vis5.mp4

The refractive solution to the coupling two incident beams to two scattered beams. The left column is the real part of the incident/non-adjoint electric fields, the second column is the real part of the scattered/adjoint fields. The third column is the final permittivity of the medium. The right column shows both field magnitudes, the red channel being the non-adjoint field and the green channel being the adjoint field

vis4.mp4

The diffractive solution to the coupling two incident beams to two scattered beams. The left column is the real part of the incident/non-adjoint electric fields, the second column is the real part of the scattered/adjoint fields. The third column is the final permittivity of the medium. The right column shows both field magnitudes, the red channel being the non-adjoint field and the green channel being the adjoint field

vis1.mp4

The diffractive solution to the coupling an incident to a scattered beam. The beam is incident from the lower left at an angle of 45 degrees and scattered to the lower right at an angle of 60 degrees. The upper left panel is the real part of the incident/non-adjoint electric field, the upper right panel is the real part of the scattered/adjoint field, the lower left is the final permittivity of the medium. the lower right panel shows both field magnitudes, the red channel being the non-adjoint field and the green channel being the adjoint field

Rhogogaster kudiana Rohwer, 1925, female from Anisimovka, Russian Far East

<p><strong><em>Rhogogaster kudiana</em></strong> ROHWER, 1925, ♀</p> <p>Current status: <em>Rhogogaster sibirica</em> Enslin, 1912</p> <p>Anisimovka (Russia: Primorskiy Kray); +43.16666 +132.80000. 07.06.1993 , leg. A. Taeger, coll. Senckenberg Deutsches Entomologisches Institut.</p> <p>Rohwer, S. A. 1925: Sawflies from the Maritime Province of Siberia. - Proceedings of the United States National Museum, Washington 68: 6.</p> <p>Original description:</p> <p>"RHOGOGASTER KUDIANUS, new species<br>This species seems to be intermediate between <em>R. viridis</em> (Linnaeus) and <em>R. dissimulans</em> (Kincaid). In general color it is much like Kincaid's species, but it differs from it in the more deepty emarginate clypeus and the dark markings at the apices of the tarsi. It may readily be separated from <em>viridis</em> by the complete absence of black on the abdomen, a slight difference in the shape of the sheath and shorter antennae.<br>Female.-—Length, 9.5 mm. Labrum broad, the apical margin almost truncate, anterior margin of the clypeus with a deep, subquadrate emargination, the lobes broad and truncate; head without punctures; postocellar furrow straight; postocellar area more than two times as broad as long ; occipital carina sharply defined ; antenna; slender, a little longer than the head and thorax, the third joint subequal with the fourth and fifth; thorax smooth; second intercubitus sinuate; fourth abscissa of cubitus one-third as long as the third; sheath stout, strongly convex below, the apex narrowly rounded. Uniformly pale-yellow (green in life) ; flagellum, except the two basal joints beneath, scape and pedicellum above, a U-shaped mark on the frons, the small spot inclosing the anterior ocellus, suture of prescutum, sides and depressed area of scutum, black; legs color of the body; apices of the four anterior femora above, the posterior femora with a complete narrow line above, narrow lines on all tibiae above, apices of all tarsi, black; wings clear hyaline, strongly iridescent: venation yellow; costa, basal, median, discoidal and anal veins, black.<br>Type-locality.— Kudia River, Amagu, Siberia.<br>Described from a single female collected July, 1923, by T. D. A. Cockerell.<br>Type.—Cat. No. 27618, U.S.N.M."</p> <p>The holotype is figured at http://usnmhymtypes.com/default.asp?Action=Show_Types&Single_Type=True&TypeID=6086.</p> <p>D.R. Smith examined the holotype: "The thorax is shiny, with small scattered pits on the mesonotum, more prominent on the front and lateral lobes; the mesoscutellum has very few. The pleurae are more densely sculptured on the lower portion... [as given in pictures of the female from Anisimovka] ... The antennal crests are more similar to <em>californica.</em> The ridges on the face are not as distinct and hollows not as deep as in <em>dryas,</em> but more like <em>californica</em> – much stronger than in <em>viridis."</em></p> <p>Photos were taken at the SDEI with a Leica DFC 495 digital camera and M205 C microscope. Composite images with an extended depth of field were created from stacks of images using the software CombineZ5.3 or CombineZP, and finally arranged and partly enhanced with Ulead PhotoImpact X3.</p

vis3.mp4

The refractive solution, with smoothing, to the coupling an incident to a scattered beam. The beam is incident from the lower left at an angle of 45 degrees and scattered to the lower right at an angle of 60 degrees. The upper left panel is the real part of the incident/non-adjoint electric field, the upper right panel is the real part of the scattered/adjoint field, the lower left is the final permittivity of the medium. the lower right panel shows both field magnitudes, the red channel being the non-adjoint field and the green channel being the adjoint field

