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Description
Membrane proteins are a vital part of cellular structure. They are directly involved in many important cellular functions, such as uptake, signaling, respiration, and photosynthesis, among others. Despite their importance, however, less than 500 unique membrane protein structures have been determined to date. This is due to several difficulties with macromolecular crystallography, primarily the difficulty of growing large, well-ordered protein crystals. Since the first proof of concept for femtosecond nanocrystallography showing that diffraction patterns can be collected on extremely small crystals, thus negating the need to grow larger crystals, there have been many exciting advancements in the field. The technique has been proven to show high spatial resolution, thus making it a viable method for structural biology. However, due to the ultrafast nature of the technique, which allows for a lack of radiation damage in imaging, even more interesting experiments are possible, and the first temporal and spatial images of an undamaged structure could be acquired. This concept was denoted as time-resolved femtosecond nanocrystallography.
This dissertation presents on the first time-resolved data set of Photosystem II where structural changes can actually be seen without radiation damage. In order to accomplish this, new crystallization techniques had to be developed so that enough crystals could be made for the liquid jet to deliver a fully hydrated stream of crystals to the high-powered X-ray source. These changes are still in the preliminary stages due to the slightly lower resolution data obtained, but they are still a promising show of the power of this new technique. With further optimization of crystal growth methods and quality, injection technique, and continued development of data analysis software, it is only a matter of time before the ability to make movies of molecules in motion from X-ray diffraction snapshots in time exists. The work presented here is the first step in that process.
This dissertation presents on the first time-resolved data set of Photosystem II where structural changes can actually be seen without radiation damage. In order to accomplish this, new crystallization techniques had to be developed so that enough crystals could be made for the liquid jet to deliver a fully hydrated stream of crystals to the high-powered X-ray source. These changes are still in the preliminary stages due to the slightly lower resolution data obtained, but they are still a promising show of the power of this new technique. With further optimization of crystal growth methods and quality, injection technique, and continued development of data analysis software, it is only a matter of time before the ability to make movies of molecules in motion from X-ray diffraction snapshots in time exists. The work presented here is the first step in that process.
ContributorsKupitz, Christopher (Author) / Fromme, Petra (Thesis advisor) / Spence, John C. (Thesis advisor) / Redding, Kevin (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2014
Description
With the advent of the X-ray free-electron laser (XFEL), an opportunity has arisen to break the nexus between radiation dose and spatial resolution in diffractive imaging, by outrunning radiation damage altogether when using single X-ray pulses so brief that they terminate before atomic motion commences. This dissertation concerns the application of XFELs to biomolecular imaging in an effort to overcome the severe challenges associated with radiation damage and macroscopic protein crystal growth. The method of femtosecond protein nanocrystallography (fsPNX) is investigated, and a new method for extracting crystallographic structure factors is demonstrated on simulated data and on the first experimental fsPNX data obtained at an XFEL. Errors are assessed based on standard metrics familiar to the crystallography community. It is shown that resulting structure factors match the quality of those measured conventionally, at least to 9 angstrom resolution. A new method for ab-initio phasing of coherently-illuminated nanocrystals is then demonstrated on simulated data. The method of correlated fluctuation small-angle X-ray scattering (CFSAXS) is also investigated as an alternative route to biomolecular structure determination, without the use of crystals. It is demonstrated that, for a constrained two-dimensional geometry, a projection image of a single particle can be formed, ab-initio and without modeling parameters, from measured diffracted intensity correlations arising from disordered ensembles of identical particles illuminated simultaneously. The method is demonstrated experimentally, based on soft X-ray diffraction from disordered but identical nanoparticles, providing the first experimental proof-of-principle result. Finally, the fundamental limitations of CFSAXS is investigated through both theory and simulations. It is found that the signal-to-noise ratio (SNR) for CFSAXS data is essentially independent of the number of particles exposed in each diffraction pattern. The dependence of SNR on particle size and resolution is considered, and realistic estimates are made (with the inclusion of solvent scatter) of the SNR for protein solution scattering experiments utilizing an XFEL source.
ContributorsKirian, Richard A (Author) / Spence, John C. H. (Committee member) / Doak, R. Bruce (Committee member) / Weierstall, Uwe (Committee member) / Bennett, Peter (Committee member) / Treacy, Michael M. J. (Committee member) / Arizona State University (Publisher)
Created2011
Description
Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only a hundred unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet would bring fully hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses ( 70 fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. At the initial experiments at the AMO beamline using 6.9- Å wavelength, Bragg peaks were recorded to 8.5- Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage. Recently, femtosecond X-ray protein nanocrystallography experiments were done at the CXI beamline of the LCLS using 1.3- Å wavelength, and Bragg reflections were recorded to 3- Å resolution; the data are currently being processed. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.
