Matching Items (17)
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
The properties of materials depend heavily on the spatial distribution and connectivity of their constituent parts. This applies equally to materials such as diamond and glasses as it does to biomolecules that are the product of billions of years of evolution. In science, insight is often gained through simple models with characteristics that are the result of the few features that have purposely been retained. Common to all research within in this thesis is the use of network-based models to describe the properties of materials. This work begins with the description of a technique for decoupling boundary effects from intrinsic properties of nanomaterials that maps the atomic distribution of nanomaterials of diverse shape and size but common atomic geometry onto a universal curve. This is followed by an investigation of correlated density fluctuations in the large length scale limit in amorphous materials through the analysis of large continuous random network models. The difficulty of estimating this limit from finite models is overcome by the development of a technique that uses the variance in the number of atoms in finite subregions to perform the extrapolation to large length scales. The technique is applied to models of amorphous silicon and vitreous silica and compared with results from recent experiments. The latter part this work applies network-based models to biological systems. The first application models force-induced protein unfolding as crack propagation on a constraint network consisting of interactions such as hydrogen bonds that cross-link and stabilize a folded polypeptide chain. Unfolding pathways generated by the model are compared with molecular dynamics simulation and experiment for a diverse set of proteins, demonstrating that the model is able to capture not only native state behavior but also partially unfolded intermediates far from the native state. This study concludes with the extension of the latter model in the development of an efficient algorithm for predicting protein structure through the flexible fitting of atomic models to low-resolution cryo-electron microscopy data. By optimizing the fit to synthetic data through directed sampling and context-dependent constraint removal, predictions are made with accuracies within the expected variability of the native state.
ContributorsDe Graff, Adam (Author) / Thorpe, Michael F. (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Matyushov, Dmitry (Committee member) / Ozkan, Sefika B. (Committee member) / Treacy, Michael M. J. (Committee member) / Arizona State University (Publisher)
Created2011
Description
HgCdTe is the dominant material currently in use for infrared (IR) focal-plane-array (FPA) technology. In this dissertation, transmission electron microscopy (TEM) was used for the characterization of epitaxial HgCdTe epilayers and HgCdTe-based devices. The microstructure of CdTe surface passivation layers deposited either by hot-wall epitaxy (HWE) or molecular beam epitaxy (MBE) on HgCdTe heterostructures was evaluated. The as-deposited CdTe passivation layers were polycrystalline and columnar. The CdTe grains were larger and more irregular when deposited by HWE, whereas those deposited by MBE were generally well-textured with mostly vertical grain boundaries. Observations and measurements using several TEM techniques showed that the CdTe/HgCdTe interface became considerably more abrupt after annealing, and the crystallinity of the CdTe layer was also improved. The microstructure and compositional profiles of CdTe(211)B/ZnTe/Si(211) heterostructures grown by MBE was investigated. Many inclined {111}-type stacking faults were present throughout the thin ZnTe layer, terminating near the point of initiation of CdTe growth. A rotation angle of about 3.5° was observed between lattice planes of the Si substrate and the final CdTe epilayer. Lattice parameter measurement and elemental profiles indicated that some local intermixing of Zn and Cd had taken place. The average widths of the ZnTe layer and the (Cd, Zn)Te transition region were found to be roughly 6.5 nm and 3.5 nm, respectively. Initial observations of CdTe(211)B/GaAs(211) heterostructures indicated much reduced defect densities near the vicinity of the substrate and within the CdTe epilayers. HgCdTe epilayers grown on CdTe(211)B/GaAs(211) composite substrate were generally of high quality, despite the presence of precipitates at the HgCdTe/CdTe interface. The microstructure of HgCdSe thin films grown by MBE on ZnTe/Si(112) and GaSb(112) substrates were investigated. The quality of the HgCdSe growth was dependent on the growth temperature and materials flux, independent of the substrate. The materials grown at 100°C were generally of high quality, while those grown at 140°C had {111}-type stacking defects and high dislocation densities. For epitaxial growth of HgCdSe on GaSb substrates, better preparation of the GaSb buffer layer will be essential in order to ensure that high-quality HgCdSe can be grown.
