Publications

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Membrane projection lithography is extended from a single layer fabrication technique to a multilayer process, adding polymeric backfill and planarization after each layer is completed. Unaligned contact lithography is used as a rapid prototyping tool to aid in process development, patterning resist membranes in seconds without requiring long e-beam write times. The fabricated multilayer structures show good resistance to solvent attack from subsequent process steps and demonstrate in-plane and out of plane multilayer metallic inclusions in a dielectric host, which is a critical step in the path to develop bulklike metamaterials at optical frequencies.

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Interaction between metamaterial elements and intersubband transitions in GaAs/AlGaAs quantum wells is observed in the mid-infrared. Transmission measurements were performed through metamaterial arrays, each having a different resonance frequency. © 2011 OSA.

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Novel low loss photopatternable matrix materials for IR metamaterial applications were synthesized using the ring opening metathesis polymerization reaction (ROMP) of norbornene followed by a partial hydrogenation to remove most of the IR absorbing olefin groups which absorb in the 8-12 {micro}m range. Photopatterning was achieved via crosslinking of the remaining olefin groups with alpha, omega-dithiols via the thiol-ene coupling reaction. Since ROMP is a living polymerization the molecular weight of the polymer can be controlled simply by varying the ratio of catalyst to monomer. In order to determine the optimum photopattenable IR matrix material we varied the amount of olefin remaining after the partial hydrogenation. Hydrogenation was accomplished using tosyl hydrazide. The degree of hydrogenation can be controlled by altering the reaction time or reaction stoichiometry and the by-products can be easily removed during workup by precipitation into ethanol. Several polymers have been prepared using this reduction scheme including two polymers which had 54% and 68% olefin remaining. Free standing films (approx. 12 {micro}m) were prepared from the 68% olefin material using draw-down technique and subsequently irradiated with a UV lamp (365 nm) for thirty minutes to induce crosslinking via thiol-ene reaction. After crosslinking, the olefin IR-absorption band disappeared and the Tg of the matrix material increased; both desirable properties for IR metamaterial applications. The polymer system has inherent photopatternable behavior primarily because of solubility differences between the pre-polymer and cross-linked matrix. Photopatterned structures using the 54% as well as the 68% olefin material were easily obtained. The synthesis, processing, and IR absorption data and the ramifications to dielectric metamaterials will be discussed.

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A considerable amount research is being conducted on microalgae, since microalgae are becoming a promising source of renewable energy. Most of this research is centered on lipid production in microalgae because microalgae produce triacylglycerol which is ideal for biodiesel fuels. Although we are interested in research to increase lipid production in algae, we are also interested in research to sustain healthy algal cultures in large scale biomass production farms or facilities. The early detection of fluctuations in algal health, productivity, and invasive predators must be developed to ensure that algae are an efficient and cost-effective source of biofuel. Therefore we are developing technologies to monitor the health of algae using spectroscopic measurements in the field. To do this, we have proposed to spectroscopically monitor large algal cultivations using LIDAR (Light Detection And Ranging) remote sensing technology. Before we can deploy this type of technology, we must first characterize the spectral bio-signatures that are related to algal health. Recently, we have adapted our confocal hyperspectral imaging microscope at Sandia to have two-photon excitation capabilities using a chameleon tunable laser. We are using this microscope to understand the spectroscopic signatures necessary to characterize microalgae at the cellular level prior to using these signatures to classify the health of bulk samples, with the eventual goal of using of LIDAR to monitor large scale ponds and raceways. By imaging algal cultures using a tunable laser to excite at several different wavelengths we will be able to select the optimal excitation/emission wavelengths needed to characterize algal cultures. To analyze the hyperspectral images generated from this two-photon microscope, we are using Multivariate Curve Resolution (MCR) algorithms to extract the spectral signatures and their associated relative intensities from the data. For this presentation, I will show our two-photon hyperspectral imaging results on a variety of microalgae species and show how these results can be used to characterize algal ponds and raceways.

