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Faddegon B, Descovich M, Chen K, Ramos-Méndez J, Iii MR, Wahl N, Taylor P, Griffin K, Lee C. A digital male pelvis phantom series showing anatomical variations over the course of fractionated radiotherapy treatment. Med Phys 2024; 51:3034-3044. [PMID: 38071746 DOI: 10.1002/mp.16865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Daily IGRT images show day-to-day anatomical variations in patients undergoing fractionated prostate radiotherapy. This is of particular importance in particle beam treatments. PURPOSE To develop a digital phantom series showing variation in pelvic anatomy for evaluating treatment planning and IGRT procedures in particle radiotherapy. METHODS A pelvic phantom series was developed from the planning MRI and kVCT (planning CT) images along with six of the daily serial MVCT images taken of a single patient treated with a full bladder on a Tomotherapy unit. The selected patient had clearly visible yet unexceptional internal anatomy variation. Prostate, urethra, bladder, rectum, bowel, bowel gas, bone and soft tissue were contoured and a single Hounsfield Unit was assigned to each region. Treatment plans developed on the kVCT for photon, proton and carbon beams were recalculated on each phantom to demonstrate a clinical application of the series. Proton plans were developed with and without robust optimization. RESULTS Limited to axial slices with prostate, the bladder volume varied from 6 to 46 cm3, the rectal volume (excluding gas) from 22 to 52 cm3, and rectal gas volume from zero to 18 cm3. The water equivalent path length to the prostate varied by up to 1.5 cm . The variations resulted in larger changes in the RBE-weighted Dose Volume Histograms of the non-robust proton plan and the carbon plan compared to the robust proton plan, the latter similar to the photon plan. The prostate coverage (V100%) decreased by an average of 18% in the carbon plan, 16% in the non-robust proton plan, 1.8% in the robust proton plan, and 4.4% in the photon plan. The volume of rectum receiving 75% of the prescription dose (V75%) increased by an average of 3.7 cm3, 4.7 cm3, 1.9 cm3, and 0.6 cm3 in those four plans, respectively. CONCLUSIONS The digital pelvic phantom series provides for quantitative investigation of IGRT procedures and new methods for improving accuracy in particle therapy and may be used in cross-institutional comparisons for clinical trial quality assurance.
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Affiliation(s)
- Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - Martina Descovich
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - Katherine Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - Mack Roach Iii
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - Niklas Wahl
- Division of Medical Physics in Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO) and National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Paige Taylor
- Department of Radiation Physics, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Keith Griffin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Choonsik Lee
- Department of Radiation Physics, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Ortiz R, Faddegon B. Creating uniform cluster dose spread-out Bragg peaks for proton and carbon beams. Med Phys 2024. [PMID: 38376446 DOI: 10.1002/mp.16991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Preliminary data have shown a close association of the generalized ionization cluster size dose (in short, cluster dose) with cell survival, independent of particle type, and energy, when cluster dose is derived from an ionization detail parameter preferred for its association with cell survival. Such results suggest cluster dose has the potential to replace RBE-weighted dose in proton and ion beam radiotherapy treatment plan optimization, should a uniform cluster dose lead to comparable biological effects. However, further preclinical investigations are warranted to confirm this premise. PURPOSE To present an analytical approach to create uniform cluster dose spread-out Bragg peaks (SOBP) for evaluation of the potential of cluster dose to result in uniform biological effect. METHODS We modified the coefficients of the Bortfeld and Schlegel weight formula, an analytical method typically used for the creation of radiation dose SOBP in particle therapy, to produce uniform cluster dose SOBP of different widths (1-5 cm) at relevant clinical proton and carbon beam energies. Optimum parameters were found by minimization of the ratio between the maximum and minimum cluster dose in the SOBP region using the Nelder-Mead method. RESULTS The coefficients of the Bortfeld and Schlegel weight formula leading to uniform cluster dose SOBPs were determined for each combination of beam energy and SOBP width studied. The uniformity of the resulting cluster dose SOBPs, calculated as the relative difference between the maximum and minimum cluster dose within the SOBP, was within 0.3%-3.5% for the evaluated proton beams and 1.3%-3.4% for the evaluated carbon beams. CONCLUSIONS The modifications to the analytical approach to create radiation dose SOBPs resulted in uniform cluster dose proton and carbon SOBPs over a wide range of beam energies and SOBP widths. Such SOBPs should prove valuable in preclinical investigations for the selection of nanodosimetric quantities to be used in proton and ion therapy treatment planning.
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Affiliation(s)
- Ramon Ortiz
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
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Faddegon B, Blakely EA, Burigo L, Censor Y, Dokic I, Kondo ND, Ortiz R, Méndez JR, Rucinski A, Schubert K, Wahl N, Schulte R. Ionization detail parameters and cluster dose: a mathematical model for selection of nanodosimetric quantities for use in treatment planning in charged particle radiotherapy. Phys Med Biol 2023; 68:10.1088/1361-6560/acea16. [PMID: 37489619 PMCID: PMC10565507 DOI: 10.1088/1361-6560/acea16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/24/2023] [Indexed: 07/26/2023]
Abstract
Objective. To propose a mathematical model for applying ionization detail (ID), the detailed spatial distribution of ionization along a particle track, to proton and ion beam radiotherapy treatment planning (RTP).Approach. Our model provides for selection of preferred ID parameters (Ip) for RTP, that associate closest to biological effects. Cluster dose is proposed to bridge the large gap between nanoscopicIpand macroscopic RTP. Selection ofIpis demonstrated using published cell survival measurements for protons through argon, comparing results for nineteenIp:Nk,k= 2, 3, …, 10, the number of ionizations in clusters ofkor more per particle, andFk,k= 1, 2, …, 10, the number of clusters ofkor more per particle. We then describe application of the model to ID-based RTP and propose a path to clinical translation.Main results. The preferredIpwereN4andF5for aerobic cells,N5andF7for hypoxic cells. Significant differences were found in cell survival for beams having the same LET or the preferredNk. Conversely, there was no significant difference forF5for aerobic cells andF7for hypoxic cells, regardless of ion beam atomic number or energy. Further, cells irradiated with the same cluster dose for theseIphad the same cell survival. Based on these preliminary results and other compelling results in nanodosimetry, it is reasonable to assert thatIpexist that are more closely associated with biological effects than current LET-based approaches and microdosimetric RBE-based models used in particle RTP. However, more biological variables such as cell line and cycle phase, as well as ion beam pulse structure and rate still need investigation.Significance. Our model provides a practical means to select preferredIpfrom radiobiological data, and to convertIpto the macroscopic cluster dose for particle RTP.
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Affiliation(s)
- Bruce Faddegon
- University of California San Francisco, Department of Radiation Oncology 1600 Divisadero Street, San Francisco, CA 94143 United States of America
| | - Eleanor A. Blakely
- Loma Linda University School of Medicine, 11175 Campus St, Loma Linda,CA92350, United States of America
| | - Lucas Burigo
- Division of Medical Physics in Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Radiation Research in Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany
| | - Yair Censor
- Department of Mathematics, University of Haifa, 199 Aba Khoushy Ave. Mount Carmel, Haifa, 3498838, Israel
| | - Ivana Dokic
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Consortium (DKTK) Core-Center Heidelberg, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Molecular and Translational Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), 69120 Heidelberg, Germany
- Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Oncology (NCRO), Heidelberg University Hospital and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Naoki Domínguez Kondo
- University of California San Francisco, Department of Radiation Oncology 1600 Divisadero Street, San Francisco, CA 94143 United States of America
| | - Ramon Ortiz
- University of California San Francisco, Department of Radiation Oncology 1600 Divisadero Street, San Francisco, CA 94143 United States of America
| | - José Ramos Méndez
- University of California San Francisco, Department of Radiation Oncology 1600 Divisadero Street, San Francisco, CA 94143 United States of America
| | - Antoni Rucinski
- Institute of Nuclear Physics Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland
| | - Keith Schubert
- Baylor University, 1311 S 5th St, Waco, TX 76706, United States of America
| | - Niklas Wahl
- Division of Medical Physics in Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Radiation Research in Oncology (NCRO), Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg, Germany
| | - Reinhard Schulte
- Loma Linda University School of Medicine, 11085 Campus St, Loma Linda, CA92350, United States of America
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Lee H, Cheon BW, Feld JW, Grogg K, Perl J, Ramos-Méndez JA, Faddegon B, Min CH, Paganetti H, Schuemann J. TOPAS-imaging: extensions to the TOPAS simulation toolkit for medical imaging systems. Phys Med Biol 2023; 68:10.1088/1361-6560/acc565. [PMID: 36930985 PMCID: PMC10164408 DOI: 10.1088/1361-6560/acc565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/17/2023] [Indexed: 03/19/2023]
Abstract
Objective. The TOol for PArticle Simulation (TOPAS) is a Geant4-based Monte Carlo software application that has been used for both research and clinical studies in medical physics. So far, most users of TOPAS have focused on radiotherapy-related studies, such as modeling radiation therapy delivery systems or patient dose calculation. Here, we present the first set of TOPAS extensions to make it easier for TOPAS users to model medical imaging systems.Approach. We used the extension system of TOPAS to implement pre-built, user-configurable geometry components such as detectors (e.g. flat-panel and multi-planar detectors) for various imaging modalities and pre-built, user-configurable scorers for medical imaging systems (e.g. digitizer chain).Main results. We developed a flexible set of extensions that can be adapted to solve research questions for a variety of imaging modalities. We then utilized these extensions to model specific examples of cone-beam CT (CBCT), positron emission tomography (PET), and prompt gamma (PG) systems. The first of these new geometry components, the FlatImager, was used to model example CBCT and PG systems. Detected signals were accumulated in each detector pixel to obtain the intensity of x-rays penetrating objects or prompt gammas from proton-nuclear interaction. The second of these new geometry components, the RingImager, was used to model an example PET system. Positron-electron annihilation signals were recorded in crystals of the RingImager and coincidences were detected. The simulated data were processed using corresponding post-processing algorithms for each modality and obtained results in good agreement with the expected true signals or experimental measurement.Significance. The newly developed extension is a first step to making it easier for TOPAS users to build and simulate medical imaging systems. Together with existing TOPAS tools, this extension can help integrate medical imaging systems with radiotherapy simulations for image-guided radiotherapy.