ContributorsHunter, Mark (Author) / Fromme, Petra (Thesis advisor) / Wolf, George (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2011
Description
Many species e.g. sea urchin form amorphous calcium carbonate (ACC) precursor phases that subsequently transform into crystalline CaCO3. It is certainly possible that the biogenic ACC might have more than 10 wt% Mg and ∼ 3 wt% of water. The structure of ACC and the mechanisms by which it transforms to crystalline phase are still poorly understood. In this dissertation our goal is to determine an atomic structure model that is consistent with diffraction and IR measurements of ACC. For this purpose a calcite supercell with 24 formula units, containing 120 atoms, was constructed. Various configurations with substitution of Ca by 6 Mg ions (6 wt.%) and insertion of 3-5 H2O molecules (2.25-3.75 wt.%) in the interstitial positions of the supercell, were relaxed using a robust density function code VASP. The most noticeable effects were the tilts of CO3 groups and the distortion of Ca sub-lattice, especially in the hydrated case. The distributions of Ca-Ca nearest neighbor distance and CO3 tilts were extracted from various configurations. The same methods were also applied to aragonite. Sampling from the calculated distortion distributions, we built models for amorphous calcite/aragonite of size ∼ 1700 nm3 based on a multi-scale modeling scheme. We used these models to generate diffraction patterns and profiles with our diffraction code. We found that the induced distortions were not enough to generate a diffraction profile typical of an amorphous material. We then studied the diffraction profiles from several nano-crystallites as recent studies suggest that ACC might be a random array of nanocryatallites. It was found that the generated diffraction profile from a nano-crystallite of size ∼ 2 nm3 is similar to that from the ACC.
ContributorsSinha, Sourabh (Author) / Rez, Peter (Thesis advisor) / Bearat, Hamdallah A. (Committee member) / Bennett, Peter A. (Committee member) / McCartney, Martha R. (Committee member) / Peng, Xihong (Committee member) / Arizona State University (Publisher)
Created2012
Description
The rapid progress of solution-phase synthesis has led colloidal nanocrystals one of the most versatile nanoscale materials, provided opportunities to tailor material's properties, and boosted related technological innovations. Colloidal nanocrystal-based materials have been demonstrated success in a variety of applications, such as LEDs, electronics, solar cells and thermoelectrics. In each of these applications, the thermal transport property plays a big role. An undesirable temperature rise due to inefficient heat dissipation could lead to deleterious effects on devices' performance and lifetime. Hence, the first project is focused on investigating the thermal transport in colloidal nanocrystal solids. This study answers the question that how the molecular structure of nanocrystals affect the thermal transport, and provides insights for future device designs. In particular, PbS nanocrystals is used as a monitoring system, and the core diameter, ligand length and ligand binding group are systematically varied to study the corresponding effect on thermal transport.
Next, a fundamental study is presented on the phase stability and solid-liquid transformation of metallic (In, Sn and Bi) colloidal nanocrystals. Although the phase change of nanoparticles has been a long-standing research topic, the melting behavior of colloidal nanocrytstals is largely unexplored. In addition, this study is of practical importance to nanocrystal-based applications that operate at elevated temperatures. Embedding colloidal nanocrystals into thermally-stable polymer matrices allows preserving nanocrystal size throughout melt-freeze cycles, and therefore enabling observation of stable melting features. Size-dependent melting temperature, melting enthalpy and melting entropy have all been measured and discussed.
In the next two chapters, focus has been switched to developing colloidal nanocrystal-based phase change composites for thermal energy storage applications. In Chapter 4, a polymer matrix phase change nanocomposite has been created. In this composite, the melting temperature and energy density could be independently controlled by tuning nanocrystal diameter and volume fractions. In Chapter 5, a solution-phase synthesis on metal matrix-metal nanocrytal composite is presented. This approach enables excellent morphological control over nanocrystals and demonstrated a phase change composite with a thermal conductivity 2 - 3 orders of magnitude greater than typical phase change materials, such as organics and molten salts.