An overwhelming majority of metamaterial designs that have been proposed thus far rely on the use of metallic resonators to afford properties that are unprecedented in nature. Though well suited for applications at radio and microwave frequencies, metals experience severe ohmic losses at higher frequencies rendering their use at such frequencies impractical. Certainly the future of metamaterials lies in their implementation in the visible and long wavelength infrared (LWIR, 8-12 {micro}m). Thus, alternative design protocols and material components tailored specifically for these frequencies are highly attractive. Herein, we present low permittivity, low permeability polymer dielectric materials that are well suited substrates for LWIR-metamaterial applications. These materials lack vibrational absorption bands in the 8-12 {micro}m range are 3D fabrication compatible, photopatternable, and high temperature tolerant. Thus, these materials are ideal for fabrication of 3D metamaterial structures operating in the LWIR and can also serve as negative photoresists for contact lithography applications.

We will present a study of the structure-property relations in Reststrahlen materials that possess a band of negative permittivities in the infrared. It will be shown that sub-micron defects strongly affect the optical response, resulting in significantly diminished permittivities. This work has implications on the use of ionic materials in IR-metamaterials.

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The role of crystal coherence length on the infrared optical response of MgO thin films was investigated with regard to Reststrahlen band photon-phonon coupling. Preferentially (001)-oriented sputtered and evaporated ion-beam assisted deposited thin films were prepared on silicon and annealed to vary film microstructure. Film crystalline coherence was characterized by x-ray diffraction line broadening and transmission electron microscopy. The infrared dielectric response revealed a strong dependence of dielectric resonance magnitude on crystalline coherence. Shifts to lower transverse optical phonon frequencies were observed with increased crystalline coherence. Increased optical phonon damping is attributed to increasing granularity and intergrain misorientation.

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This paper introduces an effective-media toolset that can be used for the design of metamaterial structures based on metallic components such as split-ring resonators and dipoles, as well as dielectric spherical resonators. For demonstration purposes the toolset will be used to generate infrared metamaterial designs, and the predicted performances will be verified with full-wave numerical simulations.

Metamaterials form a new class of artificial electromagnetic materials that provides the device designer with the ability to manipulate the flow of electromagnetic energy in ways that are not achievable with naturally occurring materials. However, progress toward practical implementation of metamaterials, particularly at infrared and visible frequencies, has been hampered by a combination of absorptive losses; the narrow band nature of the resonant metamaterial response; and the difficulty in fabricating fully 3-dimensional structures. They describe the progress of a recently initiated program at Sandia National Laboratories directed toward the development of practical 3D metamaterials operating in the thermal infrared. They discuss their analysis of fundamental loss limits for different classes of metamaterials. In addition, they discuss new design approaches that they are pursuing which reduce the reliance on metallic structures in an effort to minimize ohmic losses.

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We present a new fabrication technique called Membrane Projection Lithography for the production of three-dimensional metamaterials at infrared wavelengths. Using this technique, multilayer infrared metamaterials that include both in-plane and out-of-plane resonators can be fabricated.

Dielectric resonators are an effective means to realize isotropic, low-loss optical metamaterials. As proof of this concept, a cubic resonator is analytically designed and then tested in the long-wave infrared.

The authors have developed two versions of a flexible fabrication technique known as membrane projection lithography that can produce nearly arbitrary patterns in '212 D' and fully three-dimensional (3D) structures. The authors have applied this new technique to the fabrication of split ring resonator-based metamaterials in the midinfrared. The technique utilizes electron beam lithography for resolution, pattern design flexibility, and alignment. The resulting structures are nearly three orders of magnitude smaller than equivalent microwave structures that were first used to demonstrate a negative index material. The fully 3D structures are highly isotropic and exhibit both electrically and magnetically excited resonances for incident transverse electromagnetic waves.

