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- All Subjects: tem
- All Subjects: Molecular Dynamics
- Creators: Chamberlin, Ralph
Description
The research described in this dissertation has involved the use of transmission electron microcopy (TEM) to characterize the structural properties of II-VI and III-V compound semiconductor heterostructures and superlattices. The microstructure of thick ZnTe epilayers (~2.4 µm) grown by molecular beam epitaxy (MBE) under virtually identical conditions on GaSb, InAs, InP and GaAs (100) substrates were compared using TEM. High-resolution electron micrographs revealed a highly coherent interface for the ZnTe/GaSb sample, and showed extensive areas with well-separated interfacial misfit dislocations for the ZnTe/InAs sample. Lomer edge dislocations and 60o dislocations were commonly observed at the interfaces of the ZnTe/InP and ZnTe/GaAs samples. The amount of residual strain at the interfaces was estimated to be 0.01% for the ZnTe/InP sample and -0.09% for the ZnTe/GaAs sample. Strong PL spectra for all ZnTe samples were observed from 80 to 300 K. High quality GaSb grown by MBE on ZnTe/GaSb (001) virtual substrates with a temperature ramp at the beginning of the GaSb growth has been demonstrated. High-resolution X-ray diffraction (XRD) showed clear Pendellösung thickness fringes from both GaSb and ZnTe epilayers. Cross-section TEM images showed excellent crystallinity and smooth morphology for both ZnTe/GaSb and GaSb/ZnTe interfaces. Plan-view TEM image revealed the presence of Lomer dislocations at the interfaces and threading dislocations in the top GaSb layer. The defect density was estimated to be ~1 x107/cm2. The PL spectra showed improved optical properties when using the GaSb transition layer grown on ZnTe with a temperature ramp. The structural properties of strain-balanced InAs/InAs1-xSbx SLs grown on GaSb (001) substrates by metalorganic chemical vapor deposition (MOCVD) and MBE, have been studied using XRD and TEM. Excellent structural quality of the InAs/InAs1-xSbx SLs grown by MOCVD has been demonstrated. Well-defined ordered-alloy structures within individual InAs1-xSbx layers were observed for samples grown by modulated MBE. However, the ordering disappeared when defects propagating through the SL layers appeared during growth. For samples grown by conventional MBE, high-resolution images revealed that interfaces for InAs1-xSbx grown on InAs layers were sharper than for InAs grown on InAs1-xSbx layers, most likely due to a Sb surfactant segregation effect.
ContributorsOuyang, Lu (Author) / Smith, David J. (Thesis advisor) / McCartney, Martha (Committee member) / Ponce, Fernando (Committee member) / Chamberlin, Ralph (Committee member) / Menéndez, Jose (Committee member) / Arizona State University (Publisher)
Created2012
Description
Soft magnetic alloys play a significant role for magnetic recording applications and highly sensitivity magnetic field sensors. In order to sustain the magnetic areal density growth, development of new synthesis techniques and materials is necessary. In this work, the effect of oxygen incorporation during electrodeposition of CoFe alloys on magnetic properties, magnetoresistance and structural properties has been studied. Understanding the magnetic properties often required knowledge of oxygen distribution and structural properties of the grown films. Transmission electron microscopy (TEM) was a powerful tool in this study to correlate the oxygen-distribution nanostructure to the magnetic properties of deposited films. Off-axis electron holography in TEM was used to measure magnetic domain wall width in the deposited films. Elemental depth profiles of Fe, Co, O were investigated by secondary ion mass spectroscopy (SIMS). Magnetic properties have been determined by superconducting quantum interference device (SQUID) measurements. Oxygen content in the CoFe deposited films was controlled by electrolyte composition. Films were deposited on Si 100 substrates and on other substrates such as Cu and Al. However, a good film quality was achieved on Si substrate. Electron energy loss and x-ray spectroscopies showed that the low oxygen films contained intragranular Fe2+ oxide (FeO) particles and that the high oxygen films contained intergranular Fe3+ (Fe2O3) along grain boundaries. The films with oxide present at the grain boundary had significantly increased coercivity, magnetoresistance and reduced saturation magnetization relative to the lower oxygen content films with intragranular oxide. The differences in magnetic properties between low oxygen and high oxygen concentration films were attributed to stronger mobile domain wall interactions with the grain boundary oxide layers. The very high magnetoresistance values were achieved for magnetic devices with nanocontact dimension < 100 nm and oxide incorporation in this nanoconfined geometry. The content of oxide phase in nanocontact was controlled by concentration of the Fe3+ ions in the electrodeposition solution. Magnetic device integrity was improved by varying amount of additive into plating solution. These results indicated that electrodeposited CoFe nanocontact is a novel class of materials with large application for magnetic field sensors.
