Bruce Faddegon, PhD
Professor
Radiation Oncology
School of Medicine

The overall objective of Dr. Faddegon’s research is to allow for more aggressive treatment in sites where side effects, local control, and even metastases are a problem through cost-effective solutions to improve the therapeutic ratio.

Current research includes developing TOPAS, the Tool for Particle Simulation, a collaboration of UCSF, MGH and SLAC supported by NIH to improve advanced simulation of radiotherapy in conjunction with the open source Geant4 Monte Carlo simulation toolkit. The initial grant focussed on proton therapy. The renewal grant focused on organ and cell radiobiology. The current NIH U24 grant is through the NCI Informatics Technology for Cancer Research (ITCR) to extend TOPAS to conventional radiotherapy and imaging. Work in parallel is being done to develop TOPAS-nBio with enhanced track structure simulation capabilities in conjunction with Geant4-DNA for physicists, chemists and biologists to better establish the relationship between ionization deposition details, radiation chemistry, and biological effect.

Dr. Faddegons clinical responsibility is physics support of radiotherapy. This includes installation, commissioning, maintenance and quality assurance of equipment and procedures used in radiation treatment planning and delivery. Highlights of Dr. Faddegon’s published clinical development work at UCSF include developing new x-ray targets that are implemented on linacs worldwide for low-dose megavoltage imaging and to reduce downtime, developing the means to treat the whole body over a short distance (3 meters), implementing high precision graticules for patient localization, and determining the means to detect and correct defective circuitry in treatments using virtual wedges.

• Impact of DNA Geometry and Scoring on Monte Carlo Track-Structure Simulations of Initial Radiation-Induced Damage.
  Radiation research 2022 Bertolet A, Ramos-Méndez J, McNamara A, Yoo D, Ingram S, Henthorn N, Warmenhoven JW, Faddegon B, Merchant M, McMahon SJ, Paganetti H, Schuemann J
• TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields.
  Physics in medicine and biology 2022 Ramos-Méndez J, García-García O, Domínguez-Kondo J, LaVerne JA, Schuemann J, Moreno-Barbosa E, Faddegon B
• DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions.
  Physics in medicine and biology 2021 D-Kondo N, Moreno-Barbosa E, Štephán V, Stefanová K, Perrot Y, Villagrasa C, Incerti S, De Celis Alonso B, Schuemann J, Faddegon B, Ramos-Méndez J
• TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation.
  Physics in medicine and biology 2021 Ramos-Méndez J, LaVerne JA, Domínguez-Kondo N, Milligan J, Štepán V, Stefanová K, Perrot Y, Villagrasa C, Shin WG, Incerti S, McNamara A, Paganetti H, Perl J, Schuemann J, Faddegon B
• Publisher's Note: "Dispersion calibration for the National Ignition Facility electron-positron-proton spectrometers for intense laser matter interactions" [Rev. Sci. Instrum. 92, 033516 (2021)].
  The Review of scientific instruments 2021 von der Linden J, Ramos-Mendez J, Faddegon B, Massin D, Fiksel G, Holder JP, Willingale L, Peebles J, Edwards MR, Chen H
• Dispersion calibration for the National Ignition Facility electron-positron-proton spectrometers for intense laser matter interactions.
  The Review of scientific instruments 2021 von der Linden J, Ramos-Méndez J, Faddegon B, Massin D, Fiksel G, Holder JP, Willingale L, Peebles J, Edwards MR, Chen H
• Assessment of DNA damage with an adapted independent reaction time approach implemented in Geant4-DNA for the simulation of diffusion-controlled reactions between radio-induced reactive species and a chromatin fiber.
  Medical physics 2020 Tran HN, Ramos-Méndez J, Shin WG, Perrot Y, Faddegon B, Okada S, Karamitros M, Davídková M, Štepán V, Incerti S, Villagrasa C
• Report on G4-Med, a Geant4 benchmarking system for medical physics applications developed by the Geant4 Medical Simulation Benchmarking Group.
