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

TL;DR

This paper discusses the design and optimization of the European XFEL's SPB instrument for imaging single protein molecules, focusing on X-ray source, optics, and simulations to achieve near-atomic resolution.

Contribution

It demonstrates how to optimize the XFEL beamline parameters for single biomolecule imaging with minimal additional costs through end-to-end simulations.

Findings

Achieved diffraction with about 0.5 photons per Shannon pixel at 4 keV.

Generated 1e13 photons in a 4 fs pulse at 4 keV.

Focused beam of 100 nm diameter with a fluence of 1e23 ph/cm^2.

Abstract

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.