Geant4-DNA example applications for track structure simulations in liquid water: A report from the Geant4-DNA Project

Ionization Detail Parameters for DNA Damage Evaluation in Charged Particle Radiotherapy: Simulation Study Based on Cell Survival Database

Details of excitation and ionization acts hide a description of the biological effects of charged particle traversal through living tissue. Nanodosimetry enables the introduction of novel quantities that characterize and quantify the particle track structure while also serving as a foundation for assessing biological effects based on this quantification. This presents an opportunity to enhance the planning of charged particle radiotherapy by taking into account the ionization detail. This work uses Monte Carlo simulations with Geant4-DNA code for a wide variety of charged particles and their radiation qualities to analyze the distribution of ionization cluster sizes within nanometer-scale volumes, similar to DNA diameter. By correlating these results with biological parameters extracted from the PIDE database for the V79 cell line, a novel parameter R2 based on ionization details is proposed for the evaluation of radiation quality in terms of biological consequences, i.e., radiobiological cross section for inactivation. By incorporating the probability p of sub-lethal damage caused by a single ionization, we address limitations associated with the usually proposed nanodosimetric parameter Fk for characterizing the biological effects of radiation. We show that the new parameter R2 correlates well with radiobiological data and can be used to predict biological outcomes.

Estimation of the relative biological effectiveness for double strand break induction of clinical kilovoltage beams using Monte Carlo simulations

BACKGROUND

The Relative Biological Effectiveness (RBE) of kilovoltage photon beams has been previously investigated in vitro and in silico using analytical methods. The estimated values range from 1.03 to 1.82 depending on the methodology and beam energies examined.

PURPOSE

The focus of this work was to independently estimate RBE values for a range of clinically used kilovoltage beams (70-200 kVp) while investigating the suitability of using TOPAS-nBio for this task.

METHODS

Previously validated spectra of clinical beams were used to generate secondary electron spectra at several depths in a water tank phantom via TOPAS Monte Carlo (MC) simulations. Cell geometry was irradiated with the secondary electrons in TOPAS-nBio MC simulations. The deposited dose and the calculated number of DNA strand breaks were used to estimate RBE values.

RESULTS

Monoenergetic secondary electron simulations revealed the highest direct and indirect double strand break yield at approximately 20 keV. The average RBE value for the kilovoltage beams was calculated to be 1.14.

CONCLUSIONS

TOPAS-nBio was successfully used to estimate the RBE values for a range of clinical radiotherapy beams. The calculated value was in agreement with previous estimates, providing confidence in its clinical use in the future.

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.

Efficient computational modeling of electronic stopping power of organic polymers for proton therapy optimization

This comprehensive study delves into the intricate interplay between protons and organic polymers, offering insights into proton therapy in cancer treatment. Focusing on the influence of the spatial electron density distribution on stopping power estimates, we employed real-time time-dependent density functional theory coupled with the Penn method. Surprisingly, the assumption of electron density homogeneity in polymers is fundamentally flawed, resulting in an overestimation of stopping power values at energies below 2 MeV. Moreover, the Bragg rule application in specific compounds exhibited significant deviations from experimental data around the stopping maximum, challenging established norms.

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.

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.

Short life fission products extracted from molten salt reactor fuel for radiopharmaceutical applications

This work studies the potential of using short life fission product (AFp) radioisotopes e.g. 82Br, 86Rb, (90Sr) - 90mY, (99Mo) - 99mTc, 103Ru - 103mRh, 111Ag, 127Sb - 127(m)Te, 126I, 131I, 133Xe, 136Cs, 141Ce, 143Ce, 143Pr, 147Nd - 147Pm, 149Pm, 153Sm, 156Eu, 159Gd and 161Tb, extracted from a molten salt reactor and their separation using specific thermodynamic and radiochemical conditions. Their utilisation for coupled radiodiagnostics and radiotherapy is a key consideration. A molten salt reactor produces fission products during operation. These radioisotopes can be separated at line from the liquid fuel by evaporation/distillation, chemical reduction (using H2 doped gas), electro-deposition and/or chemical oxidation (using Cl2 doped gas). They can be refined and chemically treated for radiopharmaceutical use for imaging and radiodiagnostics utilising γ radioscopy or positron emission tomography, and potentially in radiotherapy to target specific cancers or viral diseases using β- emitters. Some of the AFp isotopes are currently used for radiodiagnostics because they emit γ rays of energy 50-200 keV. However, some may also be used in parallel for radiotherapy utilising their β- (EMean ≈ 100 keV) emission whose mean free pathway of c.a. 100 nm in biological tissue is much smaller than their penetration depth. Focus is given to 86Rb, 90Y, 99mTc, 131I and 133Xe as well as on the ALn isotopes (141Ce, 143Ce - 143Pr, 147Nd - 147Pm, 149Pm and 153Sm) because of their strong potential for complexation with bio-ligands (e.g. DOTA) or for their ability to form micro-nano-spheres, and because of their potential for dual radiodiagnostics and radiotherapy. It is shown that these radio-lanthanides could also replace 177Lu for the treatment of specific cancers.