  Medical physics 2020 Arce P, Bolst D, Bordage MC, Brown JMC, Cirrone P, Cortés-Giraldo MA, Cutajar D, Cuttone G, Desorgher L, Dondero P, Dotti A, Faddegon B, Fedon C, Guatelli S, Incerti S, Ivanchenko V, Konstantinov D, …
• Independent reaction times method in Geant4-DNA: Implementation and performance.
  Medical physics 2020 Ramos-Méndez J, Shin WG, Karamitros M, Domínguez-Kondo J, Tran NH, Incerti S, Villagrasa C, Perrot Y, Štepán V, Okada S, Moreno-Barbosa E, Faddegon B
• LET-Dependent Intertrack Yields in Proton Irradiation at Ultra-High Dose Rates Relevant for FLASH Therapy.
  Radiation research 2020 Ramos-Méndez J, Domínguez-Kondo N, Schuemann J, McNamara A, Moreno-Barbosa E, Faddegon B
• A Millimeter-scale Single Charged Particle Dosimeter for Cancer Radiotherapy.
  IEEE journal of solid-state circuits 2020 Lee K, Scholey J, Norman EB, Daftari IK, Mishra KK, Faddegon BA, Maharbiz MM, Anwar M
• Monte Carlo track-structure for the radionuclide Copper-64: characterization of S-values, nanodosimetry and quantification of direct damage to DNA.
  Physics in medicine and biology 2020 Carrasco-Hernández J, Ramos-Méndez J, Faddegon B, Jalilian AR, Moranchel M, Ávila-Rodríguez MA
• Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio.
  Radiation research 2020 Zhu H, McNamara AL, McMahon SJ, Ramos-Mendez J, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J
• A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio.
  Physics in medicine and biology 2020 Zhu H, McNamara AL, Ramos-Mendez J, McMahon SJ, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J
• The TOPAS tool for particle simulation, a Monte Carlo simulation tool for physics, biology and clinical research.
  Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) 2020 Faddegon B, Ramos-Méndez J, Schuemann J, McNamara A, Shin J, Perl J, Paganetti H
• Beam modeling and beam model commissioning for Monte Carlo dose calculation-based radiation therapy treatment planning: Report of AAPM Task Group 157.
  Medical physics 2019 Ma CMC, Chetty IJ, Deng J, Faddegon B, Jiang SB, Li J, Seuntjens J, Siebers JV, Traneus E
• Three discipline collaborative radiation therapy (3DCRT) special debate: The United States needs at least one carbon ion facility.
  Journal of applied clinical medical physics 2019 Blakely EA, Faddegon B, Tinkle C, Bloch C, Dominello M, Griffin RJ, Joiner MC, Burmeister J
• Monte Carlo Processing on a Chip (MCoaC)-preliminary experiments toward the realization of optimal-hardware for TOPAS/Geant4 to drive discovery.
  Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) 2019 Abhyankar YS, Dev S, Sarun OS, Saxena A, Joshi R, Darbari H, Sajish C, Sonavane UB, Gavane V, Deshpande A, Dixit T, Harsh R, Badwe R, Rath GK, Laskar S, Faddegon B, Perl J, Paganetti H, Schuemann J, …
• The microdosimetric extension in TOPAS: development and comparison with published data.
  Physics in medicine and biology 2019 Zhu H, Chen Y, Sung W, McNamara AL, Tran LT, Burigo LN, Rosenfeld AB, Li J, Faddegon B, Schuemann J, Paganetti H
• Simultaneous optimization of RBE-weighted dose and nanometric ionization distributions in treatment planning with carbon ions.
  Physics in medicine and biology 2019 Burigo LN, Ramos-Méndez J, Bangert M, Schulte RW, Faddegon B
• TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology.
