Electromagnetic modeling of large subwavelength-patterned highly resonant structures.

The rigorous modeling of large (hundreds of wavelengths) optical resonant components patterned at a subwavelength scale remains a major issue, especially when long range interactions cannot be neglected. In this Letter, we compare the performances of the discrete dipole approximation approach to that of the Fourier modal, the finite element and the finite difference time domain methods, for simulating the spectral behavior of a cavity resonator integrated grating filter (CRIGF). When the component is invariant along one axis (two-dimensional configuration), the four techniques yield similar results, despite the modeling difficulty of such a structure. We also demonstrate, for the first time to the best of our knowledge, the rigorous modeling of a three-dimensional CRIGF.

Tomographic diffractive microscopy with agile illuminations for imaging targets in a noisy background.

Tomographic diffractive microscopy is a marker-free optical digital imaging technique in which three-dimensional samples are reconstructed from a set of holograms recorded under different angles of incidence. We show experimentally that, by processing the holograms with singular value decomposition, it is possible to image objects in a noisy background that are invisible with classical wide-field microscopy and conventional tomographic reconstruction procedure. The targets can be further characterized with a selective quantitative inversion.

Experimental demonstration of 1D crossed gratings for polarization-independent high-Q filtering.

We demonstrate experimentally a spectral filter with high Q-factor (≃3238), wide accordability range (1500-1600 nm) with respect to the angle of incidence, and record polarization independence. This work is an experimental validation of the theoretical work reported in [Opt. Lett. 36, 1662 (2011)]: the filter is composed of two 1D crossed gratings engraved on each side of a planar waveguide. We provide a good comparison with theory and physical interpretations of the features observed experimentally.

Structured illumination fluorescence microscopy with distorted excitations using a filtered blind-SIM algorithm.

Structured illumination microscopy (SIM) is a powerful technique for obtaining super-resolved fluorescence maps of samples, but it is very sensitive to aberrations or misalignments affecting the excitation patterns. Here, we present a reconstruction algorithm that is able to process SIM data even if the illuminations are strongly distorted. The approach is an extension of the recent blind-SIM technique, which reconstructs simultaneously the sample and the excitation patterns without a priori information on the latter. Our algorithm was checked on synthetic and experimental data using distorted and nondistorted illuminations. The reconstructions were similar to that obtained by up-to-date SIM methods when the illuminations were periodic and remained artifact-free when the illuminations were strongly distorted.

Total absorption of light by a nanoparticle: an electromagnetic sink in the optical regime.

In this Letter, we give a general description of the illumination and object properties for obtaining total absorption. We show theoretically and numerically that properly designed sub-100 nm metallic particles are able to absorb all the energy of an incident beam if the latter is adequately shaped. In addition to their interest as absorbers, these particles act as efficient near-field probes as they convert the incident propagating beam into a localized nonradiative field.

Full-polarized tomographic diffraction microscopy achieves a resolution about one-fourth of the wavelength.

We present a marker-free microscope that records the phase, amplitude, and polarization state of the field diffracted by the sample for different illumination directions. The data are processed with an appropriate inversion method to yield the sample permittivity map. We observe that the full-polarized information ameliorates significantly the three-dimensional image of weakly scattering subdiffraction objects. A resolution about one-fourth of the illumination wavelength is experimentally demonstrated on complex samples.

Far-field optical control of a movable subdiffraction light grid.

We demonstrate experimentally a subdiffraction light pattern, with a period down to 150 nm, at the surface of an optimized silicon nanostructured thin film. We show, using near-field and far-field characterization, that this subdiffraction pattern can be translated and rotated just by changing the illumination angle. The movable high frequency light pattern paves the way for subdiffraction resolution surface imaging microscopy without scanning near-field probes.

Tomographic diffractive microscopy with a wavefront sensor.

Tomographic diffractive microscopy is a recent imaging technique that reconstructs quantitatively the three-dimensional permittivity map of a sample with a resolution better than that of conventional wide-field microscopy. Its main drawbacks lie in the complexity of the setup and in the slowness of the image recording as both the amplitude and the phase of the field scattered by the sample need to be measured for hundreds of successive illumination angles. In this Letter, we show that, using a wavefront sensor, tomographic diffractive microscopy can be implemented easily on a conventional microscope. Moreover, the number of illuminations can be dramatically decreased if a constrained reconstruction algorithm is used to recover the sample map of permittivity.

