Matching Items (2)
Filtering by
- All Subjects: Applied physics
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
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