  Radiation research 2019 Schuemann J, McNamara AL, Ramos-Méndez J, Perl J, Held KD, Paganetti H, Incerti S, Faddegon B
• Fast calculation of nanodosimetric quantities in treatment planning of proton and ion therapy.
  Physics in medicine and biology 2018 Ramos-Méndez J, Burigo LN, Schulte R, Chuang C, Faddegon B
• A New Standard DNA Damage (SDD) Data Format.
  Radiation research 2018 Schuemann J, McNamara AL, Warmenhoven JW, Henthorn NT, Kirkby KJ, Merchant MJ, Ingram S, Paganetti H, Held KD, Ramos-Mendez J, Faddegon B, Perl J, Goodhead DT, Plante I, Rabus H, Nettelbeck H, …
• Clinical trials involving carbon-ion radiation therapy and the path forward.
  Cancer 2018 Lazar AA, Schulte R, Faddegon B, Blakely EA, Roach M
• Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit.
  Physics in medicine and biology 2018 McNamara AL, Ramos-Méndez J, Perl J, Held K, Dominguez N, Moreno E, Henthorn NT, Kirkby KJ, Meylan S, Villagrasa C, Incerti S, Faddegon B, Paganetti H, Schuemann J
• Helium CT: Monte Carlo simulation results for an ideal source and detector with comparison to proton CT.
  Medical physics 2018 Piersimoni P, Faddegon BA, Méndez JR, Schulte RW, Volz L, Seco J
• Monte Carlo simulation of chemistry following radiolysis with TOPAS-nBio.
  Physics in medicine and biology 2018 Ramos-Méndez J, Perl J, Schuemann J, McNamara A, Paganetti H, Faddegon B
• Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations.
  Physics in medicine and biology 2017 Ramos-Méndez J, Schuemann J, Incerti S, Paganetti H, Schulte R, Faddegon B
• The effect of beam purity and scanner complexity on proton CT accuracy.
  Medical physics 2017 Piersimoni P, Ramos-Méndez J, Geoghegan T, Bashkirov VA, Schulte RW, Faddegon BA
• Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries.
  Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) 2016 McNamara A, Geng C, Turner R, Mendez JR, Perl J, Held K, Faddegon B, Paganetti H, Schuemann J
• Technical Note: Preferred dosimeter size and associated correction factors in commissioning high dose per pulse, flattening filter free x-ray beams.
  Medical physics 2016 Sudhyadhom A, Kirby N, Faddegon B, Chuang CF
• New Clinical and Research Programs in Particle Beam Radiation Therapy: The University of California San Francisco Perspective.
  International journal of particle therapy 2016 Roach M, Schulte R, Mishra K, Faddegon B, Barani I, Lazar A, Blakely EA
• Dose assessment for the fetus considering scattered and secondary radiation from photon and proton therapy when treating a brain tumor of the mother.
  Physics in medicine and biology 2015 Geng C, Moteabbed M, Seco J, Gao Y, Xu XG, Ramos-Méndez J, Faddegon B, Paganetti H
• Experimental depth dose curves of a 67.5 MeV proton beam for benchmarking and validation of Monte Carlo simulation.
  Medical physics 2015 Faddegon BA, Shin J, Castenada CM, Ramos-Méndez J, Daftari IK
• A framework for implementation of organ effect models in TOPAS with benchmarks extended to proton therapy.
  Physics in medicine and biology 2015 Ramos-Méndez J, Perl J, Schümann J, Shin J, Paganetti H, Faddegon B
• Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endpoints.
  Physics in medicine and biology 2015 Polster L, Schuemann J, Rinaldi I, Burigo L, McNamara AL, Stewart RD, Attili A, Carlson DJ, Sato T, Ramos Méndez J, Faddegon B, Perl J, Paganetti H
• Improved efficiency in Monte Carlo simulation for passive-scattering proton therapy.
