@article{MandlOestlinDawodetal.,
  author    = {Mandl, Thomas and {\"O}stlin, Christofer and Dawod, Ibrahim E. and Brodmerkel, Maxim N. and Marklund, Erik G. and Martin, Andrew V. and Timneanu, Nicusor and Caleman, Carl},
  title     = {Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers},
  series = {The Journal of Physical Chemistry Letters},
  volume    = {2020},
  journal   = {The Journal of Physical Chemistry Letters},
  number    = {Volume 11, Issue 15},
  pages     = {6077 -- 6083},
  abstract  = {One of the challenges facing single particle imaging with ultrafast X-ray pulses is the structural heterogeneity of the sample to be imaged. For the method to succeed with weakly scattering samples, the diffracted images from a large number of individual proteins need to be averaged. The more the individual proteins differ in structure, the lower the achievable resolution in the final reconstructed image. We use molecular dynamics to simulate two globular proteins in vacuum, fully desolvated as well as with two different solvation layers, at various temperatures. We calculate the diffraction patterns based on the simulations and evaluate the noise in the averaged patterns arising from the structural differences and the surrounding water. Our simulations show that the presence of a minimal water coverage with an average 3 {\AA} thickness will stabilize the protein, reducing the noise associated with structural heterogeneity, whereas additional water will generate more background noise.},
  subject      = {Protein structure},
  language  = {en}
}
@article{KierspelKadekBarranetal.,
  author    = {Kierspel, Thomas and Kadek, Alan and Barran, Perdita and Bellina, Bruno and Bijedic, Adi and Brodmerkel, Maxim N. and Commandeur, Jan and Caleman, Carl and Damjanovic, Tomislav and Dawod, Ibrahim and De Santis, Emiliano and Lekkas, Alexandros and Lorenzen, Kristina and L{\´o}pez Morillo, Luis and Mandl, Thomas and Marklund, Erik G. and Papanastasiou, Dimitris and Ramakers, Lennart A. I. and Schweikhard, Lutz and Simke, Florian and Sinelnikova, Anna and Smyrnakis, Athanasios and Timneanu, Nicusor and Uetrecht, Charlotte},
  title     = {Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC},
  series = {Analytical and Bioanalytical Chemistry},
  volume    = {2023},
  journal   = {Analytical and Bioanalytical Chemistry},
  number    = {415},
  doi       = {https://doi.org/10.1007/s00216-023-04658-y},
  pages     = {4209 -- 4220},
  abstract  = {MS SPIDOC is a novel sample delivery system designed for single (isolated) particle imaging at X-ray Free-Electron Lasers that is adaptable towards most large-scale facility beamlines. Biological samples can range from small proteins to MDa particles. Following nano-electrospray ionization, ionic samples can be m/z-filtered and structurally separated before being oriented at the interaction zone. Here, we present the simulation package developed alongside this prototype. The first part describes how the front-to-end ion trajectory simulations have been conducted. Highlighted is a quadrant lens; a simple but efficient device that steers the ion beam within the vicinity of the strong DC orientation field in the interaction zone to ensure spatial overlap with the X-rays. The second part focuses on protein orientation and discusses its potential with respect to diffractive imaging methods. Last, coherent diffractive imaging of prototypical T = 1 and T = 3 norovirus capsids is shown. We use realistic experimental parameters from the SPB/SFX instrument at the European XFEL to demonstrate that low- resolution diffractive imaging data (q < 0.3 nm -1 ) can be collected with only a few X-ray pulses. Such low-resolution data are sufficient to distinguish between both symmetries of the capsids, allowing to probe low abundant species in a beam if MS SPIDOC is used as sample delivery.},
  subject      = {SPI},
  language  = {en}
}