Most far-field optical imaging systems rely on a lens and spatially-resolved detection to probe distinct locations on the object. We describe and demonstrate a novel high-speed wide-field approach to imaging that instead measures the complex spatial Fourier transform of the object by detecting its spatially-integrated response to dynamic acousto-optically synthesized structured illumination. Tomographic filtered backprojection is applied to reconstruct the object in two or three dimensions. This technique decouples depth-of-field and working-distance from resolution, in contrast to conventional imaging, and can be used to image biological and synthetic structures in fluoresced or scattered light employing coherent or broadband illumination. We discuss the electronically programmable transfer function of the optical system and its implications for imaging dynamic processes. Finally, we present for the first time two-dimensional high-resolution image reconstructions demonstrating a three-orders-of-magnitude improvement in depth-of-field over conventional lens-based microscopy.

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3-D cubic unit cell arrays containing split ring resonators were fabricated and characterized. The unit cells are {approx}3 orders-of-magnitude smaller than microwave SRR-based metamaterials and exhibit both electrically and magnetically excited resonances for normally incident TEM waves in addition to showing improved isotropic response.

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We describe a time-domain spectroscopy system in the thermal infrared used for complete transmission and reflection characterization of metamaterials in amplitude and phase. The system uses a triple-output near-infrared ultrafast fiber laser, phase-locked difference frequency generation and phase-matched electro-optic sampling. We will present measurements of several metamaterials designs.

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The authors experimentally demonstrate a resonant hybridization between the magnetic dipole structural resonance in the permeability of a fishnet metamaterial and an electric dipole material resonance in the permittivity of the dielectric spacer layer. The hybrid resonances in the permeability and the negative index response exhibit an anticrossing behavior. A simple analytic model and numerical simulations using a rigorous coupled-wave analysis are in excellent qualitative agreement with the experiment. © 2010 American Vacuum Society.

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Cellular autofluorescence, though ubiquitous when imaging cells and tissues, is often assumed to be small in comparison to the signal of interest. Uniform estimates of autofluorescence intensity obtained from separate control specimens are commonly employed to correct for autofluorescence. While these may be sufficient for high signal-to-background applications, improvements in detector and probe technologies and introduction of spectral imaging microscopes have increased the sensitivity of fluorescence imaging methods, exposing the possibility of effectively probing the low signal-to-background regime. With spectral imaging, reliable monitoring of signals near or even below the noise levels of the microscope is possible if autofluorescence and background signals can be accurately compensated for. We demonstrate the importance of accurate autofluorescence determination and utility of spectral imaging and multivariate analysis methods using a case study focusing on fluorescence confocal spectral imaging of host-pathogen interactions. In this application fluorescent proteins are produced when bacteria invade host cells. Unfortunately the analyte signal is spectrally overlapped and typically weaker than the cellular autofluorescence. In addition to discussing the advantages of spectral imaging for following pathogen invasion, we present the spectral properties of mouse macrophage autofluorescence. The imaging and analysis methods developed are widely applicable to cell and tissue imaging. © 2008 Copyright SPIE - The International Society for Optical Engineering.

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We have developed a system to measure the directional thermal emission from a surface, and in turn, calculate its emissivity. This approach avoids inaccuracies sometimes encountered with the traditional method for calculating emissivity, which relies upon subtracting the measured total reflectivity and total transmissivity from unity. Typical total reflectivity measurements suffer from an inability to detect backscattered light, and may not be accurate for high angles of incidence. Our design allows us to vary the measurement angle (θ) from near-normal to ∼80°, and can accommodate samples as small as 7 mm on a side by controlling the sample interrogation area. The sample mount is open-backed to eliminate shine-through, can be heated up to 200°C, and is kept under vacuum to avoid oxidizing the sample. A cold shield reduces the background noise and stray signals reflected off the sample. We describe the strengths, weaknesses, trade-offs, and limitations of our system design, data analysis methods, the measurement process, and present the results of our validation of this Variable-Angle Directional Emissometer.