  Physics in medicine and biology 2015 Méndez JR, Perl J, Schümann J, Shin J, Paganetti H, Faddegon B
• TH2-Polarized CD4(+) T Cells and Macrophages Limit Efficacy of Radiotherapy.
  Cancer immunology research 2015 Shiao SL, Ruffell B, DeNardo DG, Faddegon BA, Park CC, Coussens LM
• Experimental validation of the TOPAS Monte Carlo system for passive scattering proton therapy.
  Medical physics 2013 Testa M, Schümann J, Lu HM, Shin J, Faddegon B, Perl J, Paganetti H
• Geometrical splitting technique to improve the computational efficiency in Monte Carlo calculations for proton therapy.
  Medical physics 2013 Ramos-Méndez J, Perl J, Faddegon B, Schümann J, Paganetti H
• TOPAS: an innovative proton Monte Carlo platform for research and clinical applications.
  Medical physics 2012 Perl J, Shin J, Schumann J, Faddegon B, Paganetti H
• Genetically mediated Nf1 loss in mice promotes diverse radiation-induced tumors modeling second malignant neoplasms.
  Cancer research 2012 Choi G, Huang B, Pinarbasi E, Braunstein SE, Horvai AE, Kogan S, Bhatia S, Faddegon B, Nakamura JL
• SU-E-T-473: Performance Assessment of the TOPAS Tool for Particle Simulation for Proton Therapy Applications.
  Medical physics 2012 Perl J, Shin J, Schuemann J, Faddegon B, Paganetti H
• SU-E-T-478: Geometrical Splitting Technique to Improve the Computational Efficiency in Monte Carlo Calculations for Proton Therapy.
  Medical physics 2012 Ramos-Mendez J, Perl J, Faddegon B, Paganetti H
• SU-E-T-500: Pencil-Beam versus Monte Carlo Based Dose Calculation for Proton Therapy Patients with Complex Geometries. Clinical Use of the TOPAS Monte Carlo System.
  Medical physics 2012 Schuemann J, Shin J, Perl J, Grassberger C, Verburg J, Faddegon B, Paganetti H
• A modular method to handle multiple time-dependent quantities in Monte Carlo simulations.
  Physics in medicine and biology 2012 Shin J, Perl J, Schümann J, Paganetti H, Faddegon BA
• Efficient voxel navigation for proton therapy dose calculation in TOPAS and Geant4.
  Physics in medicine and biology 2012 Schümann J, Paganetti H, Shin J, Faddegon B, Perl J
• Sensitivity analysis of an asymmetric Monte Carlo beam model of a Siemens Primus accelerator.
  Journal of applied clinical medical physics 2012 Schreiber EC, Sawkey DL, Faddegon BA
• Characterization of an extendable multi-leaf collimator for clinical electron beams.
  Physics in medicine and biology 2011 O'Shea TP, Ge Y, Foley MJ, Faddegon BA
• Study of intensity-modulated photon-electron radiation therapy using digital phantoms.
  Physics in medicine and biology 2011 Ge Y, Faddegon BA
• Accounting for the fringe magnetic field from the bending magnet in a Monte Carlo accelerator treatment head simulation.
  Medical physics 2011 O'Shea TP, Foley MJ, Faddegon BA
• Dose-dependent effects of focal fractionated irradiation on secondary malignant neoplasms in Nf1 mutant mice.
  Cancer research 2011 Nakamura JL, Phong C, Pinarbasi E, Kogan SC, Vandenberg S, Horvai AE, Faddegon BA, Fiedler D, Shokat K, Houseman BT, Chao R, Pieper RO, Shannon K
• Practical quantitative measurement of graticule misalignment relative to collimator axis of rotation.
  Journal of applied clinical medical physics 2010 Halabi T, Faddegon B
• Monte Carlo commissioning of clinical electron beams using large field measurements.
  Physics in medicine and biology 2010 O'Shea TP, Sawkey DL, Foley MJ, Faddegon BA
• Comparison of patient megavoltage cone beam CT images acquired with an unflattened beam from a carbon target and a flattened treatment beam.
