Improved dynamic headspace sampling and detection using capillary microextraction of volatiles coupled to gas chromatography mass spectrometry

Sampling and preconcentration techniques play a critical role in headspace analysis in analytical chemistry. My dissertation presents a novel sampling design, capillary microextraction of volatiles (CMV), that improves the preconcentration of volatiles and semivolatiles in a headspace with high throughput, near quantitative analysis, high recovery and unambiguous identification of compounds when coupled to mass spectrometry. The CMV devices use sol-gel polydimethylsiloxane (PDMS) coated microglass fibers as the sampling/preconcentration sorbent when these fibers are stacked into open-ended capillary tubes. The design allows for dynamic headspace sampling by connecting the device to a hand-held vacuum pump. The inexpensive device can be fitted into a thermal desorption probe for thermal desorption of the extracted volatile compounds into a gas chromatography-mass spectrometer (GC-MS). The performance of the CMV devices was compared with two other existing preconcentration techniques, solid phase microextraction (SPME) and planar solid phase microextraction (PSPME). Compared to SPME fibers, the CMV devices have an improved surface area and phase volume of 5000 times and 80 times, respectively. One (1) minute dynamic CMV air sampling resulted in similar performance as a 30 min static extraction using a SPME fiber. The PSPME devices have been fashioned to easily interface with ion mobility spectrometers (IMS) for explosives or drugs detection. The CMV devices are shown to offer dynamic sampling and can now be coupled to COTS GC-MS instruments. Several compound classes representing explosives have been analyzed with minimum breakthrough even after a 60 min. sampling time. The extracted volatile compounds were retained in the CMV devices when preserved in aluminum foils after sampling. Finally, the CMV sampling device were used for several different headspace profiling applications which involved sampling a shipping facility, six illicit drugs, seven military explosives and eighteen different bacteria strains. Successful detection of the target analytes at ng levels of the target signature volatile compounds in these applications suggests that the CMV devices can provide high throughput qualitative and quantitative analysis with high recovery and unambiguous identification of analytes.

Anomaly detection from time-changing environmental sensor data streams

This thesis stems from the project with real-time environmental monitoring company EMSAT Corporation. They were looking for methods to automatically ag spikes and other anomalies in their environmental sensor data streams. The problem presents several challenges: near real-time anomaly detection, absence of labeled data and time-changing data streams. Here, we address this problem using both a statistical parametric approach as well as a non-parametric approach like Kernel Density Estimation (KDE). The main contribution of this thesis is extending the KDE to work more effectively for evolving data streams, particularly in presence of concept drift. To address that, we have developed a framework for integrating Adaptive Windowing (ADWIN) change detection algorithm with KDE. We have tested this approach on several real world data sets and received positive feedback from our industry collaborator. Some results appearing in this thesis have been presented at ECML PKDD 2015 Doctoral Consortium.

Multiscale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe.

Photoacoustic tomography (PAT) of genetically encoded probes allows for imaging of targeted biological processes deep in tissues with high spatial resolution; however, high background signals from blood can limit the achievable detection sensitivity. Here we describe a reversibly switchable nonfluorescent bacterial phytochrome for use in multiscale photoacoustic imaging, BphP1, with the most red-shifted absorption among genetically encoded probes. BphP1 binds a heme-derived biliverdin chromophore and is reversibly photoconvertible between red and near-infrared light-absorption states. We combined single-wavelength PAT with efficient BphP1 photoswitching, which enabled differential imaging with substantially decreased background signals, enhanced detection sensitivity, increased penetration depth and improved spatial resolution. We monitored tumor growth and metastasis with ∼ 100-μm resolution at depths approaching 10 mm using photoacoustic computed tomography, and we imaged individual cancer cells with a suboptical-diffraction resolution of ∼ 140 nm using photoacoustic microscopy. This technology is promising for biomedical studies at several scales.