The Effects of Particle LET and Fluence on the Complexity and Frequency of Clustered DNA Damage

Motivation

Clustered DNA-lesions are predominantly induced by ionizing radiation, particularly by high-LET particles, and considered as lethal damage. Quantification of this specific type of damage as a function of radiation parameters such as LET, dose rate, dose, and particle type can be informative for the prediction of biological outcome in radiobiological studies. This study investigated the induction and complexity of clustered DNA damage for three different types of particles at an LET range of 0.5-250 keV/μm.

Methods

Nanometric volumes (36.0 nm3) of 15 base-pair DNA with its hydration shell was modeled. Electron, proton, and alpha particles at various energies were simulated to irradiate the nanometric volumes. The number of ionization events, low-energy electron spectra, and chemical yields for the formation of °OH, H°, e aq - , and H2O2 were calculated for each particle as a function of LET. Single- and double-strand breaks (SSB and DSB), base release, and clustered DNA-lesions were computed from the Monte-Carlo based quantification of the reactive species and measured yields of the species responsible for the DNA lesion formation.

Results

The total amount of DNA damage depends on particle type and LET. The number of ionization events underestimates the quantity of DNA damage at LETs higher than 10 keV/μm. Minimum LETs of 9.4 and 11.5 keV/μm are required to induce clustered damage by a single track of proton and alpha particles, respectively. For a given radiation dose, an increase in LET reduces the number of particle tracks, leading to more complex clustered DNA damage, but a smaller number of separated clustered damage sites.

Conclusions

The dependency of the number and the complexity of clustered DNA damage on LET and fluence suggests that the quantification of this damage can be a useful method for the estimation of the biological effectiveness of radiation. These results also suggest that medium-LET particles are more appropriate for the treatment of bulk targets, whereas high-LET particles can be more effective for small targets.

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.

Comparison of two methods simulating inter-track interactions using the radiobiological Monte Carlo toolkit TOPAS-nBio

Objective.To compare two independently developed methods that enable modelling inter-track interactions in TOPAS-nBio by examining the yield of radiolytic species in radiobiological Monte Carlo track structure simulations. One method uses a phase space file to assign more than one primary to one event, allowing for inter-track interaction between these primary particles. This method has previously been developed by this working group and published earlier. Using the other method, chemical reactions are simulated based on a new version of the independent reaction time approach to allow inter-track interactions.Approach.G-values were calculated and compared using both methods for different numbers of tracks able to undergo inter-track interactions.Main results.Differences in theG-values simulated with the two methods strongly depend on the molecule type, and deviations can range up to 3.9% (H2O2), although, on average, the deviations are smaller than 1.5%.Significance.Both methods seem to be suitable for simulating inter-track interactions, as they provide comparableG-values even though both techniques were developed independently of each other.

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.

An inter-comparison between radiobiological characteristics of a commercial low-energy IORT system by Geant4-DNA and MCDS Monte Carlo codes

INTRODUCTION

The need for accurate relative biological effectiveness (RBE) estimation for low energy therapeutic X-rays (corresponding to 50 kV nominal energy of a commercial low-energy IORT system (INTRABEAM)) is a crucial issue due to increased radiobiological effects, respect to high energy photons. Modeling of radiation-induced DNA damage through Monte Carlo (MC) simulation approaches can give useful information. Hence, this study aimed to evaluate and compare RBE of low energy therapeutic X-rays using Geant4-DNA toolkit and Monte Carlo damage simulation (MCDS) code.

