Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides.

The challenge of the Human Genome Project is to increase the rate of DNA sequence acquisition by two orders of magnitude to complete sequencing of the human genome by the year 2000. The present work describes a rapid detection method using a two-dimensional optical wave guide that allows measurement of real-time binding or melting of a light-scattering label on a DNA array. A particulate label on the target DNA acts as a light-scattering source when illuminated by the evanescent wave of the wave guide and only the label bound to the surface generates a signal. Imaging/visual examination of the scattered light permits interrogation of the entire array simultaneously. Hybridization specificity is equivalent to that obtained with a conventional system using autoradiography. Wave guide melting curves are consistent with those obtained in the liquid phase and single-base discrimination is facile. Dilution experiments showed an apparent lower limit of detection at 0.4 nM oligonucleotide. This performance is comparable to the best currently known fluorescence-based systems. In addition, wave guide detection allows manipulation of hybridization stringency during detection and thereby reduces DNA chip complexity. It is anticipated that this methodology will provide a powerful tool for diagnostic applications that require rapid cost-effective detection of variations from known sequences.

Rossby wave propagation tracks in southern hemisphere mean basic flows associated to generalized frosts over southern South America

Based on previous observational studies on cold extreme events over southern South America, some recent studies suggest a possible relationship between Rossby wave propagation remotely triggered and the occurrence of frost. Using the concept of linear theory of Rossby wave propagation, this paper analyzes the propagation of such waves in two different basic states that correspond to austral winters with maximum and minimum generalized frost frequency of occurrence in the Wet Pampa (central-northwest Argentina). In order to determine the wave trajectories, the ray tracing technique is used in this study. Some theoretical discussion about this technique is also presented. The analysis of the basic state, from a theoretical point of view and based on the calculation of ray tracings, corroborates that remotely excited Rossby waves is the mechanism that favors the maximum occurrence of generalized frosts. The basic state in which the waves propagate is what conditions the places where they are excited. The Rossby waves are excited in determined places of the atmosphere, propagating towards South America along the jet streams that act as wave guides, favoring the generation of generalized frosts. In summary, this paper presents an overview of the ray tracing technique and how it can be used to investigate an important synoptic event, such as frost in a specific region, and its relationship with the propagation of large scale planetary waves.

The efficiency of excitation of a surface wave on a dielectric cylinder /

Vita.

Two-dimensional photonic crystals in antimony-based films fabricated by holography

In this work, we demonstrated the fabrication of two-dimensional (2D) photonic crystals layers (2D-PCLs) by combining holographic recording and the evaporation of antimony-based glasses. Such materials present high refractive indices that can be tuned from 1.8 to 2.4, depending on the film composition; thus, they are interesting dielectric materials for fabrication of 2D-PCLs. The good quality of the obtained samples allowed the measurement of their PC properties through the well-defined Fano resonances that appear in the transmittance spectrum measurements at different incidence angles. The experimental results are in good agreement with the calculated band diagram for the hexagonal asymmetric structure. (C) 2008 American Institute of Physics.

A Study on Unconditionally Stable FDTD Methods for the Modeling of Metamaterials

We assess the performance of three unconditionally stable finite-difference time-domain (FDTD) methods for the modeling of doubly dispersive metamaterials: 1) locally one-dimensional FDTD; 2) locally one-dimensional FDTD with Strang splitting; and (3) alternating direction implicit FDTD. We use both double-negative media and zero-index media as benchmarks.

MEMS-based incandescent microlamps for integrated optics applications

In this work we present the fabrication and operation of incandescent microlamps for integrated optics applications. This microlamp emits white and infrared light from a chromium resistor embedded in a free-standing silicon oxynitride (SiO(x)N(y)) cantilever that can be coupled to an optical waveguide. In fact, the chromium resistor is sandwiched between layers of SiO(x)N(y) that isolate it from the atmosphere, while electric current heats the resistor to incandescent temperatures. The same SiO(x)N(y) material used in the microlamp fabrication is also used to produce the optical waveguides to allow a monolithic integration of light source and optical circuit. Front-side bulk micromachining of the silicon substrate in potassium hydroxide (KOH) solution is used to fabricate the cantilevers that thermally isolate the resistors from the substrate, thus reducing the heat transfer and the current required to light the lamp.

