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Description
Human breath is a concoction of thousands of compounds having in it a breath-print of physiological processes in the body. Though breath provides a non-invasive and easy to handle biological fluid, its analysis for clinical diagnosis is not very common. Partly the reason for this absence is unavailability of cost effective and convenient tools for such analysis. Scientific literature is full of novel sensor ideas but it is challenging to develop a working device, which are few. These challenges include trace level detection, presence of hundreds of interfering compounds, excessive humidity, different sampling regulations and personal variability. To meet these challenges as well as deliver a low cost solution, optical sensors based on specific colorimetric chemical reactions on mesoporous membranes have been developed. Sensor hardware utilizing cost effective and ubiquitously available light source (LED) and detector (webcam/photo diodes) has been developed and optimized for sensitive detection. Sample conditioning mouthpiece suitable for portable sensors is developed and integrated. The sensors are capable of communication with mobile phones realizing the idea of m-health for easy personal health monitoring in free living conditions. Nitric oxide and Acetone are chosen as analytes of interest. Nitric oxide levels in the breath correlate with lung inflammation which makes it useful for asthma management. Acetone levels increase during ketosis resulting from fat metabolism in the body. Monitoring breath acetone thus provides useful information to people with type1 diabetes, epileptic children on ketogenic diets and people following fitness plans for weight loss.
ContributorsPrabhakar, Amlendu (Author) / Tao, Nongjian (Thesis advisor) / Forzani, Erica (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2013
Description
Measurements of the response of superconducting nanowire single photon detector (SNSPD) devices to changes in various forms of input power can be used for characterization of the devices and for probing device-level physics. Two niobium nitride (NbN) superconducting nanowires developed for use as SNSPD devices are embedded as the inductive (L) component in resonant inductor/capacitor (LC) circuits coupled to a microwave transmission line. The capacitors are low loss commercial chip capacitors which limit the internal quality factor of the resonators to approximately $Qi = 170$. The resonator quality factor, approximately $Qr = 23$, is dominated by the coupling to the feedline and limits the detection bandwidth to on the order of 1MHz. In our experiments with this first generation device, we measure the response of the SNSPD devices to changes in thermal and optical power in both the time domain and the frequency domain. Additionally, we explore the non-linear response of the devices to an applied bias current. For these nanowires, we find that the band-gap energy is $\Delta_0 \approx 1.1$meV and that the density of states at the Fermi energy is $N_0 \sim 10^{10}$/eV/$\mu$m$^3$.
We present the results of experimentation with a superconducting nanowire that can be operated in two detection modes: i) as a kinetic inductance detector (KID) or ii) as a single photon detector (SPD). When operated as a KID mode in linear mode, the detectors are AC-biased with tones at their resonant frequencies of 45.85 and 91.81MHz. When operated as an SPD in Geiger mode, the resonators are DC biased through cryogenic bias tees and each photon produces a sharp voltage step followed by a ringdown signal at the resonant frequency of the detector. We show that a high AC bias in KID mode is inferior for photon counting experiments compared to operation in a DC-biased SPD mode due to the small fraction of time spent near the critical current with an AC bias. We find a photon count rate of $\Gamma_{KID} = 150~$photons/s/mA in a critically biased KID mode and a photon count rate of $\Gamma_{SPD} = 10^6~$photons/s/mA in SPD mode.
This dissertation additionally presents simulations of a DC-biased, frequency-multiplexed readout of SNSPD devices in Advanced Design System (ADS), LTspice, and Sonnet. A multiplexing factor of 100 is achievable with a total count rate of $>5$MHz. This readout could enable a 10000-pixel array for astronomy or quantum communications. Finally, we present a prototype array design based on lumped element components. An early implementation of the array is presented with 16 pixels in the frequency range of 74.9 to 161MHz. We find good agreement between simulation and experimental data in both the time domain and the frequency domain and present modifications for future versions of the array.
