A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser
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The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.
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XMDYN is part of the start-to-end simulation package for biomolecular imaging at the European XFEL [114].
“XMDYN is part of the start-to-end simulation package for biomolecular imaging at the European XFEL [114].”
From Roadmap of ultrafast x-ray atomic and molecular physics (2018) · cites this paper as [114]
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Shen, Z., Teo, C., Ayyer, K., & Loh, N. D. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2007.03054 · Cited by 1 · see citing works
Self-citationPetrova, T. E., & Lunin, V. Y. (2020) · Mathematical Biology and Bioinformatics · doi:10.17537/2020.15.t52
Single particle imaging of biological specimens
Cheng, G., & Yu, J. (2024) · Conference on Frontiers in Optical Imaging Technology and Applications · doi:10.1117/12.3017901
- Authors
- Yoon, C. H., Yurkov, M. V., Schneidmiller, E. A., Samoylova, L., Buzmakov, A., Jurek, Z., Ziaja, B., Santra, R., Loh, N. D., Tschentscher, T., & Mancuso, A. P.
- Affiliations
- Deutsches Elektronen-Synchrotron DESY (DE)
- European X-Ray Free-Electron Laser (DE)
- Russian Academy of Sciences (RU)
- Universität Hamburg (DE)
- National University of Singapore (SG)
- Corresponding author
- Yoon, Chun Hong
- ORCID
- Venue
- Scientific Reports
- Published
- 2016-04-25
- Volume
- 6
- Issue
- 1
- Pages
- 24791-24791
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC4842992
- OpenAlex
- W2344801351
- Cited by
- 51
- References
- 45
- Citations by year
- 2025: 1 · 2024: 7 · 2023: 3 · 2022: 7 · 2021: 7 · 2020: 6 · 2019: 3 · 2018: 6 · 2017: 7 · 2016: 4
- FWCI
- 7.46
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Reports (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Desy Publications Database (Deutsches Elektronen-Synchrotron DESY) (submittedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- European XFEL (submittedVersion, cc-by)
- National University of Singapore (submittedVersion, cc-by)
- DESY Publication Database (PUBDB) (Deutsches Elektronen-Synchrotron)
- Topics
- Physical Sciences › Physics and Astronomy › Radiation › Advanced X-ray Imaging Techniques
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Engineering › Electrical and Electronic Engineering › Particle Accelerators and Free-Electron Lasers
- Keywords
- X-ray free-electron laser, single-particle imaging, incoherent scattering, phase retrieval, nitrogenase iron protein, experimental design, coherent X-ray imaging
- MeSH terms
- Computer Simulation, Electrons, Lasers, Models, Theoretical, Oxidoreductases, Protein Conformation, X-Ray Diffraction, Photons, Crystallography, X-Ray, Imaging, Three-Dimensional
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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