Matching Items (48)
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
After a decade of efforts, accurate and affordable DNA sequencing continues to remain an important goal in current research landscape. This thesis starts with a brief overview of the recent updates in the field of DNA sequencing technologies followed by description of the nanofluidics route to single molecule DNA detection. Chapter 2 presents discusses carbon nanotube(CNT) based nanofluidics. The fabrication and DNA sensing measurements of CNT forest membrane devices are presented. Chapter 3 gives the background for functionalization and recognition aspects of reader molecules. Chapter 4 marks the transition to solid state nanopore nanofluidics. The fabrication of Imidazole functionalized nanopores is discussed. The Single Molecule detection results of DNA from Palladium nanopore devices are presented next. Combining chemical recognition to nanopore technology, it has been possible to prolong the duration of single molecule events from the order of a few micro seconds to upto a few milliseconds. Overall, the work presented in this thesis promises longer single molecule detection time in a nanofludic set up and paves way for novel nanopore- tunnel junction devices that combine recognition chemistry, tunneling device and nanopore approach.
ContributorsKrishnakumar, Padmini (Author) / Lindsay, Stuart (Thesis advisor) / He, Jin (Committee member) / Vaiana, Sara (Committee member) / Schmidt, Kevin (Committee member) / Arizona State University (Publisher)
Created2013
Description
Solution conformations and dynamics of proteins and protein-DNA complexes are often difficult to predict from their crystal structures. The crystal structure only shows a snapshot of the different conformations these biological molecules can have in solution. Multiple different conformations can exist in solution and potentially have more importance in the biological activity. DNA sliding clamps are a family of proteins with known crystal structures. These clamps encircle the DNA and enable other proteins to interact more efficiently with the DNA. Eukaryotic PCNA and prokaryotic β clamp are two of these clamps, some of the most stable homo-oligomers known. However, their solution stability and conformational equilibrium have not been investigated in depth before. Presented here are the studies involving two sliding clamps: yeast PCNA and bacterial β clamp. These studies show that the β clamp has a very different solution stability than PCNA. These conclusions were reached through various different fluorescence-based experiments, including fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET), single molecule fluorescence, and various time resolved fluorescence techniques. Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
ContributorsRanjit, Suman (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Ribulose-1, 5-bisphosphate carboxylase oxygenase, commonly known as RuBisCO, is an enzyme involved in carbon fixation in photosynthetic organisms. The enzyme is subject to a mechanism-based deactivation during its catalytic cycle. RuBisCO activase (Rca), an ancillary enzyme belonging to the AAA+ family of the ATP-ases, rescues RuBisCO by facilitating the removal of the tightly bound sugar phosphates from the active sites of RuBisCO. In this work, we investigated the ATP/ADP dependent oligomerization equilibrium of fluorescently tagged Rca for a wide range of concentrations using fluorescence correlation spectroscopy. Results show that in the presence of ADP-Mg2+, the oligomerization state of Rca gradually changes in steps of two subunits. The most probable association model supports the dissociation constants (K_d) of ∼4, 1, 1 μM for the monomer-dimer, dimer-tetramer, and tetramer-hexamer equlibria, respectively. Rca continues to assemble at higher concentrations which are indicative of the formation of aggregates. In the presence of ATP-Mg2+, a similar stepwise assembly is observed. However, at higher concentrations (30-75 µM), the average oligomeric size remains relatively unchanged around six subunits per oligomer. This is in sharp contrast with observations in ADP-Mg2+, where a marked decrease in the diffusion coefficient of Rca was observed, consistent with the formation of aggregates. The estimated K_d values obtained from the analysis of the FCS decays were similar for the first steps of the assembly process in both ADP-Mg2+ and ATP-Mg2+. However, the formation of the hexamer from the tetramer is much more favored in ATP-Mg2+, as evidenced from 20 fold lower K_d associated with this assembly step. This suggests that the formation of a hexameric ring in the presence of ATP-Mg2+. In addition to that, Rca aggregation is largely suppressed in the presence of ATP-Mg2+, as evidenced from the 1000 fold larger K_d value for the hexamer-24 mer association step. In essence, a fluorescence-based method was developed to monitor in vitro protein oligomerization and was successfully applied with Rca. The results provide a strong hint at the active oligomeric structure of Rca, and this information will hopefully help the ongoing research on the mechanistic enzymology of Rca.
