Nancy Stoffel

Fast PCR Thermal Cycling Device

A novel flow-through device for performing fast PCR thermal cycling is presented. The thermal gradient thermal cycling device is comprised of layers of highly thermally conducting material separated by insulating layers. Channels etched in the conducting and insulating layers create one continuous path through the device. When the device is held between platens at different temperatures and PCR sample mix is pumped through it, every fluid particle undergoes the time-temperature protocol necessary for PCR but with a temperature change rate not possible with conventional cyclers. Ultrafast thermal cycling makes it ideal for bio-defense applications, such as the instantaneous bio-aerosol agent identification system under development for the Department of Homeland Security. Its compact size and simplicity of use make it a natural choice for diagnostics, forensics, food and water testing and other DNA testing applications. Herein we describe the design and fabrication of the device developed for IBADS and the subsequent performance with various assays using plasmid and genomic template DNA. Performance under some circumstances was exceptional: Amplification rates of up to two decades per minute were recorded and total amplification of up to eight decades in 30 cycles was seen. We discuss how to optimize the performance of a device that pushes PCR to its fundamental limits and review a wide variety of performance data.

Diamond shaped ring laser characterization, package design and performance

A semiconductor diamond-shaped ring laser was fabricated and packaged for further test and analysis as an element in digital photonic logic. The optical characteristics of the ring laser were quantified in order to design a prototype package. The mode field was found to be quasi-circular. Based on the mode field of the laser, coupling curves were calculated and Corning OptiFocustrade lensed fiber was chosen to use for the four fiber outputs. Each fiber placement was actively optimized. Output power measurements were made for each facet before and after fiber coupling. Reflections from fiber tips were found to affect the final output power distribution of the device even though the fibers were anti-reflection (AR) coated, and additional effort was put into minimizing its variance. The packaged devices were tested for performance in digital photonic logic applications. Tests conducted to this point indicate that the packaging enabled a multiple port device of this type to be sufficiently portable for field testing

Injection characterization of packaged bi-directional diamond shaped ring lasers at 1550 nm

The Air Force Research Laboratory, Binoptics Corp., and Infotonics Technology Center worked collaboratively to package and characterize recently developed diode based ring lasers that operate at 1550 nm in a diamond shaped cavity. The laser modes propagate bi-directionally; however, uniaxial propagation may be induced by optical injection or by integrating a mirror. Round trip cavity length was 500 μm in 3.5 μm wide ridge waveguides, and four polarization-maintaining lensed fibers provided access to the input and output modes. A signal from a tunable diode laser, incident at one port, served to injection lock both of the counter-propagating circulating modes. When the input signal was time-encoded by an optical modulator, the encoding was transferred to both modes with an inverted time-intensity profile. Performance, in terms of fidelity and extinction ratio, is characterized for selected pulsed and monochromatic formats from low frequencies to those exceeding 12 GHz. A rate equation model is proposed to account for certain aspects of the observed behavior and analog and digital applications are discussed.

Characterization of an electroabsorption modulator design with high-dynamic range for broadband analog applications

An electroabsorption modulator (EAM) is designed to optimize dynamic range performance over 20 GHz bandwidth. The single stripe waveguide enables an extremely compact and integrated package to be fabricated with single mode fiber pigtails. The transfer functions shape permits suppression of higher order intermodulation products, yielding a spur-free dynamic range exceeding that of Mach- Zehnder designs. A dilute optical core diverts energy flow from absorbing layers into low loss waveguide; the 20 dBm optical power tolerance is significantly higher than that of commercially available electroabsorption devices. The tunable performance over 20 GHz is characterized and applications are discussed. New approaches to the broadband impedance matching requirements are calculated and the impact on system performance is assessed.