MATERIALS AND METHODS

RBE calculations were performed considering the emitted secondary electron spectra through interactions of low energy X-rays inside the medium. In Geant4-DNA, the DNA strand breaks were obtained by employing a B-DNA model in physical stage with 10.79 eV energy-threshold and the probability of hydroxyl radical's chemical reactions of about 0.13%. Furthermore, RBE estimations by MCDS code were performed under fully aerobic conditions.

RESULTS

Acquired results by two considered MC codes showed that the same trend is found for RBEDSB and RBESSB variations. Totally, a reasonable agreement between the calculated RBE values (both RBESSB and RBEDSB) existed between the two considered MC codes. The mean differences of 9.2% and 1.8% were obtained between the estimated RBESSB and RBEDSB values by two codes, respectively.

CONCLUSION

Based on the obtained results, it can be concluded that a tolerable accordance is found between the calculated RBEDSB values through MCDS and Geant4-DNA, a fact which appropriates both codes for RBE evaluations of low energy therapeutic X-rays, especially in the case of RBEDSB where lethal damages are regarded.

Experimental validation in a neutron exposure frame of the MINAS TIRITH for cell damage simulation

In the domains of medicine and space exploration, refining risk assessment models for protecting healthy tissue from ionizing radiation is crucial. Understanding radiation-induced effects requires biological experimentations at the cellular population level and the cellular scale modeling using Monte Carlo track structure codes. We present MINAS TIRITH, a tool using Geant4-DNA Monte Carlo-generated databases to study DNA damage distribution at the cell population scale. It introduces a DNA damage location module and proposes a method to convert double-strand breaks (DSB) into DNA Damage Response foci. We evaluate damage location precision and DSB-foci conversion parameters. MINAS TIRITH's accuracy is validated againstγ-H2AX foci distribution from cell population exposed to monoenergetic neutron beams (2.5 or 15.1 MeV) under different configurations, yielding mixed radiation fields. Strong agreement between simulation and experimental results was found demonstrating MINAS TIRITH's predictive precision in radiation-induced DNA damage topology. Additionally, modeling intercellular damage variability within a population subjected to a specific macroscopic dose identifies subpopulations, enhancing realistic fate models. This approach advances our understanding of radiation-induced effects on cellular systems for risk assessment improvement.

First-principles simulation of an ejected electron produced by monochromatic deposition energy to water at the femtosecond order

This study uses a time-dependent first-principles simulation code to investigate the transient dynamics of an ejected electron produced in the monochromatic deposition energy from 11 to 19 eV in water. The energy deposition forms a three-body single spur comprising a hydroxyl radical (OH˙), hydronium ion (H3O+), and hydrated electron (eaq-). The earliest formation involves electron thermalization and delocalization dominated by the molecular excitation of water. Our simulation results show that the transient electron dynamics primarily depends on the amount of deposition energy to water; the thermalization time varies from 200 to 500 fs, and the delocalization varies from 3 to 10 nm in this energy range. These features are crucial for determining the earliest single-spur formation and facilitating a sequential simulation from an energy deposition to a chemical reaction in water photolysis or radiolysis. The spur radius obtained from the simulation correlates reasonably with the experimental-based estimations. Our results should provide universalistic insights for analysing ultrafast phenomena dominated by the molecular excitation of water in the femtosecond order.

Electric Fields in Liquid Water Irradiated with Protons at Ultrahigh Dose Rates

We study the effects of irradiating water with 3 MeV protons at high doses by observing the motion of charged polystyrene beads outside the proton beam. By single-particle tracking, we measure a radial velocity of the order of microns per second. Combining electrokinetic theory with simulations of the beam-generated reaction products and their outward diffusion, we find that the bead motion is due to electrophoresis in the electric field induced by the mobility contrast of cations and anions. This work sheds light on the perturbation of biological systems by high-dose radiations and paves the way for the manipulation of colloid or macromolecular dispersions by radiation-induced diffusiophoresis.