ContributorsChakraborty, Manas (Author) / Levitus, Marcia (Thesis advisor) / Angell, Charles (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2014
Description
Concrete is the most widely used infrastructure material worldwide. Production of portland cement, the main binding component in concrete, has been shown to require significant energy and account for approximately 5-7% of global carbon dioxide production. The expected continued increased use of concrete over the coming decades indicates this is an ideal time to implement sustainable binder technologies. The current work aims to explore enhanced sustainability concretes, primarily in the context of limestone and flow. Aspects such as hydration kinetics, hydration product formation and pore structure add to the understanding of the strength development and potential durability characteristics of these binder systems. Two main strategies for enhancing this sustainability are explored in this work: (i) the use of high volume limestone in combination with other alternative cementitious materials to decrease the portland cement quantity in concrete and (ii) the use of geopolymers as the binder phase in concrete. The first phase of the work investigates the use of fine limestone as cement replacement from the perspective of hydration, strength development, and pore structure. The nature of the potential synergistic benefit of limestone and alumina will be explored. The second phase will focus on the rheological characterization of these materials in the fresh state, as well as a more general investigation of the rheological characterization of suspensions. The results of this work indicate several key ideas. (i) There is a potential synergistic benefit for strength, hydration, and pore structure by using alumina and in portland limestone cements, (ii) the limestone in these systems is shown to react to some extent, and fine limestone is shown to accelerate hydration, (iii) rheological characteristics of cementitious suspensions are complex, and strongly dependent on several key parameters including: the solid loading, interparticle forces, surface area of the particles present, particle size distribution of the particles, and rheological nature of the media in which the particles are suspended, and (iv) stress plateau method is proposed for the determination of rheological properties of concentrated suspensions, as it more accurately predicts apparent yield stress and is shown to correlate well with other viscoelastic properties of the suspensions.
ContributorsVance, Kirk (Author) / Neithalath, Narayanan (Thesis advisor) / Rajan, Subramaniam D. (Committee member) / Mobasher, Barzin (Committee member) / Chawla, Nikhilesh (Committee member) / Marzke, Robert (Committee member) / Arizona State University (Publisher)
Created2014
Description
Single molecule identification is one essential application area of nanotechnology. The application areas including DNA sequencing, peptide sequencing, early disease detection and other industrial applications such as quantitative and quantitative analysis of impurities, etc. The recognition tunneling technique we have developed shows that after functionalization of the probe and substrate of a conventional Scanning Tunneling Microscope with recognition molecules ("tethered molecule-pair" configuration), analyte molecules trapped in the gap that is formed by probe and substrate will bond with the reagent molecules. The stochastic bond formation/breakage fluctuations give insight into the nature of the intermolecular bonding at a single molecule-pair level. The distinct time domain and frequency domain features of tunneling signals were extracted from raw signals of analytes such as amino acids and their enantiomers. The Support Vector Machine (a machine-learning method) was used to do classification and predication based on the signal features generated by analytes, giving over 90% accuracy of separation of up to seven analytes. This opens up a new interface between chemistry and electronics with immediate implications for rapid Peptide/DNA sequencing and molecule identification at single molecule level.
ContributorsZhao, Yanan, 1986- (Author) / Lindsay, Stuart (Thesis advisor) / Nemanich, Robert (Committee member) / Qing, Quan (Committee member) / Ros, Robert (Committee member) / Zhang, Peiming (Committee member) / Arizona State University (Publisher)
Created2014
Description
Calcitonin Gene-Related Peptide (CGRP) is an intrinsically disordered protein
that has no regular secondary structure, but plays an important role in vasodilation and pain transmission in migraine. Little is known about the structure and dynamics of the monomeric state of CGRP or how CGRP is able to function in the cell, despite the lack of regular secondary structure. This work focuses characterizing the non-local structural and dynamical properties of the CGRP monomer in solution, and understanding how these are affected by the sequence and the solution environment. The unbound, free state of CGRP is measured using a nanosecond laser-pump spectrophotometer, which allows measuring the end-to-end distance (a non-local structural property) and the rate of end-to-end contact formation (intra-chain diffusional dynamics). The data presented in this work show that electrostatic interactions strongly modulate the structure of CGRP, and that peptide-solvent interactions are sequence and charge dependent and can have a significant effect on the internal dynamics of the peptide. In the last few years migraine research has shifted focus to disrupting the CGRP-receptor pathway through the design of pharmacological drugs that bind to either CGRP or its receptor, inhibiting receptor activation and therefore preventing or reducing the frequency of migraine attacks. Understanding what types of intra- and inter-chain interactions dominate in CGRP can help better design drugs that disrupt the binding of CGRP to its receptor.