Coherent x-ray wavefront reconstruction of a partially illuminated Fresnel zone plate.

A detailed characterization of the coherent x-ray wavefront produced by a partially illuminated Fresnel zone plate is presented. We show, by numerical and experimental approaches, how the beam size and the focal depth are strongly influenced by the illumination conditions, while the phase of the focal spot remains constant. These results confirm that the partial illumination can be used for coherent diffraction experiments. Finally, we demonstrate the possibility of reconstructing the complex-valued illumination function by simple measurement of the far field intensity in the specific case of partial illumination.

Cramer-Rao analysis of steady-state and time-domain fluorescence diffuse optical imaging.

Using a Cramer-Rao analysis, we study the theoretical performances of a time and spatially resolved fDOT imaging system for jointly estimating the position and the concentration of a point-wide fluorescent volume in a diffusive sample. We show that the fluorescence lifetime is a critical parameter for the precision of the technique. A time resolved fDOT system that does not use spatial information is also considered. In certain cases, a simple steady-state configuration may be as efficient as this time resolved fDOT system.

Tunable, polarization independent, narrow-band filtering with one-dimensional crossed resonant gratings.

We propose an optical component for widely tunable, narrow-band filtering. It takes advantage of the tunability properties, with respect to the angle of incidence, of guided-mode resonance filters. The intrinsic polarization sensitivity of the resonances is suppressed by exciting the modes through two identical, differently oriented one-dimensional gratings flanking a thick substrate. An example is provided that theoretically shows a polarization independent peak at 1.6 µm with a Q factor of 13,000 and a reflectivity greater than 99% at resonance, which is tunable over 100 nm. Finally, we discuss the fabrication limitations and conclude that the proposed configuration is realistic.

Full wave optical profilometry.

We show that tomographic diffractive microscopy can be used for profilometry applications with high transverse resolution. We present an iterative reconstruction procedure, based on a rigorous wave scattering model, that permits us to retrieve the profile of rough metallic interfaces from the complex scattered field. The transversal resolution is subwavelength, and can even fall below the classical resolution limit if the profile is rough enough for multiple interactions to occur. Large profiles, with tens of wavelength size, can be investigated.

Measurement and modeling of 2D hexagonal resonant-grating filter performance.

We report the measurement of a polarization-independent guided-mode resonant filter with a Q factor of approximately 2200 functioning near normal incidence in the near infrared (850 nm). Besides this remarkable performance, we provide a detailed optical and structural characterization of the component, which points out the origins of the limitation of the experimental performance. We conclude that the defaults in question can be corrected by improving the lithography process, and we are confident that even greater performance will be obtained in future realizations.

Mirror-assisted tomographic diffractive microscopy with isotropic resolution.

We demonstrate that the axial resolution of a reflection tomographic diffractive microscope is drastically improved when the sample is placed in front of a perfect mirror. We show analytically and with rigorous simulations that this approach permits us to obtain images with the same isotropic resolution as that obtained when the sample is illuminated and observed from every possible angle. The main difficulty lies in accounting properly for the mirror in the inversion algorithm.

Analysis of the depth resolution limit of luminescence diffuse optical imaging.

We introduce a methodology to determine quantitatively the depth resolution limit in luminescence diffuse optical imaging. The approach is based on a Cramer-Rao statistical analysis, a noise model, and calculations of photon transport in tissues. We illustrate the method in the case of luminescence imaging in a brain-skull model, showing its potential applications in molecular imaging on small animals.

Scattering from rough inhomogeneous media: splitting of surface and volume scattering.

The intensity scattered by particles randomly placed beneath a rough interface is studied with rigorous simulations. It is shown that the angular intensity pattern is close to that obtained by adding the intensity scattered by particles under a flat surface to that scattered by a rough homogeneous surface whose permittivity is evaluated with an effective-medium theory. This heuristic splitting rule is accurate for a large range of parameters that are well beyond any perturbative treatment.

