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Description
The objective of the present investigations is to experimentally determine the fundamental molecular properties of the transient metal containing pieces. The transient molecules have been generated using laser ablation production technique and detected by using laser induced fluorescence technique. Ultra-high resolution spectra of the diatomic molecules, 87SrF, 135&137BaF, YbF, HfF,

The objective of the present investigations is to experimentally determine the fundamental molecular properties of the transient metal containing pieces. The transient molecules have been generated using laser ablation production technique and detected by using laser induced fluorescence technique. Ultra-high resolution spectra of the diatomic molecules, 87SrF, 135&137BaF, YbF, HfF, and IrSi were recorded at a resolution of approximately 30 Mhz. The fine and hyperfine structure of these molecules were determined for the ground and the excited state. The optical Stark splittings of 180HfF and IrSi were recorded and analyzed to determine the permanent electric dipole moments of the ground and the excited state. An effective Hamiltonian operator, including the rotational, centrifugal distortion, spin-orbit, spin-spin, spin-rotation, Λ-doubling, magnetic hyperfine and quadrupole interactions, and Stark effect, was employed to model and analyze the recorded spectra. The electronic spectra of the triatomic molecules, TiO2 and ZrO2, were recorded using pulsed dye laser, LIF, spectrometer at a resolution of 300MHz. These molecules have C2v symmetry. The harmonic frequencies, lifetime measurements were determined. These spectra of ZrO2 and TiO2 were modeled using a normal coordinate analysis and Franck-Condon factor predictions. High resolution field-free and Stark effect spectra of ZrO2 were recorded and for future investigation.
ContributorsLe, Anh Thun (Author) / Steimle, Timothy C (Thesis advisor) / Richert, Ranko (Committee member) / Chizmeshya, Andrew (Committee member) / Arizona State University (Publisher)
Created2013
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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

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
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Description
This dissertation is focused on material property exploration and analysis using computational quantum mechanics methods. Theoretical calculations were performed on the recently discovered hexahydride materials A2SiH6 (A=Rb, K) to calculate the lattice dynamics of the systems in order to check for structural stability, verify the experimental Raman and infrared spectrospcopy

This dissertation is focused on material property exploration and analysis using computational quantum mechanics methods. Theoretical calculations were performed on the recently discovered hexahydride materials A2SiH6 (A=Rb, K) to calculate the lattice dynamics of the systems in order to check for structural stability, verify the experimental Raman and infrared spectrospcopy results, and obtain the theoretical free energies of formation. The electronic structure of the systems was calculated and the bonding and ionic properties of the systems were analyzed. The novel hexahydrides were compared to the important hydrogen storage material KSiH3. This showed that the hypervalent nature of the SiH62- ions reduced the Si-H bonding strength considerably. These hydrogen rich compounds could have promising energy applications as they link to alternative hydrogen fuel technology. The carbide systems Li-C (A=Li,Ca,Mg) were studied using \emph{ab initio} and evolutionary algorithms at high pressures. At ambient pressure Li2C2 and CaC2 are known to contain C22- dumbbell anions and CaC2 is polymorphic. At elevated pressure both CaC2 and Li2C2 display polymorphism. At ambient pressure the Mg-C system contains several experimentally known phases, however, all known phases are shown to be metastable with respect to the pure elements Mg and C. First principle investigation of the configurational space of these compounds via evolutionary algorithms results in a variety of metastable and unique structures. The binary compounds ZnSb and ZnAs are II-V electron-poor semiconductors with interesting thermoelectric properties. They contain rhomboid rings composed of Zn2Sb2 (Zn2As2) with multi-centered covalent bonds which are in turn covalently bonded to other rings via two-centered, two-electron bonds. Ionicity was explored via Bader charge analysis and it appears that the low ionicity that these materials display is a necessary condition of their multicentered bonding. Both compounds were found to have narrow, indirect band gaps with multi-valley valence and conduction bands; which are important characteristics for high thermopower in thermoelectric materials. Future work is needed to analyze the lattice properties of the II-V CdSb-type systems, especially in order to find the origin of the extremely low thermal conductivity that these systems display.
ContributorsBenson, Daryn Eugene (Author) / Häussermann, Ulrich (Thesis advisor) / Shumway, John (Thesis advisor) / Chamberlin, Ralph (Committee member) / Sankey, Otto (Committee member) / Treacy, Mike (Committee member) / Arizona State University (Publisher)
Created2013
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Description
This thesis describes the studies for two groups of molecules in the gas-phase: (a) copper monofluoride (CuF) and copper hydroxide (CuOH); (b) thorium monoxide (ThO) and tungsten carbide (WC). Copper-containing molecules (Group a) are selected to investigate the ionic bonding in transition metal-containing molecules because they have a relatively simple