Near-real-time service provision during effusive crises at Etna and Stromboli: basis and implementation of satellite-based IR operations

Using the NEODAAS-Dundee AVHRR receiving station (Scotland), NEODAAS-Plymouth can provide calibrated brightness temperature data to end users or interim users in near-real time. Between 2000 and 2009 these data were used to undertake volcano hot spot detection, reporting and time-average discharge rate dissemination during effusive crises at Mount Etna and Stromboli (Italy). Data were passed via FTP, within an hour of image generation, to the hot spot detection system maintained at Hawaii Institute of Geophysics and Planetology (HIGP, University of Hawaii at Manoa, Honolulu, USA). Final product generation and quality control were completed manually at HIGP once a day, so as to provide information to onsite monitoring agencies for their incorporation into daily reporting duties to Italian Civil Protection. We here describe the processing and dissemination chain, which was designed so as to provide timely, useable, quality-controlled and relevant information for ‘one voice’ reporting by the responsible monitoring agencies.

Near-real-time service provision during effusive crises at Etna and Stromboli: basis and implementation of satellite-based IR operations

Using the NEODAAS-Dundee AVHRR receiving station (Scotland), NEODAAS-Plymouth can provide calibrated brightness temperature data to end users or interim users in near-real time. Between 2000 and 2009 these data were used to undertake volcano hot spot detection, reporting and time-average discharge rate dissemination during effusive crises at Mount Etna and Stromboli (Italy). Data were passed via FTP, within an hour of image generation, to the hot spot detection system maintained at Hawaii Institute of Geophysics and Planetology (HIGP, University of Hawaii at Manoa, Honolulu, USA). Final product generation and quality control were completed manually at HIGP once a day, so as to provide information to onsite monitoring agencies for their incorporation into daily reporting duties to Italian Civil Protection. We here describe the processing and dissemination chain, which was designed so as to provide timely, useable, quality-controlled and relevant information for ‘one voice’ reporting by the responsible monitoring agencies.

Detection of H2O and Evidence for TiO/VO in an Ultra-hot Exoplanet Atmosphere

We present a primary transit observation for the ultra-hot (T eq ~ 2400 K) gas giant expolanet WASP-121b, made using the Hubble Space Telescope Wide Field Camera 3 in spectroscopic mode across the 1.12–1.64 μm wavelength range. The 1.4 μm water absorption band is detected at high confidence (5.4σ) in the planetary atmosphere. We also reanalyze ground-based photometric light curves taken in the B, r', and z' filters. Significantly deeper transits are measured in these optical bandpasses relative to the near-infrared wavelengths. We conclude that scattering by high-altitude haze alone is unlikely to account for this difference and instead interpret it as evidence for titanium oxide and vanadium oxide absorption. Enhanced opacity is also inferred across the 1.12–1.3 μm wavelength range, possibly due to iron hydride absorption. If confirmed, WASP-121b will be the first exoplanet with titanium oxide, vanadium oxide, and iron hydride detected in transmission. The latter are important species in M/L dwarfs and their presence is likely to have a significant effect on the overall physics and chemistry of the atmosphere, including the production of a strong thermal inversion.

Subliminal or not? : An appraisal of semantic processing in the near absence of visual awareness

Stimuli that cannot be perceived (i.e., that are subliminal) can still elicit neural responses in an observer, but can such stimuli influence behavior and higher-order cognition? Empirical evidence for such effects has periodically been accepted and rejected over the last six decades. Today, many psychologists seem to consider such effects well-established and recent studies have extended the power of subliminal processing to new limits. In this thesis, I examine whether this shift in zeitgeist is matched by a shift in evidential strength for the phenomenon. This thesis consists of three empirical studies involving more than 250 participants, a simulation study, and a quantitative review. The conclusion based on these efforts is that several methodological, statistical, and theoretical issues remain in studies of subliminal processing. These issues mean that claimed subliminal effects might be caused by occasional or weak percepts (given the experimenters’ own definitions of perception) and that it is still unclear what evidence there is for the cognitive processing of subliminal stimuli. New data are presented suggesting that even in conditions traditionally claimed as “subliminal”, occasional or weak percepts may in fact influence cognitive processing more strongly than do the physical stimuli, possibly leading to reversed priming effects. I also summarize and provide methodological, statistical, and theoretical recommendations that could benefit future research aspiring to provide solid evidence for subliminal cognitive processing.