Assessing radiation dosimetry for microorganisms in naturally radioactive mineral springs using GATE and Geant4-DNA Monte Carlo simulations

Mineral springs in Massif Central, France can be characterized by higher levels of natural radioactivity in comparison to the background. The biota in these waters is constantly under radiation exposure mainly from the α-emitters of the natural decay chains, with 226Ra in sediments ranging from 21 Bq/g to 43 Bq/g and 222Rn activity concentrations in water up to 4600 Bq/L. This study couples for the first time micro- and nanodosimetric approaches to radioecology by combining GATE and Geant4-DNA to assess the dose rates and DNA damages to microorganisms living in these naturally radioactive ecosystems. It focuses on unicellular eukaryotic microalgae (diatoms) which display an exceptional abundance of teratological forms in the most radioactive mineral springs in Auvergne. Using spherical geometries for the microorganisms and based on γ-spectrometric analyses, we evaluate the impact of the external exposure to 1000 Bq/L 222Rn dissolved in the water and 30 Bq/g 226Ra in the sediments. Our results show that the external dose rates for diatoms are significant (9.7 μGy/h) and comparable to the threshold (10 μGy/h) for the protection of the ecosystems suggested by the literature. In a first attempt of simulating the radiation induced DNA damage on this species, the rate of DNA Double Strand Breaks per day is estimated to 1.11E-04. Our study confirms the significant mutational pressure from natural radioactivity to which microbial biodiversity has been exposed since Earth origin in hydrothermal springs.

Energy imparted and ionisation yield at the nanometre scale: results for extended beams

The metrological problem of interpreting ionisation-based micro- and nanodosimetric measurements in terms of quantities proportional to energy imparted becomes particularly relevant when the sensitive volume (SV) size is in the nanometre range. At these scales, a constant W-value cannot be assumed, and the stochastics of the energy transfer per single collision could play a more important role. This problem was recently analysed by our group by means of track-structure Monte Carlo simulations with the Geant4-DNA code, finding a strong correlation between the energy imparted and ionisation yield also for SV diameters of 1 nm. As the previous study was limited to primary beams of radius zero crossing the sensitive sphere along its diameter, it is the aim of the present work to extend the analysis to beams with a radius larger than the dimensions of the SV, to better assess the role played by secondary electrons.

Calculation of electron interaction models in N2 and O2

Cosmic rays have the potential to significantly affect the atmospheric composition by increasing the rate and changing the types of chemical reactions through ion production. The amount and states of ionization, and the spatial distribution of ions produced are still open questions for atmospheric models. To precisely estimate these quantities, it is necessary to simulate particle-molecule interactions, down to very low energies. Models enabling such simulations require interaction probabilities over a broad energy range and for all energetically allowed scattering processes. In this paper, we focus on electron interaction with the two most abundant molecules in the atmosphere, i.e., N2 and O2, as an initial step. A set of elastic and inelastic cross section models for electron transportation in oxygen and nitrogen molecules valid in the energy range 10 eV - 1 MeV, is presented. Comparison is made with available theoretical and experimental data and a reasonable good agreement is observed. Stopping power is calculated and compared with published data to assess the general consistency and reliability of our results. Good overall agreement is observed, with relative differences lower than 6% with the ESTAR database.

H2O˙+ and OH+ reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage

Radiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This work reports the first experimental study of the ion-molecule reactions of the H2O˙+ and OH+ ions, produced by photoionization with synchrotron radiation, with a furan (c-C4H4O) molecule, a template for deoxyribose sugar in DNA. The present experiments, performed as a function of the collision energy of the ions and the tunable photoionization energy, provide key parameters for the theoretical modelling of the effect of radiation dose, like the absolute cross sections for producing protonated furan (furanH+) and a radical cation (furan˙+), the most abundant products, which can amount up to 200 Å2 at very low collision energies (<1.0 eV). The experimental results show that furanH+ is more fragile, indicating how the protonation of the sugar component of the DNA may favor its dissociation with possible major radiosensitizing effects. Moreover, the ring opening of furanH+ isomers and the potential energy surface of the most important fragmentation channels have been explored by molecular dynamics simulations and quantum chemistry calculations. The results show that, in the most stable isomer of furanH+, the ring opening occurs via a low energy pathway with carbon-oxygen bond cleavage, followed by the loss of neutral carbon monoxide and the formation of the allyl cation CH2CHCH2+, which instead is not observed in the fragmentation of furan˙+. At higher energies the ring opening through the carbon-carbon bond is accompanied by the loss of formaldehyde, producing HCCCH2+, the most intense fragment ion detected in the experiments. This work highlights the importance of the secondary processes, like the ion-molecule reactions at low energies in the radiation damage due to their very large cross sections, and it aims to provide benchmark data for the development of suitable models to approach this low collision energy range.