ContributorsZhao, Wenfeng (Author) / Smith, David J. (Thesis advisor) / McCartney, Martha (Committee member) / Carpenter, Ray (Committee member) / Bennett, Peter (Committee member) / Treacy, Michael J. (Committee member) / Arizona State University (Publisher)
Created2011
Description
In this project, a novel method is presented for measuring the resistivity of nanoscale metallic conductors (nanowires) using a variable-spacing 2-point method with a modified ultrahigh vacuum scanning tunneling microscope. An auxiliary field emission imaging method that allows for scanning insulating surfaces using a large gap distance (20nm) is also presented. Using these methods, the resistivity of self-assembled endotaxial FeSi2 nanowires (NWs) on Si(110) was measured. The resistivity was found to vary inversely with NW width, being rhoNW = 200 uOhm cm at 12 nm and 300 uOhm cm at 2 nm. The increase at small w is attributed to boundary scattering, and is fit to the Fuchs-Sondheimer model, yielding values of rho0 = 150 uOhm cm and lambda = 2.4 nm, for specularity parameter p = 0.5. These results are attributed to a high concentration of point defects in the FeSi2 structure, with a correspondingly short inelastic electron scattering length. It is remarkable that the defect concentration persists in very small structures, and is not changed by surface oxidation.
ContributorsTobler, Samuel (Author) / Bennett, Peter (Thesis advisor) / McCartney, Martha (Committee member) / Tao, Nongjian (Committee member) / Doak, Bruce (Committee member) / Chen, Tingyong (Committee member) / Arizona State University (Publisher)
Created2011
Description
Studying charge transport through single molecules tethered between two metal electrodes is of fundamental importance in molecular electronics. Over the years, a variety of methods have been developed in attempts of performing such measurements. However, the limitation of these techniques is still one of the factors that prohibit one from gaining a thorough understanding of single molecule junctions. Firstly, the time resolution of experiments is typically limited to milli to microseconds, while molecular dynamics simulations are carried out on the time scale of pico to nanoseconds. A huge gap therefore persists between the theory and the experiments. This thesis demonstrates a nanosecond scale measurement of the gold atomic contact breakdown process. A combined setup of DC and AC circuits is employed, where the AC circuit reveals interesting observations in nanosecond scale not previously seen using conventional DC circuits. The breakdown time of gold atomic contacts is determined to be faster than 0.1 ns and subtle atomic events are observed within nanoseconds. Furthermore, a new method based on the scanning tunneling microscope break junction (STM-BJ) technique is developed to rapidly record thousands of I-V curves from repeatedly formed single molecule junctions. 2-dimensional I-V and conductance-voltage (G-V) histograms constructed using the acquired data allow for more meaningful statistical analysis to single molecule I-V characteristics. The bias voltage adds an additional dimension to the conventional single molecule conductance measurement. This method also allows one to perform transition voltage spectra (TVS) for individual junctions and to study the correlation between the conductance and the tunneling barrier height. The variation of measured conductance values is found to be primarily determined by the poorly defined contact geometry between the molecule and metal electrodes, rather than the tunnel barrier height. In addition, the rapid I-V technique is also found useful in studying thermoelectric effect in single molecule junctions. When applying a temperature gradient between the STM tip and substrate in air, the offset current at zero bias in the I-V characteristics is a measure of thermoelectric current. The rapid I-V technique allows for statistical analysis of such offset current at different temperature gradients and thus the Seebeck coefficient of single molecule junctions is measured. Combining with single molecule TVS, the Seebeck coefficient is also found to be a measure of tunnel barrier height.