Fast and accurate hand pose detection for human-robot interaction

[EN]Enabling natural human-robot interaction using computer vision based applications requires fast and accurate hand detection. However, previous works in this field assume different constraints, like a limitation in the number of detected gestures, because hands are highly complex objects difficult to locate. This paper presents an approach which integrates temporal coherence cues and hand detection based on wrists using a cascade classifier. With this approach, we introduce three main contributions: (1) a transparent initialization mechanism without user participation for segmenting hands independently of their gesture, (2) a larger number of detected gestures as well as a faster training phase than previous cascade classifier based methods and (3) near real-time performance for hand pose detection in video streams.

Ionospheric Turbulence Near the Upper Hybrid Layer: Theory and Experiment

The thesis presents experimental results, simulations, and theory on turbulence excited in magnetized plasmas near the ionosphere’s upper hybrid layer. The results include: The first experimental observations of super small striations (SSS) excited by the High-Frequency Auroral Research Project (HAARP) The first detection of high-frequency (HF) waves from the HAARP transmitter over a distance of 16x10^3 km The first simulations indicating that upper hybrid (UH) turbulence excites electron Bernstein waves associated with all nearby gyroharmonics Simulation results that indicate that the resulting bulk electron heating near the upper hybrid (UH) resonance is caused primarily by electron Bernstein waves parametrically excited near the first gyroharmonic. On the experimental side we present two sets of experiments performed at the HAARP heating facility in Alaska. In the first set of experiments, we present the first detection of super-small (cm scale) striations (SSS) at the HAARP facility. We detected density structures smaller than 30 cm for the first time through a combination of satellite and ground based measurements. In the second set of experiments, we present the results of a novel diagnostic implemented by the Ukrainian Antarctic Station (UAS) in Verdansky. The technique allowed the detection of the HAARP signal at a distance of nearly 16 Mm, and established that the HAARP signal was injected into the ionospheric waveguide by direct scattering off of dekameter-scale density structures induced by the heater. On the theoretical side, we present results of Vlasov simulations near the upper hybrid layer. These results are consistent with the bulk heating required by previous work on the theory of the formation of descending artificial ionospheric layers (DIALs), and with the new observations of DIALs at HAARP’s upgraded effective radiated power (ERP). The simulations that frequency sweeps, and demonstrate that the heating changes from a bulk heating between gyroharmonics, to a tail acceleration as the pump frequency is swept through the fourth gyroharmonic. These simulations are in good agreement with experiments. We also incorporate test particle simulations that isolate the effects of specific wave modes on heating, and we find important contributions from both electron Bernstein waves and upper hybrid waves, the former of which have not yet been detected by experiments, and have not been previously explored as a driver of heating. In presenting these results, we analyzed data from HAARP diagnostics and assisted in planning the second round of experiments. We integrated the data into a picture of experiments that demonstrated the detection of SSS, hysteresis effects in simulated electromagnetic emission (SEE) features, and the direct scattering of the HF pump into the ionospheric waveguide. We performed simulations and analyzed simulation data to build the understanding of collisionless heating near the upper hybrid layer, and we used these simulations to show that bulk electron heating at the upper hybrid layer is possible, which is required by current theories of DAIL formation. We wrote a test particle simulation to isolate the effects of electron Bernstein waves and upper hybrid layers on collisionless heating, and integrated this code to work with both the output of Vlasov simulations and the input for simulations of DAIL formation.

Comparison of adhesion layers of gold on silicate glasses for SERS detection

Gold is one of the most widely used metals for building up plasmonic devices. Although slightly less efficient than silver for producing sharp resonance, its chemical properties make it one of the best choices for designing sensors. Sticking gold on a silicate glass substrate requires an adhesion layer, whose effect has to be taken into account. Traditionally, metals (Cr or Ti) or dielectric materials (TiO2 or Cr2O3 ) are deposited between the glass and the nanoparticle. Recently, indium tin oxide and (3-mercaptopropyl)trimethoxysilane (MPTMS) were used as a new adhesion layer. The aim of this work is to compare these six adhesion layers for surface- enhanced Raman scattering sensors by numerical modeling. The near-field and the far-field optical responses of gold nanocylinders on the different adhesion layers are then calculated. It is shown that MPTMS leads to the highest field enhancement, slightly larger than other dielectric materials. We attributed this effect to the lower refractive index of MPTMS compared with the others.