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Affiliation(s)
- Hoyeon Lee
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, United States of America
| | - Bo-Wi Cheon
- Department of Radiation Convergence Engineering, Yonsei University, Wonju, Gangwon-do 26493, Republic of Korea
| | - Joseph W Feld
- Electrical Engineering and Computer Science Department, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Kira Grogg
- The Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, United States of America
| | - Joseph Perl
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 United States of America
| | - José A Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115 United States of America
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115 United States of America
| | - Chul Hee Min
- Department of Radiation Convergence Engineering, Yonsei University, Wonju, Gangwon-do 26493, Republic of Korea
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, United States of America
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, United States of America
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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. Impact of DNA Geometry and Scoring on Monte Carlo Track-Structure Simulations of Initial Radiation-Induced Damage. Radiat Res 2022; 198:207-220. [PMID: 35767729 PMCID: PMC9458623 DOI: 10.1667/rade-21-00179.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/07/2022] [Indexed: 11/03/2022]
Abstract
Track structure Monte Carlo simulations are a useful tool to investigate the damage induced to DNA by ionizing radiation. These simulations usually rely on simplified geometrical representations of the DNA subcomponents. DNA damage is determined by the physical and physicochemical processes occurring within these volumes. In particular, damage to the DNA backbone is generally assumed to result in strand breaks. DNA damage can be categorized as direct (ionization of an atom part of the DNA molecule) or indirect (damage from reactive chemical species following water radiolysis). We also consider quasi-direct effects, i.e., damage originated by charge transfers after ionization of the hydration shell surrounding the DNA. DNA geometries are needed to account for the damage induced by ionizing radiation, and different geometry models can be used for speed or accuracy reasons. In this work, we use the Monte Carlo track structure tool TOPAS-nBio, built on top of Geant4-DNA, for simulation at the nanometer scale to evaluate differences among three DNA geometrical models in an entire cell nucleus, including a sphere/spheroid model specifically designed for this work. In addition to strand breaks, we explicitly consider the direct, quasi-direct, and indirect damage induced to DNA base moieties. We use results from the literature to determine the best values for the relevant parameters. For example, the proportion of hydroxyl radical reactions between base moieties was 80%, and between backbone, moieties was 20%, the proportion of radical attacks leading to a strand break was 11%, and the expected ratio of base damages and strand breaks was 2.5-3. Our results show that failure to update parameters for new geometric models can lead to significant differences in predicted damage yields.
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Affiliation(s)
- Alejandro Bertolet
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Aimee McNamara
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Dohyeon Yoo
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Samuel Ingram
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Nicholas Henthorn
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - John-William Warmenhoven
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Michael Merchant
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, United Kingdom
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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Ramos-Méndez J, García-García O, Domínguez-Kondo J, LaVerne JA, Schuemann J, Moreno-Barbosa E, Faddegon B. TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields. Phys Med Biol 2022; 67. [DOI: 10.1088/1361-6560/ac79f9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/17/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Current Monte Carlo simulations of DNA damage have been reported only at ambient temperature. The aim of this work is to use TOPAS-nBio to simulate the yields of DNA single-strand breaks (SSBs) and double-strand breaks (DSBs) produced in plasmids under low-LET irradiation incorporating the effect of the temperature changes in the environment. A new feature was implemented in TOPAS-nBio to incorporate reaction rates used in the simulation of the chemical stage of water radiolysis as a function of temperature. The implemented feature was verified by simulating temperature-dependent G-values of chemical species in liquid water from 20 °C to 90 °C. For radiobiology applications, temperature dependent SSB and DSB yields were calculated from 0 °C to 42 °C, the range of available published measured data. For that, supercoiled DNA plasmids dissolved in aerated solutions containing EDTA irradiated by Cobalt-60 gamma-rays were simulated. TOPAS-nBio well reproduced published temperature-dependent G-values in liquid water and the yields of SSB and DSB for the temperature range considered. For strand break simulations, the model shows that the yield of SSB and DSB increased linearly with the temperature at a rate of (2.94 ± 0.17) × 10−10 Gy–1 Da–1 °C–1 (R
2 = 0.99) and (0.13 ± 0.01) × 10−10 Gy–1 Da–1 °C–1 (R
2 = 0.99), respectively. The extended capability of TOPAS-nBio is a complementary tool to simulate realistic conditions for a large range of environmental temperatures, allowing refined investigations of the biological effects of radiation.
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Nanni E, Tantawi S, Loo B, Snively E, Schulte R, Faddegon B, Pankuch M, Li Z, Dolgashev V, Ramos J. FLASH Modalities Track (Oral Presentations) 3D HIGH SPEED RF BEAM SCANNER FOR HADRON THERAPY OF CANCER. Phys Med 2022. [DOI: 10.1016/s1120-1797(22)01532-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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D-Kondo N, Moreno-Barbosa E, Štěphán V, Stefanová K, Perrot Y, Villagrasa C, Incerti S, De Celis Alonso B, Schuemann J, Faddegon B, Ramos-Méndez J. DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions. Phys Med Biol 2021; 66. [PMID: 34787099 DOI: 10.1088/1361-6560/ac3a22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022]
Abstract
The chemical stage of the Monte Carlo track-structure (MCTS) code Geant4-DNA was extended for its use in DNA strand break (SB) simulations and compared against published experimental data. Geant4-DNA simulations were performed using pUC19 plasmids (2686 base pairs) in a buffered solution of DMSO irradiated by60Co or137Csγ-rays. A comprehensive evaluation of SSB yields was performed considering DMSO, DNA concentration, dose and plasmid supercoiling. The latter was measured using the super helix density value used in a Brownian dynamics plasmid generation algorithm. The Geant4-DNA implementation of the independent reaction times method (IRT), developed to simulate the reaction kinetics of radiochemical species, allowed to score the fraction of supercoiled, relaxed and linearized plasmid fractions as a function of the absorbed dose. The percentage of the number of SB after •OH + DNA and H• + DNA reactions, referred as SSB efficiency, obtained using MCTS were 13.77% and 0.74% respectively. This is in reasonable agreement with published values of 12% and 0.8%. The SSB yields as a function of DMSO concentration, DNA concentration and super helix density recreated the expected published experimental behaviors within 5%, one standard deviation. The dose response of SSB and DSB yields agreed with published measurements within 5%, one standard deviation. We demonstrated that the developed extension of IRT in Geant4-DNA, facilitated the reproduction of experimental conditions. Furthermore, its calculations were strongly in agreement with experimental data. These two facts will facilitate the use of this extension in future radiobiological applications, aiding the study of DNA damage mechanisms with a high level of detail.
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Affiliation(s)
- N D-Kondo
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - E Moreno-Barbosa
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - V Štěphán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Stefanová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - Y Perrot
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - C Villagrasa
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - S Incerti
- Univ. Bordeaux, CNRS/IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - B De Celis Alonso
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - J Schuemann
- Department of Radiation Oncology, Massachusets General Hospital and Hardvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
| | - J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
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Ramos-Méndez J, LaVerne JA, Domínguez-Kondo N, Milligan J, Štěpán V, Stefanová K, Perrot Y, Villagrasa C, Shin WG, Incerti S, McNamara A, Paganetti H, Perl J, Schuemann J, Faddegon B. TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation. Phys Med Biol 2021; 66. [PMID: 34412044 DOI: 10.1088/1361-6560/ac1f39] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 11/12/2022]
Abstract
The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependentGvalues in pure liquid water for·OH, e-aq, and H2with published experimental data. For H2O2and H·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by137Csγ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependentGvalues and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for·OH and H·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.
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Affiliation(s)
- J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
| | - J A LaVerne
- Radiation Laboratory and Department of Physics, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - N Domínguez-Kondo
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico
| | - J Milligan
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, United States of America
| | - V Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Stefanová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - Y Perrot
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - C Villagrasa
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - W-G Shin
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - S Incerti
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, F-33170 Gradignan, France
| | - A McNamara
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - H Paganetti
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - J Perl
- SLAC National Accelerator Laboratory, Menlo Park, CA, United States of America
| | - J Schuemann
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
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von der Linden J, Ramos-Mendez J, Faddegon B, Massin D, Fiksel G, Holder JP, Willingale L, Peebles J, Edwards MR, Chen H. 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)]. Rev Sci Instrum 2021; 92:059902. [PMID: 34243233 DOI: 10.1063/5.0054243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 06/13/2023]
Affiliation(s)
| | - Jose Ramos-Mendez
- Radiation Oncology, University of California, San Francisco, California 94143, USA
| | - Bruce Faddegon
- Radiation Oncology, University of California, San Francisco, California 94143, USA
| | - Devan Massin
- Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA
| | - Gennady Fiksel
- Center for Ultrafast Optical Science, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Joe P Holder
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Louise Willingale
- Center for Ultrafast Optical Science, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jonathan Peebles
- Laboratory for Laser Energetics, University of Rochester, Rochester, New York 14623, USA
| | - Matthew R Edwards
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Hui Chen
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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11
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von der Linden J, Ramos-Méndez 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. Rev Sci Instrum 2021; 92:033516. [PMID: 33820046 DOI: 10.1063/5.0040624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Electron-positron pairs, produced in intense laser-solid interactions, are diagnosed using magnetic spectrometers with image plates, such as the National Ignition Facility Electron-Positron-Proton Spectrometers (EPPSs). Although modeling can help infer the quantitative value, the accuracy of the models needs to be verified to ensure measurement quality. The dispersion of low-energy electrons and positrons may be affected by fringe magnetic fields near the entrance of the EPPS. We have calibrated the EPPS with six electron beams from a Siemens Oncor linear accelerator (linac) ranging in energy from 2.7 MeV to 15.2 MeV as they enter the spectrometer. A Geant4 traveling-wave optical parametric amplifier of superfluorescence Monte Carlo simulation was set up to match depth dose curves and lateral profiles measured in water at 100 cm source-surface distance. An accurate relationship was established between the bending magnet current setting and the energy of the electron beam at the exit window. The simulations and measurements were used to determine the energy distributions of the six electron beams at the EPPS slit. Analysis of the scanned image plates together with the determined energy distribution arriving in the spectrometer provides improved dispersion curves for the EPPS.
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Affiliation(s)
| | - José Ramos-Méndez
- Radiation Oncology, University of California, San Francisco, California 94143, USA
| | - Bruce Faddegon
- Radiation Oncology, University of California, San Francisco, California 94143, USA
| | - Devan Massin
- Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA
| | - Gennady Fiksel
- Center for Ultrafast Optical Science, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Joe P Holder
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Louise Willingale
- Center for Ultrafast Optical Science, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jonathan Peebles
- Laboratory for Laser Energetics, University of Rochester, Rochester, New York 14623, USA
| | - Matthew R Edwards
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Hui Chen
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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12
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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, Kyriakou I, Latyshev G, Le A, Mancini-Terracciano C, Maire M, Mantero A, Novak M, Omachi C, Pandola L, Perales A, Perrot Y, Petringa G, Quesada JM, Ramos-Méndez J, Romano F, Rosenfeld AB, Sarmiento LG, Sakata D, Sasaki T, Sechopoulos I, Simpson EC, Toshito T, Wright DH. Report on G4-Med, a Geant4 benchmarking system for medical physics applications developed by the Geant4 Medical Simulation Benchmarking Group. Med Phys 2021; 48:19-56. [PMID: 32392626 PMCID: PMC8054528 DOI: 10.1002/mp.14226] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 04/26/2020] [Accepted: 04/30/2020] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Geant4 is a Monte Carlo code extensively used in medical physics for a wide range of applications, such as dosimetry, micro- and nanodosimetry, imaging, radiation protection, and nuclear medicine. Geant4 is continuously evolving, so it is crucial to have a system that benchmarks this Monte Carlo code for medical physics against reference data and to perform regression testing. AIMS To respond to these needs, we developed G4-Med, a benchmarking and regression testing system of Geant4 for medical physics. MATERIALS AND METHODS G4-Med currently includes 18 tests. They range from the benchmarking of fundamental physics quantities to the testing of Monte Carlo simulation setups typical of medical physics applications. Both electromagnetic and hadronic physics processes and models within the prebuilt Geant4 physics lists are tested. The tests included in G4-Med are executed on the CERN computing infrastructure via the use of the geant-val web application, developed at CERN for Geant4 testing. The physical observables can be compared to reference data for benchmarking and to results of previous Geant4 versions for regression testing purposes. RESULTS This paper describes the tests included in G4-Med and shows the results derived from the benchmarking of Geant4 10.5 against reference data. DISCUSSION Our results indicate that the Geant4 electromagnetic physics constructor G4EmStandardPhysics_option4 gives a good agreement with the reference data for all the tests. The QGSP_BIC_HP physics list provided an overall adequate description of the physics involved in hadron therapy, including proton and carbon ion therapy. New tests should be included in the next stage of the project to extend the benchmarking to other physical quantities and application scenarios of interest for medical physics. CONCLUSION The results presented and discussed in this paper will aid users in tailoring physics lists to their particular application.
