Matching Items (56)
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
One of the most important issues in femtosecond free electron laser X-ray diraction is to reconstruct the 3D charge density of molecule from a mass of diraction snapshots. In order to determine the orientation of single molecule from diraction patterns, we rst determine the moments and products of inertia of this from 2D experiment data (diraction patterns or EM images to obtain the elements of the inertia tensor. If diraction patterns from uniformly random orientations or some preferred orientations are collected, the principal axes of the molecule can be extracted, together with the Euler angles which relate the principal axes of the molecule to the laboratory frame axes. This is achieved by nding the maximum and minimum values for the measured moments from many single-molecule patterns. Simulations for GroEL protein indicates that the calculation of the autocorrelation help eliminate the Poisson noise in Cryo- EM images and can make correct orientation determination. The eect of water jacket surrounding the protein molecule is studied based on molecular dynamics simulation result. The intensities from water and interference is found to suppress those from protein itself. A method is proposed and applied to the simulation data to show the possibility for it to overcome the water background problem. The scattering between Bragg re ections from nanocrystals is used to aid solution of the phase problem. We describe a method for reconstructing the charge density of a typical molecule within a single unit cell, if suciently nely-sampled diraction data are available from many nanocrystals of dierent sizes lying in the same orientations without knowledge of the distribution of particle size or requiring atomic-resolution data. Triple correlation of the diraction patterns are made use of to reconiii
ContributorsWang, Xiaoyu (Author) / Spence, John C.H. (Thesis advisor) / Schmidt, Kevin (Committee member) / Doak, R. Bruce (Committee member) / Weierstall, Uwe (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2011
Description
Black Laurel is a book-length manuscript which has at its center poems that reveal and explore issues related to Michele Poulos's identity as a Greek-American writer, discovering the connections that link the past and present of both Greece and America. These poems often work as a quest to recover identity. They explore the idea that it is her own privileged perspective as an educated Greek-American woman that both allows and in some ways prevents her seeing herself in the Greeks who today are struggling economically, emotionally, and psychologically. Many of the poems work to achieve a complex understanding of both an individual as well as a broader cultural history. These poems sometimes take on the personas of striking figures from other times and other landscapes, while others draw on materials which are somewhat more autobiographical. In one poem titled "Before My Mother Set Herself on Fire," the speaker is an imagined daughter in a modern-day Greek family. The poem, inspired by a news story about an elderly man who shot himself in the head in front of Syntagma Square in Athens to protest the austerity measures imposed on the Greek population, explores the various ways in which a national crisis may affect an individual family. Alternatively, Poulos delves into her personal family history in "When the Wind Falls," a poem about the Nazi invasions of northern Greece. At the same time, this focus on past and present Greece is only one strand in a wide-ranging manuscript woven of materials which also include a variety of subjects related to science, history, eroticism, mysticism, and much more.
ContributorsPoulos, Michele (Author) / Dubie, Norman (Thesis advisor) / Hogue, Cynthia (Committee member) / Hummer, Terry (Committee member) / Arizona State University (Publisher)
Created2013
Description
Chris Miller's Souvenirs of Sleep is as serious as it is whimsical, if this is a possibility. The "Museum of the Zoo-real" may be an equally appropriate title as animals are often in performance. In this visual and spiritual investigation, childhood, dream, and the loss of a mother to suicide are the currents. Miller's work is informed by the cinema of Werner Herzog, Andrei Tarkovsky, Robert Bresson and beyond. Miller believes in the power of implication. The poems begin with intense focus, but are often in the business of expansion. Souvenirs of Sleep is a journey toward sense-making, a search for language that might allow it.
ContributorsMiller, Christopher (Author) / Dubie, Norman (Thesis advisor) / Hogue, Cynthia (Committee member) / Ball, Sally (Committee member) / Arizona State University (Publisher)
Created2013
Description
Cruz del Sur is an exploration of what it means to be an outsider: as a resident, as a foreigner, from the perspective of the human eye, or from the perspective of a camera lens. An unlikely blending of voices, these poems embark the reader on a journey across a continent, and also into an interior: a mystical quest.
