Publications

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A novel hyperspectral fluorescence microscope for high-resolution 3D optical sectioning of cells and other structures has been designed, constructed, and used to investigate a number of different problems. We have significantly extended new multivariate curve resolution (MCR) data analysis methods to deconvolve the hyperspectral image data and to rapidly extract quantitative 3D concentration distribution maps of all emitting species. The imaging system has many advantages over current confocal imaging systems including simultaneous monitoring of numerous highly overlapped fluorophores, immunity to autofluorescence or impurity fluorescence, enhanced sensitivity, and dramatically improved accuracy, reliability, and dynamic range. Efficient data compression in the spectral dimension has allowed personal computers to perform quantitative analysis of hyperspectral images of large size without loss of image quality. We have also developed and tested software to perform analysis of time resolved hyperspectral images using trilinear multivariate analysis methods. The new imaging system is an enabling technology for numerous applications including (1) 3D composition mapping analysis of multicomponent processes occurring during host-pathogen interactions, (2) monitoring microfluidic processes, (3) imaging of molecular motors and (4) understanding photosynthetic processes in wild type and mutant Synechocystis cyanobacteria.

Sandia National Laboratories, in partnership with the Consumer Product Safety Commission (CPSC), has developed an optical-based sensor for the detection of CO in appliances such as residential furnaces. The device is correlation radiometer based on detection of the difference signal between the transmission spectrum of the sample multiplied by two alternating synthetic spectra (called Eigen spectra). These Eigen spectra are derived from a priori knowledge of the interferents present in the exhaust stream. They may be determined empirically for simple spectra, or using a singular value decomposition algorithm for more complex spectra. Data is presented on the details of the design of the instrument and Eigen spectra along with results from detection of CO in background N{sub 2}, and CO in N{sub 2} with large quantities of interferent CO{sub 2}. Results indicate that using the Eigen spectra technique, CO can be measured at levels well below acceptable limits in the presence of strongly interfering species. In addition, a conceptual design is presented for reducing the complexity and cost of the instrument to a level compatible with consumer products.

We describe the design and operation of a long-working-distance, incoherent light interference microscope that has been developed to address the growing demand for new microsystem characterization tools. The design of the new microscope is similar to that of a Linnik interference microscope and thus preserves the full working distance of the long-working-distance objectives utilized. However, in contrast to a traditional Linnik microscope, the new microscope does not rely on the use of matched objectives in the sample and the reference arms of the interferometer. An adjustable optical configuration has been devised that allows the total optical path length, wavefront curvature, and dispersion of the reference arm to be matched to the sample arm of the interferometer. The reference arm configuration can be adjusted to provide matching for 5×, 10×, and 20× long-working-distance objectives in the sample arm. In addition to retaining the full working distance of the sample arm objectives, the new design allows interference images to be acquired in situations in which intervening windows are necessary, such as occur with packaged microsystems, microfluidic devices, and cryogenic, vacuum, or environmental chamber studies of microsystem performance. The interference microscope is compatible with phase-shifting interferometry, vertical scanning interferometry, and stroboscopic measurement of dynamic processes. © 2005 Optical Society of America.

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The objective of this LDRD project was to develop a programmable diffraction grating fabricated in SUMMiT V{trademark}. Two types of grating elements (vertical and rotational) were designed and demonstrated. The vertical grating element utilized compound leveraged bending and the rotational grating element used vertical comb drive actuation. This work resulted in two technical advances and one patent application. Also a new optical configuration of the Polychromator was demonstrated. The new optical configuration improved the optical efficiency of the system without degrading any other aspect of the system. The new configuration also relaxes some constraint on the programmable diffraction grating.

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This report summarizes the development of new biocompatible self-assembly procedures enabling the immobilization of genetically engineered cells in a compact, self-sustaining, remotely addressable sensor platform. We used evaporation induced self-assembly (EISA) to immobilize cells within periodic silica nanostructures, characterized by unimodal pore sizes and pore connectivity, that can be patterned using ink-jet printing or photo patterning. We constructed cell lines for the expression of fluorescent proteins and induced reporter protein expression in immobilized cells. We investigated the role of the abiotic/biotic interface during cell-mediated self-assembly of synthetic materials.