Near-infrared Instrumentation For Rapid-response Astronomy

Ɣ-ray bursts (GRBs) are the Universe's most luminous transient events. Since the discovery of GRBs was announced in 1973, efforts have been ongoing to obtain data over a broader range of the electromagnetic spectrum at the earliest possible times following the initial detection. The discovery of the theorized ``afterglow'' emission in radio through X-ray bands in the late 1990s confirmed the cosmological nature of these events. At present, GRB afterglows are among the best probes of the early Universe (z ≳ 9). In addition to informing theories about GRBs themselves, observations of afterglows probe the circum-burst medium (CBM), properties of the host galaxies and the progress of cosmic reionization. To explore the early-time variability of afterglows, I have developed a generalized analysis framework which models near-infrared (NIR), optical, ultra-violet (UV) and X-ray light curves without assuming an underlying model. These fits are then used to construct the spectral energy distribution (SED) of afterglows at arbitrary times within the observed window. Physical models are then used to explore the evolution of the SED parameter space with time. I demonstrate that this framework produces evidence of the photodestruction of dust in the CBM of GRB 120119A, similar to the findings from a previous study of this afterglow. The framework is additionally applied to the afterglows of GRB 140419A and GRB 080607. In these cases the evolution of the SEDs appears consistent with the standard fireball model. Having introduced the scientific motivations for early-time observations, I introduce the Rapid Infrared Imager-Spectrometer (RIMAS). Once commissioned on the 4.3 meter Discovery Channel Telescope (DCT), RIMAS will be used to study the afterglows of GRBs through photometric and spectroscopic observations beginning within minutes of the initial burst. The instrument will operate in the NIR, from 0.97 μm to 2.37 μm, permitting the detection of very high redshift (z ≳ 7) afterglows which are attenuated at shorter wavelengths by Lyman-ɑ absorption in the intergalactic medium (IGM). A majority of my graduate work has been spent designing and aligning RIMAS's cryogenic (~80 K) optical systems. Design efforts have included an original camera used to image the field surrounding spectroscopic slits, tolerancing and optimizing all of the instrument's optics, thermal modeling of optomechanical systems, and modeling the diffraction efficiencies for some of the dispersive elements. To align the cryogenic optics, I developed a procedure that was successfully used for a majority of the instrument's sub-assemblies. My work on this cryogenic instrument has necessitated experimental and computational projects to design and validate designs of several subsystems. Two of these projects describe simple and effective measurements of optomechanical components in vacuum and at cryogenic temperatures using an 8-bit CCD camera. Models of heat transfer via electrical harnesses used to provide current to motors located within the cryostat are also presented.

Two roads to planet detection

One of the most exciting discoveries in astrophysics of the last last decade is of the sheer diversity of planetary systems. These include "hot Jupiters", giant planets so close to their host stars that they orbit once every few days; "Super-Earths", planets with sizes intermediate to those of Earth and Neptune, of which no analogs exist in our own solar system; multi-planet systems with planets smaller than Mars to larger than Jupiter; planets orbiting binary stars; free-floating planets flying through the emptiness of space without any star; even planets orbiting pulsars. Despite these remarkable discoveries, the field is still young, and there are many areas about which precious little is known. In particular, we don't know the planets orbiting Sun-like stars nearest to our own solar system, and we know very little about the compositions of extrasolar planets. This thesis provides developments in those directions, through two instrumentation projects.

The first chapter of this thesis concerns detecting planets in the Solar neighborhood using precision stellar radial velocities, also known as the Doppler technique. We present an analysis determining the most efficient way to detect planets considering factors such as spectral type, wavelengths of observation, spectrograph resolution, observing time, and instrumental sensitivity. We show that G and K dwarfs observed at 400-600 nm are the best targets for surveys complete down to a given planet mass and out to a specified orbital period. Overall we find that M dwarfs observed at 700-800 nm are the best targets for habitable-zone planets, particularly when including the effects of systematic noise floors caused by instrumental imperfections. Somewhat surprisingly, we demonstrate that a modestly sized observatory, with a dedicated observing program, is up to the task of discovering such planets.

