Matching Items (4)
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
The rigidity of a material is the property that enables it to preserve its structure when deformed. In a rigid body, no internal motion is possible since the degrees of freedom of the system are limited to translations and rotations only. In the macroscopic scale, the rigidity and response of a material to external load can be studied using continuum elasticity theory. But when it comes to the microscopic scale, a simple yet powerful approach is to model the structure of the material and its interparticle interactions as a ball$-$and$-$spring network. This model allows a full description of rigidity in terms of the vibrational modes and the balance between degrees of freedom and constraints in the system.
In the present work, we aim to establish a microscopic description of rigidity in \emph{disordered} networks. The studied networks can be designed to have a specific number of degrees of freedom and/or elastic properties. We first look into the rigidity transition in three types of networks including randomly diluted triangular networks, stress diluted triangular networks and jammed networks. It appears that the rigidity and linear response of these three types of systems are significantly different. In particular, jammed networks display higher levels of self-organization and a non-zero bulk modulus near the transition point. This is a unique set of properties that have not been observed in any other types of disordered networks. We incorporate these properties into a new definition of jamming that requires a network to hold one extra constraint in excess of isostaticity and have a finite non-zero bulk modulus. We then follow this definition by using a tuning by pruning algorithm to build spring networks that have both these properties and show that they behave exactly like jammed networks. We finally step into designing new disordered materials with desired elastic properties and show how disordered auxetic materials with a fully convex geometry can be produced.
In the present work, we aim to establish a microscopic description of rigidity in \emph{disordered} networks. The studied networks can be designed to have a specific number of degrees of freedom and/or elastic properties. We first look into the rigidity transition in three types of networks including randomly diluted triangular networks, stress diluted triangular networks and jammed networks. It appears that the rigidity and linear response of these three types of systems are significantly different. In particular, jammed networks display higher levels of self-organization and a non-zero bulk modulus near the transition point. This is a unique set of properties that have not been observed in any other types of disordered networks. We incorporate these properties into a new definition of jamming that requires a network to hold one extra constraint in excess of isostaticity and have a finite non-zero bulk modulus. We then follow this definition by using a tuning by pruning algorithm to build spring networks that have both these properties and show that they behave exactly like jammed networks. We finally step into designing new disordered materials with desired elastic properties and show how disordered auxetic materials with a fully convex geometry can be produced.
ContributorsFaghir Hagh, Varda (Author) / Thorpe, Michael F. (Thesis advisor) / Beckstein, Oliver (Committee member) / Chamberlin, Ralph V. (Committee member) / Schmidt, kevin E. (Committee member) / Arizona State University (Publisher)
Created2018
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