Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit

Recent updates of the MPEXS2.1-DNA Monte Carlo code for simulations of water radiolysis under ion irradiation

To improve radiotherapy, especially that with ion beams such as proton and carbon ion beams, the mechanisms of interactions induced by ionizing radiation must be understood. MPEXS2.1-DNA is a Monte Carlo simulation code developed for water radiolysis studies and DNA damage simulations that uses GPU devices for fast computation. However, the original chemistry model in MPEXS2.1-DNA did not include detailed chemical reactions for reactive oxygen species (ROS), e.g., O•-, O2, O2•-, HO2•, HO2-. In the present study, drawing the former work on the step-by-step (SBS) model for the RITRACKS code, we implemented an alternative SBS model into MPEXS2.1-DNA to increase the capabilities and computational speed of water radiolysis simulations under ion irradiation. This model is based on the theory of Green's function of the diffusion equation (GFDE-SBS). Also, we implemented multiple ionization processes which enhance ROS generation under high-LET irradiation. We compared the simulation results obtained by GFDE-SBS with experimental data from previous studies. The validation results demonstrated that the GFDE-SBS model accurately reproduced the measured radiation chemical yields of major species, such as hydroxyl radicals and hydrogen peroxide. Furthermore, the computational speed of GFDE-SBS was increased approximately ten times faster than the original model due to the changes in time stepping. Additionally, simulations using a Fricke dosimeter confirmed that this model is reliable for long-term simulations over seconds. These improvements enable simulations of radiation interactions and can help in the study of DNA damage mechanisms.

Investigating radical yield variations in FLASH and conventional proton irradiation via microscopic Monte Carlo simulations

Objective.Ultra-high-dose rate (UHDR) FLASH radiation therapy has shown remarkable tissue sparing effects compared to that at conventional dose rates (CDR). Radical production modulated by dose rate is expected to be one of the factors triggering different radiobiological responses. This study investigates the impacts of dose rate on radical yields in UHDR FLASH and CDR proton irradiation via GPU-based microscopic Monte Carlo (MC) simulations.Approach.We considered a region of interest (ROI) irradiated by a proton beam produced with a synchrotron pulse structure. The number of protons entering into the ROI was estimated in UHDR and CDR conditions. We sampled protons entering the ROI with randomly distributed spatial and temporal positions. An in-house developed GPU-based microscopic MC simulation package was used to model radiation physics and chemical processes with a periodic boundary condition. The temporal evolution of the radical yields was computed for different radical types, which in this work are hydrated electroneh, hydroxyl⋅OH, hydrogen radicalH⋅and hydrogen peroxideH2O2. We also examined radical yields with different proton energies from 1 to 142.4 MeV.Main results.Under the UHDR FLASH conditions, radical production was altered as a result of the spatial and temporal overlap of radicals produced by different protons, causing a change in their interactions. For the case with 142.4 MeV protons after 50 micropulses, the chemical yield of⋅OHunder the FLASH scheme was decreased by ∼14% compared with that under the CDR condition. The percentage of reduction increased with the number of micropulses and decreased with proton energy.Significance.We modeled microscopic phenomena of radiation physics and chemistry triggered by synchrotron proton irradiation under UHDR FLASH and CDR conditions. Our results provided insights into the underlying mechanisms responsible for the FLASH effect.

Extending TOPAS with an analytical microdosimetric function: application and benchmarking with nBio track structure simulations

Microdosimetric distributions are important to accurately describe the biological impact of ionizing radiation, particularly in ion therapy. The computational demands of track structure simulations, a gold standard for modeling microscopic energy deposition, limit their practicality for large-scale or clinical applications. The analytical microdosimetric function (AMF) is a computationally efficient function that reproduces track structure simulation results. First introduced in the particle and heavy ion transport code system Monte Carlo code in 2006 and updated in 2023, the AMF offers a promising alternative for calculating microdosimetric spectra. This study implements the AMF within the Geant4-based Tool for Particle Therapy (TOPAS) platform, enabling efficient calculation of microdosimetric spectra and radiobiological metrics, including dose-mean lineal energy (y¯D) and relative biological effectiveness (RBE) using clinically relevant models, including the modified microdosimetric kinetic model and Mayo Clinic Florida MKM. Using OpenTOPAS (v4.0.0), the AMF extension was benchmarked against TOPAS-nBio track structure simulations for ions relevant to radiotherapy and space applications (1H,4He,7Li,12C,16O,20Ne,40Ar,56Fe). AMF results were further compared with TOPAS-nBio at different depths within the mixed radiation field of a carbon spread-out Bragg peak (SOBP). The AMF extension demonstrated reasonable agreement with TOPAS-nBio track structure simulations for most ions and energies. Microdosimetric spectra and derived metrics,y¯Dand RBE, showed average discrepancies under 10% for most cases. Deviations were largely attributed to differences in Monte Carlo stopping power models and ionization cross-sections. In an SOBP, the RBE calculated using TOPAS-nBio and AMF consistently agreed within 5%. Additionally, the AMF achieved significant computational efficiency, reducing simulation times by over 98% compared to TOPAS-nBio at discrete depths in an SOBP. The AMF extension in TOPAS provides a computationally efficient alternative to track structure simulations for microdosimetric analysis and RBE modeling. Its integration with advanced RBE models enables rapid, accurate calculations critical for particle therapy research and clinical treatment planning.

Verification of Geant4-DNA step-by-step-reaction-diffusion master equation model for long-term radiolysis simulation

PURPOSE

This paper describes the verification of the step-by-step-reaction-diffusion Master Equation (SBS-RDME) model, implemented in Geant4-DNA, for long-term radiolysis simulations in the Fricke dosimeter.

METHODS

Scaling for reaction rate constants due to the high acidity of the Fricke solution was applied. The secondary electrons generated by gamma irradiation from Co-60 were used as the radiation source for the simulations. Model parameters were optimized by observing changes in output and computation time in response to variations in the starting time t and initial voxel resolution ℎ of the compartment-based simulation. The yields of ferric ion G(Fe3+) and chemical species influencing its formation were calculated using the SBS-RDME model and using the IRT method for comparison. The time evolution of the yields of Fe3+, OH, H, HO2, H2O2, and H2 were compared, and the reactions affecting the yield of each chemical species were analyzed.

RESULTS

The model parameters were set to t = 5 ns and h = 12.5 nm. The yield trends over time for chemical species were consistent between the SBS-RDME model and the IRT method. At 50 s, the G(Fe3+) from the two calculations agreed within 3.2 %. Contribution analysis of the reactions affecting the generation/removal of each chemical species indicated that the main reason for this discrepancy between the two calculations might be the inability of the SBS method to consider specific reaction types during simulation.

CONCLUSIONS

The SBS-RDME model was verified for long-term simulations by comparing its results to those obtained from the IRT method.

Results of a Geant4 benchmarking study for bio-medical applications, performed with the G4-Med system

BACKGROUND

Geant4, a Monte Carlo Simulation Toolkit extensively used in bio-medical physics, is in continuous evolution to include newest research findings to improve its accuracy and to respond to the evolving needs of a very diverse user community. In 2014, the G4-Med benchmarking system was born from the effort of the Geant4 Medical Simulation Benchmarking Group, to benchmark and monitor the evolution of Geant4 for medical physics applications. The G4-Med system was first described in our Medical Physics Special Report published in 2021. Results of the tests were reported for Geant4 10.5.

PURPOSE

In this work, we describe the evolution of the G4-Med benchmarking system.

METHODS

The G4-Med benchmarking suite currently includes 23 tests, which benchmark Geant4 from the calculation of basic physical quantities to the simulation of more clinically relevant set-ups. New tests concern the benchmarking of Geant4-DNA physics and chemistry components for regression testing purposes, dosimetry for brachytherapy with a125 I $^{125}I$ source, dosimetry for external x-ray and electron FLASH radiotherapy, experimental microdosimetry for proton therapy, and in vivo PET for carbon and oxygen beams. Regression testing has been performed between Geant4 10.5 and 11.1. Finally, a simple Geant4 simulation has been developed and used to compare Geant4 EM physics constructors and physics lists in terms of execution times.

RESULTS

In summary, our EM tests show that the parameters of the multiple scattering in the Geant4 EM constructor G4EmStandardPhysics_option3 in Geant4 11.1, while improving the modeling of the electron backscattering in high atomic number targets, are not adequate for dosimetry for clinical x-ray and electron beams. Therefore, these parameters have been reverted back to those of Geant4 10.5 in Geant4 11.2.1. The x-ray radiotherapy test shows significant differences in the modeling of the bremsstrahlung process, especially between G4EmPenelopePhysics and the other constructors under study (G4EmLivermorePhysics, G4EmStandardPhysics_option3, and G4EmStandardPhysics_option4). These differences will be studied in an in-depth investigation within our Group. Improvement in Geant4 11.1 has been observed for the modeling of the proton and carbon ion Bragg peak with energies of clinical interest, thanks to the adoption of ICRU90 to calculate the low energy proton stopping powers in water and of the Linhard-Sorensen ion model, available in Geant4 since version 11.0. Nuclear fragmentation tests of interest for carbon ion therapy show differences between Geant4 10.5 and 11.1 in terms of fragment yields. In particular, a higher production of boron fragments is observed with Geant4 11.1, leading to a better agreement with reference data for this fragment.

CONCLUSIONS

Based on the overall results of our tests, we recommend to use G4EmStandardPhysics_option4 as EM constructor and QGSP_BIC_HP with G4EmStandardPhysics_option4, for hadrontherapy applications. The Geant4-DNA physics lists report differences in modeling electron interactions in water, however, the tests have a pure regression testing purpose so no recommendation can be formulated.

