira. Its fruits are widely consumed raw or processed as fruit jam, juices and ice creams, which have made it a target of intense exploitation. The extractive activities and intense human activity on the environment of natural occurrence of H. speciosa has caused genetic erosion in the species and little is known about the ecology or genetic structure of natural populations. The objective of this research was the evaluation of the genetic diversity and genetic structure of H. speciosa var. speciosa. The genetic variability was assessed using 11 allozyme loci with a sample of 164 individuals distributed in six natural populations located in the States of Pernambuco and Alagoas, Northeastern Brazil. The results showed a high level of genetic diversity within the species (<img border=0 id="_x0000_i1026" src="/img/revistas/rbf/v34n4/a23img01.jpg" align=absmiddle>e= 0.36) seeing that the most of the genetic variability of H. speciosa var. speciosa is within its natural populations with low difference among populations ( <img border=0 id="_x0000_i1027" src="/img/revistas/rbf/v34n4/a23img02.jpg" align=absmiddle > or = 0.081). The inbreeding values within (<img border=0 id="_x0000_i1028" src="/img/revistas/rbf/v34n4/a23img03.jpg" align=absmiddle> = -0.555) and among populations (<img border=0 id="_x0000_i1029" src="/img/revistas/rbf/v34n4/a23img04.jpg" align=absmiddle> =-0.428) were low showing lacking of endogamy and a surplus of heterozygotes. The estimated gene flow ( <img border=0 id="_x0000_i1030" src="/img/revistas/rbf/v34n4/a23img05.jpg" align=absmiddle>m ) was high, ranging from 2.20 to 13.18, indicating to be enough to prevent the effects of genetic drift and genetic differentiation among populations. The multivariate analyses indicated that there is a relationship between genetic and geographical distances, which was confirmed by a spatial pattern analysis using Mantel test (r = 0.3598; p = 0.0920) with 1000 random permutations. The high genetic diversity index in these populations indicates potential for in situ genetic conservation

Tilted fiber Bragg grating sensor interrogation system using a high-resolution silicon-on-insulator arrayed waveguide grating

We report a compact high-resolution arrayed waveguide grating (AWG) interrogator system designed to measure the relative wavelength spacing between two individual resonances of a tilted fiber Bragg grating (TFBG) refractometer. The TFBG refractometer benefits from an internal wavelength and power reference provided by the core mode reflection resonance that can be used to determine cladding mode perturbations with high accuracy. The AWG interrogator is a planar waveguide device fabricated on a silicon-on-insulator platform, having 50 channels with a 0.18 nm wavelength separation and a footprint of 8 mm × 8 mm. By overlaying two adjacent interference orders of the AWG we demonstrate simultaneous monitoring of two widely separated resonances in real time with high wavelength resolution. The standard deviation of the measured wavelength shifts is 1.2 pm, and it is limited by the resolution of the optical spectrum analyzer used for the interrogator calibration measurements

Synthetic Biology Open Language (SBOL) Version 1.1.0

In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.1.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data model, a common computational representation

NFIRAOS adaptive optics for the Thirty Meter Telescope

NFIRAOS (Narrow-Field InfraRed Adaptive Optics System) will be the first-light multi-conjugate adaptive optics system for the Thirty Meter Telescope (TMT). NFIRAOS houses all of its opto-mechanical sub-systems within an optics enclosure cooled to precisely -30°C in order to improve sensitivity in the near-infrared. It supports up to three client science instruments, including the first-light InfraRed Imaging Spectrograph (IRIS). Powering NFIRAOS is a Real Time Controller that will process the signals from six laser wavefront sensors, one natural guide star pyramid WFS, up to three low-order on-instrument WFS and up to four guide windows on the client instrument’s science detector in order to correct for atmospheric turbulence, windshake, optical errors and plate-scale distortion. NFIRAOS is currently preparing for its final design review in late June 2018 at NRC Herzberg in Victoria, British Columbia in partnership with Canadian industry and TMT