This thesis describes the studies for two groups of molecules in the gas-phase: (a) copper monofluoride (CuF) and copper hydroxide (CuOH); (b) thorium monoxide (ThO) and tungsten carbide (WC). Copper-containing molecules (Group a) are selected to investigate the ionic bonding in transition metal-containing molecules because they have a relatively simple electronic state distribution due to the nearly filled 3d-orbital. ThO and WC (Group b) are in support of particle physics for the determination of electron electric dipole moment (eEDM), de, the existence of which indicates new physics beyond the Standard Model. The determination of the tiny eEDM requires large electric fields applied to the electron. The 3(Delta)1 states for heavy polar molecules were proposed [E. R. Meyer, J. L. Bohn, and M. P. Deskevich, Phys. Rev. A 73, 062108 (2006)] to determine de with the following attractive features: (1) large electric dipole moments; (2) large internal electric fields, Eeff, experienced by valence electrons; (3) nearly degenerate omega-doublets; (4) extremely small magnetic dipole moments. The H3(Delta)1 state for ThO and the X3(Delta)1 state for WC are both good candidates. Spectroscopic parameters (i.e. molecular electric and magnetic dipole moments, omega-doubling parameters, etc) are required for the 3(Delta)1 states of ThO and WC. High resolution optical spectra (linewidth ~50 MHz) of CuF, CuOH, ThO and WC were recorded field-free and in the presence of a static electric field (or magnetic field) using laser ablation source/supersonic expansion and laser induced fluorescence (LIF) detection. The spectra were modeled by a zero-field effective Hamiltonian operator and a Stark (or Zeeman) Hamiltonian operator with various molecular parameters. The determined molecular parameters are compared to theoretical predictions. The small omega-doubling parameter was well determined using the pump/probe microwave optical double resonance (PPMODR) technique with a much higher resolution (linewidth ~60 kHz) than optical spectroscopy. In addition to the above mentioned studies of the two groups of molecules, a resonance enhanced multi-photon ionization (REMPI) combined with a time-of-flight mass spectrometer (TOFMS) has been developed to identify the molecules responsible for observed LIF signals. The operation of this spectrometer has been tested by recording the mass spectrum of Ti/O2 and the REMPI spectrum for TiO using a two-color excitation scheme.
ContributorsWang, Fang (Author) / Steimle, Timothy C (Thesis advisor) / Chizmeshya, Andrew (Committee member) / Wolf, George (Committee member) / Arizona State University (Publisher)
Created2012
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Description
Spider dragline silk is well known for its outstanding mechanical properties - a combination of strength and extensibility that makes it one of the toughest materials known. Two proteins, major ampullate spidroin 1 (MaSp1) and 2 (MaSp2), comprise dragline silk fibers. There has been considerable focus placed on understanding the

