Richard A. Kirian

Arizona State University

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Co-Authors

Henry N. Chapman

Universität Hamburg

109

Anton Barty

Deutsches Elektronen-Synchrotron DESY

Petra Fromme

Arizona State University

Mark S. Hunter

SLAC National Accelerator Laboratory

Uwe Weierstall

Arizona State University

Andrew Aquila

Linac Coherent Light Source

John C. H. Spence

Arizona State University

Filipe R. N. C. Maia

Lawrence Berkeley National Laboratory

Thomas A. White

Deutsches Elektronen-Synchrotron DESY

M. Seibert

Uppsala University

Cooperative Institutions

SLAC National Accelerator Laboratory

246

Universität Hamburg

187

Deutsches Elektronen-Synchrotron DESY

179

Arizona State University

170

Center for Free-Electron Laser Science

154

Stanford University

128

Linac Coherent Light Source

120

European X-Ray Free-Electron Laser

118

Menlo School

113

Lawrence Berkeley National Laboratory

107

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Research Field

Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data

Journal of Applied Crystallography (2014)

Anton Barty Richard A. Kirian Filipe R. N. C. Maia Max F. Hantke Chun Hong Yoon

The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.

Data Reduction

Software portability

10.1107/s1600576714007626

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Citations (388)

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

Scientific Data (2016)

Anna Munke Jakob Andreasson Andrew Aquila Salah Awel Kartik Ayyer

Abstract Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.

Coherent diffraction imaging

10.1038/sdata.2016.64

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Citations (77)

A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy

Ultramicroscopy (2021)

Joe Chen K. E. Schmidt J. C. H. Spence Richard A. Kirian

10.1016/j.ultramic.2021.113234

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Citations (11)

3D diffractive imaging of nanoparticle ensembles using an x-ray laser

Optica (2020)

Kartik Ayyer P. Lourdu Xavier Johan Bielecki Zhou Shen Benedikt J. Daurer

Single particle imaging at x-ray free electron lasers (XFELs) has the potential to determine the structure and dynamics of single biomolecules at room temperature. Two major hurdles have prevented this potential from being reached, namely, the collection of sufficient high-quality diffraction patterns and robust computational purification to overcome structural heterogeneity. We report the breaking of both of these barriers using gold nanoparticle test samples, recording around 10 million diffraction patterns at the European XFEL and structurally and orientationally sorting the patterns to obtain better than 3-nm-resolution 3D reconstructions for each of four samples. With these new developments, integrating advancements in x-ray sources, fast-framing detectors, efficient sample delivery, and data analysis algorithms, we illuminate the path towards sub-nanometer biomolecular imaging. The methods developed here can also be extended to characterize ensembles that are inherently diverse to obtain their full structural landscape.

Biomolecule

10.1364/optica.410851

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Citations (59)

Megahertz single-particle imaging at the European XFEL

arXiv (Cornell University) (2019)

E. V. Sobolev С. Н. Золотарев Klaus Giewekemeyer Johan Bielecki Kenta Okamoto

The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL will soon provide 27,000 pulses per second, more than two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The obtained results pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

Repetition (rhetorical device)

Pulse repetition frequency

Particle (ecology)

10.48550/arxiv.1912.10796

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Citations (4)

An advanced workflow for single particle imaging with the limited data at an X-ray free-electron laser

arXiv (Cornell University) (2020)

Dameli Assalauova Young Yong Kim Sergey G. Bobkov Ruslan Khubbutdinov M. Franklin Rose

An improved analysis for single particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the AMO instrument at the Linac Coherent Light Source (LCLS) as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from the half of the detector and small fraction of single hits. General SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus structure determination step. The presented processing pipeline allowed us to determine the three-dimensional structure of the bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.

10.48550/arxiv.2006.08345

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Citations (0)

Optical Injector of Particles for X-ray Diffractive Imaging

Optics in the Life Sciences (2013)

Niko Eckerskorn Richard A. Kirian Jochen Küpper Daniel P. DePonte Wiesław Królikowski

We apply a high aspect-ratio first order Bessel beam, formed by imaging a vortex beam through an axicon, to guide biological macromolecules and viruses to the focus of femtosecond x-ray free-electron-laser for coherent diffractive imaging.

Axicon

Bessel beam

X-ray optics

Filamentation

10.1364/ota.2013.tm4d.3

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Citations (0)

Rapid sample delivery for megahertz serial crystallography at X-ray FELs

IUCrJ (2018)

Max O. Wiedorn Salah Awel Andrew J. Morgan Kartik Ayyer Y. Gevorkov

Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s −1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.

Sample (material)

10.1107/s2052252518008369

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Citations (58)

Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs

Research Square (Research Square) (2023)

Sebastian Westenhoff Patrick Konold Leonardo Monrroy Alfredo Bellisario Diogo de Matos Filipe

Abstract Detecting microsecond structural perturbations in biomolecules has wide relevance in biology, chemistry, and medicine. Here, we show how MHz repetition rates at X-ray free electron lasers (XFELs) can be used to produce microsecond time-series of protein scattering with exceptionally low noise levels of 0.001%. We demonstrate the approach by deriving new mechanistic insight into Jα helix unfolding of a Light-Oxygen-Voltage (LOV) photosensory domain. This time-resolved acquisition strategy is easy to implement and widely applicable for direct observation of structural dynamics of many biochemical processes.

Microsecond

Biomolecule

Repetition (rhetorical device)

10.21203/rs.3.rs-3638353/v1

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Citations (0)

Imaging of Objects by Coherent Diffraction of X-Ray FEL Pulses

Springer eBooks (2015)

Richard A. Kirian Henry N. Chapman

Coherent diffraction imaging

Free-electron laser

10.1007/978-3-319-04507-8_27-1

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Citations (0)