Publications

Key TOPAS Papers to Cite when TOPAS is Used in Your Research:

• J Perl, J Shin, J Schümann,  B Faddegon, H Paganetti. "TOPAS: an innovative proton Monte Carlo platform for research and clinical applications." Med Phys. 2012 Nov; 39(11):6818-37. View in: PubMed

• B Faddegon, J Ramos-Méndez, J Schümann, A McNamara, J Shin, J Perl, H Paganetti. "The TOPAS Tool for Particle Simulation, a Monte Carlo Simulation Tool for Physics, Biology and Clinical Research." Phys Med. 2020 Apr 02; 72:114-121. PMID: 32247964. PMCID: PMC7192305

Some other papers funded in whole or in part by the NIH Grants

• R01 CA140735 (2009-2016)

• U24 CA215123 (2018-2023)

(Note: This list has not been updated for several  years. It is far from complete)

• T Akagi, T Aso, B Faddegon, A Kimuar, N Matsufuji, T Nishio, C Omachi, H Paganetti, J Perl, T Sasaki, D Sawkey, J Schümann, J Sin, Toshito T, T Yamashita, H Yoshida. “The PTSim and TOPAS Projects, Bringing Geant4 to the Particle Therapy Clinic.” Progress in Nuclear Science and Technology 2011 2: 912-917 

• J Schümann, H Paganetti, J Shin, B Faddegon,  J Perl. "Efficient voxel navigation for proton therapy dose calculation in TOPAS and Geant4." Phys Med Biol. 2012 Jun 7; 57(11):3281-93. View in: PubMed

• J Shin,  J Perl,  J Schümann, H Paganetti, BA Faddegon. "A modular method to handle multiple time-dependent quantities in Monte Carlo simulations." Phys Med Biol. 2012 Jun 7; 57(11):3295-308. View in: PubMed

• M Testa,  J Schümann,  HM. Lu,  J Shin,  B Faddegon,  J Perl,  H Paganetti. "Experimental validation of the TOPAS Monte Carlo system for passive scattering proton therapy." Med Phys. 2013 Dec; 40(12):121719. View in: PubMed

• J Ramos-Méndez, J Perl, B Faddegon, J Schümann, H Paganetti. "Geometrical splitting technique to improve the computational efficiency in Monte Carlo calculations for proton therapy." Med Phys. 2013 Apr; 40(4):041718. View in: PubMed

• J Perl. "Formal quality control for a proton Monte Carlo system in radiation therapy." Journal of Physics: Conference Series 489 (2014) 012021. View in: IOPScience

• M Testa, CH Min, JM Verburg, J Schümann, HM Lu, H Paganetti. "Range verification of passively scattered proton beams based on prompt gamma time patterns." Phys Med Biol. 2014 Jul 8; 59(15):4181-95. View in: PubMed

• J Ramos-Méndez, J Perl, J Schuemann, J Shin, H Paganetti,  B Faddegon. “A framework for implementation of organ effect models in TOPAS with benchmarks extended to proton therapy," Phys Med Biol. 60(13): 5037-5052, 2015, PMID: 26061583

• L Polster, J Schümann, I Rinaldi, L Burigo, A McNamara, R Stewart, A Attili, D Carlson, T Sato, J Ramos-Méndez, B Faddegon, J Perl, H Paganetti, “Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endpoints.” Physics in Medicine and Biology 2015 60, 5053-5070

• J Ramos-Méndez, J Perl, J Schümann, J Shin, H Paganetti, B Faddegon, “Improved efficiency in Monte Carlo simulation for passive-scattering proton therapy.” Physics in Medicine and Biology 2015 60, 5019-5035 

• J Ramos-Méndez, J Schümann, S Incerti, H Paganetti, R Schulte, B Faddegon, “Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations.” Physics in Medicine and Biology 2017 62, 5908-5925

• H Zhu, Y Chen, W Sung, AL McNamara, LT Tran, LN Burigo, Rosenfeld AB, J Li, B Faddegon, J Schümann, H Paganetti, “The microdosimetric extension in TOPAS: Development and comparison with published data.” Physics in Medicine and Biology: 2019, 64 145004

• YS Abhyankar, S Dev, OS Sarun, A Saxena, R Joshi, H Darbari, C Sajish, UB Sonavane, V Gavane, A Deshpande, T Dixit, R Harsh, R Badwe, GK Rath, S Laskar, Faddegon B, J Perl, H Paganetti, J Schümann, A Srivastava, C Obcemea, AK Nath, A Sharma, J Buchsbaum, “Monte Carlo Processing on a Chip (MCoaC)-preliminary experiments toward the realization of optimal-hardware for TOPAS/Geant4 to drive discovery.” European Journal of Medical Physics 2019, 64 166-173

• P Arce, D Bolst, D Cutajar, S Guatelli, D Sakata, M-C Bordage, P Cirrone, G Cuttone, L Pandola, G Petringa, MA Cortes-Giraldo, JM Quesada, L Desorgher, P Dondero, A Mantero, A Dotti, D Wright, B Faddegon, J Ramos-Mendez, C Fedon, S Incerti, V Ivanchenko, D Konstantinov, G Latyshev, I Kyriakou, C Mancini-Terraccciano, M Maire, M Novak, C Omachi, T Toshito, A Perales, V Perrot, F Romano, L Sarmiento, T Sasaki, I Sechopoulos, EC Simpson. "Report on G4-Med, a Geant4 benchmarking system for medical physics applications developed by the Geant4 Medical Physics Benchmarking Group." In press, Med Phys, April 2020 Manuscript #19SR-897R1

• L B Skinner, T Niedermayr, N Prionas, J Perl, BP Fahimian, E Kidd. "Intensity modulated Ir-192 brachytherapy using high-Z 3D printed applicators." In Press. Phys Med Biol. 2020 Jun 10. doi: 10.1088/1361-6560/ab9b54.