Spider dragline silk is well known for its outstanding mechanical properties - a combination of strength and extensibility that makes it one of the toughest materials known. Two proteins, major ampullate spidroin 1 (MaSp1) and 2 (MaSp2), comprise dragline silk fibers. There has been considerable focus placed on understanding the source of spider silk's unique mechanical properties by investigating the protein composition, molecular structure and dynamics. Chemical compositional heterogeneity of spider silk fiber is critical to understand as it provides important information for the interactions between MaSp1 and MaSp2. Here, the amino acid composition of dragline silk protein was precisely determined using a solution-state nuclear magnetic resonance (NMR) approach on hydrolyzed silk fibers. In a similar fashion, solution-state NMR was applied to probe the "13"C/"15"N incorporation in silk, which is essential to understand for designing particular solid-state NMR methods for silk structural characterization. Solid-state NMR was used to elucidate silk protein molecular dynamics and the supercontraction mechanism. A "2"H-"13"C heteronuclear correlation (HETCOR) solid-state NMR technique was developed to extract site-specific "2"H quadrupole patterns and spin-lattice relaxation rates for understanding backbone and side-chain dynamics. Using this technique, molecular dynamics were determined for a number of repetitive motifs in silk proteins - Ala residing nanocrystalline &beta-sheet; domains, 3"1"-helical regions, and, Gly-Pro-Gly-XX &beta-turn; motifs. The protein backbone and side-chain dynamics of silk fibers in both dry and wet states reveal the impact of water on motifs with different secondary structures. Spider venom is comprised of a diverse range of molecules including salts, small organics, acylpolyamines, peptides and proteins. Neurotoxins are an important family of peptides in spider venom and have been shown to target and modulate various ion channels. The neurotoxins are Cys-rich and share an inhibitor Cys knot (ICK) fold. Here, the molecular structure of one G. rosea tarantula neurotoxin, GsAF2, was determined by solution-state NMR. In addition, the interaction between neurotoxins and model lipid bilayers was probed with solid-state NMR and negative-staining (NS) transmission electron microscopy (TEM). It is shown that the neurotoxins influence lipid bilayer assembly and morphology with the formation of nanodiscs, worm-like micelles and small vesicles.
ContributorsShi, Xiangyan (Author) / Yarger, Jeffery L (Thesis advisor) / Holland, Gregory P (Thesis advisor) / Levitus, Marcia (Committee member) / Marzke, Robert F (Committee member) / Arizona State University (Publisher)
Created2014
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Description
CubeSats are a newly emerging, low-cost, rapid development platform for space exploration research. They are small spacecraft with a mass and volume of up to 12 kg and 12,000 cm3, respectively. To date, CubeSats have only been flown in Low Earth Orbit (LEO), though a large number are currently being

CubeSats are a newly emerging, low-cost, rapid development platform for space exploration research. They are small spacecraft with a mass and volume of up to 12 kg and 12,000 cm3, respectively. To date, CubeSats have only been flown in Low Earth Orbit (LEO), though a large number are currently being designed to be dropped off by a mother ship on Earth escape trajectories intended for Lunar and Martian flyby missions. Advancements in propulsion technologies now enable these spacecraft to achieve capture orbits around the moon and Mars, providing a wealth of scientific data at low-cost. However, the mass, volume and launch constraints of CubeSats severely limit viable propulsion options.

We present an innovative propulsion solution using energy generated by onboard photovoltaic panels to electrolyze water, thus producing combustible hydrogen and oxygen for low-thrust applications. Water has a high storage density allowing for sufficient fuel within volume constraints. Its high enthalpy of formation provides more fuel that translates into increased ∆V and vastly reduced risk for the launch vehicle. This innovative technology poses significant challenges including the design and operation of electrolyzers at ultra-cold temperatures, the efficient separation of the resultant hydrogen and oxygen gases from liquid water in a microgravity environment, as well as the effective utilization of thrust to produce desired trajectories.

Analysis of the gas combustion and flow through the nozzle using both theoretical equations and finite-volume CFD modeling suggests an expected specific impulse of 360 s. Preliminary results from AGI's Satellite Toolkit (STK) indicate that the ΔV produced by the system for an 8kg CubeSat with 6kg of propellant in a LEO orbit (370 km altitude) is sufficient for an earth escape trajectory, lunar capture orbit or even a Mars capture orbit. These results suggest a promising pathway for an in-depth study supported by laboratory experiments to characterize the strengths and weaknesses of the proposed concept.
ContributorsPothamsetti, Ramana Kumar (Author) / Thangavelautham, Jekanthan (Thesis advisor) / Dahm, Werner J.A (Committee member) / Solanki, Kiran N (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Fluorescence spectroscopy is a popular technique that has been particularly useful in probing biological systems, especially with the invention of single molecule fluorescence. For example, Förster resonance energy transfer (FRET) is one tool that has been helpful in probing distances and conformational changes in biomolecules. In this work, important properties

