Matching Items (21)
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
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
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
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
Description
This thesis describes several experiments based on carbon nanotube nanofludic devices and field-effect transistors. The first experiment detected ion and molecule translocation through one single-walled carbon nanotube (SWCNT) that spans a barrier between two fluid reservoirs. The electrical ionic current is measured. Translocation of small single stranded DNA oligomers is marked by large transient increases in current through the tube and confirmed by a PCR (polymerase chain reaction) analysis. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurement, and open new avenues for control of DNA translocation. The second experiment constructed devices in which the interior of a single-walled carbon nanotube field-effect transistor (CNT-FET) acts as a nanofluidic channel that connects two fluid reservoirs, permitting measurement of the electronic properties of the SWCNT as it is wetted by an analyte. Wetting of the inside of the SWCNT by water turns the transistor on, while wetting of the outside has little effect. This finding may provide a new method to investigate water behavior at nanoscale. This also opens a new avenue for building sensors in which the SWCNT functions as an electronic detector. This thesis also presents some experiments that related to nanofabrication, such as construction of FET with tin sulfide (SnS) quantum ribbon. This work demonstrates the application of solution processed IV-VI semiconductor nanostructures in nanoscale devices.
ContributorsCao, Zhai (Author) / Lindsay, Stuart (Thesis advisor) / Vaiana, Sara (Committee member) / Ros, Robert (Committee member) / Marzke, Robert (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
The behaviors of various amorphous materials are characterized at high pressures to deduce phase transitions, coordination changes, densification, and other structural or electronic alterations in the system. Alongside, improvements on high pressure techniques are presented to measure equations of state of glassy materials and probe liquids using in-situ high resolution nuclear magnetic resonance (NMR) spectroscopy. 27Al NMR is used to quantify coordination changes in CaAl2O4 glass pressure cycled to 16 GPa. The structure and coordination environments remain unchanged up to 8 GPa at which 93% of the recovered glass exists as 4-fold Al, whereas the remaining population exists as [5,6]Al. Upon densification, [5,6]Al comprise nearly 30% of observed Al, most likely through the generation of 3-coordinated oxygen. A method to determine the volumetric equation of state of amorphous solids using optical microscopy in a diamond anvil cell is also described. The method relies on two dimensional image acquisition and analysis to quantify changes in the projected image area with compression. The area analysis method is used to determine the compression of cubic crystals, yielding results in good agreement with diffraction and volumetric measurements. A NMR probe capable of reaching 3 GPa is built to understand the nature of magnetic field gradients and improve upon the resolution of high pressure studies conducted in a diamond anvil cell. Field gradients in strength up to 6 G/cm are caused largely by mismatches in the magnetic susceptibility between the sample and gasket, which is proven to shift the chemical shift distribution by use of several different metallic gaskets. Polyamorphic behavior in triphenyl phosphite is studied at pressures up to 0.7 GPa to elucidate the formation of the glacial phase at high pressures. A perceived liquid-liquid phase transition is shown to follow a positive Clapeyron slope, and closely follows the predicted glass transition line up to 0.4 GPa and temperatures below 270 K. A drastic change in morphology is indicative of a transformation from liquid I to liquid II and followed by optical microscopy.
ContributorsAmin, Samrat A (Author) / Yarger, Jeffery L (Thesis advisor) / Wolf, George (Committee member) / Marzke, Robert (Committee member) / Arizona State University (Publisher)
Created2012
Description
The goal of this theoretical study of infrared spectra was to ascertain to what degree molecules may be identified from their IR spectra and which spectral regions are best suited for this purpose. The frequencies considered range from the lowest frequency molecular vibrations in the far-IR, terahertz region (below ~3 THz or 100 cm-1) up to the highest frequency vibrations (~120 THz or 4000 cm-1). An emphasis was placed on the IR spectra of chemical and biological threat molecules in the interest of detection and prevention. To calculate IR spectra, the technique of normal mode analysis was applied to organic molecules ranging in size from 8 to 11,352 atoms. The IR intensities of the vibrational modes were calculated in terms of the derivative of the molecular dipole moment with respect to each normal coordinate. Three sets of molecules were studied: the organophosphorus G- and V-type nerve agents and chemically related simulants (15 molecules ranging in size from 11 to 40 atoms); 21 other small molecules ranging in size from 8 to 24 atoms; and 13 proteins ranging in size from 304 to 11,352 atoms. Spectra for the first two sets of molecules were calculated using quantum chemistry software, the last two sets using force fields. The "middle" set used both methods, allowing for comparison between them and with experimental spectra from the NIST/EPA Gas-Phase Infrared Library. The calculated spectra of proteins, for which only force field calculations are practical, reproduced the experimentally observed amide I and II bands, but they were shifted by approximately +40 cm-1 relative to experiment. Considering the entire spectrum of protein vibrations, the most promising frequency range for differentiating between proteins was approximately 600-1300 cm-1 where water has low absorption and the proteins show some differences.