Estimation of relative biological effectiveness of 225Ac compared to 177Lu during [225Ac]Ac-PSMA and [177Lu]Lu-PSMA radiopharmaceutical therapy using TOPAS/TOPAS-nBio/MEDRAS

AIM

Over recent years, [225Ac]Ac-PSMA and [177Lu]Lu-PSMA radiopharmaceutical therapy have evolved as a promising treatment option for advanced prostate cancer. Especially for alpha particle emitter treatments, there is still a need for improving dosimetry, which requires accurate values of relative biological effectiveness (RBE). To achieve that, consideration of DNA damages in the cell nucleus and knowledge of the energy deposition in the location of the DNA at the nanometer scale are required. Monte Carlo particle track structure simulations provide access to interactions at this level. The aim of this study was to estimate the RBE of 225Ac compared to 177Lu. The initial damage distribution after radionuclide decay and the residual damage after DNA repair were considered.

METHODS

This study employed the TOol for PArtcile Simulation (TOPAS) based on the Geant4 simulation toolkit. Simulation of the nuclear DNA and damage scoring were performed using the TOPAS-nBio extension of TOPAS. DNA repair was modeled utilizing the Python-based program MEDRAS (Mechanistic DNA Repair and Survival). Five different cell geometries of equal volume and two radionuclide internalization assumptions as well as two cell arrangement scenarios were investigated. The radionuclide activity (number of source points) was adopted based on SPECT images of patients undergoing the above-mentioned therapies.

RESULTS

Based on the simulated dose-effect curves, the RBE of 225Ac compared to 177Lu was determined in a wide range of absorbed doses to the nucleus. In the case of spherical geometry, 3D cell arrangement and full radionuclide internalization, the RBE based on the initial damage had a constant value of approximately 2.14. Accounting for damage repair resulted in RBE values ranging between 9.38 and 1.46 for 225Ac absorbed doses to the nucleus between 0 and 50 Gy, respectively.

CONCLUSION

In this work, the consideration of DNA repair of the damage from [225Ac]Ac-PSMA and [177Lu]Lu-PSMA revealed a dose dependency of the RBE. Hence, this work suggested that DNA repair is an important aspect to understand response to different radiation qualities.

Evaluation of the Yield of DNA Double-Strand Breaks for Carbon Ions Using Monte Carlo Simulation and DNA Fragment Distribution

PURPOSE

The aim of this work was to provide a method to evaluate the yield of DNA double-strand breaks (DSBs) for carbon ions, overcoming the bias in existing methods due to the nonrandom distribution of DSBs.

METHODS AND MATERIALS

A previously established biophysical program based on the radiation track structure and a multilevel chromosome model was used to simulate DNA damage induced by x-rays and carbon ions. The fraction of activity retained (FAR) as a function of absorbed dose or particle fluence was obtained by counting the fraction of DNA fragments larger than 6 Mbp. Simulated FAR curves for the 250 kV x-rays and carbon ions at various energies were compared with measurements using constant-field gel electrophoresis. The doses or fluences at the FAR of 0.7 based on linear interpolation were used to estimate the simulation error for the production of DSBs.

RESULTS

The relative difference of doses at the FAR of 0.7 between simulation and experiment was -8.5% for the 250 kV x-rays. The relative differences of fluences at the FAR of 0.7 between simulations and experiments were -17.5%, -42.2%, -18.2%, -3.1%, 10.8%, and -14.5% for the 34, 65, 130, 217, 2232, and 3132 MeV carbon ions, respectively. In comparison, the measurement uncertainty was about 20%. Carbon ions produced remarkably more DSBs and DSB clusters per unit dose than x-rays. The yield of DSBs for carbon ions, ranging from 10 to 16 Gbp-1Gy-1, increased with linear energy transfer (LET) but plateaued in the high-LET end. The yield of DSB clusters first increased and then decreased with LET. This pattern was similar to the relative biological effectiveness for cell survival for heavy ions.

CONCLUSIONS

The estimated yields of DSBs for carbon ions increased from 10 Gbp-1Gy-1 in the low-LET end to 16 Gbp-1Gy-1 in the high-LET end with 20% uncertainty.

