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Rational Design of Nanoplasmonic Array Geometries for Biosensing

Background: Molecular diagnostics provide early and accurate diagnosis, which is essential for the prevention and treatment of infectious as well as chronic diseases. These tests are designed to detect disease-specific bioanalytes such as nucleic acid (DNA or RNA) or protein (antigens, antibodies) biomarkers. In the context of infectious disease diagnosis, nucleic acid-based detection methods are known to provide more specific and sensitive results. Here, the presence of a unique sequence belonging to the pathogenic genomic material is targeted to identify species, organism, genera and/or antimicrobial resistant gene markers. The majority of the common nucleic acid based diagnostic techniques require amplification (polymerase chain reaction, isothermal amplification etc.) of the pathogenic genetic material prior to detection impacting diagnostic speed, complexity, and cost thereby limiting ease of use. Thus, the development of simplified nucleic acid-based diagnostics that can be even used in resource-poor settings may hugely benefit patients across the globe. Nanopath is a molecular diagnostics company utilizing a solid-state nanosensor to enable sequence-specific detection of target nucleic acids without the need of amplification. These nanostructures enable ultra-sensitive biomarker detection using geometric, feature-dependent properties highly dependent on the local dielectric environment, allowing them to be sensitive to low concentration binding events. This paper describes an application of this approach to provide highly relevant clinical information within a single doctor’s office visit. Intro: The Nanopath team is in collaboration with NASA (National Aeronautics and Space Administration) and NIST (National Institute of Standards and Technology) to push the bounds of the fundamental physics associated with their biosensing platform. The ability of metals to support electromagnetic surface waves gives rise to surface plasmons when optically illuminated. This property, and its strong sensitivity to changes in the local refractive index, allows for the use of metal nanoparticles as ultra-sensitive transducers. In prior work by members of this team, ensembles of randomly oriented nanoparticles (i.e., colloidal nanorods dispersed on chip) were employed for sequence-specific nucleic acid sensing (1-3). While these particle sensors have the advantage of rapid fabrication, they suffer from low sensitivity and quality factor due to the random particle dispersity. In contrast, in this study we employ ordered array nanoparticle ensembles which can be used to improve sensor sensitivity and figure-of-merit. Study Methods Overview: In this talk, we detail the results of sensing experiments and computational simulations to outline a rational design of the structure of these plasmonic nanoparticle arrays for biomolecular sensing. Through simulation and experiment, we iteratively tailor nanostructure dimension to provide high quality signal and large resonance shifts upon modeled nucleic acid binding. In particular, full-wave electromagnetic simulations were conducted using Lumerical photonic simulation software in which periodic boundary conditions were applied in the x- and y- dimensions for each of the nanoplasmonic sensor geometries. To simulate the resonance response to changes in the bulk solution in contact with the sensor surface, the refractive index of the surrounding media was changed appropriately. Nucleic acid hybridization events were modeled using either using spherical structures approximating the relevant radius of genomic material as estimated by polymer models, or as conformal layers with the known refractive indices for nucleic acids. On the basis of initial simulations, nanosensors were fabricated using traditional electron-beam lithography protocols at NIST. To evaluate consensus between simulations and experiments, bulk sensing experiments were carried out in which the resonance peaks were obtained by submerging the sensors in refractive index standards. Key nanosensor characteristics including resonance peak locations, resonance peak shifts as a function of refractive index, and figure of merit (FOM) of extinction curves were examined between the experimental and simulation results prior to proceeding with simulations on additional geometries and more complex solution conditions, and further device fabrication. This iterative process is repeated toward a rational design of nanoplasmonic array geometries for biosensing optimizing response for targeted disease detection. In summary, this study puts forth a methodology for rational design and characterization of regularly spaced nanoparticle arrays for optics-based biosensing. The results of this study will allow for more informed design of nanostructure geometries towards sequence-specific nucleic acid detection. These improved designs have the potential to improve clinical sensitivity and limit-of-detection across disease indication.