High throughput instruments and analysis techniques are required in order to make good use of the genomic sequences that have recently become available for many species, including humans. These instruments and methods must work with tens of thousands of genes simultaneously, and must be able to identify the small subsets of those genes that are implicated in the observed phenotypes, or, for instance, in responses to therapies. Microarrays represent one such high throughput method, which continue to find increasingly broad application. This project has improved microarray technology in several important areas. First, we developed the hyperspectral scanner, which has discovered and diagnosed numerous flaws in techniques broadly employed by microarray researchers. Second, we used a series of statistically designed experiments to identify and correct errors in our microarray data to dramatically improve the accuracy, precision, and repeatability of the microarray gene expression data. Third, our research developed new informatics techniques to identify genes with significantly different expression levels. Finally, natural language processing techniques were applied to improve our ability to make use of online literature annotating the important genes. In combination, this research has improved the reliability and precision of laboratory methods and instruments, while also enabling substantially faster analysis and discovery.

This project combined nanocomposite materials with microfabricated optical device structures for the development of microsensor arrays. For the nanocomposite materials we have designed, developed, and characterized self-assembling, organic/inorganic hybrid optical sensor materials that offer highly selective, sensitive, and reversible sensing capability with unique hierarchical nanoarchitecture. Lipid bilayers and micellar polydiacetylene provided selective optical response towards metal ions (Pb(II), Hg(II)), a lectin protein (Concanavalin A), temperature, and organic solvent vapor. These materials formed as composites in silica sol-gels to impart physical protection of the self-assembled structures, provide a means for thin film surface coatings, and allow facile transport of analytes. The microoptical devices were designed and prepared with two- and four-level diffraction gratings coupled with conformal gold coatings on fused silica. The structure created a number of light reflections that illuminated multiple spots along the silica surface. These points of illumination would act as the excitation light for the fluorescence response of the sensor materials. Finally, we demonstrate an integrated device using the two-level diffraction grating coupled with the polydiacetylene/silica material.

Polycrystalline silicon (polysilicon) surface micromachining is a new technology for building micrometer ({micro}m) scale mechanical devices on silicon wafers using techniques and process tools borrowed from the manufacture of integrated circuits. Sandia National Laboratories has invested a significant effort in demonstrating the viability of polysilicon surface micromachining and has developed the Sandia Ultraplanar Micromachining Technology (SUMMiT V{trademark} ) process, which consists of five structural levels of polysilicon. A major advantage of polysilicon surface micromachining over other micromachining methods is that thousands to millions of thin film mechanical devices can be built on multiple wafers in a single fabrication lot and will operate without post-processing assembly. However, if thin film mechanical or surface properties do not lie within certain tightly set bounds, micromachined devices will fail and yield will be low. This results in high fabrication costs to attain a certain number of working devices. An important factor in determining the yield of devices in this parallel-processing method is the uniformity of these properties across a wafer and from wafer to wafer. No metrology tool exists that can routinely and accurately quantify such properties. Such a tool would enable micromachining process engineers to understand trends and thereby improve yield of micromachined devices. In this LDRD project, we demonstrated the feasibility of and made significant progress towards automatically mapping mechanical and surface properties of thin films across a wafer. The MEMS parametrics measurement team has implemented a subset of this platform, and approximately 30 wafer lots have been characterized. While more remains to be done to achieve routine characterization of all these properties, we have demonstrated the essential technologies. These include: (1) well-understood test structures fabricated side-by-side with MEMS devices, (2) well-developed analysis methods, (3) new metrologies (i.e., long working distance interferometry) and (4) a hardware/software platform that integrates (1), (2) and (3). In this report, we summarize the major focus areas of our LDRD project. We describe the contents of several articles that provide the details of our approach. We also describe hardware and software innovations we made to realize a fully automatic wafer prober system for MEMS mechanical and surface property characterization across wafers and from wafer-lot to wafer-lot.