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Production of renewable biofuels to displace fossil fuels currently consumed in the transportation sector is a pressing multi-agency national priority. Currently, nearly all fuel ethanol is produced from corn-derived starch. Dedicated 'energy crops' and agricultural waste are preferred long-term solutions for renewable, cheap, and globally available biofuels as they avoid some of the market pressures and secondary greenhouse gas emission challenges currently facing corn ethanol. These sources of lignocellulosic biomass are converted to fermentable sugars using a variety of chemical and thermochemical pretreatments, which disrupt cellulose and lignin cross-links, allowing exogenously added recombinant microbial enzymes to more efficiently hydrolyze the cellulose for 'deconstruction' into glucose. This process is plagued with inefficiencies, primarily due to the recalcitrance of cellulosic biomass, mass transfer issues during deconstruction, and low activity of recombinant deconstruction enzymes. Costs are also high due to the requirement for enzymes and reagents, and energy-intensive and cumbersome pretreatment steps. One potential solution to these problems is found in synthetic biology; they propose to engineer plants that self-produce a suite of cellulase enzymes targeted to the apoplast for cleaving the linkages between lignin and cellulosic fibers; the genes encoding the degradation enzymes, also known as cellulases, are obtained from extremophilic organisms that grow at high temperatures (60-100 C) and acidic pH levels (<5). These enzymes will remain inactive during the life cycle of the plant but become active during hydrothermal pretreatment i.e., elevated temperatures. Deconstruction can be integrated into a one-step process, thereby increasing efficiency (cellulose-cellulase mass-transfer rates) and reducing costs. The proposed disruptive technologies address biomass deconstruction processes by developing transgenic plants encoding a suite of enzymes used in cellulosic deconstruction. The unique aspects of this technology are the rationally engineered, highly productive extremophilic enzymes, targeted to specific cellular locations (apoplast) and their dormancy during normal plant proliferation, which become Trojan horses during pretreatment conditions. They have been leveraging established Sandia's enzyme-engineering and imaging capabilities. Their technical approach not only targets the recalcitrance and mass-transfer problem during biomass degradation but also eliminates the costs associated with industrial-scale production of microbial enzymes added during processing.

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The combination of hyperspectral confocal fluorescence microscopy and multivariate curve resolution (MCR) provides an ideal system for improved quantitative imaging when multiple fluorophores are present. However, the presence of multiple noise sources limits the ability of MCR to accurately extract pure-component spectra when there is high spectral and/or spatial overlap between multiple fluorophores. Previously, MCR results were improved by weighting the spectral images for Poisson-distributed noise, but additional noise sources are often present. We have identified and quantified all the major noise sources in hyperspectral fluorescence images. Two primary noise sources were found: Poisson-distributed noise and detector-read noise. We present methods to quantify detector-read noise variance and to empirically determine the electron multiplying CCD (EMCCD) gain factor required to compute the Poisson noise variance. We have found that properly weighting spectral image data to account for both noise sources improved MCR accuracy. In this paper, we demonstrate three weighting schemes applied to a real hyperspectral corn leaf image and to simulated data based upon this same image. MCR applied to both real and simulated hyperspectral images weighted to compensate for the two major noise sources greatly improved the extracted pure emission spectra and their concentrations relative to MCR with either unweighted or Poisson-only weighted data. Thus, properly identifying and accounting for the major noise sources in hyperspectral images can serve to improve the MCR results. These methods are very general and can be applied to the multivariate analysis of spectral images whenever CCD or EMCCD detectors are used. Copyright © 2008 John Wiley & Sons, Ltd.

