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- Genre: Doctoral Dissertation
Description
Off-axis electron holography (EH) has been used to characterize electrostatic potential, active dopant concentrations and charge distribution in semiconductor nanostructures, including ZnO nanowires (NWs) and thin films, ZnTe thin films, Si NWs with axial p-n junctions, Si-Ge axial heterojunction NWs, and Ge/LixGe core/shell NW.
The mean inner potential (MIP) and inelastic mean free path (IMFP) of ZnO NWs have been measured to be 15.3V±0.2V and 55±3nm, respectively, for 200keV electrons. These values were then used to characterize the thickness of a ZnO nano-sheet and gave consistent values. The MIP and IMFP for ZnTe thin films were measured to be 13.7±0.6V and 46±2nm, respectively, for 200keV electrons. A thin film expected to have a p-n junction was studied, but no signal due to the junction was observed. The importance of dynamical effects was systematically studied using Bloch wave simulations.
The built-in potentials in Si NWs across the doped p-n junction and the Schottky junction due to Au catalyst were measured to be 1.0±0.3V and 0.5±0.3V, respectively. Simulations indicated that the dopant concentrations were ~1019cm-3 for donors and ~1017 cm-3 for acceptors. The effects of positively charged Au catalyst, a possible n+-n--p junction transition region and possible surface charge, were also systematically studied using simulations.
Si-Ge heterojunction NWs were studied. Dopant concentrations were extracted by atom probe tomography. The built-in potential offset was measured to be 0.4±0.2V, with the Ge side lower. Comparisons with simulations indicated that Ga present in the Si region was only partially activated. In situ EH biasing experiments combined with simulations indicated the B dopant in Ge was mostly activated but not the P dopant in Si. I-V characteristic curves were measured and explained using simulations.
The Ge/LixGe core/shell structure was studied during lithiation. The MIP for LixGe decreased with time due to increased Li content. A model was proposed to explain the lower measured Ge potential, and the trapped electron density in Ge core was calculated to be 3×1018 electrons/cm3. The Li amount during lithiation was also calculated using MIP and volume ratio, indicating that it was lower than the fully lithiated phase.
The mean inner potential (MIP) and inelastic mean free path (IMFP) of ZnO NWs have been measured to be 15.3V±0.2V and 55±3nm, respectively, for 200keV electrons. These values were then used to characterize the thickness of a ZnO nano-sheet and gave consistent values. The MIP and IMFP for ZnTe thin films were measured to be 13.7±0.6V and 46±2nm, respectively, for 200keV electrons. A thin film expected to have a p-n junction was studied, but no signal due to the junction was observed. The importance of dynamical effects was systematically studied using Bloch wave simulations.
The built-in potentials in Si NWs across the doped p-n junction and the Schottky junction due to Au catalyst were measured to be 1.0±0.3V and 0.5±0.3V, respectively. Simulations indicated that the dopant concentrations were ~1019cm-3 for donors and ~1017 cm-3 for acceptors. The effects of positively charged Au catalyst, a possible n+-n--p junction transition region and possible surface charge, were also systematically studied using simulations.
Si-Ge heterojunction NWs were studied. Dopant concentrations were extracted by atom probe tomography. The built-in potential offset was measured to be 0.4±0.2V, with the Ge side lower. Comparisons with simulations indicated that Ga present in the Si region was only partially activated. In situ EH biasing experiments combined with simulations indicated the B dopant in Ge was mostly activated but not the P dopant in Si. I-V characteristic curves were measured and explained using simulations.
The Ge/LixGe core/shell structure was studied during lithiation. The MIP for LixGe decreased with time due to increased Li content. A model was proposed to explain the lower measured Ge potential, and the trapped electron density in Ge core was calculated to be 3×1018 electrons/cm3. The Li amount during lithiation was also calculated using MIP and volume ratio, indicating that it was lower than the fully lithiated phase.
