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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 "
pH and oxygen are amongst the most important and frequently measured analytes in the life and material sciences, indicating, e.g., diseases and corrosion processes. This includes the optical monitoring of pH in living cells for studying cellular internalization pathways, such as phagocytosis, endocytosis, and receptor ligand internalization with the aid of molecular and nanoscale fluorescent sensors. Nanoparticle (NP)-based sensors, that are labeled or stained with a multitude of sensor dyes, have several advantages as compare to conventional molecular probes like enhanced brightness, i.e., amplified signals, ease of designing ratiometric systems by combining analyte sensitive and inert reference dyes, and increased photostability. Moreover, this can enable the use of hydrophobic dyes in aqueous environments. Versatile templates and carriers for the fabrication of nanosensors by the staining and/or labelling with different fluorophores and sensor molecules or surface functionalized NP like silica (SiO2-NP) and polystyrene (PS-NP) particles provide. Here we present the design of a versatile platform of color emissive nanosensors and stimuli-responsive microparticles for the measurement of pH, oxygen, and other targets utilizing both types of matrices and sets of spectrally distinguishable sensor and reference dyes and their characterization and demonstrate the applicability of representative sensor particle for cellular studies.