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Hyperspectral imaging confocal microscopy (HSI-CM) is a powerful tool for the analysis of cellular processes such as the immune response. HSI-CM is a data rich technique that routinely generates two-way data having a spectral domain and an image or concentration domain. Using a variety of modifications to the instrument or experimental protocols, one can readily produce three-way data with HSI-CM. These data are often amenable to trilinear analysis. For example we have used a time series of 18 images acquired during photobleaching of the fluorophores in an effort to identify fluorescence resonance energy transfer (FRET). The resulting images represent intensity as a function of concentration, wavelength and photodegradation in time, to which we apply our techniques of trilinear decomposition. We have successfully employed trilinear decomposition of photobleaching spectral image data from fixed A549 cells transfected with yellow and green fluorescent proteins (YFP and GFP) as molecular probes of cellular proteins involved in the cellular immune response. While useful in the interpretation biological processes, the size of the data generated with the HSI-CM can be difficult to manage computationally. The 208 x 204 x 512 x 18 elements in the image data require careful processing and efficient analysis algorithms. Accordingly, we have implemented fast algorithms that can quickly perform the trilinear decomposition. In this paper we describe how three-way data are produced and the methods we have used to process them. Specifically, we show that co-adding spectra in a spatial neighborhood is a highly effective method for improving the performance of these algorithms without sacrificing resolution. Copyright © 2008 John Wiley & Sons, Ltd.

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Simultaneous imaging of multiple cellular components is of tremendous importance in the study of complex biological systems, but the inability to use probes with similar emission spectra and the time consuming nature of collecting images on a confocal microscope are prohibitive. Hyperspectral imaging technology, originally developed for remote sensing applications, has been adapted to measure multiple genes in complex biological tissues. A spectral imaging microscope was used to acquire overlapping fluorescence emissions from specific mRNAs in brain tissue by scanning the samples using a single fluorescence excitation wavelength. The underlying component spectra obtained from the samples are then separated into their respective spectral signatures using multivariate analyses, enabling the simultaneous quantitative measurement of multiple genes either at regional or cellular levels. © 2006 Elsevier B.V. All rights reserved.

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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.

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Multivariate data analysis applied to hyperspectral images offers the unique opportunity to dramatically increase the amount of information gained from a single biological sample. Numerous fluorescent tags can be used to perform multiple studies in parallel from a single hyperspectral image scan. Highly spatially and spectrally overlapping fluorophores can be separated even amidst a large autofluorescence background with the use of multivariate curve resolution methods. The results of two biological samples with multiple fluorescent labels are shown and compared to a traditional filter-based multispectral system. These examples illustrate the combined power of the hyperspectral microscope hardware and the multivariate image analysis software for biomedical imaging. This technique has the potential to be applied to a broad array of biological applications where fluorescent tags are a central and ubiquitous tool, and to biomedical areas that focus on the discovery and identification of weak, broad spectrum native fluorescence. © 2006 IEEE.

We have developed a new, high performance, hyperspectral microscope for biological and other applications. For each voxel within a three-dimensional specimen, the microscope simultaneously records the emission spectrum from 500 nm to 800 nm, with better than 3 nm spectral resolution. The microscope features a fully confocal design to ensure high spatial resolution and high quality optical sectioning. Optical throughput and detection efficiency are maximized through the use of a custom prism spectrometer and a backside thinned electron multiplying charge coupled device (EMCCD) array. A custom readout mode and synchronization scheme enable 512-point spectra to be recorded at a rate of 8300 spectra per second. In addition, the EMCCD readout mode eliminates curvature and keystone artifacts that often plague spectral imaging systems. The architecture of the new microscope is described in detail, and hyperspectral images from several specimens are presented.

Hyperspectral imaging provides complex image data with spectral information from many fluorescent species contained within the sample such as the fluorescent labels and cellular or pigment autofluorescence. To maximize the utility of this spectral imaging technique it is necessary to couple hyperspectral imaging with sophisticated multivariate analysis methods to extract meaningful relationships from the overlapped spectra. Many commonly employed multivariate analysis techniques require the identity of the emission spectra of each component to be known or pure component pixels within the image, a condition rarely met in biological samples. Multivariate curve resolution (MCR) has proven extremely useful for analyzing hyperspectral and multispectral images of biological specimens because it can operate with little or no a priori information about the emitting species, making it appropriate for interrogating samples containing autofluorescence and unanticipated contaminating fluorescence. To demonstrate the unique ability of our hyperspectral imaging system coupled with MCR analysis techniques we will analyze hyperspectral images of four-color in-situ hybridized rat brain tissue containing 455 spectral pixels from 550 - 850 nm. Even though there were only four colors imparted onto the tissue in this case, analysis revealed seven fluorescent species, including contributions from cellular autofluorescence and the tissue mounting media. Spectral image analysis will be presented along with a detailed discussion of the origin of the fluorescence and specific illustrations of the adverse effects of ignoring these additional fluorescent species in a traditional microscopy experiment and a hyperspectral imaging system.

