Matching Items (6)
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
Zeolites are a class of microporous materials that are immensely useful as molecular sieves and catalysts. While there exist millions of hypothetical zeolite topologies, only 206 have been recognized to exist in nature, and the question remains: What distinguishes known zeolite topologies from their hypothetical counterparts? It has been found that all 206 of the known zeolites can be represented as networks of rigid perfect tetrahedra that hinge freely at the connected corners. The range of configurations over which the corresponding geometric constraints can be met has been termed the "flexibility window". Only a small percentage of hypothetical types exhibit a flexibility window, and it is thus proposed that this simple geometric property, the existence of a flexibility window, provides a reliable benchmark for distinguishing potentially realizable hypothetical structures from their infeasible counterparts. As a first approximation of the behavior of real zeolite materials, the flexibility window provides additional useful insights into structure and composition. In this thesis, various methods for locating and exploring the flexibility window are discussed. Also examined is the assumption that the tetrahedral corners are force-free. This is a reasonable approximation in silicates for Si-O-Si angles above ~135°. However, the approximation is poor for germanates, where Ge-O-Ge angles are constrained to the range ~120°-145°. Lastly, a class of interesting low-density hypothetical zeolites is evaluated based on the feasibility criteria introduced.
ContributorsDawson, Colby (Author) / Treacy, Michael M. J. (Thesis advisor) / O'Keeffe, Michael (Committee member) / Thorpe, Michael F. (Committee member) / Rez, Peter (Committee member) / Bennett, Peter (Committee member) / Arizona State University (Publisher)
Created2013
Description
A time-dependent semiclassical formalism is developed for the theory of incoherentdiffractive imaging (IDI), an atomically-precise imaging technique based on the principles of
intensity interferometry. The technique is applied to image inner-shell X-ray fluorescence
from heavy atoms excited by the femtosecond pulses of an X-ray free-electron laser (XFEL).
Interference between emission from different atoms is expected when the XFEL pulse duration
is shorter than the fluorescence lifetime. Simulations for atoms at the vertices of a simple
icosahedral virus capsid are used to generate mock IDI diffraction patterns. These are then
used to reconstruct the geometry by phase retrieval of the intensity correlation function between
photons emitted independently from many different atoms at two different detector
pixels. The dependence of the intensity correlation function on fluorescence lifetime relative
to XFEL pulse duration is computed, and a simple expression for the visibility (or contrast)
of IDI speckle as well as an upper bound on the IDI signal-to-noise ratio are obtained as a
function of XFEL flux and lifetime. This indicates that compact XFELs, with reduced flux
but attosecond pulses, should be ideally suited to 3D, atomic-resolution mapping of heavy
atoms in materials science, chemistry, and biology. As IDI is a new technique, not much has
yet been written about it in the literature. The current theoretical and experimental results
are reviewed, including a discussion of signal-to-noise issues that have been raised regarding
the idea that IDI is suitable for structural biology.
ContributorsShevchuk, Andrew Stewart Hegeman (Author) / Kirian, Richard A (Thesis advisor) / Schmidt, Kevin E (Committee member) / Weierstall, Uwe (Committee member) / Graves, William S (Committee member) / Arizona State University (Publisher)
Created2022
Description
X-ray free electron lasers (XFELs) provide several orders of magnitude brighter x-rays than 3rd generation sources. However, the electron beamlines and undulator magnets required are on the scale of kilometers, costing billions of dollars with only a half dozen or so currently operating worldwide. One way to overcome these limitations is to prebunch the electron beam on the scale of the x-ray wavelength. In this paper one such scheme is discussed, which uses a nanopatterned grating called a dynamical beam stop. This uses diffraction from crystal planes of the etched portion of a grating to impart a transverse modulation which becomes a temporal modulation via an emittance exchange (EEX). To expand upon this topic, dynamical electron diffraction intensities for a 200 nm thick Si(001) unpatterned membrane are simulated via the multislice method and compared to experiment for various crystallographic orientations at MeV energies. From this as well as an analysis of the experimental inelastic plasmon diffuse scattering, it is determined that the optimal transverse modulation would be formed from a bright field image of the beam stop, with the nanopattern being etched all the way through the membrane. A model quantifying the quality of the modulation - the bunching factor - as a function of contrast and duty factor is formulated and the optimal modulation is determined analytically. A prototype beam stop is then imaged in a transmission electron microscope (TEM) at 200 KeV, with the measured bunching factor of 0.5 agreeing with the model and approaching a saturated XFEL. Using the angular spectrum method, it is determined that the spatial coherence of the MeV energy electron beam is insufficient for significant self-imaging to occur for gratings with pitches of hundreds of nanometers. Finally, the first-order EEX input requirements for the electron beam are examined in the transverse dimension as are newly proposed longitudinal requirements to compensate for lingering correlations between the initial and final longitudinal phase spaces.
ContributorsMalin, Lucas Earle (Author) / Graves, William S (Thesis advisor) / Kirian, Richard A (Committee member) / Smith, David J. (Committee member) / Spence, John C. H. (Committee member) / Arizona State University (Publisher)
Created2020
Description
Optical trapping schemes that exploit radiation forces, such as optical tweezers, are well understood and widely used to manipulate microparticles; however, these are typically effective only on short (sub-millimeter) length scales. In the past decade, manipulating micron sized objects over large distances (∼0.5 meters) using photophoretic forces has been experimentally established. Photophoresis, discovered by Ehrenhaft in the early twentieth century, is the force a small particle feels when exposed to radiation while immersed in a gas. The anisotropic heating caused by the radiation results in a net momentum transfer on one side with the surrounding gas. To date, there is no theoretical evaluation of the photophoretic force in the case of an arbitrary illumination profile (i.e. not a plane wave) incident on a dielectric sphere, starting from Maxwell’s equations. Such a treatment is needed for the case of recently published photophoretic particle manipulation schemes that utilize complicated wavefronts such as diverging Laguerre-Gaussian-Bessel beams. Here the equations needed to determine the expansion coefficients for electromagnetic fields when represented as a superposition of spherical harmonics are derived. The algorithm of Driscoll and Healy for the efficient numerical integration of functions on the 2-sphere is applied and validated with the plane wave, whose analytic expansion is known. The expansion coefficients of the incident field are related to the field inside the sphere, from which the distribution of heat deposition can be evaluated. The incident beam is also related to the scattered field, from which the scattering forces may be evaluated through the Maxwell stress tensor. In future work, these results will be combined with heat diffusion/convection simulations within the sphere and a surrounding gas to predict the total forces on the sphere, which will be compared against experimental observations that so far remain unexplained.
ContributorsAlvarez, Roberto Carlos (Author) / Camacho, Erika T (Thesis advisor) / Kirian, Richard A (Thesis advisor) / Espanol, Malena I (Committee member) / Arizona State University (Publisher)
Created2021