ContributorsGuo, Shaoyin (Author) / Tao, Nongjian (Thesis advisor) / Bennett, Peter (Committee member) / Ning, Cun-Zheng (Committee member) / Yu, Hongbin (Committee member) / Arizona State University (Publisher)
Created2012
Description
A distinct characteristic of ferroelectric materials is the existence of a reversible spontaneous polarization with the application of an electric field. The relevant properties ferroelectric lithium niobate surfaces include a low density of defects and external screening of the bound polarization charge. These properties result in unique surface electric field distribution with a strong electric field in the vicinity of domain boundaries, while away from the boundaries, the field decreases rapidly. In this work, ferroelectric lithium niobate (LN) is used as a template to direct the assembly of metallic nanostructures via photo-induced reduction and a substrate for deposition of ZnO semiconducting thin films via plasma enhanced atomic layer deposition (PE-ALD). To understand the mechanism the photo-induced deposition process the following effects were considered: the illumination photon energy and intensity, the polarization screening mechanism of the lithium niobate template and the chemical concentration. Depending on the UV wavelength, variation of Ag deposition rate and boundary nanowire formation are observed and attributed to the unique surface electric field distribution of the polarity patterned template and the penetration depth of UV light. Oxygen implantation is employed to transition the surface from external screening to internal screening, which results in depressed boundary nanowire formation. The ratio of the photon flux and Ag ion flux to the surface determine the deposition pattern. Domain boundary deposition is enhanced with a high photon/Ag ion flux ratio while domain boundary deposition is depressed with a low photon/Ag ion flux ratio. These results also support the photo-induced deposition model where the process is limited by carrier generation, and the cation reduction occurs at the surface. These findings will provide a foundational understanding to employ ferroelectric templates for assembly and patterning of inorganic, organic, biological, and integrated structures. ZnO films deposited on positive and negative domain surfaces of LN demonstrate different I-V curve behavior at different temperatures. At room temperature, ZnO deposited on positive domains exhibits almost two orders of magnitude greater conductance than on negative domains. The conductance of ZnO on positive domains decreases with increasing temperature while the conductance of ZnO on negative domains increases with increasing temperature. The observations are interpreted in terms of the downward or upward band bending at the ZnO/LN interface which is induced by the ferroelectric polarization charge. Possible application of this effect in non-volatile memory devices is proposed for future work.
ContributorsSun, Yang (Author) / Nemanich, Robert (Thesis advisor) / Bennett, Peter (Committee member) / Sukharev, Maxim (Committee member) / Ros, Robert (Committee member) / McCartney, Martha (Committee member) / Arizona State University (Publisher)
Created2011
Description
Raman scattering from Ge-Si core-shell nanowires is investigated theoretically and experimentally. A theoretical model that makes it possible to extract quantitative strain information from the measured Raman spectra is presented for the first time. Geometrical and elastic simplifications are introduced to keep the model analytical, which facilitates comparison with experimental results. In particular, the nanowires are assumed to be cylindrical, and their elastic constants isotropic. The simple analytical model is subsequently validated by performing numerical calculations using realistic nanowire geometries and cubic, anisotropic elastic constants. The comparison confirms that the analytic model is an excellent approximation that greatly facilitates quantitative Raman work, with expected errors in the strain determination that do not exceed 10%. Experimental Raman spectra of a variety of core-shell nanowires are presented, and the strain in the nanowires is assessed using the models described above. It is found that all structures present a significant degree of strain relaxation relative to ideal, fully strained Ge-Si core-shell structures. The analytical models are modified to quantify this strain relaxation.
ContributorsSingh, Rachna (Author) / Menéndez, Jose (Thesis advisor) / Drucker, Jeffery (Committee member) / Ponce, Fernando (Committee member) / Tsen, Kong-Thon (Committee member) / Bennett, Peter (Committee member) / Arizona State University (Publisher)
Created2011
Description
This research focuses on the stress and structure evolution observed in-situ during the earliest stages of thin film growth in Cu on Au(111)-reconstruction. For the research, an ultra high vacuum-scanning tunneling microscopy (UHV-STM) system was modified to have the additional capabilities of in-situ deposition and in-situ stress evolution monitoring. The design and fabrication processes for the modifications are explained in detail. The deposition source enabled imaging during the deposition of Cu thin films, while also being columnar enough to avoid negatively impacting the function of the microscope. It was found that the stress-induced changes in piezo voltage occurred over a substantially longer time scale and larger piezo scale than used during imaging, allowing for the deconvolution of the two sources of piezo voltage change. The intrinsic stress evolution observed at the onset of Cu growth was tensile in character and reached a maximum of 0.19 N/m at approximately 0.8ML, with an average tensile slope of 1.0GPa. As the film thickness increased beyond 0.8 ML, the stress became less tensile as the observation of disordered stripe and trigon patterns of misfit dislocations began to appear. The transport of atoms from the surface of enlarged Cu islands into the strained layer played an important role in this stage, because they effectively reduce the activation barrier for the formation of the observed surface structures. A rich array of structures were observed in the work presented here including stripe, disordered stripe and trigon patterns co-existing in a single Cu layer. Heteroepitaxial systems in existing literature showed a uniform structure in the single layer. The non-uniform structures in the single layer of this work may be attributed to the room temperature Cu growth, which can kinetically limit uniform pattern formation. The development of the UHV-STM system with additional capabilities for this work is expected to contribute to research for the stress and structure relationships of many other heteroepitaxial systems.