that has no regular secondary structure, but plays an important role in vasodilation and pain transmission in migraine. Little is known about the structure and dynamics of the monomeric state of CGRP or how CGRP is able to function in the cell, despite the lack of regular secondary structure. This work focuses characterizing the non-local structural and dynamical properties of the CGRP monomer in solution, and understanding how these are affected by the sequence and the solution environment. The unbound, free state of CGRP is measured using a nanosecond laser-pump spectrophotometer, which allows measuring the end-to-end distance (a non-local structural property) and the rate of end-to-end contact formation (intra-chain diffusional dynamics). The data presented in this work show that electrostatic interactions strongly modulate the structure of CGRP, and that peptide-solvent interactions are sequence and charge dependent and can have a significant effect on the internal dynamics of the peptide. In the last few years migraine research has shifted focus to disrupting the CGRP-receptor pathway through the design of pharmacological drugs that bind to either CGRP or its receptor, inhibiting receptor activation and therefore preventing or reducing the frequency of migraine attacks. Understanding what types of intra- and inter-chain interactions dominate in CGRP can help better design drugs that disrupt the binding of CGRP to its receptor.
ContributorsSizemore, Sara (Author) / Vaiana, Sara (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Ros, Robert (Committee member) / Lindsay, Stuart (Committee member) / Ozkan, Sefika (Committee member) / Arizona State University (Publisher)
Created2015
Description
The central theme of this dissertation is to understand the chemical processing science of advanced ceramic materials for biomedicine, including therapy and imaging. The secondary component focuses on the chemical processing of energy materials.
Recently, layered double hydroxide (LDH) nanoparticles (NPs) with various intercalated compounds (e.g. fluorescent molecules, radio-labeled ATP, vitamins, DNA, and drugs) have exhibited versatility and promise as a combined therapeutic and diagnostic (i.e. theranostic) vector. However, its eventual acceptance in biomedicine will be contingent on understanding the processing science, reproducibly synthesizing monodispersed NPs with controlled mean particle size (MPS), and ascertaining the efficacy of the NPs for drug delivery and imaging. First, statistical design of experiments were used to optimize the wet chemistry synthesis of (Zn, Al)-LDH NPs. A synthesis model, which allows the synthesis of nearly monodispersed NPs with controlled MPS, was developed and experimentally verified. Also, the evolution of the nanostructure was characterized, from coprecipitation to hydrothermal treatment, to identify the formation mechanisms. Next, the biocompatibility, cellular uptake and drug delivery capability of LDH NPs were studied. In an in vitro study, using cultured pancreatic adenocarcinoma BXPC3 cells, valproate-intercalated LDH NPs showed an improved efficacy (~50 fold) over the sodium valproate alone. Finally, Gd(DTPA)-intercalated LDH NPs were synthesized and characterized by proton (1H) nuclear magnetic resonance. The longitudinal relaxivity (r1) of 28.38 s-1 mM-1, which is over 6 times higher than the clinically approved contrast agent, Gd(DTPA), demonstrated the potential of this vector for use in magnetic resonance imaging.
Visible light-transparent single metal-semiconductor junction devices, which convert ultraviolet photon energy into high open circuit voltage (Voc>1.5-2 V), are highly desirable for transparent photovoltaics that can potentially power an electrochromic stack for smart windows. A Schottky junction solar cell, comprised of sputtered ZnO/ZnS heterojunction with Cr/Au contacts, was fabricated and an Voc of fî1.35 V was measured. Also, a low-cost route to form ZnO/ZnS heterojunctions by partial sulfurization of solution-grown ZnO thin films (350 nm-5 fÝm thick; conductivity comparable to phosphorus-doped Si) was demonstrated. A final study was on a cathode material for Li-ion batteries. Phase-pure LiFePO4 powders were synthesized by microwave-assisted sol-gel method and characterized.
Recently, layered double hydroxide (LDH) nanoparticles (NPs) with various intercalated compounds (e.g. fluorescent molecules, radio-labeled ATP, vitamins, DNA, and drugs) have exhibited versatility and promise as a combined therapeutic and diagnostic (i.e. theranostic) vector. However, its eventual acceptance in biomedicine will be contingent on understanding the processing science, reproducibly synthesizing monodispersed NPs with controlled mean particle size (MPS), and ascertaining the efficacy of the NPs for drug delivery and imaging. First, statistical design of experiments were used to optimize the wet chemistry synthesis of (Zn, Al)-LDH NPs. A synthesis model, which allows the synthesis of nearly monodispersed NPs with controlled MPS, was developed and experimentally verified. Also, the evolution of the nanostructure was characterized, from coprecipitation to hydrothermal treatment, to identify the formation mechanisms. Next, the biocompatibility, cellular uptake and drug delivery capability of LDH NPs were studied. In an in vitro study, using cultured pancreatic adenocarcinoma BXPC3 cells, valproate-intercalated LDH NPs showed an improved efficacy (~50 fold) over the sodium valproate alone. Finally, Gd(DTPA)-intercalated LDH NPs were synthesized and characterized by proton (1H) nuclear magnetic resonance. The longitudinal relaxivity (r1) of 28.38 s-1 mM-1, which is over 6 times higher than the clinically approved contrast agent, Gd(DTPA), demonstrated the potential of this vector for use in magnetic resonance imaging.