ContributorsElhalawaty, Shereen (Author) / Carpenter, Ray (Thesis advisor) / Chamberlin, Ralph (Committee member) / McCartney, Martha (Committee member) / Alford, Terry (Committee member) / Arizona State University (Publisher)
Created2012
Description
In a typical living cell, millions to billions of proteins—nanomachines that fluctuate and cycle among many conformational states—convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics (EqMD) can capture atomistic detail and solute-solvent interactions, but even microseconds of sampling attainable nowadays still falls orders of magnitude short of transition timescales, especially for large systems, rendering observations of such "rare events" difficult or effectively impossible.
Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)—an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project—developing a hybrid atomistic-continuum method—is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.
Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)—an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project—developing a hybrid atomistic-continuum method—is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.
ContributorsSeyler, Sean L (Author) / Beckstein, Oliver (Thesis advisor) / Chamberlin, Ralph (Committee member) / Matyushov, Dmitry (Committee member) / Thorpe, Michael F (Committee member) / Vaiana, Sara (Committee member) / Arizona State University (Publisher)
Created2017
Description
Improved knowledge connecting the chemistry, structure, and properties of polymers is necessary to develop advanced materials in a materials-by-design approach. Molecular dynamics (MD) simulations can provide tremendous insight into how the fine details of chemistry, molecular architecture, and microstructure affect many physical properties; however, they face well-known restrictions in their applicable temporal and spatial scales. These limitations have motivated the development of computationally-efficient, coarse-grained methods to investigate how microstructural details affect thermophysical properties. In this dissertation, I summarize my research work in structure-based coarse-graining methods to establish the link between molecular-scale structure and macroscopic properties of two different polymers. Systematically coarse-grained models were developed to study the viscoelastic stress response of polyurea, a copolymer that segregates into rigid and viscous phases, at time scales characteristic of blast and impact loading. With the application of appropriate scaling parameters, the coarse-grained models can predict viscoelastic properties with a speed up of 5-6 orders of magnitude relative to the atomistic MD models. Coarse-grained models of polyethylene were also created to investigate the thermomechanical material response under shock loading. As structure-based coarse-grained methods are generally not transferable to states different from which they were calibrated at, their applicability for modeling non-equilibrium processes such as shock and impact is highly limited. To address this problem, a new model is developed that incorporates many-body interactions and is calibrated across a range of different thermodynamic states using a least square minimization scheme. The new model is validated by comparing shock Hugoniot properties with atomistic and experimental data for polyethylene. Lastly, a high fidelity coarse-grained model of polyethylene was constructed that reproduces the joint-probability distributions of structural variables such as the distributions of bond lengths and bond angles between sequential coarse-grained sites along polymer chains. This new model accurately represents the structure of both the amorphous and crystal phases of polyethylene and enabling investigation of how polymer processing such as cold-drawing and bulk crystallization affect material structure at significantly larger time and length scales than traditional molecular simulations.
ContributorsAgrawal, Vipin (Author) / Oswald, Jay (Thesis advisor) / Peralta, Pedro (Committee member) / Chamberlin, Ralph (Committee member) / Solanki, Kiran (Committee member) / Jiao, Yang (Committee member) / Arizona State University (Publisher)
Created2016
Description
Multifunctional oxide thin-films grown on silicon and several oxide substrates have been characterized using High Resolution (Scanning) Transmission Electron Microscopy (HRTEM), Energy-Dispersive X-ray Spectroscopy (EDX), and Electron Energy-Loss Spectroscopy (EELS). Oxide thin films grown on SrTiO3/Si pseudo-substrate showed the presence of amorphised SrTiO3 (STO) at the STO/Si interface. Oxide/oxide interfaces were observed to be atomically clean with very few defects.
