Comprehensive modeling of near-field nano-patterning

Near-field nano-patterning greatly simplifies holographic lithography, but deformations in formed structures are potentially severe. A fast and efficient comprehensive model was developed to predict geometry more rigorously. Numerical results show simple intensity-threshold methods do not accurately predict shape or optical behavior. By modeling sources with partial coherence, unpolarized light, and an angular spectrum, it is shown that standard UV lamps can be used to form 3D structures

Micro-optical spatial and spectral elements

Interference filters have a defect layer incorporated within a photonic crystal structure and generate a narrow transmission notch within a wide stop band. In this paper, we propose and demonstrate wavelength-tunable spatial filters by introducing diffractive optical elements in the defect layer. The spectral transmission through the device was a function of the local defect layer thickness under broadband illumination. For each wavelength, the spatial transmission followed the contours of equal defect layer optical thickness. The devices were implemented by depositing a one-dimensional photonic crystal with a centrally integrated defect layer on a silicon substrate using plasma-enhanced chemical vapor deposition. The defect layer was lithographically patterned with charge 2, 8-level vortex structures. The spectral transmission peak and linewidth was characterized by separately illuminating each zone of diffractive element using a tunable laser source and compared with model simulations. The spatial transmission through the device was imaged onto a CCD camera. Triangular wedge-shaped zones with wavelength-dependent orientations were observed. These novel devices with spectrally tunable spatial transmission have potential applications in pupil filtering, hyperspectral imaging, and engineered illumination systems

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study

Background Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. Methods We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008–11). We generated a parallel progression score using data from 1773 previously genotyped participants from the European Huntington's Disease Network REGISTRY study of Huntington's disease mutation carriers (data collected 2003–13). We did a genome-wide association analyses in terms of progression for 216 TRACK-HD participants and 1773 REGISTRY participants, then a meta-analysis of these results was undertaken. Findings Longitudinal motor, cognitive, and imaging scores were correlated with each other in TRACK-HD participants, justifying use of a single, cross-domain measure of disease progression in both studies. The TRACK-HD and REGISTRY progression measures were correlated with each other (r=0·674), and with age at onset (TRACK-HD, r=0·315; REGISTRY, r=0·234). The meta-analysis of progression in TRACK-HD and REGISTRY gave a genome-wide significant signal (p=1·12 × 10−10) on chromosome 5 spanning three genes: MSH3, DHFR, and MTRNR2L2. The genes in this locus were associated with progression in TRACK-HD (MSH3 p=2·94 × 10−8 DHFR p=8·37 × 10−7 MTRNR2L2 p=2·15 × 10−9) and to a lesser extent in REGISTRY (MSH3 p=9·36 × 10−4 DHFR p=8·45 × 10−4 MTRNR2L2 p=1·20 × 10−3). The lead single nucleotide polymorphism (SNP) in TRACK-HD (rs557874766) was genome-wide significant in the meta-analysis (p=1·58 × 10−8), and encodes an aminoacid change (Pro67Ala) in MSH3. In TRACK-HD, each copy of the minor allele at this SNP was associated with a 0·4 units per year (95% CI 0·16–0·66) reduction in the rate of change of the Unified Huntington's Disease Rating Scale (UHDRS) Total Motor Score, and a reduction of 0·12 units per year (95% CI 0·06–0·18) in the rate of change of UHDRS Total Functional Capacity score. These associations remained significant after adjusting for age of onset. Interpretation The multidomain progression measure in TRACK-HD was associated with a functional variant that was genome-wide significant in our meta-analysis. The association in only 216 participants implies that the progression measure is a sensitive reflection of disease burden, that the effect size at this locus is large, or both. Knockout of Msh3 reduces somatic expansion in Huntington's disease mouse models, suggesting this mechanism as an area for future therapeutic investigation

Modeling The Formation Of Photonic Crystals By Holographic Lithography

An approach is introduced to accurately explore methods of fabricating photonic crystals formed by holographic lithography. Analytical background is given for synthesizing the exposure beam configuration to form the desired lattice. This is combined with a comprehensive model that can predict lattice distortions due to physics of the photolithography process. Simulations are compared to experimental results and to results obtained by conventional intensity threshold methods