sensor↗

NASA NTRS1999

Mars Electromagnetic Sounding Experiment: MARSES

The MARSES is the sounding instrument developed of searching for water, water-ice or permafrost layers existing in some depth under the visible surface of Mars. There are many evidences that water once was abundant on Mars. There are stream lined islands formed by flowing water, flow patterns reminiscent of wadis in Earth deserts, and outflow channels thought to have been formed by sudden outrush of subterranean water. The secondary task is to measure the soil properties of the subsurface of Mars, which include porosity, electrical resistance of the liquid phase, thermal conductivity, temperature dependence. A main task of the MARSES system is to examine changes in subsurface properties of local areas regolith on the martian surface, and to relate them to optical images and other remote sensing data in order to understand the nature of different terrain forms. The dryed up regions of Martian frozen rocks is considered to have been developing during more than 3.5 bln years, so the upper layer boundary of permafrost can serve as an indicator reflecting the course of martian paleoclimate evolution. Additional information is contained in the original extended abstract.

Ozorovich, Y. R.↗

NASA NTRS2005

Chemical Sensors Based on Optical Ring Resonators

Chemical sensors based on optical ring resonators are undergoing development. A ring resonator according to this concept is a closed-circuit dielectric optical waveguide. The outermost layer of this waveguide, analogous to the optical cladding layer on an optical fiber, is a made of a polymer that (1) has an index of refraction lower than that of the waveguide core and (2) absorbs chemicals from the surrounding air. The index of refraction of the polymer changes with the concentration of absorbed chemical( s). The resonator is designed to operate with relatively strong evanescent-wave coupling between the outer polymer layer and the electromagnetic field propagating along the waveguide core. By virtue of this coupling, the chemically induced change in index of refraction of the polymer causes a measurable shift in the resonance peaks of the ring. In a prototype that has been used to demonstrate the feasibility of this sensor concept, the ring resonator is a dielectric optical waveguide laid out along a closed path resembling a racetrack (see Figure 1). The prototype was fabricated on a silicon substrate by use of standard techniques of thermal oxidation, chemical vapor deposition, photolithography, etching, and spin coating. The prototype resonator waveguide features an inner cladding of SiO2, a core of SixNy, and a chemical-sensing outer cladding of ethyl cellulose. In addition to the ring Chemical sensors based on optical ring resonators are undergoing development. A ring resonator according to this concept is a closed-circuit dielectric optical waveguide. The outermost layer of this waveguide, analogous to the optical cladding layer on an optical fiber, is a made of a polymer that (1) has an index of refraction lower than that of the waveguide core and (2) absorbs chemicals from the surrounding air. The index of refraction of the polymer changes with the concentration of absorbed chemical( s). The resonator is designed to operate with relatively strong evanescent-wave coupling between the outer polymer layer and the electromagnetic field propagating along the waveguide core. By virtue of this coupling, the chemically induced change in index of refraction of the polymer causes a measurable shift in the resonance peaks of the ring. In a prototype that has been used to demonstrate the feasibility of this sensor concept, the ring resonator is a dielectric optical waveguide laid out along a closed path resembling a racetrack (see Figure 1). The prototype was fabricated on a silicon substrate by use of standard techniques of thermal oxidation, chemical vapor deposition, photolithography, etching, and spin coating. The prototype resonator waveguide features an inner cladding of SiO2, a core of SixNy, and a chemical-sensing outer cladding of ethyl cellulose. In addition to the ring res

Homer, Margie↗

NASA NTRS2019

Going Beyond Standard Ocean Color Observations: Lidar and Polarimetry

Passive ocean color images have provided a sustained synoptic view of the distribution of ocean optical properties and color and biogeochemical parameters for the past 20-plus years. These images have revolutionized our view of the ocean. Remote sensing of ocean color has relied on measurements of the radiance emerging at the top of the atmosphere, thus neglecting the polarization and the vertical components. Ocean color remote sensing utilizes the intensity and spectral variation of visible light scattered upward from beneath the ocean surface to derive concentrations of biogeochemical constituents and inherent optical properties within the ocean surface layer. However, these measurements have some limitations. Specifically, the measured property is a weighted-integrated value over a relatively shallow depth, it provides no information during the night and retrievals are compromised by clouds, absorbing aerosols, and low Sun zenithal angles. In addition, ocean color data provide limited information on the morphology and size distribution of marine particles. Major advances in our understanding of global ocean ecosystems will require measurements from new technologies, specifically lidar and polarimetry. These new techniques have been widely used for atmospheric applications but have not had as much as interest from the ocean color community. This is due to many factors including limited access to in-situ instruments and/or space-borne sensors and lack of attention in university courses and ocean science summer schools curricula. However, lidar and polarimetry technology will complement standard ocean color products by providing depth-resolved values of attenuation and scattering parameters and additional information about particle morphology and chemical composition. This review aims at presenting the basics of these techniques, examples of applications and at advocating for the development of in-situ and space-borne sensors. Recommendations are provided on actions that would foster the embrace of lidar and polarimetry as powerful remote sensing tools by the ocean science community.