Experimental and computational analysis of the DNA damage induced in zebrafish, Danio rerio, early life stages after exposure to tritiated thymidine

Tritium is an ubiquitous radioactive hydrogen isotope. It is found in all environmental compartments, in three different forms: tritiated water (HTO), gaseous tritium (HT) and organically bound tritium (OBT). Once internalized in the organism, it can either be found free in the tissues (TFWT) or bound to organic matter (OBT). This study aims to assess if tritiated thymidine, an organic form of tritium, induces DNA breaks once internalized in a model organism and its DNA. To do so, both experimental procedures and nanodosimetry simulations have been used. Zebrafish embryos (3.5 hpf, hours post fertilization) were exposed to three tritiated thymidine activity concentrations (7.5, 40, 110 kBq/mL, leading to internal dose rates of 22, 170 and 270 μGy/h) for four days. Individuals were sampled after 1 and 4 days of exposure and DNA break levels were assessed by the comet assay. Results showed that, even at the lowest activity concentration, tritiated thymidine induced DNA breaks in both embryos (1 dpf) and larvae (4 dpf). It was also highlighted that there was no increase nor decrease in DNA break level between 1 and 4 dpf, except in the case of the exposure to 170 μGy/h, where a slight decrease was observed. Geant4-DNA Monte Carlo simulations, performed on two spherical zebrafish nuclei of two different radii (2.5 and 5 μm), highlighted that organic tritium mainly induced single strand breaks (SSB). The results also showed that most of the damage was indirectly induced. Those results, combined with various experimentations, expose tritiated thymidine genotoxic pathways that could lead to both short- and long-term health effects.

GANDALF: Generative ANsatz for DNA damage evALuation and Forecast. A neural network-based regression for estimating early DNA damage across micro-nano scales

PURPOSE

This study aims to develop a comprehensive simulation framework to connect radiation effects from the microscopic to the nanoscopic scale.

METHOD

The process begins with a Geant4-DNA simulation based on the example "molecularDNA", producing a dataset of twelve different types of early DNA damages within an Escherichia coli (E. coli) bacterium, generated by proton irradiation at different kinetic energies, giving a nano-scale view of the particle-matter interaction. Then we pass to the micro-scale with a Geant4 simulation, based on the example "radiobiology", providing a microscopic view of proton interactions with matter through the Linear Energy Transfer (LET). Then GANDALF (Generative ANsatz for DNA damage evALuation and Forecast) Machine Learning (ML) toolkit, a Neural Network (NN)-based regression system, is employed to correlate the micro-scale LET data with the nano-scale occurrences of DNA damages in the E. coli bacterium.

RESULTS

The trained ML algorithm provides a practical tool to convert LET curves versus depth in a water phantom into DNA damage curves for twelve distinct types of DNA damage. To assess the performance, we evaluated the choice and optimization of the regression system based on its interpolation and extrapolation capabilities, ensuring the model could reliably predict DNA damage under various conditions.

CONCLUSIONS

Through the synergistic integration of Geant4, Geant4-DNA and ML, the study provides a tool to easily convert the results at the micro-scale of Geant4 to those at the nano-scale of Geant4-DNA without having to deal with the high CPU time requirements of the latter.

Hyperthermal Reactions in DNA Triggered by 1-20 eV Electrons: Absolute Cross Sections for Crosslinks, Strand Breaks, Clustered Damages and Base Modifications

Absolute cross sections (ACSs) are needed to estimate cellular damage induced by high-energy radiation (HER). Low-energy electrons (LEEs), which are the most numerous secondary particles generated by HER, can trigger hyperthermal reactions in DNA. ACSs for such reactions are essential input parameters to calculate radiobiological effectiveness, particularly in targeted radiotherapy. Using a mathematical model, we generate ACSs from effective damage yields induced by LEE impact on 3197 base-pair plasmid DNA films. Direct or enzyme-revealed conformational damages, quantified by electrophoresis, provide the first complete set of ACSs for inducing crosslinks, double-strand breaks (DSBs), single-strand breaks, base-damage-related crosslinks, non-DSB clustered damages (NDCDs), and isolated base damages. These ACSs are generated across the 1-20 eV range, at one eV intervals. They exhibit a strong energy dependence with maximum values at 10 eV of 3.7 ± 0.8, 3.5 ± 0.6, 45.4 ± 4.1, 2.9 ± 1.1, 5.1 ± 1.4, and 54.0 ± 16.4 × 10-15 cm2, respectively. ACSs for DSBs, NDCDs, and crosslinks clearly indicate that lesions threatening cell function and genetic stability can be generated by a single LEE. At 5 and 10 eV, total damage ACSs are 63% and 80% larger, respectively, than those previously determined for the same plasmids bound to arginine, a constituent of histones protecting DNA.

Development of a chemical code applicable to ions based on the PHITS code for efficient and visual radiolysis simulations

Water radiolysis plays an important role in elucidating radiation-induced biological effects such as early DNA damage induction, chromosome aberrations, and carcinogenesis. Several Monte Carlo simulation codes for water radiolysis, commonly referred to as chemical simulation codes, have been developed worldwide. However, these codes typically require substantial computational time to calculate the time-dependent G values of water radiolysis species (e.g., ˙OH, e-aq, H2, and H2O2), and their application is often limited to specific ion beam types. In the Particle and Heavy Ion Transport code System (PHITS), the track-structure mode that allows the simulation of each atomic interaction in liquid water for any charged particles and the subsequent chemical code (named PHITS-Chem code) dedicated to electrons was developed previously. In this study, we developed the PHITS-Chem code to support a broader range of ion beam species. To reduce computational time, we introduced new features including a space partitioning method to increase the detection efficiency of reactions between chemical species and a radical scavenger model that reduces the lifetime of OH radicals. We benchmarked the updated PHITS-Chem code by comparing its predicted time-dependent G values for protons, α particles, and carbon ions with those reported in the literature (i.e., other simulation and measured data). The inclusion of a space partitioning method and the modified OH radical scavenger model reduced the time required by the PHITS-Chem code to calculate G values (by approximately 28-fold during radiolysis simulations under 1-MeV electron exposure) while maintaining calculation accuracy. A key advantage of the PHITS-Chem code is the four-dimensional visualization capability, integrated with PHITS' native visualization software, PHIG-3D. Considering the ability of the PHITS-Chem code to handle OH radical scavengers (i.e., tris(hydroxymethyl)aminomethane and dimethyl sulfoxide), it is anticipated to offer precise and intuitive insights into the radiation-induced biological effects of chemical species in ion-beam radiotherapy.

Enhancing Ion Emission: Insights from Molecular Dynamics and Monte Carlo Simulations

Gas cluster ion beam (GCIB) guns have found several applications in science and industry, such as surface smoothing or depth profiling and surface analysis in conjunction with secondary ion mass spectrometry (SIMS). The former application is severely hindered by the low amount of ejected secondary ions, which can be boosted by more than an order of magnitude by properly selecting the size of cluster projectiles and changing their constituent particles from argon to water. The mechanism of this phenomenon is still unknown. By combining molecular dynamics (MD) and Monte Carlo (MC) simulations with experimental results, we posit that the increase in ion yield can be attributed to proton transfer in long-lived complexes of sample molecules and hydronium (H3O+) ion from the projectile. The number of molecule-water complexes formed in simulations is directly proportional to the experimental signal intensity, with a small deviation for projectiles containing more than 7000 water molecules.

In silico analysis of radiation-induced double-strand breaks by internal ex vivo irradiation of lymphocytes for 45 alpha- and beta/gamma-emitting radionuclides

BACKGROUND

The aim of this study is to evaluate the induction of DNA damage by 45 radionuclides, including those used in medical applications and others relevant to radiation protection. The research focuses on understanding the differential effects of irradiating lymphocytes with beta/gamma- and alpha-emitting radionuclides using Monte Carlo simulations. A validated Monte Carlo simulation model was used to assess radiation-induced DNA damage in lymphocytes. The model integrates GATE for macroscopic radiation transport and Geant4-DNA for microscopic simulations at the cellular level. For the study, 45 radionuclides were selected and their S-values and DNA double-strand break (DSB) induction were investigated. For beta- and gamma-emitting radionuclides, DSBs per cell per mGy were quantified, while for alpha-emitters, alpha tracks per cell per mGy, DSBs per cell per mGy, and DSBs per micrometer of alpha track were calculated.

RESULT

For beta/gamma emitters, the lowest number of DSBs was observed with 125I at 0.006 ± 0.003 DSBs·cell⁻¹·mGy⁻¹, while 99mTc had the highest at approximately 0.015 ± 0.005 DSBs·cell⁻¹·mGy⁻¹. The S-value for lymphocyte nuclei ranked from 0.91 ± 0.14 mGy∙h⁻¹∙MBq⁻¹ (63Ni) and 1.06 ± 0.15 mGy∙h⁻¹∙MBq⁻¹ (125I) to 61.83 ± 1.17 mGy∙h⁻¹∙MBq⁻¹ (90Sr). For alpha-emitting radionuclides, 213Bi produced 0.0677 ± 0.0005 DSB·cell⁻¹·mGy⁻¹ while 232Th yielded 0.0914 ± 0.0004 DSB·cell⁻¹·mGy⁻¹. The DSB linear density for alpha tracks ranged from 7.4 ± 0.1 DSBs/µm for 252Cf to 16.8 ± 0.1 DSBs/µm for 232Th. The S-values for lymphocyte nuclei for alpha emitters varied, from 232Th (0.29 ± 0.21 Gy∙h⁻¹∙MBq⁻¹) to 227Th having the highest at 2.22 ± 0.16 Gy∙h⁻¹∙MBq⁻¹, due to cumulative energy deposition.

CONCLUSIONS

Differences were observed in DNA damage induced by beta/gamma- and alpha-emitting radionuclides. High-energy beta emitters induced DSBs similarly to gamma emitters, but with greater fluctuations in low-energy beta and gamma emitters due to heterogeneous energy deposition and varying interaction probabilities at the cellular level. This study highlights that long half-life alpha-emitting radionuclides may cause more extensive DNA damage due to their higher LET. This work provides a comprehensive S-values database for future experimental studies on radiation-induced DNA damage in lymphocytes.

Position in proton Bragg curve influences DNA damage complexity and survival in head and neck cancer cells

Background and purpose

Understanding the cellular and molecular effect of proton radiation, particularly the increased DNA damage complexity at the distal end of the Bragg curve, is current topic of investigation. This work aims to study in vitro clonogenic survival and DNA damage foci kinetics of a head and neck squamous cell carcinoma cell line at various positions along a double passively scattered Bragg curve. Complementary in silico studies are conducted to gain insights into the link between cell survival variations, experimentally yielded foci and the number and complexity of double strand breaks (DSBs).

Materials and methods

Proton irradiations are performed at the HollandPTC R&D proton beamline, using a double passively scattered setup. A custom water phantom setup is employed to accurately position the samples within the Bragg curve. FaDu cells are irradiated at the proximal 36 % point of the Bragg peak, (P36), proximal 80 % point of the Bragg peak (P80) and distal 20 % point of the Bragg peak (D20), with dose-averaged mean lineal energies (y D ¯ ) of 1.10 keV/μm, 1.80 keV/μm and 7.25 keV/μm, respectively.