Calculation of the DNA damage yield and relative biological effectiveness in boron neutron capture therapy via the Monte Carlo track structure simulation

Objective.Boron neutron capture therapy (BNCT) is an advanced cellular-level hadron therapy that has exhibited remarkable therapeutic efficacy in the treatment of locally invasive malignancies. Despite its clinical success, the intricate nature of relative biological effectiveness (RBE) and mechanisms responsible for DNA damage remains elusive. This work aims to quantify the RBE of compound particles (i.e. alpha and lithium) in BNCT based on the calculation of DNA damage yields via the Monte Carlo track structure (MCTS) simulation.Approach. The TOPAS-nBio toolkit was employed to conduct MCTS simulations. The calculations encompassed four steps: determination of the angle and energy spectra on the nuclear membrane, quantification of the database containing DNA damage yields for ions with specific angle and energy, accumulation of the database and spectra to obtain the DNA damage yields of compound particles, and calculation of the RBE by comparison yields of double-strand break (DSB) with the reference gamma-ray. Furthermore, the impact of cell size and microscopic boron distribution was thoroughly discussed.Main results. The DSB yields induced by compound particles in three types of spherical cells (radius equal to 10, 8, and 6μm) were found to be 13.28, 17.34, 22.15 Gy Gbp-1for boronophenylalanine (BPA), and 1.07, 3.45, 8.32 Gy Gbp-1for sodium borocaptate (BSH). The corresponding DSB-based RBE values were determined to be 1.90, 2.48, 3.16 for BPA and 0.15, 0.49, 1.19 for BSH. The calculated DSB-based RBE showed agreement with experimentally values of compound biological effectiveness for melanoma and gliosarcoma. Besides, the DNA damage yield and DSB-based RBE value exhibited an increasing trend as the cell radius decreased. The impact of the boron concentration ratio on RBE diminished once the drug enrichment surpasses a certain threshold.Significance. This work is potential to provide valuable guidance for accurate biological-weighted dose evaluation in BNCT.

Radiation-induced double-strand breaks by internal ex vivo irradiation of lymphocytes: Validation of a Monte Carlo simulation model using GATE and Geant4-DNA

This study describes a method to validate a radiation transport model that quantifies the number of DNA double-strand breaks (DSB) produced in the lymphocyte nucleus by internal ex vivo irradiation of whole blood with the radionuclides 90Y, 99mTc, 123I, 131I, 177Lu, 223Ra, and 225Ac in a test vial using the GATE/Geant4 code at the macroscopic level and the Geant4-DNA code at the microscopic level.

METHODS

The simulation at the macroscopic level reproduces an 8 mL cylindrical water-equivalent medium contained in a vial that mimics the geometry for internal ex vivo blood irradiation. The lymphocytes were simulated as spheres of 3.75 µm radius randomly distributed, with a concentration of 125 spheres/mL. A phase-space actor was attached to each sphere to register all the entering particles. The simulation at the microscopic level for each radionuclide was performed using the Geant4-DNA tool kit, which includes the clustering example centered on a density-based spatial clustering of applications with noise (DBSCAN) algorithm. The irradiation source was constructed by generating a single phase space from the sum of all phase spaces. The lymphocyte nucleus was defined as a water sphere of a 3.1 µm radius. The absorbed dose coefficients for lymphocyte nuclei (dLymph) were calculated and compared with macroscopic whole blood absorbed dose coefficients (dBlood). The DBSCAN algorithm was used to calculate the number of DSBs. Lastly, the number of DSB∙cell-1∙mGy-1 (simulation) was compared with the number of radiation-induced foci per cell and absorbed dose (RIF∙cell-1∙mGy-1) provided by experimental data for gamma and beta emitting radionuclides. For alpha emitters, dLymph and the number of α-tracks∙100 cell-1∙mGy-1 and DBSs∙µm-1 were calculated using experiment-based thresholds for the α-track lengths and DBSs/track values. The results were compared with the results of an ex vivo study with 223Ra.

