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An Office of Science User Facility

Coherent X-ray Imaging  (CXI)

Overview

Full Name

Coherent X-ray Imaging Instrument

Short Description

The Coherent X-Ray Imaging (CXI) instrument (Boutet et al New Journal of Physics (2010)) makes use of the unique brilliant hard X-ray pulses from LCLS to perform a wide variety of experiments utilizing various techniques. The primary capability of CXI is to make use of the high peak power of the focused x-ray beam using the “diffraction-before-destruction” method. This technique prevents damage to a sample during the measurement by performing the measurement faster than the damage or destruction process with ultrashort pulses. This is particular advantageous for biological samples that suffer from electronic and structural damage during long continuous exposures to x-rays. While designed originally to image single sub-micron particles using Coherent Diffractive Imaging (CXI) techniques, the CXI instrument consists of a highly flexible instrumentation suite to make use of hard x-rays primarily in a vacuum sample environment. It is available for Serial Femtosecond Crystallography (SFX) measurements capable of determining the structure of biomolecules using nanocrystals. It is also suitable for any forward scattering experiment requiring or benefiting from a vacuum sample environment. A variety of tools and devices have been developed that allow CXI to make use of other techniques such as X-ray Emission Spectroscopy, back-scattering, small and wide angle scattering, ion and electron time of flight spectroscopy. A flexible pump laser system is available for time-resolved experiments in the femtosecond time scale. CXI is available for any scientific field requiring use of the LCLS beam, including structural biology, material science, materials in extreme conditions, atomic molecular and optical physics, chemistry, soft condensed matter and high field x-ray science. Samples can be introduced to the x-ray beam either fixed on targets or using a particle injector that can deliver free-standing particles or samples in a liquid jet to the beam. Experiments at atmospheric pressure are possible under certain limited circumstances. High quality focusing optics are available to generate three foci (10, 1 and 0.1 micron). The CXI instrument operates primarily in the 5-11 keV range with capabilities for operation under reduced performance above 11 keV with use of the harmonics of the beam.

X-ray diffraction has long been used to determine atomic structures of biomolecules. The X-ray dose needed to achieve a given resolution for a particular sample can be calculated. It can be shown that the dose required to image a single biological molecule is much larger than the dose required to completely destroy the molecule through radiation damage processes. X-ray crystallographers mitigate this problem by spreading the damage over billions of molecules in a single crystal, greatly enhancing the diffraction signal. Since the molecules are all identical and precisely aligned in the crystal, the X-ray scattering information is preserved and the structure can be determined.

LCLS offers another way around the damage problem. Since the FEL X-ray pulse is very intense and very short, it is possible in principle to deliver the required dose to a nano-scale sample and record the scattered X-ray information before the damage processes have time to destroy the sample. In other words, an LCLS X-ray pulse can be focused onto a single molecule, which gets be destroyed – but not before the scattered X-rays are already on their way to the detector carrying the information needed to deduce the image. The Coherent X-ray Imaging (CXI) Instrument offers the possibility of determining structures at resolution beyond the damage limit for samples which do not form large crystals, including important classes of biological macromolecules.

CXI aims to provide a flexible suite of instrumentation for “diffract-before-destroy” studies in structural biology, but also suite for other techniques, such as laser pump/x-ray probe methods and a variety of scattering and spectroscopy techniques. Scientific fields such as material science, materials in extreme conditions, atomic molecular and optical physics, chemistry, soft condensed matter and high field x-ray science have found and will find applications at CXI.

Scientific Programs

Coherent Diffractive Imaging of reproducible biomolecules
Only a two-dimensional diffraction pattern can be collected from a single biomolecule before it is destroyed by the LCLS beam. Such a two-dimensional pattern encodes information about a projection image of the object onto a plane parallel to the detector. Three-dimensional structural information about highly-reproducible molecules such as viruses, large proteins or molecular complexes can be derived if a series of the molecules is delivered into the LCLS beam one after the other. Each molecule would have a different orientation and a full 3D diffraction data set can be obtained from a large number of identical copies of the sample. In theory, it could be possible to obtain high resolution structures for difficult to crystallize biomolecules. Research and development is required to demonstrate this capability.

