Matching Items (998)
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 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
Description
Silicon nanowires were grown epitaxially on Si (100) and (111) surfaces using the Vapor-Liquid-Solid (VLS) mechanism under both thermal and plasma enhanced growth conditions. Nanowire morphology was investigated as a function of temperature, time, disilane partial pressure and substrate preparation. Silicon nanowires synthesized in low temperature plasma typically curved compared to the linear nanowires grown under simple thermal conditions. The nanowires tended bend more with increasing disilane partial gas pressure up to 25 x10-3 mTorr. The nanowire curvature measured geometrically is correlated with the shift of the main silicon peak obtained in Raman spectroscopy. A mechanistic hypothesis was proposed to explain the bending during plasma activated growth. Additional driving forces related to electrostatic and Van der Waals forces were also discussed. Deduced from a systematic variation of a three-step experimental protocol, the mechanism for bending was associated with asymmetric deposition rate along the outer and inner wall of nanowire. The conditions leading to nanowire branching were also examined using a two-step growth process. Branching morphologies were examined as a function of plasma powers between 1.5 W and 3.5 W. Post-annealing thermal and plasma-assisted treatments in hydrogen were compared to understand the influences in the absence of an external silicon source (otherwise supplied by disilane). Longer and thicker nanowires were associated with longer annealing times due to an Ostwald-like ripening effect. The roles of surface diffusion, gas diffusion, etching and deposition rates were examined.
ContributorsJoun, Hee-Joung (Author) / Petuskey, William T. (Thesis advisor) / Drucker, Jeff (Committee member) / Chizmeshya, Andrew (Committee member) / Arizona State University (Publisher)
Created2011
Description
Group-IV semiconductor alloys are of interest for Si-integrated optoelectronic applications due to the band gap tunability and enhanced optical capabilities that can be achieved through compositional tuning. This work advances the field by presenting a systematic study of the optical and electronic properties of Ge1-ySny and analogous Ge1-x-ySixSny alloys.
The fundamental direct and indirect band gaps of Ge1-ySny materials are measured by room temperature photoluminescence in samples containing 0 ≤ y ≤ 0.11 and a transition to direct gap materials is found to occur at yc = 0.087. This result is enabled by the development of sample growth and processing protocols that produce high-quality materials epitaxially on Ge-buffered Si(100) substrates. Strategies to optimize the optical performance are explored by varying the film thickness, thermal and surface treatments, and n-type doping. The electrical and optical properties of diodes based on these materials are characterized by current-voltage, optical responsivity, and electroluminescence measurements. These show improved optical performance near yc with tunable emission out to 2500 nm. Measuring the carrier lifetimes in devices with strain relaxed and fully strained interfaces show significantly longer lifetimes in the fully strained case.
The direct and indirect band gaps of Sn-rich (y > x) Ge1-x-ySixSny materials are measured by room temperature photoluminescence on optimized samples. These data confirm a transition to direct gap materials occurs for the ternary alloy as well. Devices based on compositions 0.02 ≤ x ≤ 0.10 and 0.03 ≤ y ≤ 0.11 are characterized by current-voltage, optical responsivity, and electroluminescence measurements and show competitive performance with analogous devices based on Ge1-ySny materials. A detailed study of the direct gap in Ge1-xSix alloys gives parameters crucial en route to a global description of the Ge1-x-ySixSny fundamental band gaps.
Archetypal laser device designs on Si are explored by fabricating degenerate pn junction diodes and highly doped waveguide devices based on high-quality Ge1-ySny materials. The diodes showed tunnel-like current-voltage characteristics and tailored electroluminescence based on the doping profile. The waveguides demonstrate emission under optical stimulation.