Results

Clonogenic survival correlates strongly withy D ¯ , showing similar survival for P36 (D37%=3.0 Gy) and P80 (D37%=2.9 Gy), but decreased survival for D20 (D37% = 1.6 Gy). D20 irradiated samples exhibit increased 53BP1 foci shortly after irradiation, slower resolution of the foci, and larger residual 53BP1 foci after 24 h, indicating unrepaired complex breaks. These experimental observations are supported by the in silico study which demonstrates that irradiation at D20 leads to a 1.7-fold increase in complex DSBs with respect to the total number of strand breaks compared to P36 and P80.

Conclusions

This combined approach provides valuable insights into the cellular and molecular effect of proton radiation, emphasizing the increased DNA damage complexity at the distal end of the Bragg curve, and has the potential to enhance the efficacy of proton therapy.

Evaluating the biological impact of shelters on astronaut health during different solar particle events: a Geant4-DNA simulation study

Mechanistic Monte Carlo simulations have proven invaluable in tackling complex challenges in radiobiology, for example for protecting astronauts from solar particle events (SPEs) during deep space missions which remains an underexplored area. In this study, the Geant4-DNA Monte Carlo code was used to assess the DNA damage caused by SPEs and evaluate the protective effectiveness of a multilayer shelter. By examining the February 1956 and October 1989 SPEs-two extreme cases-the results showed that the proposed shelter reduced DNA damage by up to 57.9% for the October 1989 SPE and 36.7% for the February 1956 SPE. Cell repair and survival modeling further revealed enhanced cell survival with the shelter, reducing lethal DNA damage by up to 64.3% and 88.2% for February 1956 and October 1989 SPEs, respectively. The results presented here highlight the crucial importance of developing effective radiation shielding to protect astronauts during solar storms and emphasizes the need to improve predictions of solar particle events to optimize shelter design.

Analytic and Monte Carlo calculations of dose-mean lineal energy for 1 MeV-1 GeV protons with application to radiation protection quality factor

Radiation quality for determining biological effects is commonly linked to the microdosimetric quantity lineal energy ( y ) and to the dose-mean lineal energy ( y D ). Calculations of y D are typically performed by specialised Monte Carlo track-structure (MCTS) codes, which can be time-intensive. Thus, microdosimetry-based analytic models are potentially useful for practical calculations. Analytic model calculations of proton y D and radiation protection quality factor ( Q ) values in sub-micron liquid water spheres (diameter 10-1000 nm) over a broad energy range (1 MeV-1 GeV) are compared against MCTS simulations by PHITS, RITRACKS, and Geant4-DNA. Additionally, an improved analytic microdosimetry model is proposed. The original analytic model of Xapsos is refined and model parameters are updated based on Geant4-DNA physics model. Direct proton energy deposition is described by an alternative energy-loss straggling distribution and the contribution of secondary electrons is calculated using the dielectric formulation of the relativistic Born approximation. MCTS simulations of proton y D values using the latest versions of the PHITS, RITRACKS, and Geant4-DNA are reported along with the Monte Carlo Damage Simulation (MCDS) algorithm. The y D datasets are then used within the Theory of Dual Radiation Action (TDRA) to illustrate variations in Q with proton energy. By a careful selection of parameters, overall differences at the ~ 10% level between the proposed analytic model and the MCTS codes can be attained, significantly improving upon existing models. MCDS estimates of y D are generally much lower than estimates from MCTS simulations. The differences of Q among the examined methods are somewhat smaller than those of y D . Still, estimates of proton Q values by the present model are in better agreement with MCTS-based estimates than the existing analytic models. An improved microdosimetry-based analytic model is presented for calculating proton y D values over a broad range of proton energies (1 MeV-1 GeV) and target sizes (10-1000 nm) in very good agreement with state-of-the-art MCTS simulations. It is envisioned that the proposed model might be used as an alternative to CPU-intensive MCTS simulations and advance practical microdosimetry and quality factor calculations in medical, accelerator, and space radiation applications.

Effect of FLASH dose-rate and oxygen concentration in the production of H2O2in cellular-like media versus water: a Monte Carlo track-structure study

Objective. To study the effect of dose-rate in the time evolution of chemical yields produced in pure water versus a cellular-like environment for FLASH radiotherapy research.Approach.A version of TOPAS-nBio with Tau-Leaping algorithm was used to simulate the homogenous chemistry stage of water radiolysis using three chemical models: (1) liquid water model that considered scavenging ofeaq-, H•by dissolved oxygen; (2) Michaels & Hunt model that considered scavenging of•OH,eaq‒, and H•by biomolecules existing in cellular environment; (3) Wardman model that considered model 2) and the non-enzymatic antioxidant glutathione (GSH). H2O2concentrations at conventional and FLASH dose-rates were compared with published measurements. Model 3) was used to estimate DNA single-strand break (SSB) yields and compared with published data. SSBs were estimated from simulated yields of DNA hydrogen abstraction and attenuation factors to account for the scavenging capacity of the medium. The simulation setup consisted of monoenergetic protons (100 MeV) delivered in pulses at conventional (0.2857Gy s-1) and FLASH (500Gy s-1) dose rates. Dose varied from 5-20 Gy, and oxygen concentration from 10µM-1 mM.Main Results.At the steady state, for model (1), H2O2concentration differed by 81.5%± 4.0% between FLASH and conventional dose-rates. For models (2) and (3) the differences were within 8.0%± 4.8%, and calculated SSB yields agreed with published data within 3.8%± 1.2%. A maximum oxygen concentration difference of 60% and 50% for models (2) and (3) between conventional and FLASH dose-rates was found between 2 × 106and 9 × 1013ps for 20 Gy of absorbed dose.Significance.The findings highlight the importance of developing more advanced cellular models to account for both the chemical and biological factors that comprise the FLASH effect. It was found that differences between pure water and cellular environment models were significant and extrapolating results between the two should be avoided. Observed differences call for further experimental investigation.

Simulation of cell cycle effects on DNA strand break induction due to α-particles

PURPOSE

Understanding cell cycle variations in radiosensitivity is important for α-particle therapies. Differences are due to both repair response mechanisms and the quantity of initial radiation-induced DNA strand breaks. Genome compaction within the nucleus has been shown to impact the yield of strand breaks. Compaction changes during the cell cycle are therefore likely to contribute to radiosensitivity differences. Simulation allows the strand break yield to be calculated independently of repair mechanisms which would be challenging experimentally.

METHODS

Using Geant4 the impact of genome compaction changes on strand break induction due to α-particles was simulated. Genome compaction is considered to be described by three metrics: global base pair density, chromatin fibre packing fraction and chromosome condensation. Nuclei in the G1, S, G2 and M phases from two cancer cell lines and one normal cell line are simulated. Repair mechanisms are not considered to study only the impact of genome compaction changes.

RESULTS

The three compaction metrics have differing effects on the strand break yield. For all cell lines the strand break yield is greatest in G2 cells and least in G1 cells. More strand breaks are induced in the two cancer cell lines than in the normal cell line.

CONCLUSIONS

Compaction of the genome affects the initial yield of strand breaks. Some radiosensitivity differences between cell lines can be attributed to genome compaction changes between the phases of the cell cycle. This study provides a basis for further analysis of how repair deficiencies impact radiation-induced lethality in normal and malignant cells.

Oxygen Effect on 0-30 eV Electron Damage to DNA Under Different Hydration Levels: Base and Clustered Lesions, Strand Breaks and Crosslinks

Studies on radiosensitization of biological damage by O2 began about a century ago and it remains one of the most significant subjects in radiobiology. It has been related to increased production of oxygen radicals and other reactive metabolites, but only recently to the action of the numerous low-energy electrons (LEEs: 0-30 eV) produced by ionizing radiation. We provide the first complete set of G-values (yields of specific products per energy deposited) for all conformational damages induced to plasmid DNA by LEEs (GLEE (O2)) and 1.5 keV X-rays (GX(O2)) under oxygen at atmospheric pressure. The experiments are performed in a chamber, under humidity levels ranging from 2.5 to 33 water molecules/base. Photoelectrons from 0 to 30 eV are produced by X-rays incident on a tantalum substrate covered with DNA. Damage yields are measured by electrophoresis as a function of X-ray fluence. The oxygen enhancement ratio GLEE(O2)/GLEE(N2), which lies around 2 for potentially lethal cluster lesions, is similar to that found with cells. The average ratio, GLEE(O2)/GX(O2), of 12 for cluster lesions and crosslinks strongly suggest that DNA damages that harm cells are much more likely to be created by LEEs than any other initial species generated by X-rays in the presence of O2.

Integrating chromosome conformation and DNA repair in a computational framework to assess cell radiosensitivity. Phys Med Biol 2024;69:245017. [PMID: 39569898 DOI: 10.1088/1361-6560/ad94c6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Objective.The arrangement of chromosomes in the cell nucleus has implications for cell radiosensitivity. The development of new tools to utilize Hi-C chromosome conformation data in nanoscale radiation track structure simulations allows forin silicoinvestigation of this phenomenon. We have developed a framework employing Hi-C-based cell nucleus models in Monte Carlo radiation simulations, in conjunction with mechanistic models of DNA repair, to predict not only the initial radiation-induced DNA damage, but also the repair outcomes resulting from this damage, allowing us to investigate the role chromosome conformation plays in the biological outcome of radiation exposure.Approach.In this study, we used this framework to generate cell nucleus models based on Hi-C data from fibroblast and lymphoblastoid cells and explore the effects of cell type-specific chromosome structure on radiation response. The models were used to simulate external beam irradiation including DNA damage and subsequent DNA repair. The kinetics of the simulated DNA repair were compared with previous results.Main results.We found that the fibroblast models resulted in a higher rate of inter-chromosome misrepair than the lymphoblastoid model, despite having similar amounts of initial DNA damage and total misrepairs for each irradiation scenario.Significance.This framework represents a step forward in radiobiological modeling and simulation allowing for more realistic investigation of radiosensitivity in different types of cells.