Next, a fundamental study is presented on the phase stability and solid-liquid transformation of metallic (In, Sn and Bi) colloidal nanocrystals. Although the phase change of nanoparticles has been a long-standing research topic, the melting behavior of colloidal nanocrytstals is largely unexplored. In addition, this study is of practical importance to nanocrystal-based applications that operate at elevated temperatures. Embedding colloidal nanocrystals into thermally-stable polymer matrices allows preserving nanocrystal size throughout melt-freeze cycles, and therefore enabling observation of stable melting features. Size-dependent melting temperature, melting enthalpy and melting entropy have all been measured and discussed.
In the next two chapters, focus has been switched to developing colloidal nanocrystal-based phase change composites for thermal energy storage applications. In Chapter 4, a polymer matrix phase change nanocomposite has been created. In this composite, the melting temperature and energy density could be independently controlled by tuning nanocrystal diameter and volume fractions. In Chapter 5, a solution-phase synthesis on metal matrix-metal nanocrytal composite is presented. This approach enables excellent morphological control over nanocrystals and demonstrated a phase change composite with a thermal conductivity 2 - 3 orders of magnitude greater than typical phase change materials, such as organics and molten salts.
ContributorsLiu, Minglu (Author) / Wang, Robert Y (Thesis advisor) / Wang, Liping (Committee member) / Rykaczewski, Konrad (Committee member) / Phelan, Patrick (Committee member) / Dai, Lenore (Committee member) / Arizona State University (Publisher)
Created2015
Description
Proposed and tested were three different methods to deposit important layers of Silicon heterojunction solar cells (SHJs). If there were a shortage of Silver, Aluminum could be substituted for the contacts. If there were a shortage of Indium, Yttrium Zinc Oxide could be substituted. To improve the solar cell, the p and n type layers can be grown with hydrogenated nanocrystallline Silicon (nc-Si:H). 40% and 50% nc-Si:H has shown a maximum absorbance reduction of 5 times compared to hydrogenated amorphous Silicon (a-Si). The substitutions offer alternatives which increase the total possible amount of solar cell production, advancing toward completion of the Terrawatt challenge.
ContributorsCarpenter, Joe Victor (Author) / Alford, Terry (Thesis director) / Holman, Zachary (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor) / Materials Science and Engineering Program (Contributor)
Created2014-05
Description
Nanocrystalline (NC) materials experience inherent microstructural instability when exposed to elevated temperature, deformation rates or loads over long periods of time which limits its applications as well as processing. The instability arises due to the predominance of grain boundary (GB) diffusional processes which hastens coarsening. This dissertation aims to provide a solution for the very first time, through the development and characterization of a bulk NC alloy system. The NC-Cu-Ta discussed here offers exceptional thermal stability in addition to superior strength and creep resistance. The systematic study of the behavior of this material will pave the way for future development of NC materials with a multitude of optimized properties for extreme applications.
In-situ and ex-situ TEM characterization, multiple strain-rate compression testing and atomistic modeling were employed to investigate the behavior of NC-Cu-Ta under intense heating, stress/strain-rate and creep conditions. Results reveal, that temperature influences the misfit strain, leading to a significant change in flow stress, despite which (strength) remains greater than all known NC metals. Further, this alloy was found to achieve and retain strengths which were over two orders of magnitude higher than most NC metals under elevated temperature conditions. Dislocation-based slip was found to predominate at elevated temperatures for both high- and low-strain rate testing whereas twinning was favored during low temperature high-strain rate testing. The solute concentration was also found to play a role in dictating the deformation where heterogeneous twinnability was found to decrease with an increase in Ta concentration.
A paradigm-shift in the creep response of NC-materials with unprecedented property combinations is also reported, i.e., high strength with extremely high temperature creep resistance (6-8 orders higher than other NC materials), in this NC-Cu-Ta-alloy. The unique combination of properties in these NC-alloys is achieved through a processing route that creates distinct GB-pinning nanoclusters of the solute that favor kinetic stability of grains.
Overall, this dissertation provides an understanding of the mechanical response of a stable alloy system to extreme conditions, which was previously unattainable, and a perspective on the design of a new class of NC alloys exhibiting a multitude of optimized high temperature properties.
In-situ and ex-situ TEM characterization, multiple strain-rate compression testing and atomistic modeling were employed to investigate the behavior of NC-Cu-Ta under intense heating, stress/strain-rate and creep conditions. Results reveal, that temperature influences the misfit strain, leading to a significant change in flow stress, despite which (strength) remains greater than all known NC metals. Further, this alloy was found to achieve and retain strengths which were over two orders of magnitude higher than most NC metals under elevated temperature conditions. Dislocation-based slip was found to predominate at elevated temperatures for both high- and low-strain rate testing whereas twinning was favored during low temperature high-strain rate testing. The solute concentration was also found to play a role in dictating the deformation where heterogeneous twinnability was found to decrease with an increase in Ta concentration.