The fundamental direct and indirect band gaps of Ge1-ySny materials are measured by room temperature photoluminescence in samples containing 0 ≤ y ≤ 0.11 and a transition to direct gap materials is found to occur at yc = 0.087. This result is enabled by the development of sample growth and processing protocols that produce high-quality materials epitaxially on Ge-buffered Si(100) substrates. Strategies to optimize the optical performance are explored by varying the film thickness, thermal and surface treatments, and n-type doping. The electrical and optical properties of diodes based on these materials are characterized by current-voltage, optical responsivity, and electroluminescence measurements. These show improved optical performance near yc with tunable emission out to 2500 nm. Measuring the carrier lifetimes in devices with strain relaxed and fully strained interfaces show significantly longer lifetimes in the fully strained case.
The direct and indirect band gaps of Sn-rich (y > x) Ge1-x-ySixSny materials are measured by room temperature photoluminescence on optimized samples. These data confirm a transition to direct gap materials occurs for the ternary alloy as well. Devices based on compositions 0.02 ≤ x ≤ 0.10 and 0.03 ≤ y ≤ 0.11 are characterized by current-voltage, optical responsivity, and electroluminescence measurements and show competitive performance with analogous devices based on Ge1-ySny materials. A detailed study of the direct gap in Ge1-xSix alloys gives parameters crucial en route to a global description of the Ge1-x-ySixSny fundamental band gaps.
Archetypal laser device designs on Si are explored by fabricating degenerate pn junction diodes and highly doped waveguide devices based on high-quality Ge1-ySny materials. The diodes showed tunnel-like current-voltage characteristics and tailored electroluminescence based on the doping profile. The waveguides demonstrate emission under optical stimulation.
ContributorsGallagher, James Dennis (Author) / Menéndez, Jose (Thesis advisor) / Kouvetakis, John (Thesis advisor) / Chizmeshya, Andrew (Committee member) / Ponce, Fernando (Committee member) / Arizona State University (Publisher)
Created2015
Description
Ge1-xSnx and SiyGe1-x-ySnx materials are being researched intensively for applications in infra-red optoelectronic devices. Due to their direct band gap these materials may in-fact be the enabling factor in the commercial realization of silicon photonics/group IV photonics and the integration of nanophotonics with nanoelectronics. However the synthesis of these meta-stable semiconductor alloys, with a range of Sn-compositions, remains the primary technical challenge. Highly specialized epitaxial growth methods must be employed to produce single crystal layers which have sufficient quality for optoelectronic device applications. Up to this point these methods have been unfavorable from a semiconductor manufacturing perspective. In this work the growth of high-quality Si-Ge-Sn epitaxial alloys on Ge-buffered Si (100) using an industry-standard reduced pressure chemical vapor deposition reactor and a cost-effective chemistry is demonstrated. The growth kinetics are studied in detail in-order to understand the factors influencing layer composition, morphology, and defectivity. In doing so breakthrough GeSn materials and device results are achieved including methods to overcome the limits of Sn-incorporation and the realization of low-defect and strain-relaxed epitaxial layers with up to 20% Sn.
P and n-type doping methods are presented in addition to the production of SiGeSn ternary alloys. Finally optically stimulated lasing in thick GeSn layers and SiGeSn/GeSn multiple quantum wells is demonstrated. Lasing wavelengths ranging from 2-3 µm at temperatures up to 180K are realized in thick layers. Whereas SiGeSn/GeSn multiple quantum wells on a strain-relaxed GeSn buffers have enabled the first reported SiGeSn/GeSn multiple quantum well laser operating up to 80K with threshold power densities as low as 33 kW/cm2.
P and n-type doping methods are presented in addition to the production of SiGeSn ternary alloys. Finally optically stimulated lasing in thick GeSn layers and SiGeSn/GeSn multiple quantum wells is demonstrated. Lasing wavelengths ranging from 2-3 µm at temperatures up to 180K are realized in thick layers. Whereas SiGeSn/GeSn multiple quantum wells on a strain-relaxed GeSn buffers have enabled the first reported SiGeSn/GeSn multiple quantum well laser operating up to 80K with threshold power densities as low as 33 kW/cm2.