Electronic packaging of sensors for lower limb prosthetics

Millivolt level signals generated in residual muscles can be used to control sophisticated upper limb prosthetics. The low level voltages known as surface-electromyogram (sEMG) signals have seldom been applied in lower limbs due to moisture, large pressure, and shear forces which induced anomalies, and in particular triboelectric interference. An electronic module, known as a multi-sensor unit or MSU incorporates a multiplicity of sensors which promises to overcome the problems with sEMG in lower limbs. By incorporating a multiplicity of signals from what is physically happening in terms of pressure, temperature, and surface shear, it is anticipated that the sEMG signals can be corrected. Testing of the MSU with able bodied personnel and amputees is currently under way at Clarkson University. The MSU, which is totally potted is soft silicone rubber, measures sEMG, pressure, axial and tangential shear, and temperature. The 35×65×6.5mm electronic module is thin enough to be comfortably inserted between the liner of the prosthetic and the residual lower limb. As part of the program, a unique MEMS shear sensor, capable of being totally encased in silicone rubber, was developed. The temperature and pressure sensor are based on commercial off-the-shelf sensors. The design of the shear sensors is based on bonding a glass ball to a commercial off-the-shelf pressure sensor, thus avoiding the costly development of a custom shear sensor. The final MSU is both waterproof and rugged. Preliminary test results are briefly presented.

Photoacoustic spectroscopy for trace vapor detection and molecular discrimination

Photoacoustic spectroscopy (PAS) is a useful monitoring technique that is well suited for trace gas detection. This method routinely exhibits detection limits at the parts-per-million (ppm) or parts-per-billion (ppb) level for gaseous samples. PAS also possesses favorable detection characteristics when the system dimensions are scaled to a microsystem design. Current research utilizes quantum cascade lasers (QCLs) in combination with micro-electromechanical systems (MEMS)-scale photoacoustic cell designs. This sensing platform has provided favorable detection limits for a standard nerve agent simulant. The objective of the present work is to demonstrate an extremely versatile MEMS-scale photoacoustic sensor system that is able to discriminate between different analytes of interest.

Design and development of a package for a diluted waveguide electro-absorption modulator

Externally coupled electroabsorption modulators (EAM) are commonly used in order to transmit RF signals on optical fibers. Recently an alternative device design with diluted waveguide structures has been developed. [1] Bench tests show benefits of lower propagation loss, higher power handling (100 mW), and higher normalized slope efficiency. This paper addresses the specific issues involved in packaging the diluted waveguide EAM devices. An evaluation of the device requirements was done relative to the standard processes. Bench tests were performed in order to characterize the optical coupling of the EAM. The photo current maximum was offset from the optical power output maximum. The transmissions vs. bias voltage curves were measured, and an XY scanner was used to record the mode field of the light exiting from the EAM waveguide in each position. The Beam Propagation Method was used to simulate the mode field and the coupling efficiency. Based on the bench tests and simulation results, a design including mechanical, optical and RF elements was developed. A Newport Laser Welding system was utilized for fiber placement and fixation. The laser welding techniques were customized in order to meet the needs of the EAM package design.

Micro-Hermetic Packaging Technology for Active Implantable Neural Interfaces

In this paper, we propose a fused silica packaging platform with a micro-cavity designed to house and protect active electronics for neural interfaces. Proof-of-concept test vehicles were specifically designed, fabricated, and packaged in order to evaluate the ability of the packaging to protect against water and ion incursion. Accelerated degradation testing of three test vehicles in physiological saline was performed in a custom-built encapsulation test system (ETS) at 57 °C for 16 days (nominally equivalent to 68 days at 37 °C). Leakage current, as well as gross functionality of the test circuit, was evaluated and is presented as preliminary results.

Wafer Level Assembly Methods for Complex Pathway Micro-Fluidic PCR Reactor

Micro-fluidic devices were fabricated that amplify DNA segments using the polymerase chain reaction (PCR). These devices employ a unique passive heating methodology that provides ultra-fast fluidic temperature transitions. The devices consist of alternating layers of thermally conductive and insulative layers. The highly thermally conductive layers consist of silicon etched to form vias and micro-channels. The thermally insulative layers were made of polyetherimide layers with laser ablated vias. Individual layers of materials were aligned and joined together to create this device. Novel joining technologies developed for the project included the epoxy specifically targeted for adhesive printing and the mechanical alignment methods. A custom formulated epoxy was created to give a submicron bond line that is controllable, strong, and highly resistant to aqueous and solvent exposure. The bonding temperature was less than 200degC, creating leak-free continuous micro-fluidic pathways. Biocompatible coatings were applied to the entire length of the 600 mm internal pathway before use. The device was used to successfully demonstrate PCR reaction times of less than 5 minutes; this is in comparison to the conventional methods which take several hours.