Development and fabrication of an optimized thermo-electro-optic device using a Mach-Zehnder interferometer

The development and fabrication of a thermo-electro-optic sensor using a Mach-Zehnder interferometer and a resistive micro-heater placed in one of the device`s arms is presented. The Mach-Zehnder structure was fabricated on a single crystal silicon substrate using silicon oxynitride and amorphous hydrogenated silicon carbide films to form an anti-resonant reflective optical waveguide. The materials were deposited by Plasma enhanced chemical vapor deposition technique at low temperatures (similar to 320 degrees C). To optimize the heat transfer and increase the device response with current variation, part of the Mach-Zehnder sensor arm was suspended through front-side bulk micromachining of the silicon substrate in a KOH solution. With the temperature variation caused by the micro-heater, the refractive index of the core layer of the optical waveguide changes due to the thermo-optic effect. Since this variation occurs only in one of the Mach-Zehnder`s arm, a phase difference between the arms is produced, leading to electromagnetic interference. In this way, the current applied to the micro-resistor can control the device output optical power. Further, reactive ion etching technique was used in this work to define the device`s geometry, and a study of SF6 based etching rates on different composition of silicon oxynitride films is also presented. (C) 2007 Elsevier B.V. All rights reserved.

Visible and near-infrared luminescent Eu(3+) or Er(3+) doped laponite-derived xerogels and thick films: Structural and spectroscopic properties

Laponite-derived materials represent promising materials for optical applications. In this work, Eu(3+)- or Er(3+)-doped laponite xerogels and films were prepared from colloidal dispersion. Homogeneous, crack-free and transparent single layers were deposited on soda-lime substrates with a thickness of 10 mu m. Structural and spectroscopic properties were analyzed by thermal analyses, X-ray diffractometry, transmission electron microscopy, infrared spectroscopy, and luminescence spectroscopy. The addition of a rare earth ion to the laponite does not promote any changes in thermal stability or phase transition. Laponite clay was identified after annealing up to 500 degrees C, with a decrease in basal spacing when the annealing temperature is changed from 100 degrees C to 500 degrees C. Enstatite polymorphs and amorphous silicate phases were observed after heat treatment at 700 degrees C and 900 degrees C. Stationary and time-dependent luminescence spectra in the visible region for Eu(3+), and (5)D(0) lifetime are discussed in terms of thermal treatment and structural evolution. In the layered host, the Eu(3+) ions are distributed in many different local environments. However, Eu(3+) ions were found to occupy at least two symmetry sites, and the ions are preferentially incorporated into the crystalline enstatite for the materials annealed at 700 degrees C and 900 degrees C. A (5)D(0) lifetime of 1.3 ms and 3.1 ms was obtained for Eu(3+) ions in an amorphous silicate and crystalline MgSiO(3) local environment, respectively. Strong Er(3+) emission at the 1550 nm region was observed for the materials annealed at 900 degrees C, with a bandwidth of 44 nm. (C) 2008 Elsevier B.V. All rights reserved.

Sol-gel preparation of near-infrared broadband emitting Er(3+)-doped SiO(2)-Ta(2)O(5) nanocomposite films

This article reports a study on the preparation, densification process, and structural and optical properties of SiO(2)-Ta(2)O(5) nanocomposite films obtained by the sol-gel process. The films were doped with Er(3+) and the Si:Ta molar ratio was 90:10. Values of refractive index, thickness and vibrational modes in terms of the number of layers and thermal annealing time are described for the films. The densification process is accompanied by OH group elimination, increase in the refractive index, and changes in film thickness. Full densification of the film is acquired after 90 min of annealing at 900 degrees C. The onset of crystallization and devitrification, with the growth of Ta(2)O(5) nanocrystals occurs with film densification, evidenced by high-resolution transmission electron microscopy. The Er(3+)-doped nanocomposite annealed at 900 degrees C consists of Ta(2)O(5) nanoparticles, with sizes around 2 nm, dispersed in the SiO(2) amorphous phase. The main emission peak of the film is detected at around 1532 nm, which can be assigned to the (4)I(13/2)->(4)I(15/2) transition of the Er(3+) ions present in the nanocomposites. This band has a full width at half medium of 64 nm, and the lifetime measured for the (4)I(13/2) levels is 5.4 ms, which is broader compared to those of other silicate systems. In conclusion, the films obtained in this work are excellent candidates for use as active planar waveguide. (C) 2010 Elsevier B.V. All rights reserved.