ContributorsMargetis, Joseph (Author) / Zhang, Yong-Hang (Thesis advisor) / Chizmeshya, Andrew (Committee member) / Johnson, Shane (Committee member) / Arizona State University (Publisher)
Created2018
Description
The two-dimensional electron gas (2DEG) at SrTiO3-based oxide interfaces has been extensively studied recently for its high carrier density, high electron mobility, superconducting, ferromagnetic, ferrroelectric and magnetoresistance properties, with possible application for all-oxide devices. Understanding the mechanisms behind the 2DEG formation and factors affecting its properties is the primary objective of this dissertation.
Advanced electron microscopy techniques, including aberration-corrected electron microscopy and electron energy-loss spectroscopy (EELS) with energy-loss near-edge structure (ELNES) analysis, were used to characterize the interfaces. Image and spectrum data-processing algorithms, including subpixel atomic position measurement, and novel outlier detection by oversampling, subspace division based EELS background removal and bias-free endmember extraction algorithms for hyperspectral unmixing and mapping were heavily used. Results were compared with density functional theory (DFT) calculations for theoretical explanation.
For the γ-Al2O3/SrTiO3 system, negative-Cs imaging confirmed the formation of crystalline γ-Al2O3. ELNES hyperspectral unmixing combined with DFT calculations revealed that oxygen vacancies, rather than polar discontinuity, were the key to the 2DEG formation. The critical thickness can be explained by shift of the Fermi level due to Ti out diffusion from the substrate to the film.
At the LaTiO3/SrTiO3 interface, aberration-corrected imaging showed crystallinity deterioration in LaTiO3 films a few unit cells away from the interface. ELNES showed that oxygen annealing did not alter the crystallinity but converted Ti3+ near the interface into Ti4+, which explained disappearance of the conductivity.
At the EuO/SrTiO3 interface, both high-resolution imaging and ELNES confirmed EuO formation. ELNES hyperspectral unmixing showed a Ti3+ layer confined to within several unit cells of the interface on the SrTiO3 side, confirming the presence of oxygen vacancies.
At the BaTiO3/SrTiO3 interface, spontaneous polarization and local lattice parameters were measured directly in each unit cell column and compared with oxidation state mapping using ELNES with unit-cell resolution. The unusually large polarization near the interface and the polarization gradient were explained by oxygen vacancies and the piezoelectric effect due to epitaxial strain and strain gradient from relaxation.
Advanced electron microscopy techniques, including aberration-corrected electron microscopy and electron energy-loss spectroscopy (EELS) with energy-loss near-edge structure (ELNES) analysis, were used to characterize the interfaces. Image and spectrum data-processing algorithms, including subpixel atomic position measurement, and novel outlier detection by oversampling, subspace division based EELS background removal and bias-free endmember extraction algorithms for hyperspectral unmixing and mapping were heavily used. Results were compared with density functional theory (DFT) calculations for theoretical explanation.
For the γ-Al2O3/SrTiO3 system, negative-Cs imaging confirmed the formation of crystalline γ-Al2O3. ELNES hyperspectral unmixing combined with DFT calculations revealed that oxygen vacancies, rather than polar discontinuity, were the key to the 2DEG formation. The critical thickness can be explained by shift of the Fermi level due to Ti out diffusion from the substrate to the film.
At the LaTiO3/SrTiO3 interface, aberration-corrected imaging showed crystallinity deterioration in LaTiO3 films a few unit cells away from the interface. ELNES showed that oxygen annealing did not alter the crystallinity but converted Ti3+ near the interface into Ti4+, which explained disappearance of the conductivity.
At the EuO/SrTiO3 interface, both high-resolution imaging and ELNES confirmed EuO formation. ELNES hyperspectral unmixing showed a Ti3+ layer confined to within several unit cells of the interface on the SrTiO3 side, confirming the presence of oxygen vacancies.
At the BaTiO3/SrTiO3 interface, spontaneous polarization and local lattice parameters were measured directly in each unit cell column and compared with oxidation state mapping using ELNES with unit-cell resolution. The unusually large polarization near the interface and the polarization gradient were explained by oxygen vacancies and the piezoelectric effect due to epitaxial strain and strain gradient from relaxation.