We present just such an observatory in the second chapter, called the "MINiature Exoplanet Radial Velocity Array," or MINERVA. We describe the design, which uses a novel multi-aperture approach to increase stability and performance through lower system etendue, as well as keeping costs and time to deployment down. We present calculations of the expected planet yield, and data showing the system performance from our testing and development of the system at Caltech's campus. We also present the motivation, design, and performance of a fiber coupling system for the array, critical for efficiently and reliably bringing light from the telescopes to the spectrograph. We finish by presenting the current status of MINERVA, operational at Mt. Hopkins observatory in Arizona.

The second part of this thesis concerns a very different method of planet detection, direct imaging, which involves discovery and characterization of planets by collecting and analyzing their light. Directly analyzing planetary light is the most promising way to study their atmospheres, formation histories, and compositions. Direct imaging is extremely challenging, as it requires a high performance adaptive optics system to unblur the point-spread function of the parent star through the atmosphere, a coronagraph to suppress stellar diffraction, and image post-processing to remove non-common path "speckle" aberrations that can overwhelm any planetary companions.

To this end, we present the "Stellar Double Coronagraph," or SDC, a flexible coronagraphic platform for use with the 200" Hale telescope. It has two focal and pupil planes, allowing for a number of different observing modes, including multiple vortex phase masks in series for improved contrast and inner working angle behind the obscured aperture of the telescope. We present the motivation, design, performance, and data reduction pipeline of the instrument. In the following chapter, we present some early science results, including the first image of a companion to the star delta Andromeda, which had been previously hypothesized but never seen.

A further chapter presents a wavefront control code developed for the instrument, using the technique of "speckle nulling," which can remove optical aberrations from the system using the deformable mirror of the adaptive optics system. This code allows for improved contrast and inner working angles, and was written in a modular style so as to be portable to other high contrast imaging platforms. We present its performance on optical, near-infrared, and thermal infrared instruments on the Palomar and Keck telescopes, showing how it can improve contrasts by a factor of a few in less than ten iterations.

One of the large challenges in direct imaging is sensing and correcting the electric field in the focal plane to remove scattered light that can be much brighter than any planets. In the last chapter, we present a new method of focal-plane wavefront sensing, combining a coronagraph with a simple phase-shifting interferometer. We present its design and implementation on the Stellar Double Coronagraph, demonstrating its ability to create regions of high contrast by measuring and correcting for optical aberrations in the focal plane. Finally, we derive how it is possible to use the same hardware to distinguish companions from speckle errors using the principles of optical coherence. We present results observing the brown dwarf HD 49197b, demonstrating the ability to detect it despite it being buried in the speckle noise floor. We believe this is the first detection of a substellar companion using the coherence properties of light.