  Medical physics 2010 Faddegon BA, Aubin M, Bani-Hashemi A, Gangadharan B, Gottschalk AR, Morin O, Sawkey D, Wu V, Yom SS
• A diamond target for megavoltage cone-beam CT.
  Medical physics 2010 Sawkey D, Lu M, Morin O, Aubin M, Yom SS, Gottschalk AR, Bani-Hashemi A, Faddegon BA
• Fast, accurate photon beam accelerator modeling using BEAMnrc: a systematic investigation of efficiency enhancing methods and cross-section data.
  Medical physics 2009 Fragoso M, Kawrakow I, Faddegon BA, Solberg TD, Chetty IJ
• Simulation of large x-ray fields using independently measured source and geometry details.
  Medical physics 2009 Sawkey D, Faddegon BA
• Treatment head disassembly to improve the accuracy of large electron field simulation.
  Medical physics 2009 Faddegon BA, Sawkey D, O'Shea T, McEwen M, Ross C
• The accuracy of EGSnrc, Geant4 and PENELOPE Monte Carlo systems for the simulation of electron scatter in external beam radiotherapy.
  Physics in medicine and biology 2009 Faddegon BA, Kawrakow I, Kubyshin Y, Perl J, Sempau J, Urban L
• Validation of the final aperture superposition technique to calculate electron output factors and depth dose curves.
  Medical physics 2009 Chen J, Irion J, Faddegon BA
• Image quality & dosimetric property of an investigational imaging beam line MV-CBCT.
  Journal of applied clinical medical physics 2009 Beltran C, Lukose R, Gangadharan B, Bani-Hashemi A, Faddegon BA
• Determination of electron energy, spectral width, and beam divergence at the exit window for clinical megavoltage x-ray beams.
  Medical physics 2009 Sawkey DL, Faddegon BA
• Algorithm for X-ray scatter, beam-hardening, and beam profile correction in diagnostic (kilovoltage) and treatment (megavoltage) cone beam CT.
  IEEE transactions on medical imaging 2008 Maltz JS, Gangadharan B, Bose S, Hristov DH, Faddegon BA, Paidi A, Bani-Hashemi AR
• Low dose megavoltage cone beam computed tomography with an unflattened 4 MV beam from a carbon target.
  Medical physics 2008 Faddegon BA, Wu V, Pouliot J, Gangadharan B, Bani-Hashemi A
• Benchmarking of Monte Carlo simulation of bremsstrahlung from thick targets at radiotherapy energies.
  Medical physics 2008 Faddegon BA, Asai M, Perl J, Ross C, Sempau J, Tinslay J, Salvat F
• Measurement of multiple scattering of 13 and 20 MeV electrons by thin foils.
  Medical physics 2008 Ross CK, McEwen MR, McDonald AF, Cojocaru CD, Faddegon BA
• Sci-Fri PM: Planning-01: Measured electron and x-ray angular distribution data for benchmarking Monte Carlo codes.
  Medical physics 2008 Cojocaru CD, Ross CK, McEwen MR, McDonald AF, Faddegon BA
• Focused beam-stop array for the measurement of scatter in megavoltage portal and cone beam CT imaging.
  Medical physics 2008 Maltz JS, Gangadharan B, Vidal M, Paidi A, Bose S, Faddegon BA, Aubin M, Morin O, Pouliot J, Zheng Z, Svatos MM, Bani-Hashemi AR
• Prototyping a large field size IORT applicator for a mobile linear accelerator.
  Physics in medicine and biology 2008 Janssen RW, Faddegon BA, Dries WJ
• Monte Carlo simulation of large electron fields.
  Physics in medicine and biology 2008 Faddegon BA, Perl J, Asai M
• Report of the AAPM Task Group No. 105: Issues associated with clinical implementation of Monte Carlo-based photon and electron external beam treatment planning.
