Study of Strongly-Coupled Self-Assembled Superlattices Using X-ray Photon Correlation Spectroscopy and Coherent Diffractive Imaging

Description

The self-assembly of strongly-coupled nanocrystal superlattices, as a convenient bottom-up synthesis technique featuring a wide parameter space, is at the forefront of next-generation material design. To realize the full potential of such tunable, functional materials, a more complete understanding of

The self-assembly of strongly-coupled nanocrystal superlattices, as a convenient bottom-up synthesis technique featuring a wide parameter space, is at the forefront of next-generation material design. To realize the full potential of such tunable, functional materials, a more complete understanding of the self-assembly process and the artificial crystals it produces is required. In this work, we discuss the results of a hard coherent X-ray scattering experiment at the Linac Coherent Light Source, observing superlattices long after their initial nucleation. The resulting scattering intensity correlation functions have dispersion suggestive of a disordered crystalline structure and indicate the occurrence of rapid, strain-relieving events therein. We also present real space reconstructions of individual superlattices obtained via coherent diffractive imaging. Through this analysis we thus obtain high-resolution structural and dynamical information of self-assembled superlattices in their native liquid environment.

Date Created
2023-05
Agent

3D Printed Gas Dynamic Virtual Nozzles for X-Ray Laser Sample Deliveryand Optical Characterization of Microjets and Microdroplets

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Description
Gas Dynamic Virtual Nozzles (GDVN) produce microscopic flow-focused liquid jets and are widely used for sample delivery in serial femtosecond crystallography (SFX) and time-resolved solution scattering. Recently, 2-photon polymerization (2PP) made it possible to produce 3D-printed GDVNs with submicron printing

Gas Dynamic Virtual Nozzles (GDVN) produce microscopic flow-focused liquid jets and are widely used for sample delivery in serial femtosecond crystallography (SFX) and time-resolved solution scattering. Recently, 2-photon polymerization (2PP) made it possible to produce 3D-printed GDVNs with submicron printing resolution. Comparing with hand- fabricated nozzles, reproducibility, and less developing effort, and similarity of the performance of different 3D printed nozzles are among the advantages of using 3D printing techniques to develop GDVN’s. Submicron printing resolution also makes it possible to easily improve GDVN performance by optimizing the design of nozzles. In this study, 3D printed nozzles were developed to achieve low liquid and gas flow rates and high liquid jet velocities. A double-pulsed nanosecond laser imaging system was used to perform Particle Tracking Velocimetry (PTV) in order to determine jet velocities and assess jet stability/reproducibility. The testing results of pure water jets focused with He sheath gas showed that some designs can easily achieve stable liquid jets with velocities of more than 80 m/s, with pure water flowing at 3 microliters/min, and helium sheath gas flowing at less than 5 mg/min respectively. A numerical simulation pipeline was also used to characterize the performance of different 3D printed GDVNs. The results highlight the potential of making reproducible GDVNs with minimum fabrication effort, that can meet the requirements of present and future SFX and time-resolved solution scattering research.
Date Created
2020
Agent

Serial Femtosecond Crystallography of Proteins in Proteins and Cancer

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Description
This thesis focuses on serial crystallography studies with X-ray free electron lasers

(XFEL) with a special emphasis on data analysis to investigate important processes

in bioenergy conversion and medicinal applications.

First, the work on photosynthesis focuses on time-resolved femtosecond crystallography

studies of Photosystem II

This thesis focuses on serial crystallography studies with X-ray free electron lasers

(XFEL) with a special emphasis on data analysis to investigate important processes

in bioenergy conversion and medicinal applications.

First, the work on photosynthesis focuses on time-resolved femtosecond crystallography

studies of Photosystem II (PSII). The structural-dynamic studies of the water

splitting reaction centering on PSII is a current hot topic of interest in the field, the

goal of which is to capture snapshots of the structural changes during the Kok cycle.

This thesis presents results from time-resolved serial femtosecond (fs) crystallography

experiments (TR-SFX) where data sets are collected at room temperature from a

stream of crystals that intersect with the ultrashort femtosecond X-ray pulses at an

XFEL with the goal to obtain structural information from the transient state (S4)

state of the cycle where the O=O bond is formed, and oxygen is released. The most

current techniques available in SFX/TR-SFX to handle hundreds of millions of raw

diffraction patterns are discussed, including selection of the best diffraction patterns,

allowing for their indexing and further data processing. The results include two 4.0 Å

resolution structures of the ground S1 state and triple excited S4 transient state.

Second, this thesis reports on the first international XFEL user experiments in

South Korea at the Pohang Accelerator Laboratory (PAL-XFEL). The usability of this

new XFEL in a proof-of-principle experiment for the study of microcrystals of human

taspase1 (an important cancer target) by SFX has been tested. The descriptions of

experiments and discussions of specific data evaluation challenges of this project in

light of the taspase1 crystals’ high anisotropy, which limited the resolution to 4.5 Å,

are included in this report

In summary, this thesis examines current techniques that are available in the

SFX/TR-SFX domain to study crystal structures from microcrystals damage-free,

with the future potential of making movies of biological processes.
Date Created
2020
Agent

Serial femtosecond crystallography data analysis of photosystem II

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Description
Serial femtosecond crystallography (SFX) uses diffraction patterns from crystals delivered in a serial fashion to an X-Ray Free Electron Laser (XFEL) for structure determination. Typically, each diffraction pattern is a snapshot from a different crystal. SFX limits the effect of

Serial femtosecond crystallography (SFX) uses diffraction patterns from crystals delivered in a serial fashion to an X-Ray Free Electron Laser (XFEL) for structure determination. Typically, each diffraction pattern is a snapshot from a different crystal. SFX limits the effect of radiation damage and enables the use of nano/micro crystals for structure determination. However, analysis of SFX data is challenging since each snapshot is processed individually.