ContributorsNah, Jungwoo (Author) / Friesen, Cody (Thesis advisor) / Sieradzki, Karl (Committee member) / Bennett, Peter (Committee member) / Arizona State University (Publisher)
Created2012
Description
A theoretical study of a three-dimensional (3D) N/S interface with arbitrary spin
polarization and interface geometry is presented. The 3D model gives the same intrinsic
spin polarization and superconducting gap dependence as the 1D model. This
demonstrates that the 1D model can be use to t 3D data.
Using this model, a Heusler alloy is investigated. Andreev reflection measurements
show that the spin polarization is 80% in samples sputtered on unheated MgO(100)
substrates and annealed at high temperatures. However, the spin polarization is
considerably smaller in samples deposited on heated substrates.
Ferromagnetic FexSix alloys have been proposed as potential spin injectors into
silicon with a substantial spin polarization. Andreev Reflection Spectroscopy (ARS) is
utilized to determine the spin polarization of both amorphous and crystalline Fe65Si35
alloys. The amorphous phase has a significantly higher spin polarization than that of
the crystalline phase.
In this thesis, (1111) Fe SmO0:82F0:18FeAs and Pb superconductors are used to
measure the spin polarization of a highly spin-polarized material, La0:67Sr0:33MnO3.
Both materials yield the same intrinsic spin polarization, therefore, Fe-superconductors
can be used in ARS. Based on the behavior of the differential conductance for highly
spin polarized LSMO and small polarization of Au, it can be concluded that the Fe-Sc
is not a triplet superconductor.
Zero bias anomaly (ZBA), in point contact Andreev reflection (PCAR), has been
utilized as a characteristic feature to reveal many novel physics. Complexities at a
normal metal/superconducting interface often cause nonessential ZBA-like features,
which may be mistaken as ZBA. In this work, it is shown that an extrinsic ZBA,
which is due to the contact resistance, cannot be suppressed by a highly spin-polarized
current while a nonessential ZBA cannot be affected the contact resistance.
Finally, Cu/Cu multilayer GMR structures were fabricated and the GMR% measured
at 300 K and 4.5 K gave responses of 63% and 115% respectively. Not only
do the GMR structures have a large enhancement of resistance, but by applying an
external magnetic eld it is shown that, unlike most materials, the spin polarization
can be tuned to values of 0.386 to 0.415 from H = 0 kOe to H = 15 kOe.
polarization and interface geometry is presented. The 3D model gives the same intrinsic
spin polarization and superconducting gap dependence as the 1D model. This
demonstrates that the 1D model can be use to t 3D data.
Using this model, a Heusler alloy is investigated. Andreev reflection measurements
show that the spin polarization is 80% in samples sputtered on unheated MgO(100)
substrates and annealed at high temperatures. However, the spin polarization is
considerably smaller in samples deposited on heated substrates.
Ferromagnetic FexSix alloys have been proposed as potential spin injectors into
silicon with a substantial spin polarization. Andreev Reflection Spectroscopy (ARS) is
utilized to determine the spin polarization of both amorphous and crystalline Fe65Si35
alloys. The amorphous phase has a significantly higher spin polarization than that of
the crystalline phase.
In this thesis, (1111) Fe SmO0:82F0:18FeAs and Pb superconductors are used to
measure the spin polarization of a highly spin-polarized material, La0:67Sr0:33MnO3.
Both materials yield the same intrinsic spin polarization, therefore, Fe-superconductors
can be used in ARS. Based on the behavior of the differential conductance for highly
spin polarized LSMO and small polarization of Au, it can be concluded that the Fe-Sc
is not a triplet superconductor.
Zero bias anomaly (ZBA), in point contact Andreev reflection (PCAR), has been
utilized as a characteristic feature to reveal many novel physics. Complexities at a
normal metal/superconducting interface often cause nonessential ZBA-like features,
which may be mistaken as ZBA. In this work, it is shown that an extrinsic ZBA,
which is due to the contact resistance, cannot be suppressed by a highly spin-polarized
current while a nonessential ZBA cannot be affected the contact resistance.
Finally, Cu/Cu multilayer GMR structures were fabricated and the GMR% measured
at 300 K and 4.5 K gave responses of 63% and 115% respectively. Not only
do the GMR structures have a large enhancement of resistance, but by applying an
external magnetic eld it is shown that, unlike most materials, the spin polarization
can be tuned to values of 0.386 to 0.415 from H = 0 kOe to H = 15 kOe.