Monte Carlo methods to assess biological response to radiation in peripheral organs and in critical organs near the target

Background

The biological effects and clinical consequences of out-of-field radiation in peripheral organs can be difficult to determine, especially for low doses (0.1 Gy-1 Gy). In recent years, Monte Carlo (MC) methods have been proposed to more accurately predict nontarget doses. The aim of the present study was to assess the feasibility of using Monte Carlo methods to predict the biological response of tissues and critical organs to low dose radiation (0.1 to 1 Gy) based on results published in the literature.

Materials and methods

Literature review, including studies published by our group.

Results and Conclusions

It has long been assumed that radiation doses to peripheral organs located far from the target volume are too low to have any clinical impact. In recent years, however, concerns about the risk of treatment-induced secondary cancers, even in peripheral organs, have continued to grow in line with increasing life expectancy. At present, it is difficult in routine calculations to accurately determine radiation doses to the whole body and peripheral organs. Moreover, the potential clinical impact of these doses remains uncertain and the biological response to low dose radiation depends on the organ. In this context, MC methods can predict biological response in those organs. Monte Carlo methods have become a powerful tool to better predict the consequences of interactions between ionising radiation and biological matter. MC modelling can also help to characterise microscopic system dynamics and to provide a better understanding of processes occurring at the cellular, molecular, and nanoscales.

Geant4-DNA development for atmospheric applications: N2, O2 and CO2 models implementation

BACKGROUND AND AIM

Cosmic rays have the potential to induce significant changes in atmospheric chemical reactions by generating ions, thereby influencing the atmosphere's chemical composition. The use of particle-molecule interaction models that account for the molecular structure of the atmospheric medium can advance our understanding on the role of ions, and enables a quantitative analysis of the impact of ion-molecule reactions on atmospheric modifications. This study marks the initial effort to expand the Geant-DNA toolkit for atmospheric applications.

METHODS

Building on our previous work, we extended the validation of new electron impact interaction models with the nitrogen and oxygen molecules up to 10 MeV. Additionally, we introduce electron cross sections for the carbon dioxide molecule, due to its crucial role as a major greenhouse gas. We present the implementation of the cross section models in Geant4-DNA, along with their validation through simulations of stopping power and range.

RESULTS

The differential cross sections have been verified against analytical calculations, demonstrating good agreement with existing literature data for all three molecules. The implementation has been validated through simulations of stopping power and range in N2, O2, CO2, and air. Results demonstrate agreement within 6% compared to reference data from the ESTAR database.

CONCLUSIONS

The cross section models for the N2, O2, and CO2 atmospheric molecules have been implemented in the Geant4-DNA toolkit. This evolution is crucial for studying ionic reactive chemical networks in a quantitative manner, assessing the impact of ionization on chemical reactions occurring in the atmosphere and their implications for climate.

Nanoscale dosimetry for a radioisotope-labeled metal nanoparticle using MCNP6.2 and Geant4

BACKGROUND

Metal nanoparticles (MNPs) labeled with radioisotopes (RIs) are utilized as radio-enhancers due to their ability to amplify the radiation dose in their immediate vicinity. A thorough understanding of nanoscale dosimetry around MNPs enables their effective application in radiotherapy. However, nanoscale dosimetry around MNPs still requires further investigation.

PURPOSE

This study aims to provide insight into the radio-enhancement effects of MNPs by elucidating nanoscale dosimetry surrounding MNPs labeled with Auger-emitting RIs. We particularly focus on distinguishing the respective dose contributions of photons and electrons emitted by Auger-emitting RIs in the context of dose enhancement.

METHODS

A 50 nm diameter NP of silver (Ag) core and gold (Au) shell (Ag@Au NP) was assumed to emit mono-energetic electrons and photons (3, 5, 10, 20, and 30 keV), or the energy spectrum corresponding to one of three Auger-emitting RIs (103Pd, 125I, and 131Cs) from the Ag core. Nanoscale radial dose distributions around a single radioactive Ag@Au NP were evaluated in spherical shells of water. Monte Carlo simulations were conducted using single-event and track structure transport methods implemented in MCNP6.2 and Geant4-DNA-Au physics, respectively. To evaluate the extent of radio-enhancement by the Ag@Au NP, two scenarios were considered: Ag@Au NPs (Au shell included) and Ag@water NPs (Au shell replaced by water).

RESULTS

The radial doses of 10, 20, and 30 keV electrons estimated by both codes were comparable. However, the radial doses of 3 and 5 keV electrons by MCNP6.2 were much larger near the NP surface than those by Geant4. There was a dose enhancement of a few % to tens % by the Au shell in the region of the NP surface to 10 µm, depending on the electron energy. The radial doses of photons with the Au shell were higher up to their secondary electron ranges than those without the Au shell. The maximum dose enhancement factor of photons occurred at 20 keV and was 63.4 by MCNP6.2 and 50.5 by Geant4. The overall radial doses of electrons were 1-2 orders of magnitude larger than those of photons. As a result, in cases of RIs emitting both electrons and photons, the radial doses up to electron ranges were dominantly governed by electrons. The dose enhancement estimated by both codes for the RIs ranged from a few % except in the immediate vicinity of the NP surface.

CONCLUSION

Given the dominant contribution of electrons to radial doses of MNP labeled with Auger-emitting RIs, physical dose enhancement expected by interactions with photons was hindered. Since there are no available RIs emitting exclusively photons, achieving enhanced physical doses within a cell through a combination of MNPs and RIs appears currently unattainable. The radial doses of photons near the NP surface exhibited considerable discrepancies between the codes, primarily attributed to low-energy electrons. The difference may arise from higher cross-sections of Au inelastic scattering in Geant4-DNA-Au compared to MCNP6.2.

Nanodosimetric investigation of the track structure of therapeutic carbon ion radiation part2: detailed simulation

Objectivea previous study reported nanodosimetric measurements of therapeutic-energy carbon ions penetrating simulated tissue. The results are incompatible with the predicted mean energy of the carbon ions in the nanodosimeter and previous experiments with lower energy monoenergetic beams. The purpose of this study is to explore the origin of these discrepancies.Approachdetailed simulations using the Geant4 toolkit were performed to investigate the radiation field in the nanodosimeter and provide input data for track structure simulations, which were performed with a developed version of the PTra code.Main resultsthe Geant4 simulations show that with the narrow-beam geometry employed in the experiment, only a small fraction of the carbon ions traverse the nanodosimeter and their mean energy is between 12% and 30% lower than the values estimated using the SRIM software. Only about one-third or less of these carbon ions hit the trigger detector. The track structure simulations indicate that the observed enhanced ionization cluster sizes are mainly due to coincidences with events in which carbon ions miss the trigger detector. In addition, the discrepancies observed for high absorber thicknesses of carbon ions traversing the target volume could be explained by assuming an increase in thickness or interaction cross-sections in the order of 1%.Significancethe results show that even with strong collimation of the radiation field, future nanodosimetric measurements of clinical carbon ion beams will require large trigger detectors to register all events with carbon ions traversing the nanodosimeter. Energy loss calculations of the primary beam in the absorbers are insufficient and should be replaced by detailed simulations when planning such experiments. Uncertainties of the interaction cross-sections in simulation codes may shift the Bragg peak position.

Investigating ultra-high dose rate water radiolysis using the Geant4-DNA toolkit and a Geant4 model of the Oriatron eRT6 electron linac

Ultra-high dose rate FLASH radiotherapy, a promising cancer treatment approach, offers the potential to reduce healthy tissue damage during radiotherapy. As the mechanisms underlying this process remain unknown, several hypotheses have been proposed, including the altered production of radio-induced species under ultra-high dose rate (UHDR) conditions. This study explores realistic irradiation scenarios with various dose-per-pulse and investigates the role of pulse temporal structure. Using the Geant4 toolkit and its Geant4-DNA extension, we modeled the Oriatron eRT6 linac, a FLASH-validated electron beam, and conducted simulations covering four distinct dose-per-pulse scenarios - 0.17 Gy, 1 Gy, 5 Gy, and 10 Gy - all featuring a 1.8 µs pulse duration. Results show close agreement between simulated and experimental dose profiles in water, validating the eRT6 model for Geant4-DNA simulations. We observed important changes in the temporal evolution of certain species, such as the earlier fall in hydroxyl radicals ([Formula: see text]) and reduced production and lifetime of superoxide ([Formula: see text]) with higher dose-per-pulse levels. The pulse temporal structure did not influence the long-term evolution of species. Our findings encourage further investigation into different irradiation types, such as multi-pulse configurations, and emphasize the need to add components in water to account for relevant cellular processes.

Direct and Indirect Effects for Radiosensitization of Gold Nanoparticles in Proton Therapy

The radiosensitization characteristics of gold nanoparticles (GNPs) have been investigated in a single cell irradiated with monoenergetic beams of protons of various energies using TOPAS-nBio, an advanced toolkit of TOPAS. Both direct and indirect effects against single-strand breaks (SSBs) are investigated and their double-strand breaks (DSBs) have been calculated. A single spherical cell interaction with a detailed DNA structure has been modeled and simulated under different conditions such as particle sizes and concentrations of GNPs, their biodistributions and associated proton energies. The physical interaction among protons, suspension water and GNPs has been simulated using a dual physics approach, while the interaction between water radiolysis and OH radicals was considered in the chemical process to save computational time. The present simulations involve irradiating the cell geometry with a dose of 1 Gy. The range of DSBs (Gy-1 Gbp-1) obtained was 2.1 ± 0.09 to 21.74 ± 0.4 for all GNPs of sizes 6-50 nm the proton energies in the range of 5-50 MeV. Regardless of proton energy and GNP size, the calculations showed that the contribution of indirect and hybrid DSBs remains higher in all simulation types than that of direct DSBs. New simulation outcomes of the indirect DSBs illustrate a percentage increase, while we cannot get an increase in the direct and hybrid DSBs in most cases when compared with no GNPs cases. The indirect DSBs provide the highest enhancement factor of 1.89 at 30 nm GNPs in size for 30 MeV protons energy, and the direct and hybrid DSBs indicate a slight increase in enhancement. The work indicates that the use of GNPs increased indirect DNA DSBs, while hybrid DSBs show only a slight increase in enhancement, and no enhancement is shown in direct DNA DSBs. It is significant to consider other mechanisms such as DNA damage repair when investigating DNA damage.