We present the results of experimentation with a superconducting nanowire that can be operated in two detection modes: i) as a kinetic inductance detector (KID) or ii) as a single photon detector (SPD). When operated as a KID mode in linear mode, the detectors are AC-biased with tones at their resonant frequencies of 45.85 and 91.81MHz. When operated as an SPD in Geiger mode, the resonators are DC biased through cryogenic bias tees and each photon produces a sharp voltage step followed by a ringdown signal at the resonant frequency of the detector. We show that a high AC bias in KID mode is inferior for photon counting experiments compared to operation in a DC-biased SPD mode due to the small fraction of time spent near the critical current with an AC bias. We find a photon count rate of $\Gamma_{KID} = 150~$photons/s/mA in a critically biased KID mode and a photon count rate of $\Gamma_{SPD} = 10^6~$photons/s/mA in SPD mode.
This dissertation additionally presents simulations of a DC-biased, frequency-multiplexed readout of SNSPD devices in Advanced Design System (ADS), LTspice, and Sonnet. A multiplexing factor of 100 is achievable with a total count rate of $>5$MHz. This readout could enable a 10000-pixel array for astronomy or quantum communications. Finally, we present a prototype array design based on lumped element components. An early implementation of the array is presented with 16 pixels in the frequency range of 74.9 to 161MHz. We find good agreement between simulation and experimental data in both the time domain and the frequency domain and present modifications for future versions of the array.
ContributorsSchroeder, Edward, Ph.D (Author) / Mauskopf, Philip (Thesis advisor) / Chamberlin, Ralph (Committee member) / Lindsay, Stuart (Committee member) / Newman, Nathan (Committee member) / Easson, Damien (Committee member) / Arizona State University (Publisher)
Created2018
Description
Cell adhesion is an important aspect of many biological processes. The atomic force microscope (AFM) has made it possible to quantify the forces involved in cellular adhesion using a technique called single cell force spectroscopy (SCFS). AFM based SCFS offers versatile control over experimental conditions for probing directly the interaction between specific cell types and specific proteins, surfaces, or other cells. Transmembrane integrins are the primary proteins involved in cellular adhesion to the extra cellular matix (ECM). One of the chief integrins involved in the adhesion of leukocyte cells is αMβ2 (Mac-1). The experiments in this dissertation quantify the adhesion of Mac-1 expressing human embryonic kidney (HEK Mac-1), platelets, and neutrophils cells on substrates with different concentrations of fibrinogen and on fibrin gels and multi-layered fibrinogen coated fibrin gels. It was shown that multi-layered fibrinogen reduces the adhesion force of these cells considerably. A novel method was developed as part of this research combining total internal reflection microscopy (TIRFM) with SCFS allowing for optical microscopy of HEK Mac-1 cells interacting with bovine serum albumin (BSA) coated glass after interacting with multi-layered fibrinogen. HEK Mac-1 cells are able to remove fibrinogen molecules from the multi-layered fibrinogen matrix. An analysis methodology for quantifying the kinetic parameters of integrin-ligand interactions from SCFS experiments is proposed, and the kinetic parameters of the Mac-1 fibrinogen bond are quantified. Additional SCFS experiments quantify the adhesion of macrophages and HEK Mac-1 cells on functionalized glass surfaces and normal glass surfaces. Both cell types show highest adhesion on a novel functionalized glass surface that was prepared to induce macrophage fusion. These experiments demonstrate the versatility of AFM based SCFS, and how it can be applied to address many questions in cellular biology offering quantitative insights.
ContributorsChristenson, Wayne B (Author) / Ros, Robert (Thesis advisor) / Beckstein, Oliver (Committee member) / Lindsay, Stuart (Committee member) / Ugarova, Tatiana (Committee member) / Arizona State University (Publisher)
Created2016
Description
Atomic force microscopy (AFM) has become an important tool to characterize and image surfaces with nanoscale resolution. AFM imaging technique has been utilized to study a wide range of substances such as DNA, proteins, cells, silicon surfaces, nanowires etc. Hence AFM has become extremely important in the field of biochemistry, cell biology and material science. Functionalizing the AFM tip made it possible to detect molecules and their interaction using recognition imaging at single molecule level. Also the unbinding force of two molecules can be investigated based on AFM based single molecule force spectroscopy.