ContributorsGifford, Jessica Anna (Author) / Chen, Tingyong (Thesis advisor) / Bennett, Peter (Committee member) / Nemanich, Robert (Committee member) / Tsen, Kong-Thon (Committee member) / Arizona State University (Publisher)
Created2015
Description
An electrical current with high spin polarization is desirable for the performance of novel spintronics devices, such as magnetic tunnel junction and giant magnetoresistance devices. The generation of spin polarized current can be from ferromagnetic materials or triplet superconductors.
Anomalous Hall effect (AHE) is an effective way to study the properties of magnetic structures. The scattering of electrons by the magnetic moments affects the change of resistance, which can be used to detect the magnetization. In this dissertation, AHE is used to study the perpendicular magnetic anisotropy (PMA) structures, including Co/Pt and Ta/CoFeB/MgO.
Domain walls exist in all ferromagnetic materials. This dissertation studies the domain wall movement in the Ta/CoFeB/MgO structure. A single domain is observed by measuring the anomalous Hall effect. On the other hand, a zero Hall step is successfully observed in a single layer of magnetic material for the first time, which can be used to fabricate advanced domain wall spintronics devices.
Besides the normal ferromagnetic material, the generation of spin polarized current in superconductor is also important for Spintronics. The electrons in superconductors form Cooper pairs. In this dissertation, Andreev Reflection Spectroscopy (ARS) is used to study the spin configuration in Cooper pairs.
Generally, ferromagnetism and superconductivity can not co-exist. In this dissertation, the Bi/Ni bilayer structure has been studied with ARS, and the measurement results show a triplet superconductivity below 4K. The appearance of superconductivity is believed to be attributed to the Bi-Ni interface, and the triplet Cooper pair makes it a promising candidate in superconducting spintronics.
Besides, a Bi3Ni single crystal is also studied with ARS. The measurements show a singlet superconductivity in this material, which further proves the importance of the Bi/Ni interface to achieve triplet superconductivity.
Finally, ARS is also used to study NbSe2 monolayer, a 2D superconductor. The monolayer is verified by the measurements of critical temperature and critical field, which are different from the values of multilayer or bulk. Andreev reflection results show that NbSe2 monolayer is a singlet superconductor and there is no node exist in the superconducting gap for a in plane magnetic field up to 58 kOe.
Anomalous Hall effect (AHE) is an effective way to study the properties of magnetic structures. The scattering of electrons by the magnetic moments affects the change of resistance, which can be used to detect the magnetization. In this dissertation, AHE is used to study the perpendicular magnetic anisotropy (PMA) structures, including Co/Pt and Ta/CoFeB/MgO.
Domain walls exist in all ferromagnetic materials. This dissertation studies the domain wall movement in the Ta/CoFeB/MgO structure. A single domain is observed by measuring the anomalous Hall effect. On the other hand, a zero Hall step is successfully observed in a single layer of magnetic material for the first time, which can be used to fabricate advanced domain wall spintronics devices.
Besides the normal ferromagnetic material, the generation of spin polarized current in superconductor is also important for Spintronics. The electrons in superconductors form Cooper pairs. In this dissertation, Andreev Reflection Spectroscopy (ARS) is used to study the spin configuration in Cooper pairs.
Generally, ferromagnetism and superconductivity can not co-exist. In this dissertation, the Bi/Ni bilayer structure has been studied with ARS, and the measurement results show a triplet superconductivity below 4K. The appearance of superconductivity is believed to be attributed to the Bi-Ni interface, and the triplet Cooper pair makes it a promising candidate in superconducting spintronics.
Besides, a Bi3Ni single crystal is also studied with ARS. The measurements show a singlet superconductivity in this material, which further proves the importance of the Bi/Ni interface to achieve triplet superconductivity.
Finally, ARS is also used to study NbSe2 monolayer, a 2D superconductor. The monolayer is verified by the measurements of critical temperature and critical field, which are different from the values of multilayer or bulk. Andreev reflection results show that NbSe2 monolayer is a singlet superconductor and there is no node exist in the superconducting gap for a in plane magnetic field up to 58 kOe.
ContributorsZhao, Gejian (Author) / Chen, Tingyong (Thesis advisor) / Bennett, Peter (Committee member) / Nemanich, Robert (Committee member) / Qing, Quan (Committee member) / Arizona State University (Publisher)
Created2018