Serial Femtosecond Nanocrystallography
It is often the case that large crystals of a certain protein cannot be grown but a large number of very small crystals can readily be obtained. These sub-micron crystals do not scatter enough X-rays to yield an atomic structure using conventional protein crystallography techniques. The high flux of LCLS could allow these to be used for structure determination. This high flux also has the advantage of allowing in principle damage-free higher resolution of radiation-sensitive samples such as metalloenzymes for example. Assuming all the nanocrystals possess the same crystal symmetry, a series of nanocrystals can be illuminated by LCLS X-ray pulses and the diffraction patterns recorded. The variations in alignment of the crystal axes from sample to sample can be determined from indexing the Bragg peaks in the diffraction patterns. A full 3D set similar to conventional protein crystallography can be assembled from many small crystals and yield the protein structure. The nanocrystals can be delivered into the CXI beam using a liquid jet (Weierstall et all, Rev. Sci. Instrum. (2010)), LCP jet (Weirstall et al, Nature Communications (2014)), an electrospinning jet (Sierra et al, Acta Cryst D (2012)) or mounted to a suitable substrate in vacuum (Frank et al, IUCrJ (2014)). The liquid jet options provides high data rate while the substrate mounting and LCP jet can help minimize sample consumption.

Imaging of nanoparticles
LCLS makes it possible to obtain two-dimensional projections of any non-reproducible nanoparticle and three-dimensional images of reproducible objects using the diffract-the-destroy technique. Furthermore, the CXI beam can be attenuated to a level slightly below the damage threshold of an inorganic nanoparticle and a full 3D reconstruction can in principle be obtained from a single particle using multi-image tomographic techniques. The transverse coherence length of the CXI beam can allow small particles to be imaged in 3D at high resolution.

X-ray-matter interactions
The LCLS source produces hard X-ray fields of unprecedented high intensity. It allows for the first time tests of radiation damage models under such extreme conditions as well as tests of fundamental x-ray physics under extreme fields. These models are directly relevant to atomic-resolution imaging since the damage suffered during a pulse must be limited or the image reconstruction will suffer. The interaction of the powerful LCLS pulses with solid matter can be studied using the CXI instrument under unique extreme conditions using high-quality focusing optics.

Pump-probe imaging/crystallography
It is possible, with the use of an optical pump laser, to obtain dynamic information of photo-induced changes in non-crystalline and crystalline samples with sub-picosecond time resolution. A flexible pump laser system (nanosecond and femtosecond lasers) is provided at the CXI instrument to allow a wide range of dynamics studies.

Matter in Extreme Conditions
The ultrashort pulses of LCLS open new possibilities to study short lived states of matter in extreme conditions. These extreme or transient states can be created with a pump laser and then probed with high time resolution with LCLS pulses using diffraction (Milathianaki et al, Science (2013)), scattering or in principle emission techniques.

Atomic, Molecular and Optical Science
The CXI instrument is primarily an in-vacuum high peak power instrument using hard x-rays. This makes CXI the ideal home for AMO science that requires the use of x-rays above 4-5 keV. Time-of-flight spectrometers and photon detectors can be added to the CXI sample chambers to allow AMO studies.


Examples of experimental geometries and techniques at CXI

Serial Femtosecond Crystallography (SFX)

Using a Lipidic Cubic Phase Jet

Wei Liu et al "Serial Femtosecond Crystallography of G Protein–Coupled Receptors" Science 342 1521 (2013)

Using a Gas Dynamic Virtual Nozzle

Sébastien Boutet et al "High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography" Science 337 (6092) 362 (2012)

Lars Redecke et al "Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser" Science 339 6116 (2012)

Using an Electrostatic Jet

Raymond G. Sierra et al "Nanoflow electrospinning serial femtosecond crystallography " Acta Cryst D68 1584-1587 (2012)

Emmission Spectroscopy Simultaneously with SFX

Jan Kern et al "Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature" Science (2013)

Experimental Phasing of SFX Data

Thomas R. M. Barends et al "De novo protein crystal structure determination from X-ray free-electron laser data" Nature 0 (2013) doi: 10.1038/nature12773


2D Crystallography

Matthias Frank et al "Femtosecond X-ray diffraction from two-dimensional protein crystals" IUCrJ (2014)

Shock Dynamics

D. Milathianaki et al "Femtosecond Visualization of Lattice Dynamics in Shock-Compressed Matter" Science 342 6155 (2013) ​​

SLAC SLAC National Accelerator Laboratory, Menlo Park, CA
Operated by Stanford University for the U.S. Dept. of Energy