Visible light-transparent single metal-semiconductor junction devices, which convert ultraviolet photon energy into high open circuit voltage (Voc>1.5-2 V), are highly desirable for transparent photovoltaics that can potentially power an electrochromic stack for smart windows. A Schottky junction solar cell, comprised of sputtered ZnO/ZnS heterojunction with Cr/Au contacts, was fabricated and an Voc of fî1.35 V was measured. Also, a low-cost route to form ZnO/ZnS heterojunctions by partial sulfurization of solution-grown ZnO thin films (350 nm-5 fÝm thick; conductivity comparable to phosphorus-doped Si) was demonstrated. A final study was on a cathode material for Li-ion batteries. Phase-pure LiFePO4 powders were synthesized by microwave-assisted sol-gel method and characterized.
ContributorsSun Zhou, Xiao Di (Author) / Dey, Sandwip K (Thesis advisor) / Krause, Stephen (Committee member) / Nagaraj, Vinay J (Committee member) / Marzke, Robert (Committee member) / Arizona State University (Publisher)
Created2014
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 studies on aluminosilicate materials to replace traditional construction materials such as ordinary Portland cement(OPC) to reduce the effects caused has been an important research area for the past decades. Many properties like strength have already been studied and the primary focus is to learn about the reaction mechanism and the effect of the parameters on the formed products. The aim of this research was to explore the structural changes and reaction product analysis of geopolymers (Slag & Fly Ash) using Fourier transform infrared spectroscopy (FTIR) and deconvolution
techniques. Spectroscopic techniques give valuable information at a molecular level but not all methods are economic and simple. To understand the mechanisms of alkali activated aluminosilicate materials, attenuated total reflectance (ATR) FTIR has been used where the effect of the parameters on the reaction products have been analyzed. To analyze complex systems like geopolymers using FTIR, deconvolution techniques help to obtain the properties of a particular peak attributed to a certain molecular vibration.
Time and temperature dependent analysis were done on slag pastes to understand the polymerization of reactive silica in the system with time and temperature variance. For time dependent analysis slag has been activated with sodium and potassium silicates using two different `n'values and three different silica modulus [Ms- (SiO2 /M2O)] values. The temperature dependent analysis was done by curing the samples at 60C and 80C. Similarly fly ash has been studied by activating with alkali hydroxides and alkali silicates. Under the same curing conditions the fly ash samples were evaluated to analyze the effects of added silicates for alkali activation.
The peak shifts in the FTIR explains the changes in the structural nature of the matrix and can be identified using the deconvolution technique. A strong correlation is found between the concentrations of silicate monomer in the activating position of the main Si-O-T (where T is Al/Si) stretching band in the FTIR spectrum, which
gives an indication of the relative changes in the Si/Al ratio. Also, the effect of the cation and silicate concentration in the activating solution has been discussed using the Fourier self deconvolution technique.
techniques. Spectroscopic techniques give valuable information at a molecular level but not all methods are economic and simple. To understand the mechanisms of alkali activated aluminosilicate materials, attenuated total reflectance (ATR) FTIR has been used where the effect of the parameters on the reaction products have been analyzed. To analyze complex systems like geopolymers using FTIR, deconvolution techniques help to obtain the properties of a particular peak attributed to a certain molecular vibration.
Time and temperature dependent analysis were done on slag pastes to understand the polymerization of reactive silica in the system with time and temperature variance. For time dependent analysis slag has been activated with sodium and potassium silicates using two different `n'values and three different silica modulus [Ms- (SiO2 /M2O)] values. The temperature dependent analysis was done by curing the samples at 60C and 80C. Similarly fly ash has been studied by activating with alkali hydroxides and alkali silicates. Under the same curing conditions the fly ash samples were evaluated to analyze the effects of added silicates for alkali activation.
The peak shifts in the FTIR explains the changes in the structural nature of the matrix and can be identified using the deconvolution technique. A strong correlation is found between the concentrations of silicate monomer in the activating position of the main Si-O-T (where T is Al/Si) stretching band in the FTIR spectrum, which
gives an indication of the relative changes in the Si/Al ratio. Also, the effect of the cation and silicate concentration in the activating solution has been discussed using the Fourier self deconvolution technique.
ContributorsMadavarapu, Sateesh Babu (Author) / Neithalath, Narayanan (Thesis advisor) / Rajan, Subramaniam D. (Committee member) / Marzke, Robert (Committee member) / Arizona State University (Publisher)
Created2014