abstract: The superior brightness and ultra short pulse duration of X-ray free electron laser (XFEL) allows it to outrun radiation damage in coherent diffractive imaging since elastic scattering terminates before photoelectron cascades commences. This “diffract-before-destroy” feature of XFEL opened up new opportunities for biological macromolecule imaging and structure studies by breaking the limit to spatial resolution imposed by the maximum dose that is allowed before radiation damage. However, data collection in serial femto-second crystallography (SFX) using XFEL is affected by a bunch of stochastic factors, which pose great challenges to the data analysis in SFX. These stochastic factors include crystal size, shape, random orientation, X-ray photon flux, position and energy spectrum. Monte-Carlo integration proves effective and successful in extracting the structure factors by merging all diffraction patterns given that the data set is sufficiently large to average out all stochastic factors. However, this approach typically requires hundreds of thousands of patterns collected from experiments. This dissertation explores both experimental and algorithmic methods to eliminate or reduce the effect of stochastic factors in data acquisition and analysis. Coherent convergent X-ray beam diffraction (CCB) is discussed for possibilities of obtaining single-shot angular-integrated rocking curves. It is also shown the interference between Bragg disks helps ab-initio phasing. Two-color diffraction scheme is proposed for time-resolved studies and general data collection strategies are discussed based on error metrics. A new auto-indexing algorithm for sparse patterns is developed and demonstrated for both simulated and experimental data. Statistics show that indexing rate is increased by 3 times for I3C data set collected from beam time LJ69 at Linac coherent light source (LCLS). Finally, dynamical inversion from electron diffraction is explored as an alternative approach for structure determination. / Dissertation/Thesis / Doctoral Dissertation Physics 2016

abstract: X-ray free electron lasers (XFELs) provide several orders of magnitude brighter x-rays than 3rd generation sources. However, the electron beamlines and undulator magnets required are on the scale of kilometers, costing billions of dollars with only a half dozen or so currently operating worldwide. One way to overcome these limitations is to prebunch the electron beam on the scale of the x-ray wavelength. In this paper one such scheme is discussed, which uses a nanopatterned grating called a dynamical beam stop. This uses diffraction from crystal planes of the etched portion of a grating to impart a transverse modulation which becomes a temporal modulation via an emittance exchange (EEX). To expand upon this topic, dynamical electron diffraction intensities for a 200 nm thick Si(001) unpatterned membrane are simulated via the multislice method and compared to experiment for various crystallographic orientations at MeV energies. From this as well as an analysis of the experimental inelastic plasmon diffuse scattering, it is determined that the optimal transverse modulation would be formed from a bright field image of the beam stop, with the nanopattern being etched all the way through the membrane. A model quantifying the quality of the modulation - the bunching factor - as a function of contrast and duty factor is formulated and the optimal modulation is determined analytically. A prototype beam stop is then imaged in a transmission electron microscope (TEM) at 200 KeV, with the measured bunching factor of 0.5 agreeing with the model and approaching a saturated XFEL. Using the angular spectrum method, it is determined that the spatial coherence of the MeV energy electron beam is insufficient for significant self-imaging to occur for gratings with pitches of hundreds of nanometers. Finally, the first-order EEX input requirements for the electron beam are examined in the transverse dimension as are newly proposed longitudinal requirements to compensate for lingering correlations between the initial and final longitudinal phase spaces. / Dissertation/Thesis / Doctoral Dissertation Physics 2020

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第22239号 / 理博第4553号 / 新制||理||1654(附属図書館) / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)准教授 松田 和博, 教授 田中 耕一郎, 教授 佐々 真一 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

abstract: 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. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2019

abstract: Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) has enabled the determination of damage-free protein structures at ambient temperatures and of reaction intermediate species with time resolution on the order of hundreds of femtoseconds. However, currently available XFEL facility X-ray pulse structures waste the majority of continuously injected crystal sample, requiring a large quantity (up to grams) of crystal sample to solve a protein structure. Furthermore, mix-and-inject serial crystallography (MISC) at XFEL facilities requires fast mixing for short (millisecond) reaction time points (𝑡"), and current sample delivery methods have complex fabrication and assembly requirements. To reduce sample consumption during SFX, a 3D printed T-junction for generating segmented aqueous-in-oil droplets was developed. The device surface properties were characterized both with and without a surface coating for improved droplet generation stability. Additionally, the droplet generation frequency was characterized. The 3D printed device interfaced with gas dynamic virtual nozzles (GDVNs) at the Linac Coherent Light Source (LCLS), and a relationship between the aqueous phase volume and the resulting crystal hit rate was developed. Furthermore, at the European XFEL (EuXFEL) a similar quantity and quality of diffraction data was collected for segmented sample delivery using ~60% less sample volume than continuous injection, and a structure of 3-deoxy-D-manno- octulosonate 8-phosphate synthase (KDO8PS) delivered by segmented injection was solved that revealed new structural details to a resolution of 2.8 Å. For MISC, a 3D printed hydrodynamic focusing mixer for fast mixing by diffusion was developed to automate device fabrication and simplify device assembly. The mixer was characterized with numerical models and fluorescence microscopy. A variety of devices were developed to reach reaction intermediate time points, 𝑡", on the order of 100 – 103 ms. These devices include 3D printed mixers coupled to glass or 3D printed GDVNs and two designs of mixers with GDVNs integrated into the one device. A 3D printed mixer coupled to a glass GDVN was utilized at LCLS to study the oxidation of cytochrome c oxidase (CcO), and a structure of the CcO Pr intermediate was determined at 𝑡" = 8 s. / Dissertation/Thesis / Supplementary Video D.1 - Droplet formation in a 3D printed droplet generator / Doctoral Dissertation Chemistry 2019