Functionalized Carbon Micro/Nanostructures for Biomolecular Detection

Advancements in the micro-and nano-scale fabrication techniques have opened up new avenues for the development of portable, scalable and easier-to-use biosensors. Over the last few years, electrodes made of carbon have been widely used as sensing units in biosensors due to their attractive physiochemical properties. The aim of this research is to investigate different strategies to develop functionalized high surface carbon micro/nano-structures for electrochemical and biosensing devices. High aspect ratio three-dimensional carbon microarrays were fabricated via carbon microelectromechanical systems (C-MEMS) technique, which is based on pyrolyzing pre-patterned organic photoresist polymers. To further increase the surface area of the carbon microstructures, surface porosity was introduced by two strategies, i.e. (i) using F127 as porogen and (ii) oxygen reactive ion etch (RIE) treatment. Electrochemical characterization showed that porous carbon thin film electrodes prepared by using F127 as porogen had an effective surface area (Aeff 185%) compared to the conventional carbon electrode. To achieve enhanced electrochemical sensitivity for C-MEMS based functional devices, graphene was conformally coated onto high aspect ratio three-dimensional (3D) carbon micropillar arrays using electrostatic spray deposition (ESD) technique. The amperometric response of graphene/carbon micropillar electrode arrays exhibited higher electrochemical activity, improved charge transfer and a linear response towards H2O2 detection between 250μM to 5.5mM. Furthermore, carbon structures with dimensions from 50 nano-to micrometer level have been fabricated by pyrolyzing photo-nanoimprint lithography patterned organic resist polymer. Microstructure, elemental composition and resistivity characterization of the carbon nanostructures produced by this process were very similar to conventional photoresist derived carbon. Surface functionalization of the carbon nanostructures was performed using direct amination technique. Considering the need for requisite functional groups to covalently attach bioreceptors on the carbon surface for biomolecule detection, different oxidation techniques were compared to study the types of carbon–oxygen groups formed on the surface and their percentages with respect to different oxidation pretreatment times. Finally, a label-free detection strategy using signaling aptamer/protein binding complex for platelet-derived growth factor oncoprotein detection on functionalized three-dimensional carbon microarrays platform was demonstrated. The sensor showed near linear relationship between the relative fluorescence difference and protein concentration even in the sub-nanomolar range with an excellent detection limit of 5 pmol.

Improved Dynamic Headspace Sampling and Detection using Capillary Microextraction of Volatiles Coupled to Gas Chromatography Mass Spectrometry

Sampling and preconcentration techniques play a critical role in headspace analysis in analytical chemistry. My dissertation presents a novel sampling design, capillary microextraction of volatiles (CMV), that improves the preconcentration of volatiles and semivolatiles in a headspace with high throughput, near quantitative analysis, high recovery and unambiguous identification of compounds when coupled to mass spectrometry. The CMV devices use sol-gel polydimethylsiloxane (PDMS) coated microglass fibers as the sampling/preconcentration sorbent when these fibers are stacked into open-ended capillary tubes. The design allows for dynamic headspace sampling by connecting the device to a hand-held vacuum pump. The inexpensive device can be fitted into a thermal desorption probe for thermal desorption of the extracted volatile compounds into a gas chromatography-mass spectrometer (GC-MS). The performance of the CMV devices was compared with two other existing preconcentration techniques, solid phase microextraction (SPME) and planar solid phase microextraction (PSPME). Compared to SPME fibers, the CMV devices have an improved surface area and phase volume of 5000 times and 80 times, respectively. One (1) minute dynamic CMV air sampling resulted in similar performance as a 30 min static extraction using a SPME fiber. The PSPME devices have been fashioned to easily interface with ion mobility spectrometers (IMS) for explosives or drugs detection. The CMV devices are shown to offer dynamic sampling and can now be coupled to COTS GC-MS instruments. Several compound classes representing explosives have been analyzed with minimum breakthrough even after a 60 min. sampling time. The extracted volatile compounds were retained in the CMV devices when preserved in aluminum foils after sampling. Finally, the CMV sampling device were used for several different headspace profiling applications which involved sampling a shipping facility, six illicit drugs, seven military explosives and eighteen different bacteria strains. Successful detection of the target analytes at ng levels of the target signature volatile compounds in these applications suggests that the CMV devices can provide high throughput qualitative and quantitative analysis with high recovery and unambiguous identification of analytes.

Proximity detection protocols for IoT devices

In recent years, we have witnessed the growth of the Internet of Things paradigm, with its increased pervasiveness in our everyday lives. The possible applications are diverse: from a smartwatch able to measure heartbeat and communicate it to the cloud, to the device that triggers an event when we approach an exhibit in a museum. Present in many of these applications is the Proximity Detection task: for instance the heartbeat could be measured only when the wearer is near to a well defined location for medical purposes or the touristic attraction must be triggered only if someone is very close to it. Indeed, the ability of an IoT device to sense the presence of other devices nearby and calculate the distance to them can be considered the cornerstone of various applications, motivating research on this fundamental topic. The energy constraints of the IoT devices are often in contrast with the needs of continuous operations to sense the environment and to achieve high accurate distance measurements from the neighbors, thus making the design of Proximity Detection protocols a challenging task.