ContributorsGan, Zhaofeng (Author) / Mccartney, Martha R (Thesis advisor) / Smith, David J. (Thesis advisor) / Drucker, Jeffery (Committee member) / Bennett, Peter A (Committee member) / Arizona State University (Publisher)
Created2015
Description
Molecular dynamics simulations were used to study properties of water at the interface with nanometer-size solutes. We simulated nonpolar attractive Kihara cavities given by a Lennard-Jones potential shifted by a core radius. The dipolar response of the hydration layer to a uniform electric field substantially exceeds that of the bulk. For strongly attractive solutes, the collective dynamics of the hydration layer become slow compared to bulk water, as the solute size is increased. The statistics of electric field fluctuations at the solute center are Gaussian and tend toward the dielectric continuum limit with increasing solute size. A dipolar probe placed at the center of the solute is sensitive neither to the polarity excess nor to the slowed dynamics of the hydration layer. A point dipole was introduced close to the solute-water interface to further study the statistics of electric field fluctuations generated by the water. For small dipole magnitudes, the free energy surface is single-welled, with approximately Gaussian statistics. When the dipole is increased, the free energy surface becomes double-welled, before landing in an excited state, characterized again by a single-welled surface. The intermediate region is fairly broad and is characterized by electrostatic fluctuations significantly in excess of the prediction of linear response. We simulated a solute having the geometry of C180 fullerene, with dipoles introduced on each carbon. For small dipole moments, the solvent response follows the results seen for a single dipole; but for larger dipole magnitudes, the fluctuations of the solute-solvent energy pass through a second maximum. The juxtaposition of the two transitions leads to an approximately cubic scaling of the chemical potential with the dipole strengh. Umbrella sampling techniques were used to generate free energy surfaces of the electric potential fluctuations at the heme iron in Cytochrome B562. The results were unfortunately inconclusive, as the ionic background was not effectively represented in the finite-size system.
ContributorsFriesen, Allan Dwayne (Author) / Matyushov, Dmitry V (Thesis advisor) / Angell, C Austen (Thesis advisor) / Beckstein, Oliver (Committee member) / Mujica, Vladimiro (Committee member) / Arizona State University (Publisher)
Created2012
Description
The research of this dissertation involved quantitative characterization of electrostatic potential and charge distribution of semiconductor nanostructures using off-axis electron holography, as well as other electron microscopy techniques. The investigated nanostructures included Ge quantum dots, Ge/Si core/shell nanowires, and polytype heterostructures in ZnSe nanobelts. Hole densities were calculated for the first two systems, and the spontaneous polarization for wurtzite ZnSe was determined. Epitaxial Ge quantum dots (QDs) embedded in boron-doped silicon were studied. Reconstructed phase images showed extra phase shifts near the base of the QDs, which was attributed to hole accumulation in these regions. The resulting charge density was (0.03±0.003) holes
m3, which corresponded to about 30 holes localized to a pyramidal, 25-nm-wide Ge QD. This value was in reasonable agreement with the average number of holes confined to each Ge dot determined using a capacitance-voltage measurement. Hole accumulation in Ge/Si core/shell nanowires was observed and quantified using off-axis electron holography and other electron microscopy techniques. High-angle annular-dark-field scanning transmission electron microscopy images and electron holograms were obtained from specific nanowires. The intensities of the former were utilized to calculate the projected thicknesses for both the Ge core and the Si shell. The excess phase shifts measured by electron holography across the nanowires indicated the presence of holes inside the Ge cores. The hole density in the core regions was calculated to be (0.4±0.2)
m3 based on a simplified coaxial cylindrical model. Homogeneous zincblende/wurtzite heterostructure junctions in ZnSe nanobelts were studied. The observed electrostatic fields and charge accumulation were attributed to spontaneous polarization present in the wurtzite regions since the contributions from piezoelectric polarization were shown to be insignificant based on geometric phase analysis. The spontaneous polarization for the wurtzite ZnSe was calculated to be psp = -(0.0029±0.00013) C/m2, whereas a first principles' calculation gave psp = -0.0063 C/m2. The atomic arrangements and polarity continuity at the zincblende/wurtzite interface were determined through aberration-corrected high-angle annular-dark-field imaging, which revealed no polarity reversal across the interface. Overall, the successful outcomes of these studies confirmed the capability of off-axis electron holography to provide quantitative electrostatic information for nanostructured materials.