Media 1: Measurement of orientation and susceptibility ratios using a polarization-resolved second-harmonic generation holographic microscope

Originally published in Biomedical Optics Express on 01 September 2012 (boe-3-9-2004

Media 2: Measurement of orientation and susceptibility ratios using a polarization-resolved second-harmonic generation holographic microscope

Originally published in Biomedical Optics Express on 01 September 2012 (boe-3-9-2004

Nanogap-Enhanced Infrared Spectroscopy with Template-Stripped Wafer-Scale Arrays of Buried Plasmonic Cavities

We have combined atomic layer lithography and template stripping to produce a new class of substrates for surface-enhanced infrared absorption (SEIRA) spectroscopy. Our structure consists of a buried and U-shaped metal–insulator–metal waveguide whose folded vertical arms efficiently couple normally incident light. The insulator is formed by atomic layer deposition (ALD) of Al₂O₃ and precisely defines the gap size. The buried nanocavities are protected from contamination by a silicon template until ready for use and exposed by template stripping on demand. The exposed nanocavity generates strong infrared resonances, tightly confines infrared radiation into a gap that is as small as 3 nm (λ/3300), and creates a dense array of millimeter-long hotspots. After partial removal of the insulators, the gaps are backfilled with benzenethiol molecules, generating distinct Fano resonances due to strong coupling with gap plasmons, and a SEIRA enhancement factor of 10⁵ is observed for a 3 nm gap. Because of the wafer-scale manufacturability, single-digit-nanometer control of the gap size via ALD, and long-term storage enabled by template stripping, our buried plasmonic nanocavity substrates will benefit broad applications in sensing and spectroscopy

Supplement 1. R Scripting Language code used for data generation in simulations.

<h2>File List</h2><p> <a href="datgen_defs.R">datgen_defs.R</a><br> <a href="datgen_script.R">datgen_script.R</a><br> <a href="wedge.R">wedge.R</a><br> <a href="datgen.zip">datgen.zip</a> </p><h2>Description</h2><p> datgen_defs.r: This file contains the following functions: </p> <div> <ol> <li>xgen() Generates random environmental values given a distribution ID and sample size.</li> <li>mugen() Generates mean values for a negative binomial distribution over a given environmental gradient.</li> <li>ygen() Generates random count data given an environmental gradient, distribution mean, and CV.</li> </ol> </div> <p>datgen_script.r: This file generates random datasets as they were in this study.</p> <p>wedge.r: This file contains the following functions:</p> <div> <ol> <li>rwedge() Takes random draws from a wedge-shaped pdf.</li> <li>dwedge() Reports the cdf from a wedge-shaped distribution given a quantile.</li> </ol> </div> <p>datgen.zip: This zip file contains all the above files.</p

Inflated organelle genomes and a circular-mapping mtDNA probably existed at the origin of coloniality in volvocine green algae

<p>The volvocine lineage is a monophyletic grouping of unicellular, colonial and multicellular algae, and a model for studying the evolution of multicellularity. In addition to being morphologically diverse, volvocine algae boast a surprising amount of organelle genomic variation. Moreover, volvocine organelle genome complexity appears to scale positively with organismal complexity. However, the organelle DNA architecture at the origin of colonial living is not known. To examine this issue, we sequenced the plastid and mitochondrial DNAs (ptDNA and mtDNA) of the 4-celled alga <i>Tetrabaena socialis</i>, which is basal to the colonial and multicellular volvocines.</p> <p><i>Tetrabaena</i><i>socialis</i> has a circular-mapping mitochondrial genome, contrasting with the linear mtDNA architecture of its relative <i>Chlamydomonas reinhardtii</i>. This suggests that a circular-mapping mtDNA conformation emerged at or near the transition to group living in the volvocines, or represents the ancestral state of the lineage as a whole. The <i>T. socialis</i> ptDNA is very large (>405 kb) and dense with repeats, supporting the idea that a shift from a unicellular to a colonial existence coincided with organelle genomic expansion, potentially as a result of increased random genetic drift. These data reinforce the idea that volvocine algae harbour some of the most expanded plastid chromosomes from the eukaryotic tree of life. Circular-mapping mtDNAs are turning out to be more common within volvocines than originally thought, particularly for colonial and multicellular species. Altogether, volvocine organelle genomes became markedly more inflated during the evolution of multicellularity, but complex organelle genomes appear to have existed at the very beginning of colonial living.</p