An optical sensor system has been developed for the autonomous monitoring of NO{sub 2} evolution in energetic material aging studies. The system is minimally invasive, requiring only the presence of a small sensor film within the aging chamber. The sensor material is a perylene/PMMA film that is excited by a blue LED light source and the fluorescence detected with a CCD spectrometer. Detection of NO{sub 2} gas is done remotely through the glass window of the aging chamber. Irreversible reaction of NO{sub 2} with perylene, producing the non-fluorescent nitroperylene, provides the optical sensing scheme. The rate of fluorescence intensity loss over time can be modeled using a numerical solution to the coupled diffusion and a nonlinear chemical reaction problem to evaluate NO{sub 2} concentration levels. The light source, spectrometer, spectral acquisition, and data processing were controlled through a Labivew program run by a laptop PC. Due to the long times involved with materials aging studies the system was designed to turn on, warm up, acquire data, power itself off, then recycle at a specific time interval. This allowed the monitoring of aging HE material over the period of several weeks with minimal power consumption and stable LED light output. Despite inherent problems with gas leakage of the aging chamber they were able to test the sensor system in the field under an accelerated aging study of rocket propellant. They found that the propellant evolved NO{sub 2} at a rate that yielded a concentration of between 10 and 100 ppm. The sensor system further revealed that the propellant, over an aging period of 25 days, evolves NO{sub 2} with cyclic behavior between active and dormant periods.

A new instrument to accurately and verifiably measure mechanical properties across an entire MEMS wafer is under development. We have modified the optics on a conventional microelectronics probe station to enable three-dimensional imaging while maintaining the full working distance of a long working distance objective. This allows standard probes or probe cards to be used. We have proceeded to map out mechanical properties of polycrystalline silicon along a wafer column by the Interferometry for Material Property Measurement (IMaP) methodology. From interferograms of simple actuated cantilevers, out-of-plane deflection profiles at the nanometer scale are obtained. These are analyzed by integrated software routines that extract basic mechanical properties such as cantilever curvature and Young's modulus. Non-idealities such as support post compliance and beam take off angle are simultaneously quantified. Curvature and residual stress are found to depend on wafer position. Although deflections of cantilevers varied across the wafer, Young's modulus E - 161 GPa is independent of wafer position as expected. This result is achieved because the non-idealities have been taken into account.

The authors report here the design, fabrication and demonstration of an electrostatically actuated MEMS diffractive optical device, the Polychromator grating. The Polychromator grating enables a new type of correlation spectrometer for remote detection of a wide range of chemical species, offering electronic programmability, high specificity and sensitivity, fast response and ruggedness. Significant results include: (1) The first demonstrations of user-defined synthetic spectra in the 3-5 {micro}m wavelength regime based upon controlled deflection of individual grating elements in the Polychromator grating; (2) The first demonstration of gas detection by correlation spectroscopy using synthetic spectra generated by the Polychromator grating.

We report the first experimental observation of non-classical morphological equilibration of a corrugated crystalline surface. Periodic rippled structures with wavelengths of 290-550 nm were made on Si(OO1) by sputter rippling and then annealed at 650 - 750 °C. In contrast to the classical exponential decay with time, the ripple amplitude, A_{lambda}(t), followed an inverse linear decay, A_{lambda}(t)= A_{lambda}(0)/(1 +k_{lambda}t), agreeing with a prediction of Ozdemir and Zangwill. We measure the activation energy for surface relaxation to be 1.6±0.2 eV, consistent with an interpretation that dimers mediate transport.

The time evolution of the amplitude of periodic nanoscale ripple patterns formed on Ar+ sputtered Si(OOl ) surfaces was examined using a recently developed in situ spectroscopic technique. At sufficiently long times, we find that the amplitude does not continue to grow exponentially as predicted by the standard Bradley-Harper sputter rippling model. In accounting for this discrepancy, we rule out effects related to the concentration of mobile species, high surface curvature, surface energy anisotropy, and ion-surface interactions. We observe that for all wavelengths the amplitude ceases to grow when the width of the topmost terrace of the ripples is reduced to approximately 25 nm. This observation suggests that a short circuit relaxation mechanism limits amplitude . growth. A strategy for influencing the ultimate ripple amplitude is discussed.

As a first step toward the development of a new remote sensing technique that we call "holographic correlation spectroscopy," we demonstrate that diffractive optics can be used to synthesize the IR spectra of real compounds. In particular, we have designed, fabricated, and characterized a diffractive element that successfully reproduces the major features of the spectrum of gaseous HF in the region between 3600 cm-1 and 4300 cm-1. The reflection-mode diffractive optic consists of 4096 lines, each 4.5 micrometers wide, at 16 discrete depths relative to the substrate, and was fabricated on a silicon wafer using anisotropic reactive ion-beam etching in a four-mask-level process. We envision the use diffractive elements of this type to replace the cumbersome reference cells of conventional correlation spectroscopy and thereby enable a new class of compact and versatile correlation spectrometers. ©2004 Copyright SPIE - The International Society for Optical Engineering.