RESULTS

The dLymph values differed from the dBlood values by -1.0% (90Y), -5.2% (99mTc), -22.3% (123I), 0.35% (131I), 2.4% (177Lu), -5.6% (223Ra) and -6.1% (225Ac). The number of DSB∙cell-1∙mGy-1 for each radionuclide was 0.015 DSB∙cell-1∙mGy-1 (90Y), 0.012 DSB∙cell-1∙mGy-1 (99mTc), 0.014DSB∙cell-1∙mGy-1 (123I), 0.012 DSB∙cell-1∙mGy-1 (131I), and 0.016 DSB∙cell-1∙mGy-1 (177Lu). These values agree very well with experimental data. The number of α-tracks∙100 cells-1∙mGy-1 for 223Ra and 225Ac where 0.144 α-tracks∙100 cells-1∙mGy-1 and 0.151 α-tracks∙100 cells-1∙mGy-1, respectively. These values agree very well with experimental data. Moreover, the linear density of DSBs per micrometer α-track length were 11.13 ± 0.04 DSB/µm and 10.86 ± 0.06 DSB/µm for 223Ra and 225Ac, respectively.

CONCLUSION

This study describes a model to simulate the DNA DSB damage in lymphocyte nuclei validated by experimental data obtained from internal ex vivo blood irradiation with radionuclides frequently used in diagnostic and therapeutic procedures in nuclear medicine.

Ionization detail parameters and cluster dose: a mathematical model for selection of nanodosimetric quantities for use in treatment planning in charged particle radiotherapy

Objective. To propose a mathematical model for applying ionization detail (ID), the detailed spatial distribution of ionization along a particle track, to proton and ion beam radiotherapy treatment planning (RTP).Approach. Our model provides for selection of preferred ID parameters (Ip) for RTP, that associate closest to biological effects. Cluster dose is proposed to bridge the large gap between nanoscopicIpand macroscopic RTP. Selection ofIpis demonstrated using published cell survival measurements for protons through argon, comparing results for nineteenIp:Nk,k= 2, 3, …, 10, the number of ionizations in clusters ofkor more per particle, andFk,k= 1, 2, …, 10, the number of clusters ofkor more per particle. We then describe application of the model to ID-based RTP and propose a path to clinical translation.Main results. The preferredIpwereN4andF5for aerobic cells,N5andF7for hypoxic cells. Significant differences were found in cell survival for beams having the same LET or the preferredNk. Conversely, there was no significant difference forF5for aerobic cells andF7for hypoxic cells, regardless of ion beam atomic number or energy. Further, cells irradiated with the same cluster dose for theseIphad the same cell survival. Based on these preliminary results and other compelling results in nanodosimetry, it is reasonable to assert thatIpexist that are more closely associated with biological effects than current LET-based approaches and microdosimetric RBE-based models used in particle RTP. However, more biological variables such as cell line and cycle phase, as well as ion beam pulse structure and rate still need investigation.Significance. Our model provides a practical means to select preferredIpfrom radiobiological data, and to convertIpto the macroscopic cluster dose for particle RTP.

A systematic analysis of the particle irradiation data ensemble in the key of the microdosimetric kinetic model: Should clonogenic data be used for clinical relative biological effectiveness?

PURPOSE

To perform a systematic analysis of the Particle Irradiation Data Ensemble (PIDE) database for clonogenic survival assays in the context of the Microdosimetric Kinetic Model (MKM).

METHODS AND MATERIAL

Our study used data from the PIDE database containing data on various cell lines and radiation types. Two main parameters of the MKM were determined experiment-wise: the domain radius, which accounts for the increase of the linear parameter as a function of LET or lineal energy, and the nucleus radius, which accounts for the overkilling effect at LET high enough. We used experiments with LET less and more than 75 keV/μm to determine domain and nucleus radius, respectively. Experiments with cells in asynchronous phase of the cell cycle and monoenergetic beams were considered, and data from 294 out of 461 available experiments with protons, alpha, and carbon beams were used.

RESULTS

Domain and nucleus radii were determined for 32 cell lines as the median among cell-specific experiments after filtering experiments using protons, α-particles, and carbon ions, including 28 human cells and 12 rodent cells. The median values found for domain radii were 380 nm for normal human cells, 390 nm for tumor human cells, 295 nm for normal rodent cells, and 525 nm for tumor rodent cells (only one experiment with rodent tumor cells) with large variability across cell lines and across experiments on each cell line.

CONCLUSIONS

Large inter-experiment variabilities were found for the same cell lines, based on enormous experimental uncertainties and different experimental conditions. Our analysis raises questions about how convenient is to use clonogenic data to feed RBE models to be utilized in the clinical practice in particle therapy.

