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- All Subjects: X-rays
- Creators: Holland, Gregory
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
In disordered soft matter system, amorphous and crystalline components might be coexisted. The interaction between the two distinct structures and the correlation within the crystalline components are crucial to the macroscopic property of the such material. The spider dragline silk biopolymer, is one of such soft matter material that exhibits exceptional mechanical strength though its mass density is considerably small compare to structural metal. Through wide-angle X-ray scattering (WAXS), the research community learned that the silk fiber is mainly composed of amorphous backbone and $\beta$-sheet nano-crystals. However, the morphology of the crystalline system within the fiber is still not clear. Therefore, a combination of small-angle X-ray scattering experiments and stochastic simulation is designed here to reveal the nano-crystalline ordering in spider silk biopolymer. In addition, several density functional theory (DFT) calculations were performed to help understanding the interaction between amorphous backbone and the crystalline $\beta$-sheets.
By taking advantage of the prior information obtained from WAXS, a rather crude nano-crystalline model was initialized for further numerical reconstruction. Using Markov-Chain stochastic method, a hundreds of nanometer size $\beta$-sheet distribution model was reconstructed from experimental SAXS data, including silk fiber sampled from \textit{Latrodectus hesperus}, \textit{Nephila clavipes}, \textit{Argiope aurantia} and \textit{Araneus gemmoides}. The reconstruction method was implemented using MATLAB and C++ programming language and can be extended to study a broad range of disordered material systems.
By taking advantage of the prior information obtained from WAXS, a rather crude nano-crystalline model was initialized for further numerical reconstruction. Using Markov-Chain stochastic method, a hundreds of nanometer size $\beta$-sheet distribution model was reconstructed from experimental SAXS data, including silk fiber sampled from \textit{Latrodectus hesperus}, \textit{Nephila clavipes}, \textit{Argiope aurantia} and \textit{Araneus gemmoides}. The reconstruction method was implemented using MATLAB and C++ programming language and can be extended to study a broad range of disordered material systems.
ContributorsMou, Qiushi (Author) / Yarger, Jeffery (Thesis advisor) / Benmore, Chris (Committee member) / Holland, Gregory (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2015