In the first study, a new chemical approach to functionalize the AFM tip in a simple and user-friendly way has been described. Copper-free click chemistry and a vinyl sulfone PEG linker have been utilized during the process. Using this technique, human thrombin and integrin were detected in separate experiments. Then a novel tri-arm linker with two recognition molecules on it was designed and two proteins (human thrombin and integrin) were detected simultaneously in the same experiment using recognition imaging. This technique can be applied to understand many multivalent interactions taking place in nature. Using the same tri-arm linker functionalized with two biotin molecules, the interaction of streptavidin with mono-biotin and bis-biotin ligands were investigated. The thermal stability of streptavidin-biotin complex was also studied using SDS-PAGE analysis.
In the final study, structure of native chromatin extracted from normal and cancer cell lines were analyzed using AFM imaging and agarose gel electrophoresis. Different salt fractions were used to extract chromatin region depending on their solubility. Mnase sensitivity of the chromatin sample was used to understand the open and closed structures of chromatin from different sources. The amount of chromatin in different salt fractions could act as an indicator of amount of open and condensed chromatin in normal and cancer cells. Eventually this ratio of closed and open structure of chromatin could be an indicator of tumorigenic nature of particular cell lines.
In the first study, a new chemical approach to functionalize the AFM tip in a simple and user-friendly way has been described. Copper-free click chemistry and a vinyl sulfone PEG linker have been utilized during the process. Using this technique, human thrombin and integrin were detected in separate experiments. Then a novel tri-arm linker with two recognition molecules on it was designed and two proteins (human thrombin and integrin) were detected simultaneously in the same experiment using recognition imaging. This technique can be applied to understand many multivalent interactions taking place in nature. Using the same tri-arm linker functionalized with two biotin molecules, the interaction of streptavidin with mono-biotin and bis-biotin ligands were investigated. The thermal stability of streptavidin-biotin complex was also studied using SDS-PAGE analysis.
In the final study, structure of native chromatin extracted from normal and cancer cell lines were analyzed using AFM imaging and agarose gel electrophoresis. Different salt fractions were used to extract chromatin region depending on their solubility. Mnase sensitivity of the chromatin sample was used to understand the open and closed structures of chromatin from different sources. The amount of chromatin in different salt fractions could act as an indicator of amount of open and condensed chromatin in normal and cancer cells. Eventually this ratio of closed and open structure of chromatin could be an indicator of tumorigenic nature of particular cell lines.
ContributorsSenapati, Subhadip (Author) / Lindsay, Stuart (Thesis advisor) / Zhang, Peiming (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2015
Description
The atomic force microscope (AFM) is capable of directly probing the mechanics of samples with length scales from single molecules to tissues and force scales from pico to micronewtons. In particular, AFM is widely used as a tool to measure the elastic modulus of soft biological samples by collecting force-indentation relationships and fitting these to classic elastic contact models. However, the analysis of raw force-indentation data may be complicated by mechanical heterogeneity present in biological systems. An analytical model of an elastic indentation on a bonded two-layer sample was solved. This may be used to account for substrate effects and more generally address experimental design for samples with varying elasticity. This model was applied to two mechanobiology systems of interest. First, AFM was combined with confocal laser scanning fluorescence microscopy and finite element analysis to examine stiffness changes during the initial stages of invasion of MDA-MB-231 metastatic breast cells into bovine collagen I matrices. It was determined that the cells stiffen significantly as they invade, the amount of stiffening is correlated with the elastic modulus of the collagen gel, and inhibition of Rho-associated protein kinase reduces the elastic modulus of the invading cells. Second, the elastic modulus of cancer cell nuclei was investigated ex situ and in situ. It was observed that inhibition of histone deacetylation to facilitate chromatin decondenstation result in significantly more morphological and stiffness changes in cancerous cells compared to normal cells. The methods and results presented here offer novel strategies for approaching biological systems with AFM and demonstrate its applicability and necessity in studying cellular function in physiologically relevant environments.
ContributorsDoss, Bryant Lee (Author) / Ros, Robert (Thesis advisor) / Lindsay, Stuart (Committee member) / Nikkhah, Mehdi (Committee member) / Beckstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2015