Jamet, Cedric↗

NASA NTRS1981

Millimeter wave radiometry as a means of determining cometary surface and subsurface temperature

Thermal emission spectra for a variety of cometary nucleus models were evaluated by a radiative transfer technique adapted from modeling of terrestrial ice and snow fields. It appears that millimeter wave sensing from an interplanetary spacecraft is the most effective available means for distinguishing between alternate models of the nucleus and for evaluating the thermal state of the layer which is below the instantaneous surface where modern theories of the nucleus indicate that sublimation of the cometary volatiles actually occurs.

Hobbs, R. W.↗

NASA NTRS1989

Photovoltaic Hydrogen Sensor

Photovoltaic device senses hydrogen developed to test degradation of diodes with platinum flash gates on backs. Sensing element is p/n junction rather than conventional Schottky barrier or metal oxide/silicon field-effect transistor. Hydrogen-indicating electrical signal modulated optically rather than electrically. Layered structure of hydrogen detector and principle of operation resemble silicon solar photovoltaic cell. Hydrogen detector responds to hydrogen in atmosphere within minutes and recovers quickly when hydrogen removed.

Daud, Taher↗

NASA NTRS1995

Regional scale evaporation and the atmospheric boundary layer

In this review we briefly summarize some current models of evaporation and the atmospheric boundary layer (ABL) and discuss new experimental and computational oppurtunities that may aid our understanding of evaporation at these larger scales. In particular, consideration is given to remote sensing of the atmosphere, computational fluid dynamics and the role numerical models can play in understanding land-atmosphere interactions. These powerful modeling and measurement tools are allowing us to visualize and study spatial and temporal scales previously untouched, thereby increasing the oppurtunities to improve our understanding of land-atmosphere interaction.

Parlange, Marc B.↗

NASA NTRS1998

Automated Fluid Feature Extraction from Transient Simulations

In the past, feature extraction and identification were interesting concepts, but not required to understand the underlying physics of a steady flow field. This is because the results of the more traditional tools like iso-surfaces, cuts and streamlines were more interactive and easily abstracted so they could be represented to the investigator. These tools worked and properly conveyed the collected information at the expense of much interaction. For unsteady flow-fields, the investigator does not have the luxury of spending time scanning only one 'snap-shot' of the simulation. Automated assistance is required in pointing out areas of potential interest contained within the flow. This must not require a heavy compute burden (the visualization should not significantly slow down the solution procedure for co-processing environments like pV3). And methods must be developed to abstract the feature and display it in a manner that physically makes sense. The following is a list of the important physical phenomena found in transient (and steady-state) fluid flow: Shocks; Vortex ores; Regions of Recirculation; Boundary Layers; Wakes.