Many photosystem II (PSII) dataset have been collected at XFELs, several of which are time-resolved (containing both dark and laser illuminated frames). Comparison of light and dark datasets requires understanding systematic errors that can be introduced during data analysis. This dissertation describes data analysis of PSII datasets with a focus on the effect of parameters on later results. The influence of the subset of data used in the analysis is also examined and several criteria are screened for their utility in creating better subsets of data. Subsets are compared with Bragg data analysis and continuous diffuse scattering data analysis.

A new tool, DatView aids in the creation of subsets and visualization of statistics. DatView was developed to improve the loading speed to visualize statistics of large SFX datasets and simplify the creation of subsets based on the statistics. It combines the functionality of several existing visualization tools into a single interface, improving the exploratory power of the tool. In addition, it has comparison features that allow a pattern-by-pattern analysis of the effect of processing parameters. \emph{DatView} improves the efficiency of SFX data analysis by reducing loading time and providing novel visualization tools.
Date Created
2019
Agent

The Electrodynamic Ion Trap

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Description
In this experiment an Electrodynamic Ion Ring Trap was constructed and tested. Due to the nature of Electrostatic fields, the setup required an oscillating voltage source to stably trap the particles. It was built in a safe manner, The power

In this experiment an Electrodynamic Ion Ring Trap was constructed and tested. Due to the nature of Electrostatic fields, the setup required an oscillating voltage source to stably trap the particles. It was built in a safe manner, The power supply was kept in a project box to avoid incidental contact, and was connected to a small copper wire in the shape of a ring. The maximum voltage that could be experienced via incidental contact was well within safe ranges a 0.3mA. Within minutes of its completion the trap was able to trap small Lycopodium powder spores mass of approximately 1.7*10^{-11}kg in clusters of 15-30 for long timescales. The oscillations of these spores were observed to be roughly 1.01mm at their maximum, and in an attempt to understand the dynamics of the Ion Trap, a concept called the pseudo-potential of the trap was used. This method proved fairly inaccurate, involving much estimation and using a static field estimation of 9.39*10^8 N\C and a charge estimate on the particles of ~1e, a maximum oscillation distance of 1.37m was calculated. Though the derived static field strength was not far off from the field strength required to achieve the correct oscillation distance (Percent error of 9.92%, the small discrepancy caused major calculation errors. The trap's intended purpose however was to eventually trap protein molecules for mapping via XFEL laser, and after its successful construction that goal is fairly achievable. The trap was also housed in a vacuum chamber so that it could be more effectively implemented with the XFEL.
Date Created
2019-05
Agent

Ion Traps for Single Particle Imaging

Description
X-ray Free Electron Lasers (XFELs) are used for diffractive x-ray imaging of the structure of many biological particles, such as viruses and proteins. The ultimate goal for XFEL-based microscopy is atomic resolution images of non-crystalline particles. However, data collection efficiency

X-ray Free Electron Lasers (XFELs) are used for diffractive x-ray imaging of the structure of many biological particles, such as viruses and proteins. The ultimate goal for XFEL-based microscopy is atomic resolution images of non-crystalline particles. However, data collection efficiency as well as the limited amount of measurement time given annually to researchers, such high-resolution images are presently impossible to attain. Here, we consider two potential solutions to the single-particle hit rate problem; the first looks at applying static electric fields to existing aerodynamic particle injectors, and the second looks at the viability of using time-varying electric fields associated with ion traps to create high-density regions of particles. For the static solution, we looked at applying a constant electric potential to the nozzle, as well as applying a high voltage to a ring electrode in close proximity to a grounded nozzle. We considered the breakdown field strength of the helium gas used to determine how closely the ring electrode could be placed without creating an arc that could potentially destroy expensive equipment. Then, we considered the possibility of using electrodynamic ion traps to increase particle densities. We first characterized how charged particles behave in oscillating electric fields using a simple electrode geometry. Using the general results from this, we then constructed a rudimentary ion trap to test if our experiment agreed with the theory. Finally, we conducted a literature review to determine what particle densities other scientists have been able to measure using ion traps. We then compared existing ion traps to what we expect from the nozzle injectors to determine which method may be the better solution.
Date Created
2017-05
Agent

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

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Description
Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.
Date Created
2017-06-27
Agent

Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1

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Description
CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of

CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli. The first variant contained a flexible GPGP linker between CTB and MPR, and yielded crystals that diffracted to a resolution of 2.3 Å, but only the CTB region was detected in the electron-density map. A second variant, in which the CTB was directly attached to MPR, was shown to destabilize pentamer formation. A third construct containing a polyalanine linker between CTB and MPR proved to stabilize the pentameric form of the protein during purification. The purification procedure was shown to produce a homogeneously pure and monodisperse sample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered in the third dimension. Nanocrystals obtained using the same precipitant showed promising X-ray diffraction to 5 Å resolution in femtosecond nanocrystallography experiments at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The results demonstrate the utility of femtosecond X-ray crystallography to enable structural analysis based on nano/microcrystals of a protein for which no macroscopic crystals ordered in three dimensions have been observed before.
Date Created
2014-08-20
Agent

Experimental Strategies for Imaging Bioparticles With Femtosecond Hard X-Ray Pulses

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Description

This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles

This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of ∼40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from ∼35 to ∼300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 × 1012 photons per µm2 per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.

Date Created
2017-04-07
Agent

Open Data Set of Live Cyanobacterial Cells Imaged Using an X-Ray Laser

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Description

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

Date Created
2016-08-01
Agent