Maf1p, a negative effector of RNA polymerase III in Saccharomyces cerevisiae.

Although yeast RNA polymerase III (Pol III) and the auxiliary factors TFIIIC and TFIIIB are well characterized, the mechanisms of class III gene regulation are poorly understood. Previous studies identified MAF1, a gene that affects tRNA suppressor efficiency and interacts genetically with Pol III. We show here that tRNA levels are elevated in maf1 mutant cells. In keeping with the higher levels of tRNA observed in vivo, the in vitro rate of Pol III RNA synthesis is significantly increased in maf1 cell extracts. Mutations in the RPC160 gene encoding the largest subunit of Pol III which reduce tRNA levels were identified as suppressors of the maf1 growth defect. Interestingly, Maf1p is located in the nucleus and coimmunopurifies with epitope-tagged RNA Pol III. These results indicate that Maf1p acts as a negative effector of Pol III synthesis. This potential regulator of Pol III transcription is likely conserved since orthologs of Maf1p are present in other eukaryotes, including humans.

High-mobility-group proteins NHP6A and NHP6B participate in activation of the RNA polymerase III SNR6 gene.

Transcription of yeast class III genes involves the formation of a transcription initiation complex that comprises RNA polymerase III (Pol III) and the general transcription factors TFIIIB and TFIIIC. Using a genetic screen for positive regulators able to compensate for a deficiency in a promoter element of the SNR6 gene, we isolated the NHP6A and NHP6B genes. Here we show that the high-mobility-group proteins NHP6A and NHP6B are required for the efficient transcription of the SNR6 gene both in vivo and in vitro. The transcripts of wild-type and promoter-defective SNR6 genes decreased or became undetectable in an nhp6ADelta nhp6BDelta double-mutant strain, and the protection over the TATA box of the wild-type SNR6 gene was lost in nhp6ADelta nhp6BDelta cells at 37 degrees C. In vitro, NHP6B specifically stimulated the transcription of SNR6 templates up to fivefold in transcription assays using either cell nuclear extracts from nhp6ADelta nhp6BDelta cells or reconstituted transcription systems. Finally, NHP6B activated SNR6 transcription in a TFIIIC-independent assay. These results indicate that besides the general transcription factors TFIIIB and TFIIIC, additional auxillary factors are required for the optimal transcription of at least some specific Pol III genes.

The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the A43 subunit with Rrn3.

RNA polymerase I (Pol I) is dedicated to transcription of the large ribosomal DNA (rDNA). The mechanism of Pol I recruitment onto rDNA promoters is poorly understood. Here we present evidence that subunit A43 of Pol I interacts with transcription factor Rrn3: conditional mutations in A43 were found to disrupt the transcriptionally competent Pol I-Rrn3 complex, the two proteins formed a stable complex when co-expressed in Escherichia coli, overexpression of Rrn3 suppressed the mutant phenotype, and A43 and Rrn3 mutants showed synthetic lethality. Consistently, immunoelectron microscopy data showed that A43 and Rrn3 co-localize within the Pol I-Rrn3 complex. Rrn3 has several protein partners: a two-hybrid screen identified the C-terminus of subunit Rrn6 of the core factor as a Rrn3 contact, an interaction supported in vitro by affinity chromatography. Our results suggest that Rrn3 plays a central role in Pol I recruitment to rDNA promoters by bridging the enzyme to the core factor. The existence of mammalian orthologues of A43 and Rrn3 suggests evolutionary conservation of the molecular mechanisms underlying rDNA transcription in eukaryotes.

Dipole radiation into grating structures

We present a detailed electromagnetic analysis for the radiation of an electric source located inside grating structures. Our analysis is based on the differential method and uses the scattering-matrix algorithm. We show that gratings that exhibit periodic modulations along two spatial directions (crossed gratings) enable one to couple out the totality of the light emitted by the source into the guided modes of the structure. This property is investigated through the computation of the far-field radiation patterns for crossed gratings with various etching depths. One key result is the possibility to confine the emitted light in a direction about the sample normal, a property that is of interest in the context of spontaneous emission control by microcavity structures.