京都大学 / 0048 / 新制・課程博士 / 博士(エネルギー科学) / 甲第18611号 / エネ博第307号 / 新制||エネ||63(附属図書館) / 31511 / 京都大学大学院エネルギー科学研究科エネルギー応用科学専攻 / (主査)教授 大垣 英明, 教授 白井 康之, 教授 松田 一成 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(エネルギー科学) / 甲第21472号 / エネ博第377号 / 新制||エネ||74(附属図書館) / 京都大学大学院エネルギー科学研究科エネルギー変換科学専攻 / (主査)准教授 増田 開, 教授 長﨑 百伸, 教授 大垣 英明 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20071号 / 医博第4164号 / 新制||医||1018(附属図書館) / 33187 / 京都大学大学院医学研究科医学専攻 / (主査)教授 黒田 知宏, 教授 松田 文彦, 教授 楠見 明弘 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

We have built a spectrometer to investigate the Near-Infrared (NIR) range of this radiation, which is used for bunch diagnostics at the European X-ray Free-Electron Laser. This could give information on the development of microbunching, periodic features in the longitudinal charge profile of the bunches which have a negative impact on the operation of the facility. In general it offers an ability to investigate the influences of the laser heater, the compression, and other factors that affect the structure of the bunches. The CDR is generated 1934 m after the injector, at full acceleration. The spectrometer is based around the KALYPSO detector system, able to read out from a 256 pixel linear array detector at MHz frequencies, making it possible to obtain single bunch readings during current user operation of the facility, at 1.1 MHz. KALYPSO has an InGaAs sensor, sensitive in the range 0.9 – 1.7 μm. A 40 mm N-SF11 equilateral prism is used for dispersion. First measurements have been taken, and CDR has been detected. The spectrometer needs further calibration and resolution was lacking, but it can offer insight in to relative changes, and bunch-to and can be used as for fingerprinting the beam. A reduction in signal in the sensitive range and a skew towards longer wavelengths was seen when going from uncompressed to compressed beam. When varying the power of the laser heater the behavior varied from run to run, with changing machine settings. In some cases the CDR was attenuated, while FEL intensity initially increased, until the induced energy spread from the laser heater was large enough to inhibit the FEL process. Another, less expected, behaviour was also observed, where the initially low CDR intensity at first increased, while FEL intensity stayed the same, before it then followed the same pattern as in the first case.

<p>Radiation damage limits the resolution in imaging experiments. Damage is caused by energy deposited into the sample during exposure. Ultrashort and extremely bright X-ray pulses from free-electron lasers (FELs) offer the possibility to outrun key damage processes, and temporarily improve radiation tolerance. Theoretical models indicate that high detail-resolutions could be realized on non-crystalline samples with very short pulses, before plasma expansion.</p><p>Studies presented here describe the interaction of a very intense and ultrashort X-ray pulse with material, and investigate boundary conditions for flash diffractive imaging both theoretically and experimentally. In the hard X-ray regime, predictions are based on particle simulations with a continuum formulation that accounts for screening from free electrons.</p><p>First experimental results from the first soft X-ray free-electron laser, the FLASH facility in Hamburg, confirm the principle of flash imaging, and provide the first validation of our theoretical models. Specifically, experiments on nano-fabricated test objects show that an interpretable image can be obtained to high resolution before the sample is vaporized. Radiation intensity in these experiments reached 10^14 W/cm^2, and the temperature of the sample rose to 60000 Kelvin after the 25 femtosecond pulse left the sample. Further experiments with time-delay X-ray holography follow the explosion dynamics over some picoseconds after illumination.</p><p>Finally, this thesis presents results from biological flash-imaging studies on living cells. The model is based on plasma calculations and fluid-like motions of the sample, supported by the time-delay measurements. This study provides an estimate for the achievable resolutions as function of wavelength and pulse length. The technique was demonstrated by our team in an experiment where living cells were exposed to a single shot from the FLASH soft X-ray laser.</p>