Perspectives of Imaging of Single Protein Molecules with the Present Design of the European XFEL. - Part I - X-ray Source, Beamlime Optics and Instrument Simulations

The Single Particles, Clusters and Biomolecules (SPB) instrument at the European XFEL is located behind the SASE1 undulator, and aims to support imaging and structure determination of biological specimen between about 0.1 micrometer and 1 micrometer size. The instrument is designed to work at photon energies from 3 keV up to 16 keV. This wide operation range is a cause for challenges to the focusing optics. In particular, a long propagation distance of about 900 m between x-ray source and sample leads to a large lateral photon beam size at the optics. The beam divergence is the most important parameter for the optical system, and is largest for the lowest photon energies and for the shortest pulse duration (corresponding to the lowest charge). Due to the large divergence of nominal X-ray pulses with duration shorter than 10 fs, one suffers diffraction from mirror aperture, leading to a 100-fold decrease in fluence at photon energies around 4 keV, which are ideal for imaging of single biomolecules. The nominal SASE1 output power is about 50 GW. This is very far from the level required for single biomolecule imaging, even assuming perfect beamline and focusing efficiency. Here we demonstrate that the parameters of the accelerator complex and of the SASE1 undulator offer an opportunity to optimize the SPB beamline for single biomolecule imaging with minimal additional costs and time. Start to end simulations from the electron injector at the beginning of the accelerator complex up to the generation of diffraction data indicate that one can achieve diffraction without diffraction with about 0.5 photons per Shannon pixel at near-atomic resolution with 1e13 photons in a 4 fs pulse at 4 keV photon energy and in a 100 nm focus, corresponding to a fluence of 1e23 ph/cm^2. This result is exemplified using the RNA Pol II molecule as a case study

MicroED data collection and processing.

MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges

Angle-multiplexed metasurfaces: encoding independent wavefronts in a single metasurface under different illumination angles

The angular response of thin diffractive optical elements is highly correlated. For example, the angles of incidence and diffraction of a grating are locked through the grating momentum determined by the grating period. Other diffractive devices, including conventional metasurfaces, have a similar angular behavior due to the fixed locations of the Fresnel zone boundaries and the weak angular sensitivity of the meta-atoms. To alter this fundamental property, we introduce angle-multiplexed metasurfaces, composed of reflective high-contrast dielectric U-shaped meta-atoms, whose response under illumination from different angles can be controlled independently. This enables flat optical devices that impose different and independent optical transformations when illuminated from different directions, a capability not previously available in diffractive optics

Real-space study of the growth of magnesium on ruthenium

The growth of magnesium on ruthenium has been studied by low-energy electron microscopy (LEEM) and scanning tunneling microscopy (STM). In LEEM, a layer-by-layer growth is observed except in the first monolayer, where the completion of the first layer in inferred by a clear peak in electron reflectivity. Desorption from the films is readily observable at 400 K. Real-space STM and low-energy electron diffraction confirm that sub-monolayer coverage presents a moir\'e pattern with a 1.2 nm periodicity, which evolves with further Mg deposition by compressing the Mg layer to a 2.2 nm periodicity. Layer-by-layer growth is followed in LEEM up to 10 ML. On films several ML thick a substantial density of stacking faults are observed by dark-field imaging on large terraces of the substrate, while screw dislocations appear in the stepped areas. The latter are suggested to result from the mismatch in heights of the Mg and Ru steps. Quantum size effect oscillations in the reflected LEEM intensity are observed as a function of thickness, indicating an abrupt Mg/Ru interface.Comment: 21 pages, 10 figure

X-ray Raman scattering study of aligned polyfluorene

We present a non-resonant inelastic x-ray scattering study at the carbon K-edge on aligned poly[9,9-bis(2-ethylhexyl)-fluorene-2,7-diyl] and show that the x-ray Raman scattering technique can be used as a practical alternative to x-ray absorption measurements. We demonstrate that this novel method can be applied to studies on aligned $\pi$-conjugated polymers complementing diffraction and optical studies. Combining the experimental data and a very recently proposed theoretical scheme we demonstrate a unique property of x-ray Raman scattering by performing the symmetry decomposition on the density of unoccupied electronic states into $s$- and $p$-type symmetry contributions.Comment: 19 pages, 8 figure

A laboratory based system for Laue micro x-ray diffraction

A laboratory diffraction system capable of illuminating individual grains in a polycrystalline matrix is described. Using a microfocus x-ray source equipped with a tungsten anode and prefigured monocapillary optic, a micro-x-ray diffraction system with a 10 mum beam was developed. The beam profile generated by the ellipsoidal capillary was determined using the"knife edge" approach. Measurement of the capillary performance, indicated a beam divergence of 14 mrad and a useable energy bandpass from 5.5 to 19 keV. Utilizing the polychromatic nature of the incident x-ray beam and application of the Laue indexing software package X-Ray Micro-Diffraction Analysis Software, the orientation and deviatoric strain of single grains in a polycrystalline material can be studied. To highlight the system potential the grain orientation and strain distribution of individual grains in a polycrystalline magnesium alloy (Mg 0.2 wt percent Nd) was mapped before and after tensile loading. A basal (0002) orientation was identified in the as-rolled annealed alloy; after tensile loading some grains were observed to undergo an orientation change of 30 degrees with respect to (0002). The applied uniaxial load was measured as an increase in the deviatoric tensile strain parallel to the load axis (37 References)