Development of a novel computational technique to create DNA and cell geometrical models for Geant4-DNA

BACKGROUND

This study aimed to develop a novel human cell geometry for the Geant4-DNA simulation toolkit that explicitly incorporates all 23 chromosome pairs of the human cell. This approach contrasts with the existing, default human cell, geometrical model, which utilizes a continuous Hilbert curve.

METHODS

A Python-based tool named "complexDNA" was developed to facilitate the design of both simple and complex DNA geometries. This tool was employed to construct a human cell geometry with individual pairs of chromosomes. Subsequently, the performance of this chromosomal model was compared to the standard human cell model provided in the "molecularDNA" Geant4-DNA example.

RESULTS

Simulations using the new chromosomal model revealed minimal discrepancies in DNA damage yield and fragment size distribution compared to the default human cell model. Notably, the chromosomal model demonstrated significant computational efficiency, requiring approximately three times less simulation time to achieve equivalent results.

CONCLUSIONS

This work highlights the importance of incorporating chromosomal structure into human cell models for radiation biology research. The "complexDNA" tool offers a valuable resource for creating intricate DNA structures for future studies. Further refinements, such as implementing smaller voxels for euchromatin regions, are proposed to enhance the model's accuracy.

Modeling the oxygen effect in DNA strand break induced by gamma-rays with TOPAS-nBio

Objective.To present and validate a method to simulate from first principles the effect of oxygen on radiation-induced double-strand breaks (DSBs) using the Monte Carlo Track-structure code TOPAS-nBio.Approach.Two chemical models based on the oxygen fixation hypothesis (OFH) were developed in TOPAS-nBio by considering an oxygen adduct state of DNA and creating a competition kinetic mechanism between oxygen and the radioprotective molecule WR-1065. We named these models 'simple' and 'detailed' due to the way they handle the hydrogen abstraction pathways. We used the simple model to obtain additional information for the •OH-DNA hydrogen abstraction pathway probability for the detailed model. These models were calibrated and compared with published experimental data of linear and supercoiling fractions obtained with R6K plasmids, suspended in dioxane as a hydroxyl scavenger, and irradiated with137Cs gamma-rays. The reaction rates for WR-1065 and O2with DNA were taken from experimental works. Single-Strand Breaks (SSBs) and DSBs as a function of the dose for a range of oxygen concentrations [O2] (0.021%-21%) were obtained. Finally, the hypoxia reduction factor (HRF) was obtained from DSBs.Main Results.Validation results followed the trend of the experimental within 12% for the supercoiled and linear plasmid fractions for both models. The HRF agreed with measurements obtained with137Cs and 200-280 kVp x-ray within experimental uncertainties. However, the HRF at an oxygen concentration of 2.1% overestimated experimental results by a factor of 1.7 ± 0.1. Increasing the concentration of WR-1065 from 1 mM to 10-100 mM resulted in a HRF difference of 0.01, within the 8% statistical uncertainty between TOPAS-nBio and experimental data. This highlights the possibility of using these chemical models to recreate experimental HRF results.Significance.Results support the OFH as a leading cause of oxygen radio-sensitization effects given a competition between oxygen and chemical DNA repair molecules like WR-1065.

The Emission of Internal Conversion Electrons Rather Than Auger Electrons Increased the Nucleus-Absorbed Dose for 161Tb Compared with 177Lu with a Higher Dose Response for [161Tb]Tb-DOTA-LM3 Than for [161Tb]Tb-DOTATATE

Preclinical data have shown that 161Tb-labeled peptides targeting the somatostatin receptor are therapeutically more effective for peptide receptor radionuclide therapy than are their 177Lu-labeled counterparts. To further substantiate this enhanced therapeutic effect, we performed cellular dosimetry to quantify the absorbed dose to the cell nucleus and compared dose-response curves to evaluate differences in relative biological effectiveness in vitro. Methods: CA20948 cell survival was assessed after treatment with [161Tb]Tb- and [177Lu]Lu-DOTATATE (agonist) and with [161Tb]Tb- and [177Lu]Lu-DOTA-LM3 (antagonist) via a clonogenic assay. Cell binding, internalization, and dissociation assays were performed up to 7 d to acquire time-integrated activity coefficients. Separate S values for each type of particle emission (Auger/internal conversion [IC] electrons and β- particles) were computed via Monte Carlo simulations, while considering spheric cells. Once the absorbed dose to the cell nucleus was calculated, survival curves were fitted to the appropriate linear or linear-quadratic model and corresponding relative biological effectiveness was evaluated. Results: Although the radiopeptide uptake was independent of the radionuclide, [161Tb]Tb-DOTATATE and [161Tb]Tb-DOTA-LM3 delivered a 3.6 and 3.8 times higher dose to the nucleus, respectively, than their 177Lu-labeled counterparts on saturated receptor binding. This increased nucleus-absorbed dose was mainly due to the additional emission of IC and not Auger electrons by 161Tb. When activity concentrations were considered, both [161Tb]Tb-DOTATATE and [161Tb]Tb-DOTA-LM3 showed a lower survival fraction than did labeling with 177Lu. When the absorbed dose to the nucleus was considered, no significant difference could be observed between the dose-response curves for [161Tb]Tb- and [177Lu]Lu-DOTATATE. [161Tb]Tb-DOTA-LM3 showed a linear-quadratic dose response, whereas [161Tb]Tb-DOTATATE showed only a linear dose response within the observed dose range, suggesting additional cell membrane damage by Auger electrons. Conclusion: The IC, rather than Auger, electrons emitted by 161Tb resulted in a higher absorbed dose to the cell nucleus and lower clonogenic survival for [161Tb]Tb-DOTATATE and [161Tb]Tb-DOTA-LM3 than for the 177Lu-labeled analogs. In contrast, [161Tb]Tb-DOTATATE showed no higher dose response than [177Lu]Lu-DOTATATE, whereas for [161Tb]Tb-DOTA-LM3 an additional quadratic response was observed. Because of this quadratic response, potentially caused by cell membrane damage, [161Tb]Tb-DOTA-LM3 is a more effective radiopeptide than [161Tb]Tb-DOTATATE for labeling with 161Tb.

Monte Carlo simulations of microdosimetry and radiolytic species production at long time post proton irradiation using GATE and Geant4-DNA

BACKGROUND

Radiobiological effectiveness of radiation in cancer treatment can be studied at different scales (molecular till organ scale) and different time post irradiation. The production of free radicals and reactive oxygen species during water radiolysis is particularly relevant to understand the fundamental mechanisms playing a role in observed biological outcomes. The development and validation of Monte Carlo tools integrating the simulation of physical, physico-chemical and chemical stages after radiation is very important to maintain with experiments.

PURPOSE

Therefore, in this study, we propose to validate a new Geant4-DNA chemistry module through the simulation of water radiolysis and Fricke dosimetry experiments on a proton preclinical beam line.

MATERIAL AND METHODS

In this study, we used the GATE Monte Carlo simulation platform (version 9.3) to simulate a 67.5 MeV proton beam produced with the ARRONAX isochronous cyclotron (IBA Cyclone 70XP) at conventional dose rate (0.2 Gy/s) to simulate the irradiation of ultra-pure liquid water samples and Fricke dosimeter. We compared the depth dose profile with measurements performed with a plane parallel Advanced PTW 34045 Markus ionization chamber. Then, a new Geant4-DNA chemistry application proposed from Geant4 version 11.2 has been used to assess the evolution ofHO • ${\mathrm{HO}}^ \bullet $ ,e aq - ${\mathrm{e}}_{{\mathrm{aq}}}^ - $ ,H 3 O + ${{\mathrm{H}}}_3{{\mathrm{O}}}^ + $ ,H 2 O 2 ${{\mathrm{H}}}_2{{\mathrm{O}}}_2$ ,H 2 ${{\mathrm{H}}}_2$ ,HO 2 • ${\mathrm{HO}}_2^ \bullet $ ,HO 2 - , O 2 • - ${\mathrm{HO}}_2^ - ,{\mathrm{\ O}}_2^{ \bullet - }$ andHO - ${\mathrm{HO}}^ - $ reactive species along time until 1-h post-irradiation. In particular, the effect of oxygen and pH has been investigated through comparisons with experimental measurements of radiolytic yields forH 2 O 2 ${{\mathrm{H}}}_2{{\mathrm{O}}}_2$ and Fe3+.

RESULTS

GATE simulations reproduced, within 4%, the depth dose profile in liquid water. With Geant4-DNA, we were able to reproduce experimentalH 2 O 2 ${{\mathrm{H}}}_2{{\mathrm{O}}}_2$ radiolytic yields 1-h post-irradiation in aerated and deaerated conditions, showing the impact of small changes in oxygen concentrations on species evolution along time. For the Fricke dosimeter, simulated G(Fe3+) is 15.97 ± 0.2 molecules/100 eV which is 11% higher than the measured value (14.4 ± 04 molecules/100 eV).

CONCLUSIONS

These results aim to be consolidated by new comparisons involving other radiolytic species, such ase aq - ${\mathrm{e}}_{{\mathrm{aq}}}^ - $ or, O 2 • - $,{\mathrm{\ O}}_2^{ \bullet - }$ to further study the mechanisms underlying the FLASH effect observed at ultra-high dose rates (UHDR).

TOPAS-Tissue: A Framework for the Simulation of the Biological Response to Ionizing Radiation at the Multi-Cellular Level

This work aims to develop and validate a framework for the multiscale simulation of the biological response to ionizing radiation in a population of cells forming a tissue. We present TOPAS-Tissue, a framework to allow coupling two Monte Carlo (MC) codes: TOPAS with the TOPAS-nBio extension, capable of handling the track-structure simulation and subsequent chemistry, and CompuCell3D, an agent-based model simulator for biological and environmental behavior of a population of cells. We verified the implementation by simulating the experimental conditions for a clonogenic survival assay of a 2-D PC-3 cell culture model (10 cells in 10,000 µm2) irradiated by MV X-rays at several absorbed dose values from 0-8 Gy. The simulation considered cell growth and division, irradiation, DSB induction, DNA repair, and cellular response. The survival was obtained by counting the number of colonies, defined as a surviving primary (or seeded) cell with progeny, at 2.7 simulated days after irradiation. DNA repair was simulated with an MC implementation of the two-lesion kinetic model and the cell response with a p53 protein-pulse model. The simulated survival curve followed the theoretical linear-quadratic response with dose. The fitted coefficients α = 0.280 ± 0.025/Gy and β = 0.042 ± 0.006/Gy2 agreed with published experimental data within two standard deviations. TOPAS-Tissue extends previous works by simulating in an end-to-end way the effects of radiation in a cell population, from irradiation and DNA damage leading to the cell fate. In conclusion, TOPAS-Tissue offers an extensible all-in-one simulation framework that successfully couples Compucell3D and TOPAS for multiscale simulation of the biological response to radiation.