Haimes, Robert↗

NASA NTRS2017

Daily Kilometer-Scale MODIS Satellite Maps of PM2.5 Describe Wintertime Episodes

The San Joaquin Valley (SJV) suffers from severe health-endangering episodes of PM2.5 aerosol loadings in wintertime; episodes last approximately 5 days and differ in geographical distribution and composition. PM2.5 stations are scattered; consequently the use of remote sensing to map variable regional patterns of these varying respirable aerosol concentrations is desirable. High-precision AOT retrievals can capture column particulate loading. However,PM2.5 mapping is challenging due to several reasons: particularly thin mixed layers (ML) and thus relatively low aerosol optical thickness (AOT) close to current measurement limits, variable and a typical composition of the aerosols, and complex surface bidirectional reflectance. However, the West does present some advantages in analysis. Air basins are isolated from long-distance transport, and experience predominant strong meteorological subsidence. Thus these Western basin regions have fewer problematic cases of overriding aerosol layers detached from the surface. To counter such local overriding, Chu et al. have described an approach for the Eastern US, and He et al have described a synoptic classification approach useful in Shanghai. The Bay Area Air Quality Management District (BAAQMD) expands our experience with the use of AOT, with lower PM2.5 and several isolated sub-basins. We have prepared daily maps of episodes in each region. We present also a sequence of increasingly detailed statistical models, AOT initially appears to contribute little information; however, inclusion of weather information reveals its utility. Lyapustin and Wang's MultiAngle Implementation of Atmospheric Correction (MAIAC) retrieval for AOT provided the most useful operational remote sensing information for these regions. It provides high (1-km) spatial resolution maps and a high percentage of availability. Empirical regression methods have found that random effects regression models (aka mixed effects models, ME) employing AOT provide good estimates of ground PM2.5 concentrations.Here, we attempt to extend these methods and evaluate the usefulness of AOT with greater physical analysis, based on DISCOVER-AQ4 experience.

Chatfield, Robert B.↗

NASA NTRS1998

LASE measurements of aerosols and water vapor during TARFOX

The TARFOX (Tropospheric Aerosol Radiative Forcing Observational Experiment) intensive field campaign was designed to reduce uncertainties in estimates of the effects of anthropogenic aerosols on climate by measuring direct radiative effects and the optical, physical, and chemical properties of aerosols [1]. TARFOX was conducted off the East Coast of the United States between July 10-31, 1996. Ground, aircraft, and satellite-based sensors measured the sensitivity of radiative fields at various atmospheric levels to aerosol optical properties (i.e., optical thickness, phase function, single-scattering albedo) and to the vertical profile of aerosols. The LASE (Lidar Atmospheric Sensing Experiment) instrument, which was flown on the NASA ER-2 aircraft, measured vertical profiles of total scattering ratio and water vapor during a series of 9 flights. These profiles were used in real-time to help direct the other aircraft to the appropriate altitudes for intensive sampling of aerosol layers. We have subsequently used the LASE aerosol data to derive aerosol backscattering and extinction profiles. Using these aerosol extinction profiles, we derived estimates of aerosol optical thickness (AOT) and compared these with measurements of AOT from both ground and airborne sun photometers and derived from the ATSR-2 (Along Track and Scanning Radiometer 2) sensor on ERS-2 (European Remote Sensing Satellite-2). We also used the water vapor mixing ratio profiles measured simultaneously by LASE to derive precipitable water vapor and compare these to ground based measurements.

Ferrare, Richard A.↗

NASA NTRS1982

Delineation of cold-prone areas using nighttime SMS/GOES thermal data Effects of soils and water

Infrared digital data from geostationary satellites were used to demonstrate the usefulness of remotely sensed surface temperature data to delineate microscale and mesoscale climates. Nocturnal winter data (December-February) from 1976-77 to 1978-79 over Florida revealed noticeable contrasts in surface temperature patterns. Colder areas were associated with low soil moisture content in the upper layers of excessively drained and well drained sandy soils, whereas warmer areas were associated with bodies of water, wetlands, or poorly drained soils. An unexpected surface temperature pattern for one night where the north-central Florida climatic zone was colder than the north Florida climatic zone was found to be caused by differences in antecedent frontal rainfall. Differences in surface radiant energy fluxes over these two areas at 0200 EST 20 December 1977, based on average satellite-sensed surface temperatures, were compared with differences in soil heat fluxes that were computed from 1.5 m climatological temperatures and soil thermal properties by use of a simplified surface energy balance equation.

Chen, E.↗

NASA NTRS1981

Water frost and ice - The near-infrared spectral reflectance 0.65-2.5 microns

The spectral reflectance of water frost and frost on ice as a function of temperature and grain size is presented with 1-1/2% spectral resolution in the 0.65- to 2.5-micron wavelength region. The well-known 2.0-, 1.65-, and 1.5-micron solid water absorption bands are precisely defined along with the little studied 1.25-micron band and the previously unidentified (in reflectance) 1.04-, 0.90-, and 0.81-micron absorption bands. The 1.5-microns band complex is quantitatively analyzed using a nonlinear least squares algorithm to resolve the band into four Gaussian components as a function of grain size and temperature. It is found that the 1.65-micron component, which was thought to be a good temperature sensor, is highly grain-size dependent and poorly suited to temperature sensing. Another Gaussian component appears to show a dependence of width on grain size while being independent of temperature. The relative apparent band depths are different for frost layers on ice than for thick layers of frost and may explain the apparent band depths seen in many planetary reflectance spectra.