Al-doped SrTiO3 thin films grown on Si were of high crystalline quality. The Ti/O ratio estimated from EELS line scans revealed that substitution of Ti by Al created associated O vacancies. The strength of the crystal field in STO was measured using EELS, and decreased by ~1.0 eV as Ti4+ was substituted by Al3+. The damping of O-K EELS peaks confirmed the rise in oxygen vacancies. For Co-substituted STO films grown on Si, the EDS and EELS spectra across samples showed Co doping was quite random. The substitution of Ti4+ with Co3+ or Co2+ created associated oxygen vacancies for charge balance. Presence of oxygen vacancies was also confirmed by shift of Ti-L EELS peaks towards lower energy by ~0.4 eV. The crystal-field strength decreased by ~0.6 eV as Ti4+ was partially substituted by Co3+ or Co2+.
Spinel Co3O4 thin films grown on MgAl2O4 (110) were observed to have excellent crystalline quality. The structure of the Co3O4/MgAl2O4 interface was determined using HRTEM and image simulations. It was found that MgAl2O4 substrate is terminated with Al and oxygen. Stacking faults and associated strain fields in spinel Co3O4 were found along [111], [001], and [113] using Geometrical Phase Analysis.
NbO2 films on STO (111) were observed to be tetragonal with lattice parameter of 13.8 Å and NbO films on LSAT (111) were observed to be cubic with lattice parameter of 4.26 Å. HRTEM showed formation of high quality NbOx films and excellent coherent interface. HRTEM of SrAl4 on LAO (001) confirmed an island growth mode. The SrAl4 islands were highly crystalline with excellent epitaxial registry with LAO. By comparing HRTEM images with image simulations, the interface structure was determined to consist of Sr-terminated SrAl4 (001) on AlO2-terminated LAO (001).
Al-doped SrTiO3 thin films grown on Si were of high crystalline quality. The Ti/O ratio estimated from EELS line scans revealed that substitution of Ti by Al created associated O vacancies. The strength of the crystal field in STO was measured using EELS, and decreased by ~1.0 eV as Ti4+ was substituted by Al3+. The damping of O-K EELS peaks confirmed the rise in oxygen vacancies. For Co-substituted STO films grown on Si, the EDS and EELS spectra across samples showed Co doping was quite random. The substitution of Ti4+ with Co3+ or Co2+ created associated oxygen vacancies for charge balance. Presence of oxygen vacancies was also confirmed by shift of Ti-L EELS peaks towards lower energy by ~0.4 eV. The crystal-field strength decreased by ~0.6 eV as Ti4+ was partially substituted by Co3+ or Co2+.
Spinel Co3O4 thin films grown on MgAl2O4 (110) were observed to have excellent crystalline quality. The structure of the Co3O4/MgAl2O4 interface was determined using HRTEM and image simulations. It was found that MgAl2O4 substrate is terminated with Al and oxygen. Stacking faults and associated strain fields in spinel Co3O4 were found along [111], [001], and [113] using Geometrical Phase Analysis.
NbO2 films on STO (111) were observed to be tetragonal with lattice parameter of 13.8 Å and NbO films on LSAT (111) were observed to be cubic with lattice parameter of 4.26 Å. HRTEM showed formation of high quality NbOx films and excellent coherent interface. HRTEM of SrAl4 on LAO (001) confirmed an island growth mode. The SrAl4 islands were highly crystalline with excellent epitaxial registry with LAO. By comparing HRTEM images with image simulations, the interface structure was determined to consist of Sr-terminated SrAl4 (001) on AlO2-terminated LAO (001).
ContributorsDhamdhere, Ajit (Author) / Smith, David J. (Thesis advisor) / McCartney, Martha R. (Committee member) / Chamberlin, Ralph (Committee member) / Ponce, Fernando (Committee member) / Arizona State University (Publisher)
Created2015