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Affiliation(s)
| | - D Bolst
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - M-C Bordage
- CRCT (INSERM and Paul Sabatier University), Toulouse, France
| | - J M C Brown
- Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
| | | | | | - D Cutajar
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | | | - L Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital, Lausanne, Switzerland
| | | | - A Dotti
- SLAC National Accelerator Laboratory, Stanford, CA, USA
| | - B Faddegon
- University of California, San Francisco, CA, USA
| | - C Fedon
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - S Guatelli
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, France
| | - V Ivanchenko
- Tomsk State University, Tomsk, Russian Federation
- CERN, Geneva, Switzerland
| | - D Konstantinov
- NRC "Kurchatov Institute" - IHEP, Protvino, Russian Federation
| | - I Kyriakou
- Medical Physics Laboratory, University of Ioannina, Ioannina, Greece
| | - G Latyshev
- NRC "Kurchatov Institute" - IHEP, Protvino, Russian Federation
| | - A Le
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | | | | | | | | | - C Omachi
- Nagoya Proton Therapy Center, Nagoya, Japan
| | | | - A Perales
- Medical Physics Department of Clínica Universidad de Navarra, Pamplona, Spain
| | - Y Perrot
- IRSN, Fontenay-aux-Roses, France
| | | | | | | | - F Romano
- INFN Catania Section, Catania, Italy
- Medical Physics Department, National Physical Laboratory, Teddington, UK
| | - A B Rosenfeld
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | | | - D Sakata
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | | | - I Sechopoulos
- Radboud University Medical Center, Nijmegen, The Netherlands
- Dutch Expert Center for Screening (LRCB), Nijmegen, The Netherlands
| | - E C Simpson
- Department of Nuclear Physics, Research School of Physics, Australian National University, Canberra, Australia
| | - T Toshito
- Nagoya Proton Therapy Center, Nagoya, Japan
| | - D H Wright
- SLAC National Accelerator Laboratory, Stanford, CA, USA
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13
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Tran HN, Ramos-Méndez J, Shin WG, Perrot Y, Faddegon B, Okada S, Karamitros M, Davídková M, Štěpán V, Incerti S, Villagrasa C. 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. Med Phys 2020; 48:890-901. [PMID: 33232522 PMCID: PMC7986154 DOI: 10.1002/mp.14612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/11/2023] Open
Abstract
Purpose Simulation of indirect damage originating from the attack of free radical species produced by ionizing radiation on biological molecules based on the independent pair approximation is investigated in this work. In addition, a new approach, relying on the independent pair approximation that is at the origin of the independent reaction time (IRT) method, is proposed in the chemical stage of Geant4‐DNA. Methods This new approach has been designed to respect the current Geant4‐DNA chemistry framework while proposing a variant IRT method. Based on the synchronous algorithm, this implementation allows us to access the information concerning the position of radicals and may make it more convenient for biological damage simulations. Estimates of the evolution of free species as well as biological hits in a segment of DNA chromatin fiber in Geant4‐DNA were compared for the dynamic time step approach of the step‐by‐step (SBS) method, currently used in Geant4‐DNA, and this newly implemented IRT. Results Results show a gain in computation time of a factor of 30 for high LET particle tracks with a better than 10% agreement on the number of DNA hits between the value obtained with the IRT method as implemented in this work and the SBS method currently available in Geant4‐DNA. Conclusion Offering in Geant4‐DNA more efficient methods for the chemical step based on the IRT method is a task in progress. For the calculation of biological damage, information on the position of chemical species is a crucial point. This can be achieved using the method presented in this paper.
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Affiliation(s)
- Hoang Ngoc Tran
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Wook-Geun Shin
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France.,Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea
| | - Yann Perrot
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Mathieu Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, In, 46556, USA
| | - Marie Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Sébastien Incerti
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
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14
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Zhu H, McNamara AL, McMahon SJ, Ramos-Mendez J, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J. Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio. Radiat Res 2020; 194:9-21. [PMID: 32401689 DOI: 10.1667/rr15531.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/11/2020] [Indexed: 12/21/2022]
Abstract
The cellular response to ionizing radiation continues to be of significant research interest in cancer radiotherapy, and DNA is recognized as the critical target for most of the biologic effects of radiation. Incident particles can cause initial DNA damages through physical and chemical interactions within a short time scale. Initial DNA damages can undergo repair via different pathways available at different stages of the cell cycle. The misrepair of DNA damage results in genomic rearrangement and causes mutations and chromosome aberrations, which are drivers of cell death. This work presents an integrated study of simulating cell response after proton irradiation with energies of 0.5-500 MeV (LET of 60-0.2 keV/µm). A model of a whole nucleus with fractal DNA geometry was implemented in TOPAS-nBio for initial DNA damage simulations. The default physics and chemistry models in TOPAS-nBio were used to describe interactions of primary particles, secondary particles, and radiolysis products within the nucleus. The initial DNA double-strand break (DSB) yield was found to increase from 6.5 DSB/Gy/Gbp at low-linear energy transfer (LET) of 0.2 keV/µm to 21.2 DSB/Gy/Gbp at high LET of 60 keV/µm. A mechanistic repair model was applied to predict the characteristics of DNA damage repair and dose response of chromosome aberrations. It was found that more than 95% of the DSBs are repaired within the first 24 h and the misrepaired DSB fraction increases rapidly with LET and reaches 15.8% at 60 keV/µm with an estimated chromosome aberration detection threshold of 3 Mbp. The dicentric and acentric fragment yields and the dose response of micronuclei formation after proton irradiation were calculated and compared with experimental results.
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Affiliation(s)
- Hongyu Zhu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China.,Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, P.R. China
| | - Aimee L McNamara
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Stephen J McMahon
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
| | - Jose Ramos-Mendez
- Department of Radiation Oncology, University of California San Francisco, California 94143
| | - Nicholas T Henthorn
- Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, California 94143
| | - Kathryn D Held
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Joseph Perl
- SLAC National Accelerator Laboratory, Menlo Park, California
| | - Junli Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China.,Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, P.R. China
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
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15
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Ramos-Méndez J, Shin WG, Karamitros M, Domínguez-Kondo J, Tran NH, Incerti S, Villagrasa C, Perrot Y, Štěpán V, Okada S, Moreno-Barbosa E, Faddegon B. Independent reaction times method in Geant4-DNA: Implementation and performance. Med Phys 2020; 47:5919-5930. [PMID: 32970844 DOI: 10.1002/mp.14490] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/07/2020] [Accepted: 09/13/2020] [Indexed: 11/10/2022] Open
Abstract
PURPOSE The simulation of individual particle tracks and the chemical stage following water radiolysis in biological tissue is an effective means of improving our knowledge of the physico-chemical contribution to the biological effect of ionizing radiation. However, the step-by-step simulation of the reaction kinetics of radiolytic species is the most time-consuming task in Monte Carlo track-structure simulations, with long simulation times that are an impediment to research. In this work, we present the implementation of the independent reaction times (IRT) method in Geant4-DNA Monte Carlo toolkit to improve the computational efficiency of calculating G-values, defined as the number of chemical species created or lost per 100 eV of deposited energy. METHODS The computational efficiency of IRT, as implemented, is compared to that from available Geant4-DNA step-by-step simulations for electrons, protons and alpha particles covering a wide range of linear energy transfer (LET). The accuracy of both methods is verified using published measured data from fast electron irradiations for • OH and e aq - for time-dependent G-values. For IRT, simulations in the presence of scavengers irradiated by cobalt-60 γ-ray and 2 MeV protons are compared with measured data for different scavenging capacities. In addition, a qualitative assessment comparing measured LET-dependent G-values with Geant4-DNA calculations in pure liquid water is presented. RESULTS The IRT improved the computational efficiency by three orders of magnitude relative to the step-by-step method while differences in G-values by 3.9% at 1 μs were found. At 7 ps, • OH and e aq - yields calculated with IRT differed from recent published measured data by 5% ± 4% and 2% ± 4%, respectively. At 1 μs, differences were 9% ± 5% and 6% ± 7% for • OH and e aq - , respectively. Uncertainties are one standard deviation. Finally, G-values at different scavenging capacities and LET-dependent G-values reproduced the behavior of measurements for all radiation qualities. CONCLUSION The comprehensive validation of the Geant4-DNA capabilities to accurately simulate the chemistry following water radiolysis is an ongoing work. The implementation presented in this work is a necessary step to facilitate performing such a task.
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Affiliation(s)
- José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Wook-Geun Shin
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France.,Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea
| | - Mathieu Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jorge Domínguez-Kondo
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla PUE, 72000, Mexico
| | - Ngoc Hoang Tran
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France
| | - Sebastien Incerti
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, BP17, Fontenay-aux-Roses, 92262, France
| | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, BP17, Fontenay-aux-Roses, 92262, France
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Eduardo Moreno-Barbosa
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla PUE, 72000, Mexico
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
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16
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Ramos-Méndez J, Domínguez-Kondo N, Schuemann J, McNamara A, Moreno-Barbosa E, Faddegon B. LET-Dependent Intertrack Yields in Proton Irradiation at Ultra-High Dose Rates Relevant for FLASH Therapy. Radiat Res 2020; 194:351-362. [PMID: 32857855 PMCID: PMC7644138 DOI: 10.1667/rade-20-00084.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/13/2020] [Indexed: 01/01/2023]
Abstract
FLASH radiotherapy delivers a high dose (≥10 Gy) at a high rate (≥40 Gy/s). In this way, particles are delivered in pulses as short as a few nanoseconds. At that rate, intertrack reactions between chemical species produced within the same pulse may affect the heterogeneous chemistry stage of water radiolysis. This stochastic process suits the capabilities of the Monte Carlo method, which can model intertrack effects to aid in radiobiology research, including the design and interpretation of experiments. In this work, the TOPAS-nBio Monte Carlo track-structure code was expanded to allow simulations of intertrack effects in the chemical stage of water radiolysis. Simulation of the behavior of radiolytic yields over a long period of time (up to 50 s) was verified by simulating radiolysis in a Fricke dosimeter irradiated by 60Co γ rays. In addition, LET-dependent G values of protons delivered in single squared pulses of widths, 1 ns, 1 µs and 10 µs, were obtained and compared to simulations using no intertrack considerations. The Fricke simulation for the calculated G value of Fe3+ ion at 50 s was within 0.4% of the accepted value from ICRU Report 34. For LET-dependent G values at the end of the chemical stage, intertrack effects were significant at LET values below 2 keV/µm. Above 2 keV/µm the reaction kinetics remained limited locally within each track and thus, effects of intertrack reactions remained low. Therefore, when track structure simulations are used to investigate the biological damage of FLASH irradiation, these intertrack reactions should be considered. The TOPAS-nBio framework with the expansion to intertrack chemistry simulation provides a useful tool to assist in this task.
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Affiliation(s)
- J. Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - N. Domínguez-Kondo
- Facultad de Ciencias Físico-Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - J. Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - A. McNamara
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - E. Moreno-Barbosa
- Facultad de Ciencias Físico-Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
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Carrasco-Hernández J, Ramos-Méndez J, Faddegon B, Jalilian AR, Moranchel M, Ávila-Rodríguez MA. Monte Carlo track-structure for the radionuclide Copper-64: characterization of S-values, nanodosimetry and quantification of direct damage to DNA. Phys Med Biol 2020; 65:155005. [PMID: 32303013 DOI: 10.1088/1361-6560/ab8aaa] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
TOPAS-nBio was used to simulate, collision-to-collision, the complete trajectories of electrons in water generated during the explicit simulation of 64Cu decay. S-values and direct damage to the DNA were calculated representing the cell (C) and the cell nucleus (N) with concentric spheres of 5 μm and 4 μm in radius, respectively. The considered 'target'←'source' configurations, including the cell surface (Cs) and cytoplasm (Cy), were: C←C, C←Cs, N←N, N←Cy and N←Cs. Ionization cluster size distributions were also calculated in a cylinder immersed in water corresponding to a DNA segment of 10 base-pairs in length (diameter 2.3 nm, length 3.4 nm), modeling a radioactive point source moving from the central axis to the edge of the cylinder. For that, the first moment (M1) and cumulative probability of having a cluster size of 2 or more ionizations in the cylindrical volume (F2) were obtained. Finally, the direct damage to the DNA was estimated by quantifying double-strand breaks (DSBs) using the clustering algorithm DBSCAN. The S-values obtained with TOPAS-nBio for 64Cu were 7.879 × 10-4 ± 5 × 10-7, 4.351 × 10-4 ± 6 × 10-7, 1.442 × 10-3 ± 1 × 10-6, 2.596 × 10-4 ± 8 × 10-7, 1.127 × 10-4 ± 4 × 10-7 Gy Bq-s-1 for the configurations C←C, C←Cs, N←N, N←Cy and N←Cs, respectively. The difference of these values, compared with previously reported S-values for 64Cu with the code MNCP and software MIRDCell, ranged from -4% to -25% for the configurations N←N and N←Cs, respectively. On the other hand, F2 was maximum with the source at the center of the cylinder 0.373 ± 0.001, and monotonically decreased until reaching a value of 0.058 ± 0.001 at 2.3 nm. The same behavior was observed for M1 with values ranging from 2.188 ± 0.004 to 0.242 ± 0.002. Finally, the DBSCAN algorithm showed that the mean number of DNA DSBs per decay were 0.187 ± 0.001, 0.0317 ± 0.0005, and 0.0125 ± 0.0002 DSB-(Bq-s)-1 for the configurations N←N, N←Cs, and N←Cy, respectively. In conclusion, the results of the S-values show that the absorbed dose strongly depends on the distribution of the radionuclide in the cell, the dose being higher when 64Cu is internalized in the cell nucleus, which is reinforced by the nanodosimetric study by the presence of DNA DSBs attributable to the Auger electrons emitted during the decay of 64Cu.
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Affiliation(s)
- J Carrasco-Hernández
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Ciudad de México 07738, México
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Zhu H, McNamara AL, Ramos-Mendez J, McMahon SJ, 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. Phys Med Biol 2020; 65:085015. [PMID: 32101803 DOI: 10.1088/1361-6560/ab7a6b] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Monte Carlo (MC) track structure simulation tools are commonly used for predicting radiation induced DNA damage by modeling the physical and chemical reactions at the nanometer scale. However, the outcome of these MC simulations is particularly sensitive to the adopted parameters which vary significantly across studies. In this study, a previously developed full model of nuclear DNA was used to describe the DNA geometry. The TOPAS-nBio MC toolkit was used to investigate the impact of physics and chemistry models as well as three key parameters (the energy threshold for direct damage, the chemical stage time length, and the probability of damage between hydroxyl radical reactions with DNA) on the induction of DNA damage. Our results show that the difference in physics and chemistry models alone can cause differences up to 34% and 16% in the DNA double strand break (DSB) yield, respectively. Additionally, changing the direct damage threshold, chemical stage length, and hydroxyl damage probability can cause differences of up to 28%, 51%, and 71% in predicted DSB yields, respectively, for the configurations in this study.
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Affiliation(s)
- Hongyu Zhu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, United States of America. Department of Engineering Physics, Tsinghua University, Beijing 100084, People's Republic of China. Key Laboratory of Particle and Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, People's Republic of China
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19
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Faddegon B, Ramos-Méndez J, Schuemann J, McNamara A, Shin J, Perl J, Paganetti H. The TOPAS tool for particle simulation, a Monte Carlo simulation tool for physics, biology and clinical research. Phys Med 2020; 72:114-121. [PMID: 32247964 DOI: 10.1016/j.ejmp.2020.03.019] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/06/2020] [Accepted: 03/19/2020] [Indexed: 01/02/2023] Open
Abstract
PURPOSE This paper covers recent developments and applications of the TOPAS TOol for PArticle Simulation and presents the approaches used to disseminate TOPAS. MATERIALS AND METHODS Fundamental understanding of radiotherapy and imaging is greatly facilitated through accurate and detailed simulation of the passage of ionizing radiation through apparatus and into a patient using Monte Carlo (MC). TOPAS brings Geant4, a reliable, experimentally validated MC tool mainly developed for high energy physics, within easy reach of medical physicists, radiobiologists and clinicians. Requiring no programming knowledge, TOPAS provides all of the flexibility of Geant4. RESULTS After 5 years of development followed by its initial release, TOPAS was subsequently expanded from its focus on proton therapy physics to incorporate radiobiology modeling. Next, in 2018, the developers expanded their user support and code maintenance as well as the scope of TOPAS towards supporting X-ray and electron therapy and medical imaging. Improvements have been achieved in user enhancement through software engineering and a graphical user interface, calculational efficiency, validation through experimental benchmarks and QA measurements, and either newly available or recently published applications. A large and rapidly increasing user base demonstrates success in our approach to dissemination of this uniquely accessible and flexible MC research tool. CONCLUSIONS The TOPAS developers continue to make strides in addressing the needs of the medical community in applications of ionizing radiation to medicine, creating the only fully integrated platform for four-dimensional simulation of all forms of radiotherapy and imaging with ionizing radiation, with a design that promotes inter-institutional collaboration.
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Affiliation(s)
- Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Jan Schuemann
- Massachusetts General Hospital and Harvard Medical School, Boston, USA
| | - Aimee McNamara
- Massachusetts General Hospital and Harvard Medical School, Boston, USA
| | - Jungwook Shin
- Massachusetts General Hospital and Harvard Medical School, Boston, USA
| | - Joseph Perl
- SLAC National Accelerator Laboratory, Menlo Park, USA
| | - Harald Paganetti
- Massachusetts General Hospital and Harvard Medical School, Boston, USA
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Ma CMC, Chetty IJ, Deng J, Faddegon B, Jiang SB, Li J, Seuntjens J, Siebers JV, Traneus E. Beam modeling and beam model commissioning for Monte Carlo dose calculation-based radiation therapy treatment planning: Report of AAPM Task Group 157. Med Phys 2019; 47:e1-e18. [PMID: 31679157 DOI: 10.1002/mp.13898] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 10/01/2019] [Accepted: 10/18/2019] [Indexed: 11/07/2022] Open
Abstract
Dose calculation plays an important role in the accuracy of radiotherapy treatment planning and beam delivery. The Monte Carlo (MC) method is capable of achieving the highest accuracy in radiotherapy dose calculation and has been implemented in many commercial systems for radiotherapy treatment planning. The objective of this task group was to assist clinical physicists with the potentially complex task of acceptance testing and commissioning MC-based treatment planning systems (TPS) for photon and electron beam dose calculations. This report provides an overview on the general approach of clinical implementation and testing of MC-based TPS with a specific focus on models of clinical photon and electron beams. Different types of beam models are described including those that utilize MC simulation of the treatment head and those that rely on analytical methods and measurements. The trade-off between accuracy and efficiency in the various source-modeling approaches is discussed together with guidelines for acceptance testing of MC-based TPS from the clinical standpoint. Specific recommendations are given on methods and practical procedures to commission clinical beam models for MC-based TPS.
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Affiliation(s)
- Chang Ming Charlie Ma
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Indrin J Chetty
- Radiation Oncology Department, Henry Ford Health System, Detroit, MI, 48188, USA
| | - Jun Deng
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06032, USA
| | - Bruce Faddegon
- Department of Radiation Oncology, UCSF, San Francisco, CA, 94143, USA
| | - Steve B Jiang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Jan Seuntjens
- Medical Physics Unit, McGill University, Montreal, QC, H4A 3J1, Canada
| | - Jeffrey V Siebers
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Erik Traneus
- RaySearch Laboratories AB, SE-103 65, Stockholm, Sweden
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Blakely EA, Faddegon B, Tinkle C, Bloch C, Dominello M, Griffin RJ, Joiner MC, Burmeister J. Three discipline collaborative radiation therapy (3DCRT) special debate: The United States needs at least one carbon ion facility. J Appl Clin Med Phys 2019; 20:6-13. [PMID: 31573146 PMCID: PMC6839391 DOI: 10.1002/acm2.12727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 01/07/2023] Open
Affiliation(s)
| | - Bruce Faddegon
- Department of Radiation OncologyUniversity of California – San FranciscoSan FranciscoCAUSA
| | - Christopher Tinkle
- Department of Radiation OncologySt. Jude Children’s Research HospitalMemphisTNUSA
| | - Charles Bloch
- Department of Radiation OncologyUniversity of WashingtonSeattleWAUSA
| | - Michael Dominello
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Robert J Griffin
- Department of OncologyUniversity of Arkansas for Medical SciencesLittle RockARUSA
| | - Michael C Joiner
- Department of OncologyWayne State University School of MedicineDetroitMIUSA
| | - Jay Burmeister
- Department of OncologyWayne State University School of MedicineDetroitMIUSA,Gershenson Radiation Oncology CenterBarbara Ann Karmanos Cancer InstituteDetroitMIUSA
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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, Srivastava A, Obcemea C, Nath AK, Sharma A, Buchsbaum J. Monte Carlo Processing on a Chip (MCoaC)-preliminary experiments toward the realization of optimal-hardware for TOPAS/Geant4 to drive discovery. Phys Med 2019; 64:166-173. [PMID: 31515016 DOI: 10.1016/j.ejmp.2019.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/21/2019] [Accepted: 06/29/2019] [Indexed: 01/23/2023] Open
Abstract
Amongst the scientific frameworks powered by the Monte Carlo (MC) toolkit Geant4 (Agostinelli et al., 2003), the TOPAS (Tool for Particle Simulation) (Perl et al., 2012) is one. TOPAS focuses on providing ease of use, and has significant implementation in the radiation oncology space at present. TOPAS functionality extends across the full capacity of Geant4, is freely available to non-profit users, and is being extended into radiobiology via TOPAS-nBIO (Ramos-Mendez et al., 2018). A current "grand problem" in cancer therapy is to convert the dose of treatment from physical dose to biological dose, optimized ultimately to the individual context of administration of treatment. Biology MC calculations are some of the most complex and require significant computational resources. In order to enhance TOPAS's ability to become a critical tool to explore the definition and application of biological dose in radiation therapy, we chose to explore the use of Field Programmable Gate Array (FPGA) chips to speedup the Geant4 calculations at the heart of TOPAS, because this approach called "Reconfigurable Computing" (RC), has proven able to produce significant (around 90x) (Sajish et al., 2012) speed increases in scientific computing. Here, we describe initial steps to port Geant4 and TOPAS to be used on FPGA. We provide performance analysis of the current TOPAS/Geant4 code from an RC implementation perspective. Baseline benchmarks are presented. Achievable performance figures of the subsections of the code on optimal hardware are presented; Aspects of practical implementation of "Monte Carlo on a chip" are also discussed.
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Affiliation(s)
| | - Sachin Dev
- Open Health Systems Laboratory (OHSL), USA
| | - O S Sarun
- Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - Amit Saxena
- Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - Rajendra Joshi
- Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - Hemant Darbari
- Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - C Sajish
- Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - U B Sonavane
- Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - Vivek Gavane
- Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - Abhay Deshpande
- Society for Applied Microwave Electronics Engineering & Research (SAMEER), Mumbai, India
| | - Tanuja Dixit
- Society for Applied Microwave Electronics Engineering & Research (SAMEER), Mumbai, India
| | - Rajesh Harsh
- Society for Applied Microwave Electronics Engineering & Research (SAMEER), Mumbai, India
| | | | - G K Rath
- All India Institute of Medical Sciences (AIIMS), Delhi, India
| | | | | | - Joseph Perl
- SLAC National Accelerator Laboratory, Menlo Park, USA
| | - Harald Paganetti
- Massachusetts General Hospital and Harvard Medical School, Boston, USA
| | - Jan Schuemann
- Massachusetts General Hospital and Harvard Medical School, Boston, USA
| | | | | | - Asheet K Nath
- Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - Ashok Sharma
- All India Institute of Medical Sciences (AIIMS), Delhi, India
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Zhu H, Chen Y, Sung W, McNamara AL, Tran LT, Burigo LN, Rosenfeld AB, Li J, Faddegon B, Schuemann J, Paganetti H. The microdosimetric extension in TOPAS: development and comparison with published data. Phys Med Biol 2019; 64:145004. [PMID: 31117056 DOI: 10.1088/1361-6560/ab23a3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Microdosimetric energy depositions have been suggested as a key variable for the modeling of the relative biological effectiveness (RBE) in proton and ion radiation therapy. However, microdosimetry has been underutilized in radiation therapy. Recent advances in detector technology allow the design of new mico- and nano-dosimeters. At the same time Monte Carlo (MC) simulations have become more widely used in radiation therapy. In order to address the growing interest in the field, a microdosimetric extension was developed in TOPAS. The extension provides users with the functionality to simulate microdosimetric spectra as well as the contribution of secondary particles to the spectra, calculate microdosimetric parameters, and determine RBE with a biological weighting function approach or with the microdosimetric kinetic (MK) model. Simulations were conducted with the extension and the results were compared with published experimental data and other simulation results for three types of microdosimeters, a spherical tissue equivalent proportional counter (TEPC), a cylindrical TEPC and a solid state microdosimeter. The corresponding microdosimetric spectra obtained with TOPAS from the plateau region to the distal tail of the Bragg curve generally show good agreement with the published data.
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Affiliation(s)
- Hongyu Zhu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, United States of America. Department of Engineering Physics, Tsinghua University, Beijing 100084, People's Republic of China. Key Laboratory of Particle and Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, People's Republic of China
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Burigo LN, Ramos-Méndez J, Bangert M, Schulte RW, Faddegon B. Simultaneous optimization of RBE-weighted dose and nanometric ionization distributions in treatment planning with carbon ions. Phys Med Biol 2019; 64:015015. [PMID: 30523890 DOI: 10.1088/1361-6560/aaf400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Inverse treatment planning in intensity modulated particle therapy (IMPT) with scanned carbon-ion beams is currently based on the optimization of RBE-weighted dose to satisfy requirements of target coverage and limited toxicity to organs-at-risk (OARs) and healthy tissues. There are many feasible IMPT plans that meet these requirements, which allows the introduction of further criteria to narrow the selection of a biologically optimal treatment plan. We propose a novel treatment planning strategy based on the simultaneous optimization of RBE-weighted dose and nanometric ionization details (ID) as a new physical characteristic of the delivered plan beyond LET. In particular, we focus on the distribution of large ionization clusters (more than 3 ionizations) to enhance the biological effect across the target volume while minimizing biological effect in normal tissues. Carbon-ion treatment plans for different patient geometries and beam configurations generated with the simultaneous optimization strategy were compared against reference plans obtained with RBE-weighted dose optimization alone. Quality indicators, inhomogeneity index and planning volume histograms of RBE-weighted dose and large ionization clusters were used to evaluate the treatment plans. We show that with simultaneous optimization, ID distributions can be optimized in carbon-ion radiotherapy without compromising the RBE-weighted dose distributions. This strategy can potentially be used to account for optimization of endpoints closely related to radiation quality to achieve better tumor control and reduce risks of complications.
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Affiliation(s)
- Lucas N Burigo
- German Cancer Research Center-DKFZ, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany. National Center for Radiation Research in Oncology - NCRO, Heidelberg Institute for Radiation Oncology - HIRO Heidelberg, Germany. Author to whom any correspondence should be addressed
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Schuemann J, McNamara AL, Ramos-Méndez J, Perl J, Held KD, Paganetti H, Incerti S, Faddegon B. TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology. Radiat Res 2019; 191:125-138. [PMID: 30609382 DOI: 10.1667/rr15226.1] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The TOPAS Monte Carlo (MC) system is used in radiation therapy and medical imaging research, having played a significant role in making Monte Carlo simulations widely available for proton therapy related research. While TOPAS provides detailed simulations of patient scale properties, the fundamental unit of the biological response to radiation is a cell. Thus, our goal was to develop TOPAS-nBio, an extension of TOPAS dedicated to advance understanding of radiobiological effects at the (sub-)cellular, (i.e., the cellular and sub-cellular) scale. TOPAS-nBio was designed as a set of open source classes that extends TOPAS to model radiobiological experiments. TOPAS-nBio is based on and extends Geant4-DNA, which extends the Geant4 toolkit, the basis of TOPAS, to include very low-energy interactions of particles down to vibrational energies, explicitly simulates every particle interaction (i.e., without using condensed histories) and propagates radiolysis products. To further facilitate the use of TOPAS-nBio, a graphical user interface was developed. TOPAS-nBio offers full track-structure Monte Carlo simulations, integration of chemical reactions within the first millisecond, an extensive catalogue of specialized cell geometries as well as sub-cellular structures such as DNA and mitochondria, and interfaces to mechanistic models of DNA repair kinetics. We compared TOPAS-nBio simulations to measured and published data of energy deposition patterns and chemical reaction rates (G values). Our simulations agreed well within the experimental uncertainties. Additionally, we expanded the chemical reactions and species provided in Geant4-DNA and developed a new method based on independent reaction times (IRT), including a total of 72 reactions classified into 6 types between neutral and charged species. Chemical stage simulations using IRT were a factor of 145 faster than with step-by-step tracking. Finally, we applied the geometric/chemical modeling to obtain initial yields of double-strand breaks (DSBs) in DNA fibers for proton irradiations of 3 and 50 MeV and compared the effect of including chemical reactions on the number and complexity of DSB induction. Over half of the DSBs were found to include chemical reactions with approximately 5% of DSBs caused only by chemical reactions. In conclusion, the TOPAS-nBio extension to the TOPAS MC application offers access to accurate and detailed multiscale simulations, from a macroscopic description of the radiation field to microscopic description of biological outcome for selected cells. TOPAS-nBio offers detailed physics and chemistry simulations of radiobiological experiments on cells simulating the initially induced damage and links to models of DNA repair kinetics.
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Affiliation(s)
- J Schuemann
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - A L McNamara
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - J Ramos-Méndez
- b Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - J Perl
- c SLAC National Accelerator Laboratory, Menlo Park, California
| | - K D Held
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - H Paganetti
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - S Incerti
- d CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France.,e University of Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
| | - B Faddegon
- b Department of Radiation Oncology, University of California San Francisco, San Francisco, California
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Ramos-Méndez J, Burigo LN, Schulte R, Chuang C, Faddegon B. Fast calculation of nanodosimetric quantities in treatment planning of proton and ion therapy. ACTA ACUST UNITED AC 2018; 63:235015. [DOI: 10.1088/1361-6560/aaeeee] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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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, Friedland W, Kundrát P, Ottolenghi A, Baiocco G, Barbieri S, Dingfelder M, Incerti S, Villagrasa C, Bueno M, Bernal MA, Guatelli S, Sakata D, Brown JMC, Francis Z, Kyriakou I, Lampe N, Ballarini F, Carante MP, Davídková M, Štěpán V, Jia X, Cucinotta FA, Schulte R, Stewart RD, Carlson DJ, Galer S, Kuncic Z, Lacombe S, Milligan J, Cho SH, Sawakuchi G, Inaniwa T, Sato T, Li W, Solov'yov AV, Surdutovich E, Durante M, Prise KM, McMahon SJ. A New Standard DNA Damage (SDD) Data Format. Radiat Res 2018; 191:76-92. [PMID: 30407901 DOI: 10.1667/rr15209.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Our understanding of radiation-induced cellular damage has greatly improved over the past few decades. Despite this progress, there are still many obstacles to fully understand how radiation interacts with biologically relevant cellular components, such as DNA, to cause observable end points such as cell killing. Damage in DNA is identified as a major route of cell killing. One hurdle when modeling biological effects is the difficulty in directly comparing results generated by members of different research groups. Multiple Monte Carlo codes have been developed to simulate damage induction at the DNA scale, while at the same time various groups have developed models that describe DNA repair processes with varying levels of detail. These repair models are intrinsically linked to the damage model employed in their development, making it difficult to disentangle systematic effects in either part of the modeling chain. These modeling chains typically consist of track-structure Monte Carlo simulations of the physical interactions creating direct damages to DNA, followed by simulations of the production and initial reactions of chemical species causing so-called "indirect" damages. After the induction of DNA damage, DNA repair models combine the simulated damage patterns with biological models to determine the biological consequences of the damage. To date, the effect of the environment, such as molecular oxygen (normoxic vs. hypoxic), has been poorly considered. We propose a new standard DNA damage (SDD) data format to unify the interface between the simulation of damage induction in DNA and the biological modeling of DNA repair processes, and introduce the effect of the environment (molecular oxygen or other compounds) as a flexible parameter. Such a standard greatly facilitates inter-model comparisons, providing an ideal environment to tease out model assumptions and identify persistent, underlying mechanisms. Through inter-model comparisons, this unified standard has the potential to greatly advance our understanding of the underlying mechanisms of radiation-induced DNA damage and the resulting observable biological effects when radiation parameters and/or environmental conditions change.
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Affiliation(s)
- J Schuemann
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - A L McNamara
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - J W Warmenhoven
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - N T Henthorn
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - K J Kirkby
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - M J Merchant
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - S Ingram
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - H Paganetti
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - K D Held
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - J Ramos-Mendez
- c Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - B Faddegon
- c Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - J Perl
- d SLAC National Accelerator Laboratory, Menlo Park, California
| | - D T Goodhead
- e Medical Research Council, Harwell, United Kingdom
| | | | - H Rabus
- g Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany.,h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany
| | - H Nettelbeck
- g Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany.,h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany
| | - W Friedland
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - P Kundrát
- i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - A Ottolenghi
- j Physics Department, University of Pavia, Pavia, Italy
| | - G Baiocco
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,j Physics Department, University of Pavia, Pavia, Italy
| | - S Barbieri
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,j Physics Department, University of Pavia, Pavia, Italy
| | - M Dingfelder
- k Department of Physics, East Carolina University, Greenville, North Carolina
| | - S Incerti
- l CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France.,m University of Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
| | - C Villagrasa
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,n Institut de Radioprotection et Sûreté Nucléaire, F-92262 Fontenay aux Roses Cedex, France
| | - M Bueno
- n Institut de Radioprotection et Sûreté Nucléaire, F-92262 Fontenay aux Roses Cedex, France
| | - M A Bernal
- o Applied Physics Department, Gleb Wataghin Institute of Physics, State University of Campinas, Campinas, SP, Brazil
| | - S Guatelli
- p Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW, Australia
| | - D Sakata
- p Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW, Australia
| | - J M C Brown
- q Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
| | - Z Francis
- r Department of Physics, Faculty of Science, Saint Joseph University, Beirut, Lebanon
| | - I Kyriakou
- s Medical Physics Laboratory, University of Ioannina Medical School, Ioannina, Greece
| | - N Lampe
- l CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - F Ballarini
- j Physics Department, University of Pavia, Pavia, Italy.,t Italian National Institute of Nuclear Physics, Section of Pavia, I-27100 Pavia, Italy
| | - M P Carante
- j Physics Department, University of Pavia, Pavia, Italy.,t Italian National Institute of Nuclear Physics, Section of Pavia, I-27100 Pavia, Italy
| | - M Davídková
- u Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Řež, Czech Republic
| | - V Štěpán
- u Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Řež, Czech Republic
| | - X Jia
- v Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - F A Cucinotta
- w Health Physics and Diagnostic Sciences, University of Nevada Las Vegas, Las Vegas, Nevada
| | - R Schulte
- x Division of Biomedical Engineering Sciences, School of Medicine, Loma Linda University, Loma Linda, California
| | - R D Stewart
- y Department of Radiation Oncology, University of Washington, Seattle, Washington
| | - D J Carlson
- z Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut
| | - S Galer
- aa Medical Radiation Science Group, National Physical Laboratory, Teddington, United Kingdom
| | - Z Kuncic
- bb School of Physics, University of Sydney, Sydney, NSW, Australia
| | - S Lacombe
- cc Institut des Sciences Moléculaires d'Orsay (UMR 8214) University Paris-Sud, CNRS, University Paris-Saclay, 91405 Orsay Cedex, France
| | | | - S H Cho
- ee Department of Radiation Physics and Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - G Sawakuchi
- ee Department of Radiation Physics and Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - T Inaniwa
- ff Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, Chiba, Japan
| | - T Sato
- gg Japan Atomic Energy Agency, Nuclear Science and Engineering Center, Tokai 319-1196, Japan
| | - W Li
- i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,hh Task Group 7.7 "Internal Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany
| | - A V Solov'yov
- ii MBN Research Center, 60438 Frankfurt am Main, Germany
| | - E Surdutovich
- jj Department of Physics, Oakland University, Rochester, Michigan
| | - M Durante
- kk GSI Helmholtzzentrum für Schwerionenforschung, Biophysics Department, Darmstadt, Germany
| | - K M Prise
- ll Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
| | - S J McMahon
- ll Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
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Lazar AA, Schulte R, Faddegon B, Blakely EA, Roach M. Clinical trials involving carbon-ion radiation therapy and the path forward. Cancer 2018; 124:4467-4476. [PMID: 30307603 DOI: 10.1002/cncr.31662] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/22/2018] [Accepted: 06/29/2018] [Indexed: 02/06/2023]
Abstract
To describe the international landscape of clinical trials in carbon-ion radiotherapy (CIRT), the authors reviewed the current status of 63 ongoing clinical trials (median, 47 participants) involving CIRT identified from the US clinicaltrials.gov trial registry and the World Health Organization International Clinical Trials Platform Registry. The objectives were to evaluate the potential for these trials to define the role of this modality in the treatment of specific cancer types and identify the major challenges and opportunities to advance this technology. A significant body of literature suggested the potential for advantageous dose distributions and, in preclinical biologic studies, the enhanced effectiveness for CIRT compared with photons and protons. In addition, clinical evidence from phase I/II trials, although limited, indicated the potential for CIRT to improve cancer outcomes. However, current high-level phase III randomized clinical trial evidence does not exist. Although there has been an increase in the number of trials investigating CIRT since 2010, and the number of countries and sites offering CIRT is slowly growing, this progress has excluded other countries. Several recommendations are proposed to study this modality to accelerate progress in the field, including: 1) increasing the number of multinational randomized clinical trials, 2) leveraging the existing CIRT facilities to launch larger multinational trials directed at common cancers combined with high-level quality assurance; and 3) developing more compact and less expensive next-generation treatment systems integrated with radiobiologic research and preclinical testing.
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Affiliation(s)
- Ann A Lazar
- Department of Preventive and Restorative Dental Sciences, University of California San Francisco (UCSF), San Francisco, California.,Department of Epidemiology and Biostatistics, UCSF, San Francisco, California
| | - Reinhard Schulte
- Department of Radiation Oncology, UCSF, San Francisco, California.,Department of Basic Sciences, Division of Biomedical Engineering Sciences, Loma Linda University, Loma Linda, California
| | - Bruce Faddegon
- Department of Radiation Oncology, UCSF, San Francisco, California
| | - Eleanor A Blakely
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Mack Roach
- Department of Radiation Oncology, UCSF, San Francisco, California
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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. Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit. Phys Med Biol 2018; 63:175018. [PMID: 30088810 DOI: 10.1088/1361-6560/aad8eb] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Computational simulations, such as Monte Carlo track structure simulations, offer a powerful tool for quantitatively investigating radiation interactions within cells. The modelling of the spatial distribution of energy deposition events as well as diffusion of chemical free radical species, within realistic biological geometries, can help provide a comprehensive understanding of the effects of radiation on cells. Track structure simulations, however, generally require advanced computing skills to implement. The TOPAS-nBio toolkit, an extension to TOPAS (TOol for PArticle Simulation), aims to provide users with a comprehensive framework for radiobiology simulations, without the need for advanced computing skills. This includes providing users with an extensive library of advanced, realistic, biological geometries ranging from the micrometer scale (e.g. cells and organelles) down to the nanometer scale (e.g. DNA molecules and proteins). Here we present the geometries available in TOPAS-nBio.
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Affiliation(s)
- Aimee L McNamara
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, 30 Fruit St, Boston, MA 02114, United States of America
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Abstract
Simulation of water radiolysis and the subsequent chemistry provides important information on the effect of ionizing radiation on biological material. The Geant4 Monte Carlo toolkit has added chemical processes via the Geant4-DNA project. The TOPAS tool simplifies the modeling of complex radiotherapy applications with Geant4 without requiring advanced computational skills, extending the pool of users. Thus, a new extension to TOPAS, TOPAS-nBio, is under development to facilitate the configuration of track-structure simulations as well as water radiolysis simulations with Geant4-DNA for radiobiological studies. In this work, radiolysis simulations were implemented in TOPAS-nBio. Users may now easily add chemical species and their reactions, and set parameters including branching ratios, dissociation schemes, diffusion coefficients, and reaction rates. In addition, parameters for the chemical stage were re-evaluated and updated from those used by default in Geant4-DNA to improve the accuracy of chemical yields. Simulation results of time-dependent and LET-dependent primary yields Gx (chemical species per 100 eV deposited) produced at neutral pH and 25 °C by short track-segments of charged particles were compared to published measurements. The LET range was 0.05-230 keV µm-1. The calculated Gx values for electrons satisfied the material balance equation within 0.3%, similar for protons albeit with long calculation time. A smaller geometry was used to speed up proton and alpha simulations, with an acceptable difference in the balance equation of 1.3%. Available experimental data of time-dependent G-values for [Formula: see text] agreed with simulated results within 7% ± 8% over the entire time range; for [Formula: see text] over the full time range within 3% ± 4%; for H2O2 from 49% ± 7% at earliest stages and 3% ± 12% at saturation. For the LET-dependent Gx, the mean ratios to the experimental data were 1.11 ± 0.98, 1.21 ± 1.11, 1.05 ± 0.52, 1.23 ± 0.59 and 1.49 ± 0.63 (1 standard deviation) for [Formula: see text], [Formula: see text], H2, H2O2 and [Formula: see text], respectively. In conclusion, radiolysis and subsequent chemistry with Geant4-DNA has been successfully incorporated in TOPAS-nBio. Results are in reasonable agreement with published measured and simulated data.
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Affiliation(s)
- J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America. Author to whom any correspondence should be addressed
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Ramos-Méndez J, Schuemann J, Incerti S, Paganetti H, Schulte R, Faddegon B. Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations. Phys Med Biol 2017; 62:5908-5925. [PMID: 28594336 DOI: 10.1088/1361-6560/aa7831] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Flagged uniform particle splitting was implemented with two methods to improve the computational efficiency of Monte Carlo track structure simulations with TOPAS-nBio by enhancing the production of secondary electrons in ionization events. In method 1 the Geant4 kernel was modified. In method 2 Geant4 was not modified. In both methods a unique flag number assigned to each new split electron was inherited by its progeny, permitting reclassification of the split events as if produced by independent histories. Computational efficiency and accuracy were evaluated for simulations of 0.5-20 MeV protons and 1-20 MeV u-1 carbon ions for three endpoints: (1) mean of the ionization cluster size distribution, (2) mean number of DNA single-strand breaks (SSBs) and double-strand breaks (DSBs) classified with DBSCAN, and (3) mean number of SSBs and DSBs classified with a geometry-based algorithm. For endpoint (1), simulation efficiency was 3 times lower when splitting electrons generated by direct ionization events of primary particles than when splitting electrons generated by the first ionization events of secondary electrons. The latter technique was selected for further investigation. The following results are for method 2, with relative efficiencies about 4.5 times lower for method 1. For endpoint (1), relative efficiency at 128 split electrons approached maximum, increasing with energy from 47.2 ± 0.2 to 66.9 ± 0.2 for protons, decreasing with energy from 51.3 ± 0.4 to 41.7 ± 0.2 for carbon. For endpoint (2), relative efficiency increased with energy, from 20.7 ± 0.1 to 50.2 ± 0.3 for protons, 15.6 ± 0.1 to 20.2 ± 0.1 for carbon. For endpoint (3) relative efficiency increased with energy, from 31.0 ± 0.2 to 58.2 ± 0.4 for protons, 23.9 ± 0.1 to 26.2 ± 0.2 for carbon. Simulation results with and without splitting agreed within 1% (2 standard deviations) for endpoints (1) and (2), within 2% (1 standard deviation) for endpoint (3). In conclusion, standard particle splitting variance reduction techniques can be successfully implemented in Monte Carlo track structure codes.
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Affiliation(s)
- José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
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Piersimoni P, Bashkirov V, Faddegon B, Méndez JR, Schulte R, Seco J. Session 24: Imaging and image processing II – X-Ray and multimodal imaging. BIOMED ENG-BIOMED TE 2017. [DOI: 10.1515/bmt-2017-5045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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McNamara A, Geng C, Turner R, Mendez JR, Perl J, Held K, Faddegon B, Paganetti H, Schuemann J. Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries. Phys Med 2016; 33:207-215. [PMID: 28017738 DOI: 10.1016/j.ejmp.2016.12.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 12/08/2016] [Accepted: 12/11/2016] [Indexed: 11/30/2022] Open
Abstract
Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can help bridge the gap between physics, chemistry and biology. The TOPAS collaboration is tackling this challenge by extending the current Monte Carlo tool to allow for sub-cellular in silico simulations in a new extension, TOPAS-nBio. TOPAS wraps and extends the Geant4 Monte Carlo simulation toolkit and the new extension allows the modeling of particles down to vibrational energies (∼2eV) within realistic biological geometries. Here we present a validation of biological geometries available in TOPAS-nBio, by comparing our results to two previously published studies. We compare the prediction of strand breaks in a simple linear DNA strand from TOPAS-nBio to a published Monte Carlo track structure simulation study. While TOPAS-nBio confirms the trend in strand break generation, it predicts a higher frequency of events below an energy of 17.5eV compared to the alternative Monte Carlo track structure study. This is due to differences in the physics models used by each code. We also compare the experimental measurement of strand breaks from incident protons in DNA plasmids to TOPAS-nBio simulations. Our results show good agreement of single and double strand breaks predicting a similar increase in the strand break yield with increasing LET.
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Affiliation(s)
- Aimee McNamara
- Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA.
| | - Changran Geng
- Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | | | - Jose Ramos Mendez
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Joseph Perl
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kathryn Held
- Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Bruce Faddegon
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Harald Paganetti
- Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Jan Schuemann
- Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
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Sudhyadhom A, Kirby N, Faddegon B, Chuang CF. Technical Note: Preferred dosimeter size and associated correction factors in commissioning high dose per pulse, flattening filter free x-ray beams. Med Phys 2016; 43:1507-13. [PMID: 26936734 DOI: 10.1118/1.4941691] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE High dose rate flattening filter free (FFF) beams pose new challenges and considerations for accurate reference and relative dosimetry. The authors report errors associated with commonly used ion chambers and introduce simple methods to mitigate them. METHODS Dosimetric errors due to (1) ion recombination effects of high dose per pulse (DPP) FFF beams and (2) volume-averaging effects of the radial profile were examined on a TrueBeam STx. Four commonly used cylindrical ion chambers spanning a range of lengths (0.29-2.3 cm) and volumes (0.016-0.6 cm(3)) were used to determine the magnitude of these effects for 6 and 10 MV unflattened x-ray beams (6XFFF and 10XFFF, respectively). Two methods were used to determine the magnitude of ion collection efficiency: (1) direct measurement of the percent depth dose (PDD) for the clinical, high DPP beam in comparison to that obtained after reducing the DPP and (2) measurement of Pion as a function of depth. Two methods were used to quantify the magnitude of volume-averaging: (1) direct measurement of volume-averaging via cross-calibration and (2) calculation of volume-averaging from radial profiles of the beam. Finally, a simple analytical expression for the radial profile volume-averaging correction factor, Prp = [OAR(0.29L)](-1), or the inverse of the off-axis ratio of dose at 0.29L, where L is the length of the chamber's sensitive volume, is introduced to mitigate the volume-averaging effect in Farmer-type chambers. RESULTS Errors in measured PDD for the clinical beams were 1.3% ± 0.07% and 1.6% ± 0.07% at 35 cm depth for the 6XFFF and 10XFFF beam, respectively, using an IBA CC13 ion chamber, due to charge recombination with a high DPP. Volume-averaging effects were 0.4% and 0.7% for the 6XFFF and 10XFFF beam, respectively, when measured with a Farmer-type chamber. For the application of TG-51, these errors combine when using a CC13 to measure the PDD and a Farmer for absolute output dosimetry for a total error of up to 2% at dmax for the 10XFFF beam. CONCLUSIONS Relative and absolute dosimetry in high DPP, unflattened x-ray beams of 10 MV or higher requires corrections for charge recombination and/or volume-averaging when dosimeters with certain geometries are used. Chambers used for PDD measurement are available that do not require a correction for charge recombination. A simple analytical expression of the correction factor Prp was introduced in this work to account for volume-averaging effects in Farmer chambers. Choice of an appropriate dosimeter coupled with application of the established correction factors Pion and Prp reduces the uncertainty in the PDD measurement and the reference dose measurement.
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Affiliation(s)
- A Sudhyadhom
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California 94115
| | - N Kirby
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California 94115 and Department of Radiation Oncology and Radiology, UTHSCSA, San Antonio, San Antonio, Texas 78229
| | - B Faddegon
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California 94115
| | - C F Chuang
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California 94115
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McNamara A, Perl J, Piersimoni P, Ramos-Mendez J, Faddegon B, Held K, Paganetti H, Schuemann J. WE-H-BRA-04: Biological Geometries for the Monte Carlo Simulation Toolkit TOPASNBio. Med Phys 2016. [DOI: 10.1118/1.4957995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Hall D, Perl J, Schuemann J, Faddegon B, Paganetti H. SU-F-T-139: Meeting the Challenges of Quality Control in the TOPAS Monte Carlo Simulation Toolkit for Proton Therapy. Med Phys 2016. [DOI: 10.1118/1.4956275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Geng C, Moteabbed M, Seco J, Gao Y, George Xu X, Ramos-Méndez J, Faddegon B, Paganetti H. Dose assessment for the fetus considering scattered and secondary radiation from photon and proton therapy when treating a brain tumor of the mother. Phys Med Biol 2015; 61:683-95. [DOI: 10.1088/0031-9155/61/2/683] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Roach M, Schulte R, Mishra K, Faddegon B, Barani I, Lazar A, Blakely EA. New Clinical and Research Programs in Particle Beam Radiation Therapy: The University of California San Francisco Perspective. Int J Part Ther 2015; 2:471-473. [PMID: 27099866 DOI: 10.14338/ijpt-15-00025.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Mack Roach
- Department of Radiation Oncology, University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Reinhard Schulte
- Department of Radiation Oncology, University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Kavita Mishra
- Department of Radiation Oncology, University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Igor Barani
- Department of Radiation Oncology, University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Ann Lazar
- Department of Radiation Oncology, University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Division of Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Eleanor A Blakely
- Department of Radiation Oncology, University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Dou T, Ramos-Mendez J, Piersimoni P, Giacometti V, Penfold S, Censor Y, Faddegon B, Low D, Schulte R. SU-E-J-148: Tools for Development of 4D Proton CT. Med Phys 2015. [DOI: 10.1118/1.4924233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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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. Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endpoints. Phys Med Biol 2015; 60:5053-70. [PMID: 26061666 DOI: 10.1088/0031-9155/60/13/5053] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aim of this work is to extend a widely used proton Monte Carlo tool, TOPAS, towards the modeling of relative biological effect (RBE) distributions in experimental arrangements as well as patients. TOPAS provides a software core which users configure by writing parameter files to, for instance, define application specific geometries and scoring conditions. Expert users may further extend TOPAS scoring capabilities by plugging in their own additional C++ code. This structure was utilized for the implementation of eight biophysical models suited to calculate proton RBE. As far as physics parameters are concerned, four of these models are based on the proton linear energy transfer, while the others are based on DNA double strand break induction and the frequency-mean specific energy, lineal energy, or delta electron generated track structure. The biological input parameters for all models are typically inferred from fits of the models to radiobiological experiments. The model structures have been implemented in a coherent way within the TOPAS architecture. Their performance was validated against measured experimental data on proton RBE in a spread-out Bragg peak using V79 Chinese Hamster cells. This work is an important step in bringing biologically optimized treatment planning for proton therapy closer to the clinical practice as it will allow researchers to refine and compare pre-defined as well as user-defined models.
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Affiliation(s)
- Lisa Polster
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA. Experimental Radiation Oncology, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
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Ramos-Méndez J, Perl J, Schümann J, Shin J, Paganetti H, Faddegon B. A framework for implementation of organ effect models in TOPAS with benchmarks extended to proton therapy. Phys Med Biol 2015; 60:5037-52. [PMID: 26061583 DOI: 10.1088/0031-9155/60/13/5037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The aim of this work was to develop a framework for modeling organ effects within TOPAS (TOol for PArticle Simulation), a wrapper of the Geant4 Monte Carlo toolkit that facilitates particle therapy simulation. The DICOM interface for TOPAS was extended to permit contour input, used to assign voxels to organs. The following dose response models were implemented: The Lyman-Kutcher-Burman model, the critical element model, the population based critical volume model, the parallel-serial model, a sigmoid-based model of Niemierko for normal tissue complication probability and tumor control probability (TCP), and a Poisson-based model for TCP. The framework allows easy manipulation of the parameters of these models and the implementation of other models. As part of the verification, results for the parallel-serial and Poisson model for x-ray irradiation of a water phantom were compared to data from the AAPM Task Group 166. When using the task group dose-volume histograms (DVHs), results were found to be sensitive to the number of points in the DVH, with differences up to 2.4%, some of which are attributable to differences between the implemented models. New results are given with the point spacing specified. When using Monte Carlo calculations with TOPAS, despite the relatively good match to the published DVH's, differences up to 9% were found for the parallel-serial model (for a maximum DVH difference of 2%) and up to 0.5% for the Poisson model (for a maximum DVH difference of 0.5%). However, differences of 74.5% (in Rectangle1), 34.8% (in PTV) and 52.1% (in Triangle) for the critical element, critical volume and the sigmoid-based models were found respectively. We propose a new benchmark for verification of organ effect models in proton therapy. The benchmark consists of customized structures in the spread out Bragg peak plateau, normal tissue, tumor, penumbra and in the distal region. The DVH's, DVH point spacing, and results of the organ effect models are provided. The models were used to calculate dose response for a Head and Neck patient to demonstrate functionality of the new framework and indicate the degree of variability between the models in proton therapy.
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Affiliation(s)
- J Ramos-Méndez
- Deparment of Radiation Oncology, University of California at San Francisco, San Francisco, CA 94143, USA
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Méndez JR, Perl J, Schümann J, Shin J, Paganetti H, Faddegon B. Improved efficiency in Monte Carlo simulation for passive-scattering proton therapy. Phys Med Biol 2015; 60:5019-35. [PMID: 26061457 DOI: 10.1088/0031-9155/60/13/5019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The aim of this work was to improve the computational efficiency of Monte Carlo simulations when tracking protons through a proton therapy treatment head. Two proton therapy facilities were considered, the Francis H Burr Proton Therapy Center (FHBPTC) at the Massachusetts General Hospital and the Crocker Lab eye treatment facility used by University of California at San Francisco (UCSFETF). The computational efficiency was evaluated for phase space files scored at the exit of the treatment head to determine optimal parameters to improve efficiency while maintaining accuracy in the dose calculation. For FHBPTC, particles were split by a factor of 8 upstream of the second scatterer and upstream of the aperture. The radius of the region for Russian roulette was set to 2.5 or 1.5 times the radius of the aperture and a secondary particle production cut (PC) of 50 mm was applied. For UCSFETF, particles were split a factor of 16 upstream of a water absorber column and upstream of the aperture. Here, the radius of the region for Russian roulette was set to 4 times the radius of the aperture and a PC of 0.05 mm was applied. In both setups, the cylindrical symmetry of the proton beam was exploited to position the split particles randomly spaced around the beam axis. When simulating a phase space for subsequent water phantom simulations, efficiency gains between a factor of 19.9 ± 0.1 and 52.21 ± 0.04 for the FHTPC setups and 57.3 ± 0.5 for the UCSFETF setups were obtained. For a phase space used as input for simulations in a patient geometry, the gain was a factor of 78.6 ± 7.5. Lateral-dose curves in water were within the accepted clinical tolerance of 2%, with statistical uncertainties of 0.5% for the two facilities. For the patient geometry and by considering the 2% and 2mm criteria, 98.4% of the voxels showed a gamma index lower than unity. An analysis of the dose distribution resulted in systematic deviations below of 0.88% for 20% of the voxels with dose of 20% of the maximum or more.
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Affiliation(s)
- J Ramos Méndez
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA 94143, USA
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Ramos-Mendez J, Paganetti H, Faddegon B. SU-E-T-554: Monte Carlo Calculation of Source Terms and Attenuation Lengths for Neutrons Produced by 50-200 MeV Protons On Brass. Med Phys 2015. [DOI: 10.1118/1.4924916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Ramos-Mendez J, Perl J, Schuemann J, Shin J, Paganetti H, Faddegon B. SU-E-T-466: Implementation of An Extension Module for Dose Response Models in the TOPAS Monte Carlo Toolkit. Med Phys 2015. [DOI: 10.1118/1.4924828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Testa M, Schümann J, Lu HM, Shin J, Faddegon B, Perl J, Paganetti H. Experimental validation of the TOPAS Monte Carlo system for passive scattering proton therapy. Med Phys 2014; 40:121719. [PMID: 24320505 DOI: 10.1118/1.4828781] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE TOPAS (TOol for PArticle Simulation) is a particle simulation code recently developed with the specific aim of making Monte Carlo simulations user-friendly for research and clinical physicists in the particle therapy community. The authors present a thorough and extensive experimental validation of Monte Carlo simulations performed with TOPAS in a variety of setups relevant for proton therapy applications. The set of validation measurements performed in this work represents an overall end-to-end testing strategy recommended for all clinical centers planning to rely on TOPAS for quality assurance or patient dose calculation and, more generally, for all the institutions using passive-scattering proton therapy systems. METHODS The authors systematically compared TOPAS simulations with measurements that are performed routinely within the quality assurance (QA) program in our institution as well as experiments specifically designed for this validation study. First, the authors compared TOPAS simulations with measurements of depth-dose curves for spread-out Bragg peak (SOBP) fields. Second, absolute dosimetry simulations were benchmarked against measured machine output factors (OFs). Third, the authors simulated and measured 2D dose profiles and analyzed the differences in terms of field flatness and symmetry and usable field size. Fourth, the authors designed a simple experiment using a half-beam shifter to assess the effects of multiple Coulomb scattering, beam divergence, and inverse square attenuation on lateral and longitudinal dose profiles measured and simulated in a water phantom. Fifth, TOPAS' capabilities to simulate time dependent beam delivery was benchmarked against dose rate functions (i.e., dose per unit time vs time) measured at different depths inside an SOBP field. Sixth, simulations of the charge deposited by protons fully stopping in two different types of multilayer Faraday cups (MLFCs) were compared with measurements to benchmark the nuclear interaction models used in the simulations. RESULTS SOBPs' range and modulation width were reproduced, on average, with an accuracy of +1, -2 and ±3 mm, respectively. OF simulations reproduced measured data within ±3%. Simulated 2D dose-profiles show field flatness and average field radius within ±3% of measured profiles. The field symmetry resulted, on average in ±3% agreement with commissioned profiles. TOPAS accuracy in reproducing measured dose profiles downstream the half beam shifter is better than 2%. Dose rate function simulation reproduced the measurements within ∼2% showing that the four-dimensional modeling of the passively modulation system was implement correctly and millimeter accuracy can be achieved in reproducing measured data. For MLFCs simulations, 2% agreement was found between TOPAS and both sets of experimental measurements. The overall results show that TOPAS simulations are within the clinical accepted tolerances for all QA measurements performed at our institution. CONCLUSIONS Our Monte Carlo simulations reproduced accurately the experimental data acquired through all the measurements performed in this study. Thus, TOPAS can reliably be applied to quality assurance for proton therapy and also as an input for commissioning of commercial treatment planning systems. This work also provides the basis for routine clinical dose calculations in patients for all passive scattering proton therapy centers using TOPAS.
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Affiliation(s)
- M Testa
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard University Medical School, Boston, Massachusetts 02114
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Shin J, Faddegon B, Coss D, McMurry J, Farr J. SU-E-T-531: Performance Evaluation of Multithreaded Geant4 for Proton Therapy Dose Calculations in a High Performance Computing Facility. Med Phys 2014. [DOI: 10.1118/1.4888865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Schuemann J, Giantsoudi D, Rinaldi I, Perl J, Faddegon B, Paganetti H. TH-A-19A-02: Expanding TOPAS Towards Biological Modeling. Med Phys 2014. [DOI: 10.1118/1.4889535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Dong P, Faddegon B. SU-E-T-227: Least Restrictive Assignment of Dose-Distance Differences (LRAD) in IMRT On a Conventional Linac. Med Phys 2014. [DOI: 10.1118/1.4888557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Ramos-Méndez J, Perl J, Faddegon B, Schümann J, Paganetti H. Geometrical splitting technique to improve the computational efficiency in Monte Carlo calculations for proton therapy. Med Phys 2013; 40:041718. [PMID: 23556888 DOI: 10.1118/1.4795343] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE To present the implementation and validation of a geometrical based variance reduction technique for the calculation of phase space data for proton therapy dose calculation. METHODS The treatment heads at the Francis H Burr Proton Therapy Center were modeled with a new Monte Carlo tool (TOPAS based on Geant4). For variance reduction purposes, two particle-splitting planes were implemented. First, the particles were split upstream of the second scatterer or at the second ionization chamber. Then, particles reaching another plane immediately upstream of the field specific aperture were split again. In each case, particles were split by a factor of 8. At the second ionization chamber and at the latter plane, the cylindrical symmetry of the proton beam was exploited to position the split particles at randomly spaced locations rotated around the beam axis. Phase space data in IAEA format were recorded at the treatment head exit and the computational efficiency was calculated. Depth-dose curves and beam profiles were analyzed. Dose distributions were compared for a voxelized water phantom for different treatment fields for both the reference and optimized simulations. In addition, dose in two patients was simulated with and without particle splitting to compare the efficiency and accuracy of the technique. RESULTS A normalized computational efficiency gain of a factor of 10-20.3 was reached for phase space calculations for the different treatment head options simulated. Depth-dose curves and beam profiles were in reasonable agreement with the simulation done without splitting: within 1% for depth-dose with an average difference of (0.2 ± 0.4)%, 1 standard deviation, and a 0.3% statistical uncertainty of the simulations in the high dose region; 1.6% for planar fluence with an average difference of (0.4 ± 0.5)% and a statistical uncertainty of 0.3% in the high fluence region. The percentage differences between dose distributions in water for simulations done with and without particle splitting were within the accepted clinical tolerance of 2%, with a 0.4% statistical uncertainty. For the two patient geometries considered, head and prostate, the efficiency gain was 20.9 and 14.7, respectively, with the percentages of voxels with gamma indices lower than unity 98.9% and 99.7%, respectively, using 2% and 2 mm criteria. CONCLUSIONS The authors have implemented an efficient variance reduction technique with significant speed improvements for proton Monte Carlo simulations. The method can be transferred to other codes and other treatment heads.
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Affiliation(s)
- José Ramos-Méndez
- Benemérita Universidad Autónoma de Puebla, 18 Sur and San Claudio Avenue, Puebla, Puebla 72750, Mexico.
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Perl J, Shin J, Schuemann J, Paganetti H, Faddegon B. TU-A-108-01: Four-Dimensional Monte Carlo Using the TOPAS TOol for PArticle Simulation. Med Phys 2013. [DOI: 10.1118/1.4815324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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