Fully Three-Dimensional Modeling Of The Fabrication And Behavior Of Photonic Crystals Formed By Holographic Lithography

A comprehensive and fully three-dimensional model of holographic lithography is used to predict more rigorously the geometry and transmission spectra of photonic crystals formed in Epon® SU-8 photoresist. It is the first effort known to the authors to incorporate physics of exposure, postexposure baking, and developing into three-dimensional models of photonic crystals. Optical absorption, reflections, standing waves, refraction, beam coherence, acid diffusion, resist shrinkage, and developing effects combine to distort lattices from their ideal geometry. These are completely neglected by intensity-threshold methods used throughout the literature to predict lattices. Numerical simulations compare remarkably well with experimental results for a face-centered-cube (FCC) photonic crystal. Absorption is shown to produce chirped lattices with broadened bandgaps. Reflections are shown to significantly alter lattice geometry and reduce image contrast. Through simulation, a diamond lattice is formed by multiple exposures, and a hybrid trigonal-FCC lattice is formed that exhibits properties of both component lattices. © 2004 Optical Society of America

Micro-Photonic Systems Utilizing Su-8

SU-8 is a negative-tone photoresist that can serve as a complete optical bench for micro-photonic systems. Functional optical devices and passive alignment structures can all be formed in the same material system with common processing steps. Many interrelated process parameters control the final geometry of structures formed in SU-8, but all can be accurately simulated and predicted by computer modeling. In this work, a comprehensive model of the lithography process was developed and combined with rigorous electromagnetic simulation. It was applied to predict sidewall slope of a tall structures as well as the geometry and transmission spectra of a three-dimensional photonic crystal. The model is seen as an enabling step toward realizing optimized micro-photonic systems in SU-8

Modeling The Fabrication Of Nano-Optical Structures

Over the last two decades, considerable research has been devoted to micro-optic and now nano-optical structures. Fabrication methods have become sufficiently mature to realize most concepts, but due to physics inherent in the process, geometry is distorted. Edges are rounded, sidewalks are sloped, surfaces are rough, and etching or deposition not uniform. Deviations from perfect geometry can dramatically affect optical behavior. In order to address the impact of the non-perfect nature of fabrication, numerical methods for modeling fabrication is discussed and quantified for various examples. As an example, comprehensive modeling of near-field nano-patterning is described. Numerical and experimental results are presented of three-dimensional photonic crystals fabricated in a contact mask aligner using a standard UV lamp as the source

Fabrication Of 3-D Photonic Crystals By Two-Step Dry Etching Of Layered Media

Photonic crystals have received growing interest over the past decade on account of their excellent functionality to guiding and manipulating electromagnetic radiation and their diverse applications. Our approach to fabricate crystals is by a two step etching process in a semiconductor hetero-structure of gallium arsenide (GaAs) and aluminum gallium arsenide (AlGaAs) grown using molecular beam epitaxy (MBE). An array of holes was dry etched in Cl 2/Ar inductively coupled plasma. Etching selectivity between the mask and the substrate was 10:1. By using SF 6 in addition to the boron-tri-chloride (BCl 3) chemistry, the GaAs is etched selectively over the AlGaAs with selectivities over 5:1. Thus a robust two-step etching process has been developed based entirely on dry etching

Rigorous Electromagnetic Analysis Of Volumetrically Complex Media Using The Slice Absorption Method

There is tremendous demand for numerical methods to perform rigorous analysis of devices that are both large scale and complex throughout their volume. This can arise when devices must be considered with realistic geometry or when they contain artificial materials such as photonic crystals, left-handed materials, nanoparticles, or other metamaterials. The slice absorption method (SAM) was developed to address this need. The method is fully numerical and able to break large problems down into small pieces, or slices, using matrix division or Gaussian elimination instead of eigensystem computations and scattering matrix manipulations. In these regards, the SAM is an attractive alternative to popular techniques like the finite-difference time domain method, rigorous coupled-wave analysis, and the transfer matrix method. To demonstrate the utility of the SAM and benchmark its accuracy, reflection was simulated for a photonic crystal fabricated in SU-8 by multiphoton direct laser writing. Realistic geometry was incorporated into the model by simulating the microfabrication process, which yielded simulation results that matched experimental measurements remarkably well. © 2007 Optical Society of America