Clark, R. N.↗

NASA NTRS1982

COSAL: A black-box compressible stability analysis code for transition prediction in three-dimensional boundary layers

A fast computer code COSAL for transition prediction in three dimensional boundary layers using compressible stability analysis is described. The compressible stability eigenvalue problem is solved using a finite difference method, and the code is a black box in the sense that no guess of the eigenvalue is required from the user. Several optimization procedures were incorporated into COSAL to calculate integrated growth rates (N factor) for transition correlation for swept and tapered laminar flow control wings using the well known e to the Nth power method. A user's guide to the program is provided.

Malik, M. R.↗

NASA NTRS1991

Dust in the Mars atmosphere

The amount of dust suspended in the Martian atmosphere is highly variable with location and with time. The opacity of the sky is best known at the two Viking Lander sites, where visual, vertical-column optical depth never fell below a value of a few tenths during the 1.25 Mars years of observations and yet exceeded 2 to 3 during two great dust storms in 1977. Elsewhere on the planet, optical depths have been estimated from orbiter visible imaging of surface contrasts and from mapping of infrared emission from the surface and the overlying (dusty) atmosphere. In many cases these opacities (and thus dust amounts) may be uncertain by as much as a factor of two. Viking Lander observations of twilight indicate that the background dust haze is more or less uniformly mixed with altitude in the lower atmosphere. Observations from spacecraft indicate that there may be come seasonal variations to the height of these dust hazes, which sometimes extend above 30 km. (Ice haze layers may occur as high as 80 km.) The existing observations do not constrain the composition or the size distribution of the suspended dust particles very well. Remote sensing observations depend principally upon the product of the number of particles, the geometric cross-sections (and so particle size and shape), and the extinction efficiency of the particles (and so the particle composition), as integrated over the particle size distribution and along the line of sight. While the observed variation of dust opacity with wavelength constrains these quantities, it does not often permit the unique determination of the individual properties of the suspended dust. A size distribution having a cross-section weighted mean particle radius of 2.5 microns was deduced from a synthesis of the IR thermal emission spectra observed in the Southern Hemisphere by Mariner 9 during the 1971 global dust storm. Although the IR thermal emission is relatively insensitive to the sub-micron sized particles which tend to dominate visible opacity, this same size distribution was consistent with modeling of the sky brightness variation near the sun, as seen through the background haze above the Viking lander sites in the Northern Hemisphere.

Zurek, R. W.↗

NASA NTRS1992

Micro weather stations for in situ measurements in the Martian planetary boundary layer

Viking Lander meteorology measurements show that the Martian planetary boundary layer (PBL) has large diurnal and seasonal variations in pressure, wind velocity, relative humidity, and airborne dust loading. An even larger range of conditions was inferred from remote sensing observations acquired by the Mariner 9 and Viking orbiters. Numerical models indicate that these changes may be accompanied by dramatic vertical and horizontal wind shears (100 m/s/km) and rapid changes in the static stability. In-situ measurements from a relatively small number surface stations could yield global constraints on the Martian climate and atmospheric general circulation by providing ground truth for remote sensing instruments on orbiters. A more complete understanding of the meteorology of the PBL is an essential precursor to manned missions to Mars because this will be their working environment. In-situ measurements are needed for these studies because the spatial and temporal scales that characterize the important meteorological processes near the surface cannot be resolved from orbit. The Mars Environmental Survey (MESUR) Program will provide the first opportunity to deploy a network of surface weather stations for a comprehensive investigation of the Martian PBL. The feasibility and utility of a network of micro-weather stations for making in-situ meteorological measurements in the Martian PBL are assessed.