  Medical physics 2007 Chetty IJ, Curran B, Cygler JE, DeMarco JJ, Ezzell G, Faddegon BA, Kawrakow I, Keall PJ, Liu H, Ma CM, Rogers DW, Seuntjens J, Sheikh-Bagheri D, Siebers JV
• Response of intracerebral human glioblastoma xenografts to multifraction radiation exposures.
  International journal of radiation oncology, biology, physics 2006 Ozawa T, Faddegon BA, Hu LJ, Bollen AW, Lamborn KR, Deen DF
• A pulse-rate dependence of dose per monitor unit and its significant effect on wedged-shaped fields delivered with variable dose rate and a moving jaw.
  Medical physics 2006 Faddegon BA, Garde E
• Intraoperative radiation therapy using mobile electron linear accelerators: report of AAPM Radiation Therapy Committee Task Group No. 72.
  Medical physics 2006 Beddar AS, Biggs PJ, Chang S, Ezzell GA, Faddegon BA, Hensley FW, Mills MD
• Final Aperture Superposition Technique applied to fast calculation of electron output factors and depth dose curves.
  Medical physics 2005 Faddegon BA, Villarreal-Barajas JE
• Monte Carlo simulation of large electron fields.
  Physics in medicine and biology 2005 Faddegon B, Schreiber E, Ding X
• Sensitivity of large-field electron beams to variations in a Monte Carlo accelerator model.
  Physics in medicine and biology 2005 Schreiber EC, Faddegon BA
• A comparison of Monte Carlo and Fermi-Eyges-Hogstrom estimates of heart and lung dose from breast electron boost treatment.
  International journal of radiation oncology, biology, physics 2005 Coleman J, Park C, Villarreal-Barajas JE, Petti P, Faddegon B
• Dosimetry of a prototype retractable eMLC for fixed-beam electron therapy.
  Medical physics 2004 Hogstrom KR, Boyd RA, Antolak JA, Svatos MM, Faddegon BA, Rosenman JG
• Comparison of beam characteristics of a gold x-ray target and a tungsten replacement target.
  Medical physics 2004 Faddegon B, Egley B, Steinberg T
• Electron spectra derived from depth dose distributions.
  Medical physics 2000 Faddegon BA, Blevis I
• The flatness of Siemens linear accelerator x-ray fields.
  Medical physics 1999 Faddegon BA, O'Brien P, Mason DL
• Megavoltage imaging with low Z targets: implementation and characterization of an investigational system.
  Medical physics 1998 Ostapiak OZ, O'Brien PF, Faddegon BA
• Accurate characterization of Monte Carlo calculated electron beams for radiotherapy.
  Medical physics 1997 Ma CM, Faddegon BA, Rogers DW, Mackie TR
• Monte Carlo based phase-space evolution for electron dose calculation.
  Medical physics 1997 Scora D, Faddegon BA
• Calculation of x-ray spectra for radiosurgical beams.
  Medical physics 1995 Sixel KE, Faddegon BA
• BEAM: a Monte Carlo code to simulate radiotherapy treatment units.
  Medical physics 1995 Rogers DW, Faddegon BA, Ding GX, Ma CM, We J, Mackie TR
• Angular distribution of bremsstrahlung from 15-MeV electrons incident on thick targets of Be, Al, and Pb.
  Medical physics 1991 Faddegon BA, Ross CK, Rogers DW
• Forward-directed bremsstrahlung of 10- to 30-MeV electrons incident on thick targets of Al and Pb.
  Medical physics 1990 Faddegon BA, Ross CK, Rogers DW
• Computer aided design and verification of megavoltage tissue compensators for oblique beams.
  Medical physics 1988 Faddegon BA, Pfalzner P
• The effect of misonidazole as a hypoxic radiosensitizer at low dose.
  Radiation research 1984 Palcic B, Faddegon B, Skarsgard LD