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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Specific DNA binding by c-Myb: evidence for a double helix-turn-helix-related motif.

The c-Myb protein is a sequence-specific DNA binding protein that activates transcription in hematopoietic cells. Three imperfect repeats (R1, R2, and R3) that contain regularly spaced tryptophan residues form the DNA binding domain of c-Myb. A fragment of c-Myb that contained the R2 and R3 regions bound specifically to a DNA sequence recognized by c-Myb plus ten additional base pairs at the 3' end of the element. The R2R3 fragment was predicted to contain two consecutive helix-turn-helix (HTH) motifs with unconventional turns. Mutagenesis of amino acids in R2R3 at positions that correspond to DNA-contacting amino acids in other HTH-containing proteins abolished specific DNA binding without affecting nonspecific DNA interactions.

Participation of the TATA factor in transcription of the yeast U6 gene by RNA polymerase C.

Fractionation of transcription extracts has led to the identification of multiple transcription factors specific for each form of nuclear RNA polymerase. Accurate transcription in vitro of the yeast U6 RNA gene by RNA polymerase C requires at least two factors. One of them was physically and functionally indistinguishable from transcription factor IID (TFIID or BTF1), a pivotal component of polymerase B transcription complexes, which binds to the TATA element. Purified yeast TFIID (yIID) or bacterial extracts that contained recombinant yIID were equally competent to direct specific transcription of the U6 gene by RNA polymerase C. The results suggest the formation of a hybrid transcription machinery, which may imply an evolutionary relation between class B and class C transcription factors.

RNA polymerase III (C) and its transcription factors.

Transcription of small genes by RNA polymerase III or C (pol III) involves many of the strategies that are used for transcription complex formation and occasionally the same components as those used by RNA polymerase II or B (pol II). Transcription complex formation is a multistep process that leads to the binding of a single initiation factor, TFIIIB, which in turn directs the selection of pol III. The general transcription factor TFIID can be involved in both pol II and pol III transcription. These and other similarities point towards a unifying mechanism for eukaryotic transcription initiation.

A subunit of yeast TFIIIC participates in the recruitment of TATA-binding protein.

TFIIIC plays a key role in nucleating the assembly of the initiation factor TFIIIB on class III genes. We have characterized an essential gene, TFC8, encoding the 60-kDa polypeptide, tau60, present in affinity-purified TFIIIC. Hemagglutinin-tagged variants of tau60 were found to be part of TFIIIC-tDNA complexes and to reside at least in part in the downstream DNA-binding domain tauB. Unexpectedly, the thermosensitive phenotype of N-terminally tagged tau60 was suppressed by overexpression of tau95, which belongs to the tauA domain, and by two TFIIIB components, TATA-binding protein (TBP) and B"/TFIIIB90 (but not by TFIIIB70). Mutant TFIIIC was deficient in the activation of certain tRNA genes in vitro, and the transcription defect was selectively alleviated by increasing TBP concentration. Coimmunoprecipitation experiments support a direct interaction between TBP and tau60. It is suggested that tau60 links tauA and tauB domains and participates in TFIIIB assembly via its interaction with TBP.

Effect of mutations in a zinc-binding domain of yeast RNA polymerase C (III) on enzyme function and subunit association.

The conserved amino-terminal region of the largest subunit of yeast RNA polymerase C is capable of binding zinc ions in vitro. By oligonucleotide-directed mutagenesis, we show that the putative zinc-binding motif CX2CX6-12CXGHXGX24-37CX2C, present in the largest subunit of all eukaryotic and archaebacterial RNA polymerases, is essential for the function of RNA polymerase C. All mutations in the invariant cysteine and histidine residues conferred a lethal phenotype. We also obtained two conditional thermosensitive mutants affecting this region. One of these produced a form of RNA polymerase C which was thermosensitive and unstable in vitro. This instability was correlated with the loss of three of the subunits which are specific to RNA polymerase C: C82, C34, and C31.

RPC82 encodes the highly conserved, third-largest subunit of RNA polymerase C (III) from Saccharomyces cerevisiae.

RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. Here we report the cloning of the gene encoding the 82-kDa subunit, RPC82. It maps as a single-copy gene on chromosome XVI. The UCR2 gene was found in the opposite orientation only 340 bp upstream of the RPC82 start codon, and the end of the SKI3 coding sequence was found only 117 bp downstream of the RPC82 stop codon. The RPC82 gene encodes a protein with a predicted M(r) of 73,984, having no strong sequence similarity to other known proteins. Disruption of the RPC82 gene was lethal. An rpc82 temperature-sensitive mutant, constructed by in vitro mutagenesis of the gene, showed a deficient rate of tRNA relative to rRNA synthesis. Of eight RNA polymerase C genes tested, only the RPC31 gene on a multicopy plasmid was capable of suppressing the rpc82(Ts) defect, suggesting an interaction between the polymerase C 82-kDa and 31-kDa subunits. A group of RNA polymerase C-specific subunits are proposed to form a substructure of the enzyme.

The RPC31 gene of Saccharomyces cerevisiae encodes a subunit of RNA polymerase C (III) with an acidic tail.

The RPC31 gene encoding the C31 subunit of Saccharomyces cerevisiae RNA polymerase C (III) has been isolated, starting from a C-terminal fragment cloned on a lambda gt11 library. It is unique on the yeast genome and lies on the left arm of chromosome XIV, very close to a NotI site. Its coding sequence perfectly matches the amino acid sequence of two oligopeptides prepared from purified C31. It is also identical to the ACP2 gene previously described as encoding an HMG1-like protein (W. Haggren and D. Kolodrubetz, Mol. Cell. Biol. 8:1282-1289, 1988). Thus, ACP2 and RPC31 are allelic and encode a subunit of RNA polymerase C. The c31 protein has a highly acidic C-terminal tail also found in several other chromatin-interacting proteins, including animal HMG1. Outside this domain, however, there is no appreciable homology to any known protein. The growth phenotypes of a gene deletion, of insertions, and of nonsense mutations indicate that the C31 protein is strictly required for cell growth and that most of the acidic domain is essential for its function. Random mutagenesis failed to yield temperature-sensitive mutants, but a slowly growing mutant was constructed by partial suppression of a UAA nonsense allele of RPC31. Its reduced rate of tRNA synthesis in vivo relative to 5.8S rRNA supports the hypothesis that the C31 protein is a functional subunit of RNA polymerase C.