Radial dependence of ionization clustering around a gold nanoparticle irradiated by X-rays under charged particle equilibrium

Objective.This work explores the enhancement of ionization clustering and its radial dependence around a gold nanoparticle (NP), indicative of the induction of DNA lesions, a potential trigger for cell-death.Approach.Monte Carlo track structure simulations were performed to determine (a) the spectral fluence of incident photons and electrons in water around a gold NP under charged particle equilibrium conditions and (b) the density of ionization clusters produced on average as well as conditional on the occurrence of at least one interaction in the NP using Associated Volume Clustering. Absorbed dose was determined for comparison with a recent benchmark intercomparison. Reported quantities are normalized to primary fluence, allowing to establish a connection to macroscopic dosimetric quantities.Main results.The modification of the electron spectral fluence by the gold NP is minor and mainly occurs at low energies. The net fluence of electrons emitted from the NP is dominated by electrons resulting from photon interactions. Similar to the known dose enhancement, increased ionization clustering is limited to a distance from the NP surface of up to200nm. The number of clusters per energy imparted is increased at distances of up to150nm, and accordingly the enhancement in clustering notably surpasses that of dose enhancement. Smaller NPs cause noticeable peaks in the conditional frequency of clusters between50nm-100nmfrom the NP surface.Significance.This work shows that low energy electrons emitted by NPs lead to an increase of ionization clustering in their vicinity exceeding that of energy imparted. While the electron component of the radiation field plays an important role in determining the background contribution to ionization clustering and energy imparted, the dosimetric effects of NPs are governed by the interplay of secondary electron production by photon interaction and their ability to leave the NP.

Monte Carlo investigation of the nucleus size effect and cell's oxygen content on the damage efficiency of protons

Living tissues could suffer different types of DNA damage as a result of being exposed to ionizing radiations. Monte Carlo simulations of the underlying interactions have been instrumental in predicting the damage types and the processes involved. In this work, we employed Geant4-DNA and MCDS for extracting the initial DNA damage and investigating the dependence of damage efficiency on the cell's oxygen content. The frequency-mean lineal (y¯F) and specific (z¯F) energies were derived for a spherical volume of water of various diameters between 2 and 11.1 μm. This sphere would serve as the nucleus of a cell of 100 μm diameter, engulfed by a homogeneous beam of protons. These microdosimetric quantities were calculated assuming spherical samples of 1 μm diameter in MCDS. The simulation results showed that for 230 MeV protons, an increase in the oxygen content from 0 by 10% raised the frequency of single- and double-strand breaks and lowered the base damage frequency. The resulting damage frequencies appeared to be independent of nucleus diameter. For proton energies between 2 and 230 MeV,y¯Fshowed no dependence on the cell diameter and an increase of the cell size resulted in a decrease inz¯F.An increase in the proton energy slowed down the decreasing rate ofz¯Fas a function of nucleus diameter. However, the ratio ofy¯Fvalues corresponding to two proton energies of choice showed no dependence on the nucleus size and were equal to the ratio of the correspondingz¯Fvalues. Furthermore, the oxygen content of the cell did not affect these microdosimetric quantities. Contrary to damage frequencies, these quantities appeared to depend only on direct interactions due to deposited energies. Our calculations showed the near independence of DNA damages on the nucleus size of the human cells. The probabilities of different types of single and double-strand breaks increase with the oxygen content.

Modelling radiobiology

Radiotherapy has played an essential role in cancer treatment for over a century, and remains one of the best-studied methods of cancer treatment. Because of its close links with the physical sciences, it has been the subject of extensive quantitative mathematical modelling, but a complete understanding of the mechanisms of radiotherapy has remained elusive. In part this is because of the complexity and range of scales involved in radiotherapy-from physical radiation interactions occurring over nanometres to evolution of patient responses over months and years. This review presents the current status and ongoing research in modelling radiotherapy responses across these scales, including basic physical mechanisms of DNA damage, the immediate biological responses this triggers, and genetic- and patient-level determinants of response. Finally, some of the major challenges in this field and potential avenues for future improvements are also discussed.

Nanoscale gold nanoparticle (GNP)-laden tumor cell model and its use for estimation of intracellular dose from GNP-induced secondary electrons

BACKGROUND

Gold nanoparticles (GNPs) accumulated within tumor cells have been shown to sensitize tumors to radiotherapy. From a physics point of view, the observed GNP-mediated radiosensitization is due to various downstream effects of the secondary electron (SE) production from internalized GNPs such as GNP-mediated dose enhancement. Over the years, numerous computational investigations on GNP-mediated dose enhancement/radiosensitization have been conducted. However, such investigations have relied mostly on simple cellular geometry models and/or artificial GNP distributions. Thus, it is at least desirable, if not necessary, to conduct further investigations using cellular geometry models that properly reflect realistic cell morphology as well as internalized GNP distributions at the nanoscale.

PURPOSE

The primary aim of this study was to develop a nanometer-resolution geometry model of a GNP-laden tumor cell for computational investigations of GNP-mediated dose enhancement/radiosensitization. The secondary aim was to demonstrate the utility of this model by quantifying GNP-induced SE tracks/dose distribution at sub-cellular levels for further validation of a nanoscopic dose point kernel (nDPK) method against full-fledged Geant4 Monte Carlo (MC) simulation.

METHODS

A transmission electron microscopy (TEM) image of a single cell showing cytoplasm, cellular nucleus, and internalized GNPs in the cellular endosome was segmented into sub-cellular levels based on pixel value thresholding. A corresponding material density was allocated to each pixel, and, by adding a thickness, each pixel was transformed to a geometric voxel and imported as a Geant4-acceptable input geometry file. In Geant4-Penelope MC simulation, a clinical 6 MV photon beam was applied, vertically or horizontally to the cell surface, and energy deposition to the cellular nucleus and cytoplasm, due to SEs emitted by internalized GNPs, was scored. Next, nDPK calculations were performed by generating virtual electron tracks from each GNP voxel to all nucleus and cytoplasm voxels. Subsequently, another set of Geant4 simulation was performed with both Penelope and DNA physics models under the geometry closely mimicking in vitro cell irradiation with a clinical 6 MV photon beam, allowing for derivation of nDPK specific to this geometry and further comparison between Gean4 simulation and nDPK method.

RESULTS

The Geant4-calculated SE tracks and associated energy depositions showed significant dependence on photon incidence angle. For perpendicular incidence, nDPK results showed good agreement (average percentage pixel-to-pixel difference of 0.4% for cytoplasm and 0.5% for nucleus) with Geant4 results, while, for parallel incidence, the agreement became worse (-1.7%-0.7% for cytoplasm and -5.5%-0.8% for nucleus). Under the 6 MV cell irradiation geometry, nDPK results showed reasonable agreement (pixel-to-pixel Pearson's product moment correlation coefficient of 0.91 for cytoplasm and 0.98 for nucleus) with Geant4 results.

CONCLUSIONS

The currently developed TEM-based model of a GNP-laden cell offers unprecedented details of realistic intracellular GNP distributions for nanoscopic computational investigations of GNP-mediated dose enhancement/radiosensitization. A benchmarking study performed with this model showed reasonable agreement between Geant4- and nDPK-calculated intracellular dose deposition by SEs emitted from internalized GNPs, especially under perpendicular incidence - a popular cell irradiation geometry and when the Geant4-Penelope physics model was used.

A mechanistic simulation of induced DNA damage in a bacterial cell by X- and gamma rays: a parameter study

Mechanistic Monte Carlo simulations calculating DNA damage caused by ionizing radiation are highly dependent on the simulation parameters. In the present study, using the Geant4-DNA toolkit, the impact of different parameters on DNA damage induced in a bacterial cell by X- and gamma-ray irradiation was investigated. Three geometry configurations, including the simple (without DNA details), the random (a random multiplication of identical DNA segments), and the fractal (a regular replication of DNA segments using fractal Hilbert curves), were simulated. Also, three physics constructors implemented in Geant4-DNA, i.e., G4EmDNAPhysics_option2, G4EmDNAPhysics_option4, and G4EmDNAPhysics_option6, with two energy thresholds of 17.5 eV and 5-37.5 eV were compared for direct DNA damage calculations. Finally, a previously developed mathematical model of cell repair called MEDRAS (Mechanistic DNA Repair and Survival) was employed to compare the impact of physics constructors on the cell survival curve. The simple geometry leads to undesirable results compared to the random and fractal ones, highlighting the importance of simulating complex DNA structures in mechanistic simulation studies. Under the same conditions, the DNA damage calculated in the fractal geometry was more consistent with the experimental data. All physics constructors can be used alternatively with the fractal geometry, provided that an energy threshold of 17.5 eV is considered for recording direct DNA damage. All physics constructors represent a similar behavior in generating cell survival curves, although the slopes of the curves are different. Since the inverse of the slope of a bacterial cell survival curve (i.e., the D10-value) is highly sensitive to the simulation parameters, it is not logical to determine an optimal set of parameters for calculating the D10-value by Monte Carlo simulation.

Review of chemical models and applications in Geant4-DNA: Report from the ESA BioRad III Project

A chemistry module has been implemented in Geant4-DNA since Geant4 version 10.1 to simulate the radiolysis of water after irradiation. It has been used in a number of applications, including the calculation of G-values and early DNA damage, allowing the comparison with experimental data. Since the first version, numerous modifications have been made to the module to improve the computational efficiency and extend the simulation to homogeneous kinetics in bulk solution. With these new developments, new applications have been proposed and released as Geant4 examples, showing how to use chemical processes and models. This work reviews the models implemented and application developments for modeling water radiolysis in Geant4-DNA as reported in the ESA BioRad III Project.