ContributorsMontgomery, Scott (Author) / Dubie, Norman (Thesis advisor) / Hogue, Cynthia (Committee member) / Hummer, Terry (Committee member) / Arizona State University (Publisher)
Created2013
Description
The Fledglings of Anani is a universe with an underlying organizing principle of desire, auspiciousness and serendipity, the veiled doors and windows of these realms serve as fugues bridging layers of time leading us through myth and landscape intimately tied to the physical intelligence of earth and character of place. It is a voice that comes to know itself first as being, then in correspondence to nature and her elements, enters into the rhythm of human connection and ultimately circles back to comprehend itself as all these things, varying only in degree. The poems travel further and further toward an allusive center with a contemplative inner eye that embraces the complexity and vitality of life.
ContributorsPoole, Heather Lea (Author) / Dubie, Norman (Thesis advisor) / Hogue, Cynthia (Committee member) / Savard, Jeannine (Committee member) / Arizona State University (Publisher)
Created2012
Description
A collection of poems that explore what it means to be from the Atomic City-- a city built atop cleared-out rural communities in East Tennessee during World War II, and with the sole and secretive purpose of enriching uranium for the atomic bomb. The poems look back to the more isolated Appalachian culture of previous generations, discovering the identity rifts caused by such massive and rushed development. In trying to understand the poet's own cultural inheritance of both nuclear weaponry and an Appalachian hardness, the poems begin to meditate on inhabitation. They ask what it means to live in a country, a local community, a body. The poems travel far beyond the Atomic City's limits, incorporating characters that live, in some sense, at the edge of a community. As he crosses the Atlantic, the Spanish poet Jiménez wonders if either sound or vision are more trustworthy tools for perception; an aging grandmother in Tennessee realizes that she still "drives" her younger body in her dreams; an American woman becomes aroused after touring the killing fields in Cambodia; and the prophet of Oak Ridge, who supposedly predicted the Manhattan Project, considers how his baby daughter has become a thing after death. The various voices show the poet grappling with her own guilt over Hiroshima, and ultimately attempt to understand the limits of both grief and love, how one inherits a tragedy.
ContributorsSams, Sara (Author) / Hogue, Cynthia (Thesis advisor) / Ball, Sally (Committee member) / Dubie, Norman (Committee member) / Arizona State University (Publisher)
Created2013
Description
This creative thesis is a work of narrative and lyric poetry. Death and Nature are two complex themes that emerge frequently in the poems and work as well across the breadth of the manuscript. The speakers' perspectives vary and are indebted to two sub-genres of poetry, namely--The Poetry of Witness, and Ekphrastic Poetry. Their psycho-analytic underpinnings are at times indisputable, and at other times, purely subjective. Many poems address political and human rights issues in the Middle East, and in the rest of the world. It is here that the poems depend and reveal flexibility with diction and varying structures. Overall, the poems reflect and investigate possible restraints and choices, both internally by the details and images, and externally by multiple experiments with free verse forms.
ContributorsHassan, Eman (Author) / Dubie, Norman (Thesis advisor) / Hogue, Cynthia (Committee member) / Savard, Jeannine (Committee member) / Arizona State University (Publisher)
Created2012
Description
The poems in this book are lyric, meditational, and narrative approaches to autobiographical tales. These works, through various poetic forms, are an attempt to assess and equate personal life experiences with those larger human and universal occasions. Spanning both physical time (a cross-country move from Virginia to Arizona) and spatial time (Virginia and Mississippi during the civil rights movement), the works evaluate and validate the human experiences of loss. Through poems addressed to various family members and historical figures, the book attempts to terms with the often humorous, often terrifying experience of being an African American male in the United States in the 21st Century.
ContributorsBooth, Dexter (Author) / Dubie, Norman (Thesis advisor) / Hummer, Terry (Committee member) / Fritz-Goldberg, Beckian (Committee member) / Arizona State University (Publisher)
Created2012
Description
Dark Tourism explores the grief borne of losing a connection to the past. As detailed in the prologue poem, "Baucis and Philemon," the speaker's stories in Dark Tourism "have been resistant / to [their] drownings" and that refusal to stay buried has "[sent] ripples in every direction." The voices in Dark Tourism track the trajectory of these ripples by animating the past, especially through the formal work in the partial sonnet crown that acts as centerpiece to the manuscript. The sonic and rhythmic repetitions reinforce an idea central to Dark Tourism as a whole: the things we inherit from the past endure, with or without our permissions, and the speakers seek to interpret this haunting in a way that unifies past and present.
ContributorsAndoga, Rachel (Author) / Savard, Jeannine (Thesis advisor) / Dubie, Norman (Committee member) / Hogue, Cynthia (Committee member) / Arizona State University (Publisher)
Created2012