Light guiding light: Nonlinear refraction in rubidium vapor

Recently there has been experimental and theoretical interest in cross-dispersion effects in rubidium vapor, which allows one beam of light to be guided by another. We present theoretical results which account for the complications created by the D line hyperfine structure of rubidium as well as the presence of the two major isotopes of rubidium. This allows the complex frequency dependence of the effects observed in our experiments to be understood and lays the foundation for future studies of nonlinear propagation.

General electromagnetic simulation tool to predict the microwave nonlinear response of planar, arbitrarily-shaped HTS structures

This work describes a simulation tool being developed at UPC to predict the microwave nonlinear behavior of planar superconducting structures with very few restrictions on the geometry of the planar layout. The software is intended to be applicable to most structures used in planar HTS circuits, including line, patch, and quasi-lumped microstrip resonators. The tool combines Method of Moments (MoM) algorithms for general electromagnetic simulation with Harmonic Balance algorithms to take into account the nonlinearities in the HTS material. The Method of Moments code is based on discretization of the Electric Field Integral Equation in Rao, Wilton and Glisson Basis Functions. The multilayer dyadic Green's function is used with Sommerfeld integral formulation. The Harmonic Balance algorithm has been adapted to this application where the nonlinearity is distributed and where compatibility with the MoM algorithm is required. Tests of the algorithm in TM010 disk resonators agree with closed-form equations for both the fundamental and third-order intermodulation currents. Simulations of hairpin resonators show good qualitative agreement with previously published results, but it is found that a finer meshing would be necessary to get correct quantitative results. Possible improvements are suggested.

Diffraction grating couplers milled in Si3N4 rib waveguides with a focused ion beam

Focused ion beam milling is a processing technology which allows flexible direct writing of nanometer scale features efficiently substituting electron beam lithography. No mask need results in ability for patterns writing even on fragile micromechanical devices. In this work we studied the abilities of the tool for fabrication of diffraction grating couplers in silicon nitride waveguides. The gratings were fabricated on a chip with extra fragile cantilevers of sub micron thickness. Optical characterization of the couplers was done using excitation of the waveguides in visible range by focused Gaussian beams of different waist sizes. Influence of Ga+ implantation on the device performance was studied.

Filmes de titânio-silício preparados por "spin" e "dip-coating"

The conditions for the preparation of luminescent materials, consisting of Eu3+ ions entrapped in a titanium matrix, in the forma of a thin film, using the sol-gel process, are described. The films were obtained from sols prepared with TEOS and TEOT, in the presence of acetylacetone as the hidrolysis-retarding agent, using the dip-coating and spin-coating techniques. The influence of these techniques on the films based on titanium and silicon are presented. The Eu3+ was used as a luminescent probe. The films have been characterized by luminescence, reflection and transmittance. The thickness of the films could be related to the preparation procedure. Transparent thin films have been prepared by dip-coating technique.

Development and Analysis of a Compact Dual-Band Coplanar Antenna

The coplanar wave guide is an attractive device in microwave integrated circuits due to its uniplanar nature, ease of fabrication and low production cost. Several attempts are already done to explore the radiating modes in coplanar wave guide transmission lines. Usually coplanar wave guides are excited by an SMA connector with its centre conductor connected to the exact middle of the centre strip and the outer ground conductor to the two ground strips. The mode excited on it is purely a bound mode. The E-field distribution in the two slots are out of phase and there for cancels at the far field. This thesis addresses an attempt to excite an in phase E-field distribution in the two slots of the co planar wave guide by employing a feed asymmetry, in order to get radiation from the two large slot discontinuities of the coplanar waveguide. The omni directional distribution of the radiating energy can be achieved by widening the centre strip.The first part of the thesis deals with the investigations on the resonance phenomena of conventional coplanar waveguides at higher frequency bands. Then an offset fed open circuited coplanar waveguide supporting resonance/radiation phenomena is analyzed. Finally, a novel compact co planar antenna geometry with dual band characteristics, suitable for mobile terminal applications is designed and characterized using the inferences from the above study.

Laser microstructuring of azopolymers via surface relief gratings: controlling hydrophobicity

In this paper the large-scale mass transport mechanism is used to microstructure azopolymeric films, aiming at controllable hydrophobic surfaces. Using an Ar(+) laser with intensity of 70 mW/cm(2), we produced egg-crate-like surfaces with periods from 1.0 to 3.5 mu m that present distinct wetting properties. The static contact angle of water was measured on the microstructured surfaces, and the results revealed an increase of approximately 9 degrees for a surface pattern period of 2 mu m. Our results indicate the use of the microstructuring method described here for the fabrication of devices with controllable hydrophobicity.