Matching Items (3)
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Description
ABSTRACT

X-Ray crystallography and NMR are two major ways of achieving atomic

resolution of structure determination for macro biomolecules such as proteins. Recently, new developments of hard X-ray pulsed free electron laser XFEL opened up new possibilities to break the dilemma of radiation dose and spatial resolution in diffraction imaging by outrunning

ABSTRACT

X-Ray crystallography and NMR are two major ways of achieving atomic

resolution of structure determination for macro biomolecules such as proteins. Recently, new developments of hard X-ray pulsed free electron laser XFEL opened up new possibilities to break the dilemma of radiation dose and spatial resolution in diffraction imaging by outrunning radiation damage with ultra high brightness femtosecond X-ray pulses, which is so short in time that the pulse terminates before atomic motion starts. A variety of experimental techniques for structure determination of macro biomolecules is now available including imaging of protein nanocrystals, single particles such as viruses, pump-probe experiments for time-resolved nanocrystallography, and snapshot wide- angle x-ray scattering (WAXS) from molecules in solution. However, due to the nature of the "diffract-then-destroy" process, each protein crystal would be destroyed once

probed. Hence a new sample delivery system is required to replenish the target crystal at a high rate. In this dissertation, the sample delivery systems for the application of XFELs to biomolecular imaging will be discussed and the severe challenges related to the delivering of macroscopic protein crystal in a stable controllable way with minimum waste of sample and maximum hit rate will be tackled with several different development of injector designs and approaches. New developments of the sample delivery system such as liquid mixing jet also opens up new experimental methods which gives opportunities to study of the chemical dynamics in biomolecules in a molecular structural level. The design and characterization of the system will be discussed along with future possible developments and applications. Finally, LCP injector will be discussed which is critical for the success in various applications.
ContributorsWang, Dingjie (Author) / Spence, John CH (Thesis advisor) / Weierstall, Uwe (Committee member) / Schmidt, Kevin (Committee member) / Fromme, Petra (Committee member) / Ozkan, Banu (Committee member) / Arizona State University (Publisher)
Created2014
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Description

Serial femtosecond crystallography (SFX) with an X-ray free-electron laser (XFEL) has enabled the determination of protein structures and protein reaction intermediates in millisecond to microsecond time resolutions. Mix-and-Inject crystallography (MISC) at XFELs enables fast mixing in the magnitude of milliseconds in order to achieve desired reaction time points. For these

Serial femtosecond crystallography (SFX) with an X-ray free-electron laser (XFEL) has enabled the determination of protein structures and protein reaction intermediates in millisecond to microsecond time resolutions. Mix-and-Inject crystallography (MISC) at XFELs enables fast mixing in the magnitude of milliseconds in order to achieve desired reaction time points. For these experiments, numerical simulations of a hydrodynamic flow mixer capable of fast mixing by diffusion has been developed using both COMSOL Multiphysics 5.6 and QuickerSims Computational Fluid Dynamics (CFD) Toolbox for MATLAB. These simulation programs were compared by calculations of mixing times and concentration flow profiles. Mixing times in the range of 1-10 ms were calculated in COMSOL under certain flow rate conditions whereas mixing times in the range of 6-15 ms were calculated with QuickerSims. From these mixing times, reaction intermediates can be varied from sub-millisecond to several hundred millisecond time points for a MISC experiment. Explanations for the discrepancies between the two models were attributed to variations in parameter definitions and meshing. Further analysis on the mixing characteristics were investigated by calculating an analytical solution to the convection-diffusion equation for fluid flow in a two-dimensional rectangular channel. The concentration profile along the width of the channel for the analytical solution was compared with the numerical solution obtained with COMSOL and QuickerSims. Upon comparison, it was determined that the diffusion coefficient may not be a significant factor for the disagreement between the two hydrodynamic flow models.

ContributorsGuzman, Manuel Alexander (Author) / Ros, Alexandra (Thesis director) / Williams, Peter (Committee member) / Hayes, Mark (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description
The current work aims to understand the influence of particles on scalar transport in particle-laden turbulent jets using point-particle direct numerical simulations (DNS). Such turbulence phenomena are observed in many applications, such as aircraft and rocket engines (e.g., engines operating in dusty environments and when close to the surface) and

The current work aims to understand the influence of particles on scalar transport in particle-laden turbulent jets using point-particle direct numerical simulations (DNS). Such turbulence phenomena are observed in many applications, such as aircraft and rocket engines (e.g., engines operating in dusty environments and when close to the surface) and geophysical flows (sediment-laden rivers discharging nutrients into the oceans), etc.This thesis looks at systematically understanding the fundamental interplay between (1) fluid turbulence, (2) inertial particles, and (3) scalar transport. This work considers a temporal jet of Reynolds number of 5000 filled with the point-particles and the influence of Stokes number (St). Three Stokes numbers, St = 1, 7.5, and 20, were considered for the current work. The simulations were solved using the NGA solver, which solves the Navier-Stokes, advection-diffusion, and particle transport equations. The statistical analysis of the mean and turbulence quantities, along with the Reynolds stresses, are estimated for the fluid and particle phases throughout the domain. The observations do not show a significant influence of St in the mean flow evolution of fluid, scalar, and particle phases. The scalar mixture fraction variance and the turbulent kinetic energy (TKE) increase slightly for the St = 1 case, compared to the particle-free and higher St cases, indicating that an optimal St exists for which the scalar variation increases. The current preliminary study establishes that the scalar variance is influenced by particles under the optimal particle St. Directions for future studies based on the current observations are presented.
ContributorsPaturu, Venkata Sai Sushant (Author) / Pathikonda, Gokul (Thesis advisor) / Kasbaoui, Mohamed Houssem (Committee member) / Kim, Jeonglae (Committee member) / Prabhakaran, Prasanth (Committee member) / Arizona State University (Publisher)
Created2023