m3, which corresponded to about 30 holes localized to a pyramidal, 25-nm-wide Ge QD. This value was in reasonable agreement with the average number of holes confined to each Ge dot determined using a capacitance-voltage measurement. Hole accumulation in Ge/Si core/shell nanowires was observed and quantified using off-axis electron holography and other electron microscopy techniques. High-angle annular-dark-field scanning transmission electron microscopy images and electron holograms were obtained from specific nanowires. The intensities of the former were utilized to calculate the projected thicknesses for both the Ge core and the Si shell. The excess phase shifts measured by electron holography across the nanowires indicated the presence of holes inside the Ge cores. The hole density in the core regions was calculated to be (0.4±0.2)
m3 based on a simplified coaxial cylindrical model. Homogeneous zincblende/wurtzite heterostructure junctions in ZnSe nanobelts were studied. The observed electrostatic fields and charge accumulation were attributed to spontaneous polarization present in the wurtzite regions since the contributions from piezoelectric polarization were shown to be insignificant based on geometric phase analysis. The spontaneous polarization for the wurtzite ZnSe was calculated to be psp = -(0.0029±0.00013) C/m2, whereas a first principles' calculation gave psp = -0.0063 C/m2. The atomic arrangements and polarity continuity at the zincblende/wurtzite interface were determined through aberration-corrected high-angle annular-dark-field imaging, which revealed no polarity reversal across the interface. Overall, the successful outcomes of these studies confirmed the capability of off-axis electron holography to provide quantitative electrostatic information for nanostructured materials.
ContributorsLi, Luying (Author) / McCartney, Martha R. (Thesis advisor) / Smith, David J. (Thesis advisor) / Treacy, Michael J. (Committee member) / Shumway, John (Committee member) / Drucker, Jeffery (Committee member) / Arizona State University (Publisher)
Created2011
Description
Computational models have long been used to describe and predict the outcome of complex immunological processes. The dissertation work described here centers on the construction of multiscale computational immunology models that derives biological insights at the population, systems, and atomistic levels. First, SARS-CoV-2 mortality is investigated through the lens of the predicted robustness of CD8+ T cell responses in 23 different populations. The robustness of CD8+ T cell responses in a given population was modeled by predicting the efficiency of endemic MHC-I protein variants to present peptides derived from SARS-CoV-2 proteins to circulating T cells. To accomplish this task, an algorithm, called EnsembleMHC, was developed to predict viral peptides with a high probability of being recognized by CD T cells. It was discovered that there was significant variation in the efficiency of different MHC-I protein variants to present SARS-CoV-2 derived peptides, and countries enriched with variants with high presentation efficiency had significantly lower mortality rates. Second, a biophysics-based MHC-I peptide prediction algorithm was developed. The MHC-I protein is the most polymorphic protein in the human genome with polymorphisms in the peptide binding causing striking changes in the amino acid compositions, or binding motifs, of peptide species capable of stable binding. A deep learning model, coined HLA-Inception, was trained to predict peptide binding using only biophysical properties, namely electrostatic potential. HLA-Inception was shown to be extremely accurate and efficient at predicting peptide binding motifs and was used to determine the peptide binding motifs of 5,821 MHC-I protein variants. Finally, the impact of stalk glycosylations on NL63 protein dynamics was investigated. Previous data has shown that coronavirus crown glycans play an important role in immune evasion and receptor binding, however, little is known about the role of the stalk glycans. Through the integration of computational biology, experimental data, and physics-based simulations, the stalk glycans were shown to heavily influence the bending angle of spike protein, with a particular emphasis on the glycan at position 1242. Further investigation revealed that removal of the N1242 glycan significantly reduced infectivity, highlighting a new potential therapeutic target. Overall, these investigations and associated innovations in integrative modeling.
ContributorsWilson, Eric Andrew (Author) / Anderson, Karen (Thesis advisor) / Singharoy, Abhishek (Thesis advisor) / Woodbury, Neal (Committee member) / Sulc, Petr (Committee member) / Arizona State University (Publisher)
Created2022