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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.

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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.

Basic research is needed to better understand the potential risk of dangerous biological agents that are unintentionally or intentionally introduced into a water distribution system. We report on our capabilities to conduct such studies and our preliminary investigations. In 2004, the Biofilms Laboratory was initiated for the purpose of conducting applied research related to biofilms with a focus on application, application testing and system-scale research. Capabilities within the laboratory are the ability to grow biofilms formed from known bacteria or biofilms from drinking water. Biofilms can be grown quickly in drip-flow reactors or under conditions more analogous to drinking-water distribution systems in annular reactors. Biofilms can be assessed through standard microbiological techniques (i .e, aerobic plate counts) or with various visualization techniques including epifluorescent and confocal laser scanning microscopy and confocal fluorescence hyperspectral imaging with multivariate analysis. We have demonstrated the ability to grow reproducible Pseudomonas fluorescens biofilms in the annular reactor with plate counts on the order of 10{sup 5} and 10{sup 6} CFU/cm{sup 2}. Stationary phase growth is typically reached 5 to 10 days after inoculation. We have also conducted a series of pathogen-introduction experiments, where we have observed that both polystyrene microspheres and Bacillus cereus (as a surrogate for B. anthracis) stay incorporated in the biofilms for the duration of our experiments, which lasted as long as 36 days. These results indicated that biofilms may act as a safe harbor for bio-pathogens in drinking water systems, making it difficult to decontaminate the systems.

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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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Multivariate curve resolution (MCR) using constrained alternating least squares algorithms represents a powerful analysis capability for the quantitative analysis of hyperspectral image data. We will demonstrate the application of MCR using data from a new hyperspectral fluorescence imaging microarray scanner for monitoring gene expression in cells from thousands of genes on the array. The new scanner collects the entire fluorescence spectrum from each pixel of the scanned microarray. Application of MCR with nonnegativity and equality constraints reveals several sources of undesired fluorescence that emit in the same wavelength range as the reporter fluorophores. MCR analysis of the hyperspectral images confirms that one of the sources of fluorescence is due to contaminant fluorescence under the printed DNA spots that is spot localized. Thus, traditional background subtraction methods used with data collected from the current commercial microarray scanners will lead to errors in determining the relative expression of low-expressed genes. With the new scanner and MCR analysis, we generate relative concentration maps of the background, impurity, and fluorescent labels over the entire image. Since the concentration maps of the fluorescent labels are relatively unaffected by the presence of background and impurity emissions, the accuracy and useful dynamic range of the gene expression data are both greatly improved over those obtained by commercial microarray scanners.

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.

We describe the design, construction, and operation of a hyperspectral microarray scanner for functional genomic research. The hyperspectral instrument operates with spatial resolutions ranging from 3 to 30 {micro}m and records the emission spectrum between 490 and 900 nm with a spectral resolution of 3 nm for each pixel of the microarray. This spectral information, when coupled with multivariate data analysis techniques, allows for identification and elimination of unwanted artifacts and greatly improves the accuracy of microarray experiments. Microarray results presented in this study clearly demonstrate the separation of fluorescent label emission from the spectrally overlapping emission due to the underlying glass substrate. We also demonstrate separation of the emission due to green fluorescent protein expressed by yeast cells from the spectrally overlapping autofluorescence of the yeast cells and the growth media.

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.