Fluorescence spectroscopy is a popular technique that has been particularly useful in probing biological systems, especially with the invention of single molecule fluorescence. For example, Förster resonance energy transfer (FRET) is one tool that has been helpful in probing distances and conformational changes in biomolecules. In this work, important properties necessary in the quantification of FRET were investigated while FRET was also applied to gain insight into the dynamics of biological molecules. In particular, dynamics of damaged DNA was investigated. While damages in DNA are known to affect DNA structure, what remains unclear is how the presence of a lesion, or multiple lesions, affects the flexibility of DNA, especially in relation to damage recognition by repair enzymes. DNA conformational dynamics was probed by combining FRET and fluorescence anisotropy along with biochemical assays. The focus of this work was to investigate the relationship between dynamics and enzymatic repair. In addition, to properly quantify fluorescence and FRET data, photophysical phenomena of fluorophores, such as blinking, needs to be understood. The triplet formation of the single molecule dye TAMRA and the photoisomerization yield of two different modifications of the single molecule cyanine dye Cy3 were examined spectroscopically to aid in accurate data interpretation. The combination of the biophysical and physiochemical studies illustrates how fluorescence spectroscopy can be used to answer biological questions.
ContributorsShepherd Stennett, Elana Maria (Author) / Levitus, Marcia (Thesis advisor) / Ros, Robert (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2015
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Description
This thesis focused on physicochemical and electrochemical projects directed towards two electrolyte types: 1) class of ionic liquids serving as electrolytes in the catholyte for alkali-metal ion conduction in batteries and 2) gel membrane for proton conduction in fuel cells; where overall aims were encouraged by the U.S. Department of

This thesis focused on physicochemical and electrochemical projects directed towards two electrolyte types: 1) class of ionic liquids serving as electrolytes in the catholyte for alkali-metal ion conduction in batteries and 2) gel membrane for proton conduction in fuel cells; where overall aims were encouraged by the U.S. Department of Energy.

Large-scale, sodium-ion batteries are seen as global solutions to providing undisrupted electricity from sustainable, but power-fluctuating, energy production in the near future. Foreseen ideal advantages are lower cost without sacrifice of desired high-energy densities relative to present lithium-ion and lead-acid battery systems. Na/NiCl2 (ZEBRA) and Na/S battery chemistries, suffer from high operation temperature (>300ºC) and safety concerns following major fires consequent of fuel mixing after cell-separator rupturing. Initial interest was utilizing low-melting organic ionic liquid, [EMI+][AlCl4-], with well-known molten salt, NaAlCl4, to create a low-to-moderate operating temperature version of ZEBRA batteries; which have been subject of prior sodium battery research spanning decades. Isothermal conductivities of these electrolytes revealed a fundamental kinetic problem arisen from "alkali cation-trapping effect" yet relived by heat-ramping >140ºC.

Battery testing based on [EMI+][FeCl4-] with NaAlCl4 functioned exceptional (range 150-180ºC) at an impressive energy efficiency >96%. Newly prepared inorganic ionic liquid, [PBr4+][Al2Br7-]:NaAl2Br7, melted at 94ºC. NaAl2Br7 exhibited super-ionic conductivity 10-1.75 Scm-1 at 62ºC ensued by solid-state rotator phase transition. Also improved thermal stability when tested to 265ºC and less expensive chemical synthesis. [PBr4+][Al2Br7-] demonstrated remarkable, ionic decoupling in the liquid-state due to incomplete bromide-ion transfer depicted in NMR measurements.

Fuel cells are electrochemical devices generating electrical energy reacting hydrogen/oxygen gases producing water vapor. Principle advantage is high-energy efficiency of up to 70% in contrast to an internal combustion engine <40%. Nafion-based fuel cells are prone to carbon monoxide catalytic poisoning and polymer membrane degradation unless heavily hydrated under cell-pressurization. This novel "SiPOH" solid-electrolytic gel (originally liquid-state) operated in the fuel cell at 121oC yielding current and power densities high as 731mAcm-2 and 345mWcm-2, respectively. Enhanced proton conduction significantly increased H2 fuel efficiency to 89.7% utilizing only 3.1mlmin-1 under dry, unpressurized testing conditions. All these energy devices aforementioned evidently have future promise; therefore in early developmental stages.
ContributorsTucker, Telpriore G (Author) / Angell, Charles A. (Committee member) / Moore, Ana (Committee member) / Seo, Dong-Kyun (Committee member) / Arizona State University (Publisher)
Created2014
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Description
ABSTRACT The unique structural features of deoxyribonucleic acid (DNA) that are of considerable biological interest also make it a valuable engineering material. Perhaps the most useful property of DNA for molecular engineering is its ability to self-assemble into predictable, double helical secondary structures. These interactions are exploited to design a