Quantitative analysis of dose dependent DNA fragmentation in dry pBR322 plasmid using long read sequencing and Monte Carlo simulations

Exposure to ionizing radiation can induce genetic aberrations via unrepaired DNA strand breaks. To investigate quantitatively the dose-effect relationship at the molecular level, we irradiated dry pBR322 plasmid DNA with 3 MeV protons and assessed fragmentation yields at different radiation doses using long-read sequencing from Oxford Nanopore Technologies. This technology applied to a reference DNA model revealed dose-dependent fragmentation, as evidenced by read length distributions, showing no discernible radiation sensitivity in specific genetic sequences. In addition, we propose a method for directly measuring the single-strand break (SSB) yield. Furthermore, through a comparative study with a collection of previous works on dry DNA irradiation, we show that the irradiation protocol leads to biases in the definition of ionizing sources. We support this scenario by discussing the size distributions of nanopore sequencing reads in the light of Geant4 and Geant4-DNA simulation toolkit predictions. We show that integrating long-read sequencing technologies with advanced Monte Carlo simulations paves a promising path toward advancing our comprehension and prediction of radiation-induced DNA fragmentation.

"dsbandrepair" - An updated Geant4-DNA simulation tool for evaluating the radiation-induced DNA damage and its repair

PURPOSE

Interdisciplinary scientific communities have shown large interest to achieve a mechanistic description of radiation-induced biological damage, aiming to predict biological results produced by different radiation quality exposures. Monte Carlo track-structure simulations are suitable and reliable for the study of early DNA damage induction used as input for assessing DNA damage. This study presents the most recent improvements of a Geant4-DNA simulation tool named "dsbandrepair".

METHODS

"dsbandrepair" is a Monte Carlo simulation tool based on a previous code (FullSim) that estimates the induction of early DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). It uses DNA geometries generated by the DNAFabric computational tool for simulating the induction of early single-strand breaks (SSBs) and double-strand breaks (DSBs). Moreover, the new tool includes some published radiobiological models for survival fraction and un-rejoined DSB. Its application for a human fibroblast cell and human umbilical vein endothelial cell containing both heterochromatin and euchromatin was conducted. In addition, this new version offers the possibility of using the new IRT-syn method for computing the chemical stage.

RESULTS

The direct and indirect strand breaks, SSBs, DSBs, and damage complexity obtained in this work are equivalent to those obtained with the previously published simulation tool when using the same configuration in the physical and chemical stages. Simulation results on survival fraction and un-rejoined DSB are in reasonable agreement with experimental data.

CONCLUSIONS

"dsbandrepair" is a tool for simulating DNA damage and repair, benchmarked against experimental data. It has been released as an advanced example in Geant4.11.2.

Lithium inelastic cross-sections and their impact on micro and nano dosimetry of boron neutron capture

Objective.To present a new set of lithium-ion cross-sections for (i) ionization and excitation processes down to 700 eV, and (ii) charge-exchange processes down to 1 keV u-1. To evaluate the impact of the use of these cross-sections on micro a nano dosimetric quantities in the context of boron neutron capture (BNC) applications/techniques.Approach.The Classical Trajectory Monte Carlo method was used to calculate Li ion charge-exchange cross sections in the energy range of 1 keV u-1to 10 MeV u-1. Partial Li ion charge states ionization and excitation cross-sections were calculated using a detailed charge screening factor. The cross-sections were implemented in Geant4-DNA v10.07 and simulations and verified using TOPAS-nBio by calculating stopping power and continuous slowing down approximation (CSDA) range against data from ICRU and SRIM. Further microdosimetric and nanodosimetric calculations were performed to quantify differences against other simulation approaches for low energy Li ions. These calculations were: lineal energy spectra (yf(y) andyd(y)), frequency mean lineal energyyF-, dose mean lineal energyyD-and ionization cluster size distribution analysis. Microdosimetric calculations were compared against a previous MC study that neglected charge-exchange and excitation processes. Nanodosimetric results were compared against pure ionization scaled cross-sections calculations.Main results.Calculated stopping power differences between ICRU and Geant4-DNA decreased from 33.78% to 6.9%. The CSDA range difference decreased from 621% to 34% when compared against SRIM calculations. Geant4-DNA/TOPAS calculated dose mean lineal energy differed by 128% from the previous Monte Carlo. Ionization cluster size frequency distributions for Li ions differed by 76%-344.11% for 21 keV and 2 MeV respectively. With a decrease in theN1within 9% at 10 keV and agreeing after the 100 keV. With the new set of cross-sections being able to better simulate low energy behaviors of Li ions.Significance.This work shows an increase in detail gained from the use of a more complete set of low energy cross-sections which include charge exchange processes. Significant differences to previous simulation results were found at the microdosimetric and nanodosimetric scales that suggest that Li ions cause less ionizations per path length traveled but with more energy deposits. Microdosimetry results suggest that the BNC's contribution to cellular death may be mainly due to alpha particle production when boron-based drugs are distributed in the cellular membrane and beyond and by Li when it is at the cell cytoplasm regions.

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

Monte Carlo-Based Nanoscale Dosimetry Holds Promise for Radiopharmaceutical Therapy Involving Auger Electron Emitters

Radiopharmaceutical therapy (RPT) is evolving as a promising strategy for treating cancer. As interest grows in short-range particles, like Auger electrons, understanding the dose-response relationship at the deoxyribonucleic acid (DNA) level has become essential. In this study, we used the Geant4-DNA toolkit to evaluate DNA damage caused by the Auger-electron-emitting isotope I-125. We compared the energy deposition and single strand break (SSB) yield at each base pair location in a short B-form DNA (B-DNA) geometry with existing simulation and experimental data, considering both physical direct and chemical indirect hits. Additionally, we evaluated dosimetric differences between our high-resolution B-DNA target and a previously published simple B-DNA geometry. Overall, our benchmarking results for SSB yield from I-125 decay exhibited good agreement with both simulation and experimental data. Using this simulation, we then evaluated the SSB and double strand break (DSB) yields caused by a theranostic Br-77-labeled poly ADP ribose polymerase (PARP) inhibitor radiopharmaceutical. The results indicated a predominant contribution of chemical indirect hits over physical direct hits in generating SSB and DSB. This study lays the foundation for future investigations into the nano-dosimetric properties of RPT.

Dose and DNA damage modelling of diffusing alpha-emitters radiation therapy using Geant4

PURPOSE

Diffusing alpha-emitters radiation therapy (DaRT) is a brachytherapy technique using α-particles to treat solid tumours. The high linear energy transfer (LET) and short range of α-particles make them good candidates for the targeted treatment of cancer. Treatment planning of DaRT requires a good understanding of the dose from α-particles and the other particles released in the 224Ra decay chain.

METHODS

The Geant4 Monte Carlo toolkit has been used to simulate a DaRT seed to better understand the dose contribution from all particles and simulate the DNA damage due to this treatment.

RESULTS

Close to the seed α-particles deliver the majority of dose, however at radial distances greater than 4 mm, the contribution of β-particles is greater. The RBE has been estimated as a function of number of double strand breaks (DSBs) and complex DSBs. A maximum seed spacing of 5.5 mm and 6.5 mm was found to deliver at least 20 Gy RBE weighted dose between the seeds for RBEDSB and RBEcDSB respectively.

CONCLUSIONS

The DNA damage changes with radial distance from the seed and has been found to become less complex with distance, which is potentially easier for the cell to repair. Close to the seed α-particles contribute the majority of dose, however the contribution from other particles cannot be neglected and may influence the choice of seed spacing.

Synergistic Effect of Ferroptosis-Inducing Nanoparticles and X-Ray Irradiation Combination Therapy

Ferroptosis, characterized by the induction of cell death via lipid peroxidation, has been actively studied over the last few years and has shown the potential to improve the efficacy of cancer nanomedicine in an iron-dependent manner. Radiation therapy, a common treatment method, has limitations as a stand-alone treatment due to radiation resistance and safety as it affects even normal tissues. Although ferroptosis-inducing drugs help alleviate radiation resistance, there are no safe ferroptosis-inducing drugs that can be considered for clinical application and are still in the research stage. Here, the effectiveness of combined treatment with radiotherapy with Fe and hyaluronic acid-based nanoparticles (FHA-NPs) to directly induce ferroptosis, considering the clinical applications is reported. Through the induction of ferroptosis by FHA-NPs and apoptosis by X-ray irradiation, the therapeutic efficiency of cancer is greatly improved both in vitro and in vivo. In addition, Monte Carlo simulations are performed to assess the physical interactions of the X-rays with the iron-oxide nanoparticle. The study provides a deeper understanding of the synergistic effect of ferroptosis and X-ray irradiation combination therapy. Furthermore, the study can serve as a valuable reference for elucidating the role and mechanisms of ferroptosis in radiation therapy.

Clonogenic assay and computational modeling using real cell images to study physical enhancement and cellular sensitization induced by metal nanoparticles under MV and kV X-ray irradiation

This study was initiated due to the physically unexplainable tumor controls resulting from metal nanoparticle (MNP) experiments even under MV X-ray irradiation. A more accurate explanation of the mechanism of radiosensitization induced by MNP is warranted, considering both its physical dose enhancement and biological sensitization, as related research is lacking. Thus, we aimed to examine the intricate dynamics involved in MNP-induced radiosensitization. We conducted specifically designed clonogenic assays for the A549 lung cancer cell line with MNP irradiated by 6 MV and 300 kVp X-rays. Two types of MNP were employed: one based on iron oxide, promoting ferroptosis, and the other on gold nanoparticles known for inducing a significant dose enhancement, particularly at low-energy X-rays. We introduced the lethality enhancement factor (LEF) as the fraction in the cell killing attributed to biological sensitization. Subsequently, Monte Carlo simulations were conducted to evaluate the radial dose profiles for each MNP, corresponding to the physical enhancement. Finally, the local effect model was applied to the clonogenic assay results on real cell images. The LEF and the dose enhancement in the cytoplasm were incorporated to increase the accuracy in the average lethal events and, consequently, in the survival fraction. The results reveal an increased cell killing for both of the MNP under MV and kV X-ray irradiation. In both types of MNP, the LEF reveals a biological sensitization evident. The sensitizer enhancement ratio, derived from the calculations, exhibited only 3% and 1% relative differences compared to the conventional linear-quadratic model for gold and ferroptosis inducer nanoparticles, respectively. These findings indicate that MNPs sensitize cells via radiation through mechanisms akin to ferroptosis inducers, not exclusively relying on a physical dose enhancement. Their own contributions to survival fractions were successfully integrated into computational modeling.