ContributorsLu, Sirong (Author) / Smith, David J. (Thesis advisor) / McCartney, Martha R. (Thesis advisor) / Chizmeshya, Andrew (Committee member) / Crozier, Peter A. (Committee member) / Arizona State University (Publisher)
Created2018
Description
With the new independence of adulthood, college students are a group susceptible to adopting unsupported, if not harmful, health practices. A survey of Arizona State University undergraduate students (N=200) was conducted to evaluate supplement use, trust in information sources, and beliefs about supplement regulation. Of those who reported using supplements, college students most frequently received information from friends and family. STEM majors in fields unrelated to health who were taking a supplement were found to be less likely to receive information about the supplement from a medical practitioner than those in health fields or those in non-STEM majors (-26.9%, p=0.018). STEM majors in health-related fields were 15.0% more likely to treat colds and/or cold symptoms with research-supported methods identified from reliable sources, while non-health STEM and non-STEM majors were more likely to take unsupported cold treatments (p=0.010). Surveyed students, regardless of major, also stated they would trust a medical practitioner for supplement advice above other sources (88.0%), and the majority expressed a belief that dietary supplements are approved/regulated by the government (59.8%).
ContributorsPerez, Jacob Tanner (Author) / Hendrickson, Kirstin (Thesis director) / Lefler, Scott (Committee member) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
ContributorsChandler, N. Kayla (Author) / Neisewander, Janet (Thesis director) / Sanabria, Federico (Committee member) / Olive, M. Foster (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2013-05
Description
I propose that norms regulate behaviors that negatively impact an individual's survival and reproduction. But because monitoring and enforcing of norms can be costly, individuals should be selective about which norms they police and under what circumstances they should do so. Two studies tested this idea by experimentally activating fitness-relevant motives and having participants answer questions about the policing of norms. The first study examined a norm prescribing respect for status and another proscribing sexual coercion. Results from Study 1 failed to support the hypotheses; activating a status-seeking motive did not have the predicted effects on policing of the respect-status norm nor did activating a mating motive have the predicted effects on policing of the respect-status norm or anti-coercion norm. Study 2 examined two new norms, one prescribing that people stay home when sick and the other proscribing people from having sex with another person's partners. Study 2 also manipulated whether self or others were the target of the policing. Study 2 failed to provide support; a disease avoidance motive failed to have effects on policing of the stay home when sick norm. Individuals in a relationship under a mating motive wanted less policing of others for violation of the mate poaching norm than those in a baseline condition, opposite of the predicted effects.
ContributorsSmith, M. Kristopher (Author) / Neuberg, L. Steven (Thesis director) / Presson, Clark (Committee member) / Hruschka, J. Daniel (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2013-05
Description
Literature in public administration emphasizes a growing dissatisfaction with government on the part of residents. Where there tends to be a lack in the literature is in terms of solutions to this problem. We would like to argue that the engagement process itself has the power to foster a profound attitudinal shift on the part of both residents and government. This paper explores the structural and cultural barriers to satisfactory public engagement both from literature and a combination of policy analysis, semi-structured interviews and participatory observation within the City of Tempe. We then provide recommendations to the City of Tempe on how to overcome these barriers and effect authentic public engagement practices. With these new suggested practices and mindsets, we provide a way that people can have the power to create their own community.
ContributorsRiffle, Morgan (Co-author) / Tchida, Celina (Co-author) / Ingram-Waters, Mary (Thesis director) / Grzanka, Patrick (Committee member) / King, Cheryl (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2013-05
Description
This thesis examines the relationship between unofficial, official, and parallel Islam in Uzbekistan following the end of the Soviet Union. Key touchstone moments in Uzbekistan during the twentieth-century show the history between unofficial and official Islam and the resulting precedents set for Muslims gathering against the government. This historical analysis shows how President Karimov and the Uzbek government view and approach Islam in the country following independence.
ContributorsTieslink, Evan (Author) / Batalden, Stephen (Thesis director) / Kefeli, Agnes (Committee member) / Saikia, Yasmin (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Politics and Global Studies (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2013-05