TY - GEN A1 - Hahn, Marc Benjamin T1 - TOPAS cell model with nanoparticles N2 - These files contain cell models for TOPAS/Geant4 and the inclusion of nano particles in particle scattering simulations. A simple spherical cell with nanoparticles can be generated in a fast manner. The user has the option to include the following organelles: nucleus, mitochondria, cell membrane. Additionally nanoparticles can be included in the cytosol and at the surface of the nucleus and/or the mitochondria. The C++ classes in this repository extend the functionality of the TOPAS (http://www.topasmc.org/) Monte-Carlo program, which is itself a wrapper of the Geant4 MCS Toolkit (http://geant4.org). The sourcecode together with examples and scorers are provided. "If you use this extension please cite the following literature: Hahn, M.B., Zutta Villate, J.M. "Combined cell and nanoparticle models for TOPAS to study radiation dose enhancement in cell organelles." Sci Rep 11, 6721 (2021). https://doi.org/10.1038/s41598-021-85964-2 " KW - Monte-Carlo simulation KW - MCS KW - Geant4 KW - TOPAS KW - TOPAS-nBio KW - Dosimetry KW - Nanoparticles KW - Nanoparticle KW - AuNP KW - Gold KW - Microdosimetry KW - Targeted nanoparticle KW - Simulation KW - Particle scattering KW - Cell KW - Nucleus KW - Mitochondria KW - Cancer therapy KW - Radiation therapy PY - 2020 UR - https://github.com/BAMresearch/TOPAS-CellModels UR - https://github.com/MarcBHahn/TOPAS-CellModels DO - https://doi.org/10.26272/opus4-51150 PB - Bundesanstalt für Materialforschung und -prüfung (BAM) CY - Berlin AN - OPUS4-51150 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Winkelmann, A. A1 - Britton, T. B. A1 - Nolze, Gert T1 - EBSD Kikuchi Pattern Analysis, Silicon 15kV N2 - Supplementary data and images for Si EBSD pattern analysis as presented in: A. Winkelmann, T.B. Britton, G. Nolze "Constraints on the effective electron energy spectrum in backscatter Kikuchi diffraction", Physical Review B (2019). KW - EBSD KW - Electron energy KW - Energy distribution KW - Kikuchi pattern KW - Simulation PY - 2019 DO - https://doi.org/10.5281/zenodo.2565061 PB - Zenodo CY - Geneva AN - OPUS4-51907 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Pauw, Brian Richard A1 - Laskina, Sofya A1 - Naik, Aakash Ashok A1 - Smales, Glen Jacob A1 - George, Janine A1 - Breßler, Ingo A1 - Benner, Philipp T1 - Jupyter notebook and VASP calculation details accompanying the manuscript: "Ultima Ratio: Simulating wide-range X-ray scattering and diffraction" N2 - ## Summary: This notebook and associated datasets (including VASP details) accompany a manuscript available on the ArXiv (https://doi.org/10.48550/arXiv.2303.13435) and hopefully soon in a journal as short communication as well. Most of the details needed to understand this notebook are explained in that paper with the same title as above. For convenience, the abstract is repeated here: ## Paper abstract: We demonstrate a strategy for simulating wide-range X-ray scattering patterns, which spans the small- and wide scattering angles as well as the scattering angles typically used for Pair Distribution Function (PDF) analysis. Such simulated patterns can be used to test holistic analysis models, and, since the diffraction intensity is presented coupled to the scattering intensity, may offer a novel pathway for determining the degree of crystallinity. The ``Ultima Ratio'' strategy is demonstrated on a 64-nm Metal Organic Framework (MOF) particle, calculated from $Q<0.01$\,$\mathrm{nm}^{-1}$ up to $Q\approx150$\,$\mathrm{nm}^{-1}$, with a resolution of 0.16\,\AA. The computations exploit a modified 3D Fast Fourier Transform (3D-FFT), whose modifications enable the transformations of matrices at least up to $8000^3$ voxels in size. Multiple of these modified 3D-FFTs are combined to improve the low-$Q$ behaviour. The resulting curve is compared to a wide-range scattering pattern measured on a polydisperse MOF powder. While computationally intensive, the approach is expected to be useful for simulating scattering from a wide range of realistic, complex structures, from (poly-)crystalline particles to hierarchical, multicomponent structures such as viruses and catalysts. KW - X-ray KW - Simulation KW - Scattering KW - MOUSE KW - Nanomaterials KW - XRD KW - SAXS KW - PDF KW - total scattering KW - 3D Fourier Transform KW - High Resolution KW - FFT PY - 2023 UR - https://doi.org/10.48550/arXiv.2303.13435 DO - https://doi.org/10.5281/zenodo.7764044 PB - Zenodo CY - Geneva AN - OPUS4-57207 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -