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Bian J, Duran J, Shin WG, Ramos-Méndez J, Sankey JC, Childress L, Seuntjens J, Enger SA. GEANT4-DNA simulation of temperature-dependent and pH-dependent yields of chemical radiolytic species. Phys Med Biol 2023; 68:124002. [PMID: 37230081 DOI: 10.1088/1361-6560/acd90d] [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: 12/22/2022] [Accepted: 05/25/2023] [Indexed: 05/27/2023]
Abstract
Objective.GEANT4-DNA can simulate radiation chemical yield (G-value) for radiolytic species such as the hydrated electron (eaq-) with the independent reaction times (IRT) method, however, only at room temperature and neutral pH. This work aims to modify the GEANT4-DNA source code to enable the calculation ofG-values for radiolytic species at different temperatures and pH values.Approach.In the GEANT4-DNA source code, values of chemical parameters such as reaction rate constant, diffusion coefficient, Onsager radius, and water density were replaced by corresponding temperature-dependent polynomials. The initial concentration of hydrogen ion (H+)/hydronium ion (H3O+) was scaled for a desired pH using the relationship pH = -log10[H+]. To validate our modifications, two sets of simulations were performed. (A) A water cube with 1.0 km sides and a pH of 7 was irradiated with an isotropic electron source of 1 MeV. The end time was 1μs. The temperatures varied from 25 °C to 150 °C. (B) The same setup as (A) was used, however, the temperature was set to 25 °C while the pH varied from 5 to 9. The results were compared with published experimental and simulated work.Main results.The IRT method in GEANT4-DNA was successfully modified to simulateG-values for radiolytic species at different temperatures and pH values. Our temperature-dependent results agreed with experimental data within 0.64%-9.79%, and with simulated data within 3.52%-12.47%. The pH-dependent results agreed well with experimental data within 0.52% to 3.19% except at a pH of 5 (15.99%) and with simulated data within 4.40%-5.53%. The uncertainties were below ±0.20%. Overall our results agreed better with experimental than simulation data.Significance.Modifications in the GEANT4-DNA code enabled the calculation ofG-values for radiolytic species at different temperatures and pH values.
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Affiliation(s)
- Jingyi Bian
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Juan Duran
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Wook-Geun Shin
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, MA-02114, United States of America
| | - Jose Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, CA, United States of America
| | - Jack C Sankey
- Department of Physics, McGill University, Montreal, Quebec, Canada
| | - Lilian Childress
- Department of Physics, McGill University, Montreal, Quebec, Canada
| | - Jan Seuntjens
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Shirin A Enger
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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Ramos-Méndez J, Park C, Sharma M. Dosimetric characterization of single- and dual-port temporary tissue expanders for postmastectomy radiotherapy using Monte Carlo methods. Front Oncol 2023; 13:1124838. [PMID: 37143943 PMCID: PMC10151677 DOI: 10.3389/fonc.2023.1124838] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Purpose The aim of this work was two-fold: a) to assess two treatment planning strategies for accounting CT artifacts introduced by temporary tissue-expanders (TTEs); b) to evaluate the dosimetric impact of two commercially available and one novel TTE. Methods The CT artifacts were managed using two strategies. 1) Identifying the metal in the RayStation treatment planning software (TPS) using image window-level adjustments, delineate a contour enclosing the artifact, and setting the density of the surrounding voxels to unity (RS1). 2) Registering a geometry template with dimensions and materials from the TTEs (RS2). Both strategies were compared for DermaSpan, AlloX2, and AlloX2-Pro TTEs using Collapsed Cone Convolution (CCC) in RayStation TPS, Monte Carlo simulations (MC) using TOPAS, and film measurements. Wax slab phantoms with metallic ports and breast phantoms with TTEs balloons were made and irradiated with a 6 MV AP beam and partial arc, respectively. Dose values along the AP direction calculated with CCC (RS2) and TOPAS (RS1 and RS2) were compared with film measurements. The impact in dose distributions was evaluated with RS2 by comparing TOPAS simulations with and without the metal port. Results For the wax slab phantoms, the dose differences between RS1 and RS2 were 0.5% for DermaSpan and AlloX2 but 3% for AlloX2-Pro. From TOPAS simulations of RS2, the impact in dose distributions caused by the magnet attenuation was (6.4 ± 0.4) %, (4.9 ± 0.7)%, and (2.0 ± 0.9)% for DermaSpan, AlloX2, and AlloX2-Pro, respectively. With breast phantoms, maximum differences in DVH parameters between RS1 and RS2 were as follows. For AlloX2 at the posterior region: (2.1 ± 1.0)%, (1.9 ± 1.0)% and (1.4 ± 1.0)% for D1, D10, and average dose, respectively. For AlloX2-Pro at the anterior region (-1.0 ± 1.0)%, (-0.6 ± 1.0)% and (-0.6 ± 1.0)% for D1, D10 and average dose, respectively. The impact in D10 caused by the magnet was at most (5.5 ± 1.0)% and (-0.8 ± 1.0)% for AlloX2 and AlloX2-Pro, respectively. Conclusion Two strategies for accounting for CT artifacts from three breast TTEs were assessed using CCC, MC, and film measurements. This study showed that the highest differences with respect to measurements occurred with RS1 and can be mitigated if a template with the actual port geometry and materials is used.
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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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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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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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Abstract
The amino acid derivative 4-borono-L-phenylalanine (BPA) has been used in the radiation medicine technique boron neutron capture therapy (BNCT). Here we have characterized its interaction with DNA when incorporated into a positively charged hexa-L-arginine peptide. This ligand binds strongly to DNA and induces its condensation, an effect which is attenuated at higher ionic strengths. The use of an additional tetra-L-arginine ligand enables the preparation of a DNA condensate in the presence of a negligible concentration of unbound boron. Under these conditions, Monte Carlo simulation indicates that >85% of energy deposition events resulting from thermal neutron irradiation derive from boron fission. The combination of experimental model systems and simulations that we describe here provides a valuable tool for accurate track structure modeling of the DNA damage produced by the high LET particles involved in BNCT.
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Affiliation(s)
- Chris C Perry
- Department of Basic Sciences, School of Medicine, Loma Linda University, 11085 Campus Street, Loma Linda, CA 92350, USA
| | - Jose Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, 1600 Divisadero Street, San Francisco, CA 94115, USA
| | - Jamie R Milligan
- Department of Basic Sciences, School of Medicine, Loma Linda University, 11085 Campus Street, Loma Linda, CA 92350, USA
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Rudek B, McNamara A, Ramos-Méndez J, Byrne H, Kuncic Z, Schuemann J. Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams. Phys Med Biol 2019; 64:175005. [PMID: 31295730 DOI: 10.1088/1361-6560/ab314c] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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] [Indexed: 01/08/2023]
Abstract
Gold nanoparticle (GNP) radio-enhancement is a promising technique to increase the dose deposition in a tumor while sparing neighboring healthy tissue. Previous experimental studies showed effects on cell survival and tumor control for keV x-rays but surprisingly also for MV-photons, proton and carbon-ion beams. In a systematic study, we use the Monte Carlo simulation tool TOPAS-nBio to model the GNP radio-enhancement within a cell as a function of GNP concentration, size and clustering for a wide range of energies for photons, protons and, for the first time, carbon-ions. Moreover, we include water radiolysis, which has been recognized as a major pathway of GNP mediated radio-enhancement. At a GNP concentration of 0.5% and a GNP diameter of 10 nm, the dose enhancement ratio was highest for 50 keV x-rays (1.36) and decreased in the orthovoltage (1.04 at 250 keV) and megavoltage range (1.01 at 1 MeV). The dose enhancement linearly increased with GNP concentration and decreased with GNP size and degree of clustering for all radiation modalities. While the highest physical dose enhancement at 5% concentrations was only 1.003 for 10 MeV protons and 1.004 for 100 MeV carbon-ions, we find the number of hydroxyl ([Formula: see text]) altered by 23% and 3% after 1 [Formula: see text]s at low, clinically-relevant concentrations. For the same concentration and proton-impact, the G-value is most sensitive to the nanoparticle size with 46 times more radical interactions at GNPs for 2 nm than for 50 nm GNP diameter within 1 [Formula: see text]s. Nanoparticle clustering was found to decrease the number of interactions at GNPs, e.g. for a cluster of 25 GNPs by a factor of 3.4. The changes in G-value correlate to the average distance between the chemical species and the GNPs. While the radiochemistry of GNP-loaded water has yet to be fully understood, this work offers a first relative quantification of radiolysis products for a broad parameter-set.
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Affiliation(s)
- Benedikt Rudek
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts, MA, United States of America. Department of Physics, Boston University, Boston, Massachusetts, MA, United States of America. Department of Ionizing Radiation, Physikalisch-Technische Bundesanstalt, Braunschweig, 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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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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Piersimoni P, Ramos-Méndez J, Geoghegan T, Bashkirov VA, Schulte RW, Faddegon BA. The effect of beam purity and scanner complexity on proton CT accuracy. Med Phys 2017; 44:284-298. [PMID: 28066887 DOI: 10.1002/mp.12013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 07/31/2016] [Revised: 09/06/2016] [Accepted: 11/04/2016] [Indexed: 12/20/2022] Open
Abstract
PURPOSE To determine the dependence of the accuracy in reconstruction of relative stopping power (RSP) with proton computerized tomography (pCT) scans on the purity of the proton beam and the technological complexity of the pCT scanner using standard phantoms and a digital representation of a pediatric patient. METHODS The Monte Carlo method was applied to simulate the pCT scanner, using both a pure proton beam (uniform 200 MeV mono-energetic, parallel beam) and the Northwestern Medicine Chicago Proton Center (NMCPC) clinical beam in uniform scanning mode. The accuracy of the simulation was validated with measurements performed at NMCPC including reconstructed RSP images obtained with a preclinical prototype pCT scanner. The pCT scanner energy detector was then simulated in three configurations of increasing complexity: an ideal totally absorbing detector, a single stage detector and a multi-stage detector. A set of 15 cm diameter water cylinders containing either water alone or inserts of different material, size, and position were simulated at 90 projection angles (4° steps) for the pure and clinical proton beams and the three pCT configurations. A pCT image of the head of a detailed digital pediatric phantom was also reconstructed from the simulated pCT scan with the prototype detector. RESULTS The RSP error increased for all configurations for insert sizes under 7.5 mm in radius, with a sharp increase below 5 mm in radius, attributed to a limit in spatial resolution. The highest accuracy achievable using the current pCT calibration step phantom and reconstruction algorithm, calculated for the ideal case of a pure beam with totally absorbing energy detector, was 1.3% error in RSP for inserts of 5 mm radius or more, 0.7 mm in range for the 2.5 mm radius inserts, or better. When the highest complexity of the scanner geometry was introduced, some artifacts arose in the reconstructed images, particularly in the center of the phantom. Replacing the step phantom used for calibration with a wedge phantom led to RSP accuracy close to the ideal case, with no significant dependence of RSP error on insert location or material. The accuracy with the multi-stage detector and NMCPC beam for the cylindrical phantoms was 2.2% in RSP error for inserts of 5 mm radius or more, 0.7 mm in range for the 2.5 mm radius inserts, or better. The pCT scan of the pediatric phantom resulted in mean RSP values within 1.3% of the reference RSP, with a range error under 1 mm, except in exceptional situations of parallel incidence on a boundary between low and high density. CONCLUSIONS The pCT imaging technique proved to be a precise and accurate imaging tool, rivaling the current x-rays based techniques, with the advantage of being directly sensitive to proton stopping power rather than photon interaction coefficients. Measured and simulated pCT images were obtained from a wobbled proton beam for the first time. Since the in-silico results are expected to accurately represent the prototype pCT, upcoming measurements using the wedge phantom for calibration are expected to show similar accuracy in the reconstructed RSP.
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Affiliation(s)
- P Piersimoni
- Radiation Oncology, UCSF, San Francisco, CA 94115, USA
| | | | - T Geoghegan
- Radiation Oncology, UCSF, San Francisco, CA 94115, USA
| | - V A Bashkirov
- Radiation Research Laboratories, Loma Linda University, Loma Linda, CA 92354, USA
| | - R W Schulte
- Radiation Research Laboratories, Loma Linda University, Loma Linda, CA 92354, USA
| | - B A Faddegon
- Radiation Oncology, UCSF, San Francisco, CA 94115, USA
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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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