ContributorsMott, Adam J (Author) / Rez, Peter (Thesis advisor) / Ozkan, Banu (Committee member) / Shumway, John (Committee member) / Thorpe, Michael (Committee member) / Vaiana, Sara (Committee member) / Arizona State University (Publisher)
Created2012
Description
CpG methylation is an essential requirement for the normal development of mammals, but aberrant changes in the methylation can lead to tumor progression and cancer. An in-depth understanding of this phenomenon can provide insights into the mechanism of gene repression. We present a study comparing methylated DNA and normal DNA wrt its persistence length and contour length. Although, previous experiments and studies show no difference between the physical properties of the two, the data collected and interpreted here gives a different picture to the methylation phenomena and its effect on gene silencing. The study was extended to the artificially reconstituted chromatin and its interactions with the methyl CpG binding proteins were also probed.
ContributorsKaur, Parminder (Author) / Lindsay, Stuart (Thesis advisor) / Ros, Robert (Committee member) / Tao, Nongjian (Committee member) / Vaiana, Sara (Committee member) / Beckenstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2012
Description
Increased priority on the minimization of environmental impacts of conventional construction materials in recent years has motivated increased use of waste materials or bi-products such as fly ash, blast furnace slag with a view to reduce or eliminate the manufacturing/consumption of ordinary portland cement (OPC) which accounts for approximately 5-7% of global carbon dioxide emission. The current study explores, for the first time, the possibility of carbonating waste metallic iron powder to develop carbon-negative sustainable binder systems for concrete. The fundamental premise of this work is that metallic iron will react with aqueous CO2 under controlled conditions to form complex iron carbonates which have binding capabilities. The compressive and flexural strengths of the chosen iron-based binder systems increase with carbonation duration and the specimens carbonated for 4 days exhibit mechanical properties that are comparable to those of companion ordinary portland cement systems. The optimal mixture proportion and carbonation regime for this non-conventional sustainable binder is established based on the study of carbonation efficiency of a series of mixtures using thermogravimetric analysis. The pore- and micro-structural features of this novel binding material are also evaluated. The fracture response of this novel binder is evaluated using strain energy release rate and measurement of fracture process zone using digital image correlation (DIC). The iron-based binder system exhibits significantly higher strain energy release rates when compared to those of the OPC systems in both the unreinforced and glass fiber reinforced states. The iron-based binder also exhibits higher amount of area of fracture process zone due to its ability to undergo inelastic deformation facilitated by unreacted metallic iron particle inclusions in the microstructure that helps crack bridging /deflection. The intrinsic nano-mechanical properties of carbonate reaction product are explored using statistical nanoindentation technique coupled with a stochastic deconvolution algorithm. Effect of exposure to high temperature (up to 800°C) is also studied. Iron-based binder shows significantly higher residual flexural strength after exposure to high temperatures. Results of this comprehensive study establish the viability of this binder type for concrete as an environment-friendly and economical alternative to OPC.
ContributorsDas, Sumanta (Author) / Neithalath, Narayanan (Thesis advisor) / Rajan, S.D. (Committee member) / Mobasher, Barzin (Committee member) / Marzke, Robert (Committee member) / Chawla, Nikhilesh (Committee member) / Stone, David (Committee member) / Arizona State University (Publisher)
Created2015