Forschungsdatensätze der BAM
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This dataset contains the processed and analysed small-angle X-ray scattering data associated with all samples from the publications "Bio-SAXS of Single-Stranded DNA-Binding Proteins: Radiation Protection by the Compatible Solute Ectoine" (https://doi.org/10.1039/D2CP05053F).
Files associated with McSAS3 analyses are included, alongside the relevant SAXS data, with datasets labelled in accordance to the protein (G5P), its concentration (1, 2 or 4 mg/mL), and if Ectoine is present (Ect) or absent (Pure). PEPSIsaxs simulations of the GVP monomer (PDB structure: 1GV5 ) and dimer are also included.
TOPAS-bioSAXS-dosimetry extension for TOPAS-nBio based particle scattering simulations can be obtained from https://github.com/MarcBHahn/TOPAS-bioSAXS-dosimetry which is further described in https://doi.org/10.26272/opus4-55751.
This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under grant number 442240902 (HA 8528/2-1 and SE 2999/2-1). We acknowledge Diamond Light Source for time on Beamline B21 under Proposal SM29806. This work has been supported by iNEXT-Discovery, grant number 871037, funded by the Horizon 2020 program of the European Commission.
Models for TOPAS/Geant4 to estimate the microscopic dose received by biomolecules during bioSAXS experiments.
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).
To simulate the movement of the macroscopic magnetic moment in ferromagnetic systems under the influence of elevated temperatures, the stochastic version of the Landau-Lifshitz (LL) or the Landau-Lifshitz-Gilbert equation with a spin density of one per unit cell has to be used.
To apply the stochastic LL to micromagnetic simulations, where the spin density per unit cell is generally higher, a conversion has to be performed. OOMMF sample files MIF) are provided which can be used to determine the Curie temperature for the classical bulk magnets, iron, nickel and cobalt.
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 "