Proton relative biological effectiveness for the induction of DNA double strand breaks based on Geant4

Uncertainties in the relative biological effectiveness (RBE) of proton remains a major barrier to the biological optimization of proton therapy. A large amount of experimental data suggest that proton RBE is variable. As an evolving Monte Carlo code toolkit, Geant4-DNA is able to simulate the initial DNA damage caused by particle beams through physical and chemical interactions at the nanometer scale over a short period of time. This contributes to evaluating the radiobiological effects induced by ionizing radiation. Based on the Geant4-DNA toolkit, this study constructed a DNA geometric model containing 6.32Gbp, simulated the relationship between radiochemical yields (G-values) and their corresponding chemical constructors, and calculated a detailed calculation of the sources of damage and the complexity of damage in DNA strand breaks. The damage model constructed in this study can simulate the relative biological effectiveness (RBE) in the proton Bragg peak region. The results indicate that: (1) When the electron energy is below 400 keV, the yield of OH·account for 18.1% to 25.3% of the total water radiolysis yields. (2) Under the influence of histone clearance function, the yield of indirect damage account for over 72.93% of the yield of DNA strand breaks (SBs). When linear energy transfer (LET) increased from 29.79 (keV/μm) to 64.29 (keV/μm), the yield of double strand breaks (DSB) increased from 17.27% to 32.65%. (3) By investigating the effect of proton Bragg peak depth on the yield of direct DSB (DSBdirect) and total DSB (DSBtotal), theRBEDSBtotandRBEDSBdirlevels of cells show that the RBE value of protons reaches 2.2 in the Bragg peak region.

Primary study of the relative and compound biological effectiveness model for boron neutron capture therapy based on nanodosimetry

BACKGROUND

The current radiobiological model employed for boron neutron capture therapy (BNCT) treatment planning, which relies on microdosimetry, fails to provide an accurate representation the biological effects of BNCT. The precision in calculating the relative biological effectiveness (RBE) and compound biological effectiveness (CBE) plays a pivotal role in determining the therapeutic efficacy of BNCT. Therefore, this study focuses on how to improve the accuracy of the biological effects of BNCT.

PURPOSE

The purpose of this study is to propose new radiation biology models based on nanodosimetry to accurately assess RBE and CBE for BNCT.

METHODS

Nanodosimetry, rooted in ionization cluster size distributions (ICSD), introduces a novel approach to characterize radiation quality by effectively delineating RBE through the ion track structure at the nanoscale. In the context of prior research, this study presents a computational model for the nanoscale assessment of RBE and CBE. We establish a simplified model of DNA chromatin fiber using the Monte Carlo code TOPAS-nBio to evaluate the applicability of ICSD to BNCT and compute nanodosimetric parameters.

RESULTS

Our investigation reveals that both homogeneous and heterogeneous nanodosimetric parameters, as well as the corresponding biological model coefficients α and β, along with RBE values, exhibit variations in response to varying intracellular 10B concentrations. Notably, the nanodosimetric parameterM 1 C 2 $M_1^{{{\mathrm{C}}}_2}$ effectively captures the fluctuations in model coefficients α and RBE.

CONCLUSION

Our model facilitates a nanoscale analysis of BNCT, enabling predictions of nanodosimetric quantities for secondary ions as well as RBE, CBE, and other essential biological metrics related to the distribution of boron. This contribution significantly enhances the precision of RBE calculations and holds substantial promise for future applications in treatment planning.

A simulation study on the radiosensitization properties of gold nanorods

Objective. Gold nanorods (GNRs) have emerged as versatile nanoparticles with unique properties, holding promise in various modalities of cancer treatment through drug delivery and photothermal therapy. In the rapidly evolving field of nanoparticle radiosensitization (NPRS) for cancer therapy, this study assessed the potential of gold nanorods as radiosensitizing agents by quantifying the key features of NPRS, such as secondary electron emission and dose enhancement, using Monte Carlo simulations.Approach. Employing the TOPAS track structure code, we conducted a comprehensive evaluation of the radiosensitization behavior of spherical gold nanoparticles and gold nanorods. We systematically explored the impact of nanorod geometry (in particular size and aspect ratio) and orientation on secondary electron emission and deposited energy ratio, providing validated results against previously published simulations.Main results. Our findings demonstrate that gold nanorods exhibit comparable secondary electron emission to their spherical counterparts. Notably, nanorods with smaller surface-area-to-volume ratios (SA:V) and alignment with the incident photon beam proved to be more efficient radiosensitizing agents, showing superiority in emitted electron fluence. However, in the microscale, the deposited energy ratio (DER) was not markedly influenced by the SA:V of the nanorod. Additionally, our findings revealed that the geometry of gold nanoparticles has a more significant impact on the emission of M-shell Auger electrons (with energies below 3.5 keV) than on higher-energy electrons.Significance. This research investigated the radiosensitization properties of gold nanorods, positioning them as promising alternatives to the more conventionally studied spherical gold nanoparticles in the context of cancer research. With increasing interest in multimodal cancer therapy, our findings have the potential to contribute valuable insights into the perspective of gold nanorods as effective multipurpose agents for synergistic photothermal therapy and radiotherapy. Future directions may involve exploring alternative metallic nanorods as well as further optimizing the geometry and coating materials, opening new possibilities for more effective cancer treatments.

Radium deposition in human brain tissue: A Geant4-DNA Monte Carlo toolkit study

NASA has encouraged studies on 226Ra deposition in the human brain to investigate the effects of exposure to alpha particles with high linear energy transfer, which could mimic some of the exposure astronauts face during space travel. However, this approach was criticized, noting that radium is a bone-seeker and accumulates in the skull, which means that the radiation dose from alpha particles emitted by 226Ra would be heavily concentrated in areas close to cranial bones rather than uniformly distributed throughout the brain. In the high background radiation areas of Ramsar, Iran, extremely high levels of 226Ra in soil contribute to a large proportion of the inhabitants' radiation exposure. A prospective study on Ramsar residents with a calcium-rich diet was conducted to improve the dose uniformity due to 226Ra throughout the cerebral and cerebellar parenchyma. The study found that exposure of the human brain to alpha particles did not significantly affect working memory but was significantly associated with increased reaction times. This finding is crucial because astronauts on deep space missions may face similar cognitive impairments due to exposure to high charge and energy particles. The current study was aimed to evaluate the validity of the terrestrial model using the Geant4 Monte Carlo toolkit to simulate the interactions of alpha particles and representative cosmic ray particles, acknowledging that these radiation types are only a subset of the complete space radiation environment.

Mechanistic modelling of relative biological effectiveness of carbon ion beams and comparison with experiments

Objective.Relative biological effectiveness (RBE) plays a vital role in carbon ion radiotherapy, which is a promising treatment method for reducing toxic effects on normal tissues and improving treatment efficacy. It is important to have an effective and precise way of obtaining RBE values to support clinical decisions. A method of calculating RBE from a mechanistic perspective is reported.Approach.Ratio of dose to obtain the same number of double strand breaks (DSBs) between different radiation types was used to evaluate RBE. Package gMicroMC was used to simulate DSB yields. The DSB inductions were then analyzed to calculate RBE. The RBE values were compared with experimental results.Main results.Furusawa's experiment yielded RBE values of 1.27, 2.22, 3.00 and 3.37 for carbon ion beam with dose-averaged LET of 30.3 keVμm-1, 54.5 keVμm-1, 88 keVμm-1and 137 keVμm-1, respectively. RBE values computed from gMicroMC simulations were 1.75, 2.22, 2.87 and 2.97. When it came to a more sophisticated carbon ion beam with 6 cm spread-out Bragg peak, RBE values were 1.61, 1.63, 2.19 and 2.36 for proximal, middle, distal and distal end part, respectively. Values simulated by gMicroMC were 1.50, 1.87, 2.19 and 2.34. The simulated results were in reasonable agreement with the experimental data.Significance.As a mechanistic way for the evaluation of RBE for carbon ion radiotherapy by combining the macroscopic simulation of energy spectrum and microscopic simulation of DNA damages, this work provides a promising tool for RBE calculation supporting clinical applications such as treatment planning.

A step-by-step simulation code for estimating yields of water radiolysis species based on electron track-structure mode in the PHITS code

Objective. Time-dependent yields of chemical products resulting from water radiolysis play a great role in evaluating DNA damage response after exposure to ionizing radiation. Particle and Heavy Ion Transport code System (PHITS) is a general-purpose Monte Carlo simulation code for radiation transport, which simulates atomic interactions originating from discrete energy levels of ionizations and electronic excitations as well as molecular excitations as physical stages. However, no chemical code for simulating water radiolysis products exists in the PHITS package.Approach.Here, we developed a chemical simulation code dedicated to the PHITS code, hereafter calledPHITS-Chemcode, which enables the calculation of theGvalues of water radiolysis species (•OH, eaq-, H2, H2O2etc) by electron beams.Main results.The estimatedGvalues during 1 μs are in agreement with the experimental ones and other simulations. ThisPHITS-Chemcode also simulates the radiolysis in the presence of OH radical scavengers, such as tris(hydroxymethyl)aminomethane and dimethyl sulfoxide. Thank to this feature, the contributions of direct and indirect effects on DNA damage induction under various scavenging capacities can be analyzed.Significance.This chemical code coupled with PHITS could contribute to elucidating the mechanism of radiation effects by connecting physical, physicochemical, and chemical processes.

Spectral composition of secondary electrons based on the Kiefer-Straaten ion track structure model

The major part of energy deposition of ionizing radiation is caused by secondary electrons, independent of the primary radiation type. However, their spatial concentration and their spectral properties strongly depend on the primary radiation type and finally determine the pattern of molecular damage e.g. to biological targets as the DNA, and thus the final effect of the radiation exposure. To describe the physical and to predict the biological consequences of charged ion irradiation, amorphous track structure approaches have proven to be pragmatic and helpful. There, the local dose deposition in the ion track is equated by considering the emission and slowing down of the secondary electrons from the primary particle track. In the present work we exploit the model of Kiefer and Straaten and derive the spectral composition of secondary electrons as function of the distance to the track center. The spectral composition indicates differences to spectra of low linear energy transfer (LET) photon radiation, which we confirm by a comparison with Monte Carlo studies. We demonstrate that the amorphous track structure approach provides a simple tool for evaluating the spectral electron properties within the track structure. Predictions of the LET of electrons across the track structure as well as the electronic dose build-up effect are derived. Implications for biological effects and corresponding predicting models based on amorphous track structure are discussed.