Crisp, D.↗

NASA NTRS1994

Analysis of ERS 1 synthetic aperture radar data of frozen lakes in northern Montana and implications for climate studies

Lakes that freeze each winter are good indicators of regional climate change if key parameters, such as freeze-up and breakup date and maximum ice thickness, are measured over a decade-scale time frame. Synthetic aperture radar (SAR) satellite data have proven to be especially useful for measurement of climatologically significant parameters characteristic of frozen lakes. In this paper, five lakes in Glacier National Park, Montana, have been studied both in the field and using Earth Remote-Sensing Satellite (ERS) 1 SAR data during the 1992-1993 winter. The lakes are characterized by clear ice, sometimes with tubular or rounded bubbles, and often with a layer of snow ice on top of the clear ice. They are also often snow covered. Freeze-up is detected quite easily using ERS 1 SAR data as soon as a thin layer of ice forms. The effect of snow ice on the backscatter is thought to be significant but is, as yet, undetermined. On the five lakes studied, relative backscatter was found to increase with ice thickness until a maximum was reached in February. Breakup, an often ill-defined occurrence, is difficult to detect because surface water causes the SAR signal to be absorbed, thus masking the ice below. Comparison of the bubble structure of thaw lakes in northern Alaska with lakes in northern Montana has shown that the ice structure is quite different, and this difference may contribute to differential SAR signature evolution in the lakes of the two areas.

Hall, Dorothy K.↗

NASA NTRS2001

Infrared Sensing Aeroheating Flight Experiment: STS-96 Flight Results

Major elements of an experiment called the Infrared Sensing Aeroheating Flight Experiment are discussed. The primary experiment goal is to provide reentry global temperature images from infrared measurements to define the characteristics of hypersonic boundary-layer transition during flight. Specifically, the experiment is to identify, monitor, and quantity hypersonic boundary layer windward surface transition of the X-33 vehicle during flight. In addition, the flight data will serve as a calibration and validation of current boundary layer transition prediction techniques, provide benchmark laminar, transitional, and fully turbulent global aeroheating data in order to validate existing wind tunnel and computational results, and to advance aeroheating technology. Shuttle Orbiter data from STS-96 used to validate the data acquisition and data reduction to global temperatures, in order to mitigate the experiment risks prior to the maiden flight of the X-33, is discussed. STS-96 reentry midwave (3-5 micron) infrared data were collected at the Ballistic Missile Defense Organization/Innovative Sciences and Technology Experimentation Facility site at NASA-Kennedy Space Center and subsequently mapped into global temperature contours using ground calibrations only. A series of image mapping techniques have been developed in order to compare each frame of infrared data with thermocouple data collected during the flight. Comparisons of the ground calibrated global temperature images with the corresponding thermocouple data are discussed. The differences are shown to be generally less than about 5%, which is comparable to the expected accuracy of both types of aeroheating measurements.

Blanchard, Robert C.↗

NASA NTRS2001

Infrared Sensing Aeroheating Flight Experiement: STS-96 Flight Results

Major elements of an experiment called the Infrared Sensing Aeroheating Flight Experiment are discussed. The primary experiment goal is to provide reentry global temperature images from infrared measurements to define the characteristics of hypersonic boundary-layer transition during flight. Specifically, the experiment is to identify, monitor, and quantify hypersonic boundary layer windward surface transition of the X-33 vehicle during flight. In addition, the flight data will serve as a calibration and validation of current boundary layer transition prediction techniques, provide benchmark laminar, transitional, and fully turbulent global aeroheating data in order to validate existing wind tunnel and computational results, and to advance aeroheating technology. Shuttle Orbiter data from STS-96 used to validate the data acquisition and data reduction to global temperatures, in order to mitigate the experiment risks prior to the maiden flight of the X-33, is discussed. STS-96 reentry mid-wave (3-5 Pm) infrared data were collected at the Ballistic Missile Defense Organization/Innovative Sciences and Technology Experimentation Facility site at NASA-Kennedy Space Center and subsequently mapped into global temperature contours using ground calibrations only. A series of image mapping techniques have been developed in order to compare each frame of infrared data with thermocouple data collected during the flight. Comparisons of the ground calibrated global temperature images with the corresponding thermocouple data are discussed. The differences are shown to be generally less than about 5%, which is comparable to the expected accuracy of both types of aeroheating measurements.

Blanchard, Robert C.↗