Attention
Attention
Citations
Main TOPAS-nBio publication
When using TOPAS-nBio, please be sure to cite the following paper (Featured on the Cover of Radiation Research)
Schuemann, J., McNamara, A. L., Ramos-Méndez, J., Perl, J., Held, K. D., Paganetti, H., Incerti, S., Faddegon, B. (2019). TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology. Radiation Research, 191(2), 125–138. PMID: 30609382. PMCID: PMC6377808. http://doi.org/10.1667/RR15226.1 , PubMed
Other relevant TOPAS-nBio publications
Underwood, T. S. A., Sung, W., McFadden, C. H., McMahon, S. J., Hall, D. C., McNamara, A. L., Paganetti H., Sawakuchi G. O., Schuemann J. (2017). Comparing stochastic proton interactions simulated using TOPAS-nBio to experimental data from fluorescent nuclear track detectors. Physics in Medicine and Biology, 62(8), 3237–3249. PMID: 28350546. http://doi.org/10.1088/1361-6560/aa6429
Ramos-Méndez, J., Schuemann, J., Incerti, S., Paganetti, H., Schulte, R., & Faddegon, B. (2017). Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations. Physics in Medicine and Biology, 62(15), 5908–5925. PMID: 28594336. PMCID: PMC5785278. http://doi.org/10.1088/1361-6560/aa7831
McNamara, A., Geng, C., Turner, R., Ramos-Méndez, J., Perl, J., Held, K., Faddegon B., Paganetti H., Schuemann J. (2017). Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries. Physica Medica, 33, 207–215. PMID: 28017738. PMCID: PMC529229. http://doi.org/10.1016/j.ejmp.2016.12.010
McNamara, A. L., Ramos-Méndez, J., Perl, J., Held, K., Dominguez, N., Moreno, E., Henthorn, N., Kirkby, K. J., Meylan, S., Villagrasa, C., Incerti, S., Faddegon, B., Paganetti, H., Schuemann, J. (2018). Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit. Physics in Medicine and Biology, 63(17), 175018. http://doi.org/10.1088/1361-6560/aad8eb
Ramos-Méndez, J., Perl, J., Schuemann, J., McNamara, A., Paganetti, H., & Faddegon, B. (2018). Monte Carlo simulation of chemistry following radiolysis with TOPAS-nBio. Physics in Medicine and Biology, 63(10), 105014. PMID: 29697057. PMCID: PMC6027650. http://doi.org/10.1088/1361-6560/aac04c
Ramos-Méndez, J., Burigo, L. N., Schulte, R., Chuang, C, & Faddegon, B. (2018). Fast calculation of nanodosimetric quantities in treatment planning of proton and ion therapy. Physics in Medicine and Biology 63(23), 235015-14 pp. PMID: 30484432. http://iopscience.iop.org/article/10.1088/1361-6560/aaeeee
Zhu H., Chen Y., Sung W., McNamara A. L., Linh T. T., Burigo L. N., Rosenfeld A. B., Li J., Faddegon B., Schuemann J., Paganetti H. (2019). The microdosimetric extension in TOPAS: Development and comparison with published data. Physics in Medicine and Biology; 64(14):145004. PMID: 31117056. http://doi.org/10.1088/1361-6560/ab23a3
Hahn, M.B. (2023). Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations. Journal of Physics Communications; 7(4):042001. http://doi.org/10.1088/2399-6528/accb3f
The Standard for DNA Damage (SDD)
Schuemann J., McNamara A. L., Warmenhoven J., et al. (55 authors). (2019). A new Standard DNA Damage (SDD) data format. Radiation Research; 191(1):76. PMID: 30407901. PMCID: PMC6407706. https://doi.org/10.1667/RR15209.1
Cell models with organelles and targeted nanoparticles
Hahn, M.B., Zutta Villate, J.M. (2021). Combined cell and nanoparticle models for TOPAS to study radiation dose enhancement in cell organelles. Sci Rep 11(1): 6721. PMID: 33762596. PMCID: PMC7990972. https://doi.org/10.1038/s41598-021-85964-2
A few publications where TOPAS-nBio was used
McNamara A. L., Kam W. W., Scales N., McMahon S. J., Bennett J. W., Byrne H. L., Schuemann J., Paganetti H., Banati R., Kuncic Z. (2016). Dose enhancement effects to the nucleus and mitochondria from gold nanoparticles in the cytosol. Physics in Medicine and Biology 61(16):5993-6010. PMID: 27435339; PMCID: PMC4993038. https://doi.org/10.1088/0031-9155/61/16/5993
Sung W., Ye S. J., McNamara A. L., McMahon S., Hainfeld J., Shin J., Smilowitz H., Paganetti H., Schuemann J. (2017). Dependence of gold nanoparticle radiosensitization on cell geometry. Nanoscale; 9(18):5843-5853. PMID: 28429022. PMCID: PMC5526329. https://doi.org/10.1039/c7nr01024a
Yang C., Bromma K., Sung W., Schuemann J., Chithrani D. (2018). Determining the Radiation Enhancement Effects of Gold Nanoparticles in Cells in a Combined Treatment with Cisplatin and Radiation at Therapeutic Megavoltage Energies. Cancers (Basel). 2018; 10(5). pii: E150. PMID: 29786642. PMCID: PMC5977123. https://doi.org/10.3390/cancers10050150
Sung W., Schuemann J. (2018). Energy Optimization in Gold Nanoparticle Enhanced Radiation Therapy. Physics in Medicine and Biology; 63(13): 135001. PMID: 29873303. PMCID: PMC6040581. https://doi.org/10.1088/1361-6560/aacab6
Sung W., Jeong Y., Kim H., Jeong H., Grassberger C., Jung S., Ahn G. O., Kim I. H., Schuemann J., Lee K., Ye S. J. (2018). Computational Modeling and Clonogenic Assay for Radioenhancement of Gold Nanoparticles using 3D live cell images. Radiation Research; 190(5): 558-564. PMID: 30142031. PMCID: PMC6258025. https://doi.org/10.1667/RR15134.1
Original TOPAS paper
Perl, J., Shin, J., Schuemann, J., Faddegon, B., & Paganetti, H. (2012). TOPAS: an innovative proton Monte Carlo platform for research and clinical applications. Medical Physics, 39(11), 6818–6837. PMID: 23127075. PMCID: PMC3493036. http://doi.org/10.1118/1.4758060 |
OpenTOPAS
OpenTOPAS can be downloaded from https://opentopas.github.io/index.html and the OpenTOPAS documentation can be found at: https://opentopas.readthedocs.io
The Geant4-DNA project
TOPAS-nBio is based on and extends Geant4-DNA. Information on the Geant4-DNA project can be found at: http://geant4-dna.org/