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@ARTICLE{Leidl:1009126,
      author       = {Leidl, Max Leo and Sachse, Carsten and Müller-Caspary,
                      Knut},
      title        = {{D}ynamical scattering in ice-embedded proteins in
                      conventional and scanning transmission electron microscopy},
      journal      = {IUCrJ},
      volume       = {10},
      number       = {4},
      issn         = {2052-2525},
      address      = {Chester},
      reportid     = {FZJ-2023-02656},
      pages        = {475 - 486},
      year         = {2023},
      abstract     = {Structure determination of biological macromolecules using
                      cryogenic electron microscopy is based on applying the phase
                      object (PO) assumption and the weak phase object (WPO)
                      approximation to reconstruct the 3D potential density of the
                      molecule. To enhance the understanding of image formation of
                      protein complexes embedded in glass-like ice in a
                      transmission electron microscope, this study addresses
                      multiple scattering in tobacco mosaic virus (TMV) specimens.
                      This includes the propagation inside the molecule while also
                      accounting for the effect of structural noise. The atoms in
                      biological macromolecules are light but are distributed over
                      several nanometres. Commonly, PO and WPO approximations are
                      used in most simulations and reconstruction models.
                      Therefore, dynamical multislice simulations of TMV specimens
                      embedded in glass-like ice were performed based on fully
                      atomistic molecular-dynamics simulations. In the first part,
                      the impact of multiple scattering is studied using different
                      numbers of slices. In the second part, different sample
                      thicknesses of the ice-embedded TMV are considered in terms
                      of additional ice layers. It is found that single-slice
                      models yield full frequency transfer up to a resolution of
                      2.5 Å, followed by attenuation up to 1.4 Å. Three slices
                      are sufficient to reach an information transfer up to 1.0
                      Å. In the third part, ptychographic reconstructions based
                      on scanning transmission electron microscopy (STEM) and
                      single-slice models are compared with conventional TEM
                      simulations. The ptychographic reconstructions do not need
                      the deliberate introduction of aberrations, are capable of
                      post-acquisition aberration correction and promise benefits
                      for information transfer, especially at resolutions beyond
                      1.8 Å.Keywords: amorphous ice; cryogenic electron
                      microscopy; dynamical scattering; image simulations;
                      integrative structural biology; molecular dynamics.},
      cin          = {ER-C-3},
      ddc          = {530},
      cid          = {I:(DE-Juel1)ER-C-3-20170113},
      pnm          = {5352 - Understanding the Functionality of Soft Matter and
                      Biomolecular Systems (POF4-535) / moreSTEM -
                      Momentum-resolved Scanning Transmission Electron Microscopy
                      (VH-NG-1317) / 5241 - Molecular Information Processing in
                      Cellular Systems (POF4-524)},
      pid          = {G:(DE-HGF)POF4-5352 / G:(DE-HGF)VH-NG-1317 /
                      G:(DE-HGF)POF4-5241},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {37335769},
      UT           = {WOS:001028778800012},
      doi          = {10.1107/S2052252523004505},
      url          = {https://juser.fz-juelich.de/record/1009126},
}