A paradigm-shift in the creep response of NC-materials with unprecedented property combinations is also reported, i.e., high strength with extremely high temperature creep resistance (6-8 orders higher than other NC materials), in this NC-Cu-Ta-alloy. The unique combination of properties in these NC-alloys is achieved through a processing route that creates distinct GB-pinning nanoclusters of the solute that favor kinetic stability of grains.
Overall, this dissertation provides an understanding of the mechanical response of a stable alloy system to extreme conditions, which was previously unattainable, and a perspective on the design of a new class of NC alloys exhibiting a multitude of optimized high temperature properties.
ContributorsRajagopalan, Mansa (Author) / Solanki, Kiran N. (Thesis advisor) / Alford, Terry L. (Committee member) / Jiao, Yang (Committee member) / Darling, Kris A. (Committee member) / Arizona State University (Publisher)
Created2016
Description
Nanostructured zeolites, in particular nanocrystalline zeolites, are of great interest due to their efficient use in conventional catalysis, separations, and emerging applications. Despite the recent advances, fewer than 20 zeolite framework types have been synthesized in the form of nanocrystallites and their scalable synthesis has yet to be developed and understood. Geopolymers, claimed to be “amorphous cousins of zeolites”, are a class of ceramic-like aluminosilicate materials with prominent application in construction due to their unique chemical and mechanical properties. Despite the monolith form, geopolymers are fundamentally nanostructured materials and contain zeolite nanocrystallites.
Herein, a new cost-effective and scalable synthesis of various types of nanocrystalline zeolites based on geopolymer chemistry is presented. The study includes the synthesis of highly crystalline discrete nanorods of a CAN zeolite framework structure that had not been achieved hitherto, the exploration of the Na−Al−Si−H2O kinetic phase diagram of hydrogels that gives SOD, CAN and FAU nanocrystalline zeolites, and the discovery of a unique formation mechanism of highly crystalline nanostructured FAU zeolite with intermediate gel products that possess an unprecedented uniform distribution of elements. This study demonstrated the possibility of using high-concentration hydrogels for the synthesis of nanocrystalline zeolites of additional framework structures.
Moreover, a comprehensive study on nanostructured FAU zeolites ion-exchanged with Ag+, Zn2+, Cu2+ and Fe2+ for antibacterial applications is presented, which comprises metal ion release kinetics, antibacterial properties, and cytotoxicity. For the first time, superior metal ion release performance was confirmed for the nanostructured zeolites compared to their micron-sized counterparts. The metal ion-exchanged FAU nanostructured zeolites were established as new effective antibacterial materials featuring their unique physiochemical, antibacterial, and cytotoxic properties.
Herein, a new cost-effective and scalable synthesis of various types of nanocrystalline zeolites based on geopolymer chemistry is presented. The study includes the synthesis of highly crystalline discrete nanorods of a CAN zeolite framework structure that had not been achieved hitherto, the exploration of the Na−Al−Si−H2O kinetic phase diagram of hydrogels that gives SOD, CAN and FAU nanocrystalline zeolites, and the discovery of a unique formation mechanism of highly crystalline nanostructured FAU zeolite with intermediate gel products that possess an unprecedented uniform distribution of elements. This study demonstrated the possibility of using high-concentration hydrogels for the synthesis of nanocrystalline zeolites of additional framework structures.
Moreover, a comprehensive study on nanostructured FAU zeolites ion-exchanged with Ag+, Zn2+, Cu2+ and Fe2+ for antibacterial applications is presented, which comprises metal ion release kinetics, antibacterial properties, and cytotoxicity. For the first time, superior metal ion release performance was confirmed for the nanostructured zeolites compared to their micron-sized counterparts. The metal ion-exchanged FAU nanostructured zeolites were established as new effective antibacterial materials featuring their unique physiochemical, antibacterial, and cytotoxic properties.
ContributorsChen, Shaojiang (Author) / Seo, Dong Kyun (Thesis advisor) / Trovitch, Ryan (Committee member) / Thomas, MaryLaura Lind (Committee member) / Arizona State University (Publisher)
Created2019