ABSTRACT The unique structural features of deoxyribonucleic acid (DNA) that are of considerable biological interest also make it a valuable engineering material. Perhaps the most useful property of DNA for molecular engineering is its ability to self-assemble into predictable, double helical secondary structures. These interactions are exploited to design a variety of DNA nanostructures, which can be organized into both discrete and periodic structures. This dissertation focuses on studying the dynamic behavior of DNA nanostructure recognition processes. The thermodynamics and kinetics of nanostructure binding are evaluated, with the intention of improving our ability to understand and control their assembly. Presented here are a series of studies toward this goal. First, multi-helical DNA nanostructures were used to investigate how the valency and arrangement of the connections between DNA nanostructures affect super-structure formation. The study revealed that both the number and the relative position of connections play a significant role in the stability of the final assembly. Next, several DNA nanostructures were designed to gain insight into how small changes to the nanostructure scaffolds, intended to vary their conformational flexibility, would affect their association equilibrium. This approach yielded quantitative information about the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect. Finally, a multi-helical DNA nanostructure was used as a model `chip' for the detection of a single stranded DNA target. The results revealed that the rate constant of hybridization is strongly dominated by a rate-limiting nucleation step.
ContributorsNangreave, Jeanette (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian J.-L. (Committee member) / Seo, Dong Kyun (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Conformational changes in biomolecules often take place on longer timescales than are easily accessible with unbiased molecular dynamics simulations, necessitating the use of enhanced sampling techniques, such as adaptive umbrella sampling. In this technique, the conformational free energy is calculated in terms of a designated set of reaction coordinates. At

Conformational changes in biomolecules often take place on longer timescales than are easily accessible with unbiased molecular dynamics simulations, necessitating the use of enhanced sampling techniques, such as adaptive umbrella sampling. In this technique, the conformational free energy is calculated in terms of a designated set of reaction coordinates. At the same time, estimates of this free energy are subtracted from the potential energy in order to remove free energy barriers and cause conformational changes to take place more rapidly. This dissertation presents applications of adaptive umbrella sampling to a variety of biomolecular systems. The first study investigated the effects of glycosylation in GalNAc2-MM1, an analog of glycosylated macrophage activating factor. It was found that glycosylation destabilizes the protein by increasing the solvent exposure of hydrophobic residues. The second study examined the role of bound calcium ions in promoting the isomerization of a cis peptide bond in the collagen-binding domain of Clostridium histolyticum collagenase. This study determined that the bound calcium ions reduced the barrier to the isomerization of this peptide bond as well as stabilizing the cis conformation thermodynamically, and identified some of the reasons for this. The third study represents the application of GAMUS (Gaussian mixture adaptive umbrella sampling) to on the conformational dynamics of the fluorescent dye Cy3 attached to the 5' end of DNA, and made predictions concerning the affinity of Cy3 for different base pairs, which were subsequently verified experimentally. Finally, the adaptive umbrella sampling method is extended to make use of the roll angle between adjacent base pairs as a reaction coordinate in order to examine the bending both of free DNA and of DNA bound to the archaeal protein Sac7d. It is found that when DNA bends significantly, cations from the surrounding solution congregate on the concave side, which increases the flexibility of the DNA by screening the repulsion between phosphate backbones. The flexibility of DNA on short length scales is compared to the worm-like chain model, and the contribution of cooperativity in DNA bending to protein-DNA binding is assessed.
ContributorsSpiriti, Justin Matthew (Author) / van der Vaart, Arjan (Thesis advisor) / Chizmeshya, Andrew (Thesis advisor) / Matyushov, Dmitry (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Created2011