Microdosimetric Analysis for Boron Neutron Capture Therapy via Monte Carlo Track Structure Simulation with Modified Lithium Cross-sections

Boron neutron capture therapy (BNCT) is a cellular-level hadron therapy achieving therapeutic effects via the synergistic action of multiple particles, including Lithium, alpha, proton, and photon. However, evaluating the relative biological effectiveness (RBE) in BNCT remains challenging. In this research, we performed a microdosimetric calculation for BNCT using the Monte Carlo track structure (MCTS) simulation toolkit, TOPAS-nBio. This paper reports the first attempt to derive the ionization cross-sections of low-energy (>0.025 MeV/u) Lithium for MCTS simulation based on the effective charge cross-section scalation method and phenomenological double-parameter modification. The fitting parameters λ1=1.101,λ2=3.486 were determined to reproduce the range and stopping power data from the ICRU report 73. Besides, the lineal energy spectra of charged particles in BNCT were calculated, and the influence of sensitive volume (SV) size was discussed. Condensed history simulation obtained similar results with MCTS when using Micron-SV while overestimating the lineal energy when using Nano-SV. Furthermore, we found that the microscopic boron distribution can significantly affect the lineal energy for Lithium, while the effect for alpha is minimal. Similar results to the published data by PHITS simulation were observed for the compound particles and monoenergetic protons when using micron-SV. Spectra with nano-SV reflected that the different track densities and absorbed doses in the nucleus together result in the dramatic difference in the macroscopic biological response of BPA and BSH. This work and the developed methodology could impact the research fields in BNCT where understanding radiation effects is crucial, such as the treatment planning system, source evaluation, and new boron drug development.

In-silico calculations of DNA damage induced by α-particles in the 224Ra DaRT decay chain for a better understanding of the radiobiological effectiveness of this treatment

Diffusing alpha-emitters radiation Therapy (DaRT) is an interstitial brachytherapy technique using 224Ra seeds. For accurate treatment planning a good understanding of the early DNA damage due to α-particles is required. Geant4-DNA was used to calculate the initial DNA damage and radiobiological effectiveness due to α-particles with linear energy transfer (LET) values in the range 57.5-225.9 keV/μm from the 224Ra decay chain. The impact of DNA base pair density on DNA damage has been modelled, as this parameter varies between human cell lines. Results show that the quantity and complexity of DNA damage changes with LET as expected. Indirect damage, due to water radical reactions with the DNA, decreases and becomes less significant at higher LET values as shown in previous studies. As expected, the yield of complex double strand breaks (DSBs), which are harder for a cell to repair, increases approximately linearly with LET. The level of complexity of DSBs and radiobiological effectiveness have been found to increase with LET as expected. The quantity of DNA damage has been shown to increase for increased DNA density in the expected base pair density range of human cells. The change in damage yield as a function of base pair density is largest for higher LET α-particles, an increase of over 50% for individual strand breaks between 62.7 and 127.4 keV/μm. This change in yield shows that the DNA base pair density is an important parameter for modelling DNA damage particularly at higher LET where the DNA damage is greatest and most complex.

Multiple Mesh-type Real Human Cell Models for Dosimetric Application Coupled with Monte Carlo Simulations

The mesh-type models are superior to voxel models in cellular dose assessment coupled with Monte Carlo codes. The aim of this study was to expand the micron-scale mesh-type models based on the fluorescence tomography of real human cells, and to investigate the feasibility of these models in the application of various irradiation scenarios and Monte Carlo codes. Six different human cell lines, including pulmonary epithelial BEAS-2B, embryonic kidney 293T, hepatocyte L-02, B-lymphoblastoid HMy2.CIR, Gastric mucosal GES-1, and intestine epithelial FHs74Int, were adopted for single mesh-type models reconstruction and optimization based on laser confocal tomography images. Mesh-type models were transformed into the format of polygon mesh and tetrahedral mesh for the GATE and PHITS Monte Carlo codes, respectively. The effect of model reduction was analyzed by dose assessment and geometry consideration. The cytoplasm and nucleus doses were obtained by designating monoenergetic electrons and protons as external irradiation, and S values with different "target-source" combinations were calculated by assigning radioisotopes as internal exposure. Four kinds of Monte Carlo codes were employed, i.e., GATE with "Livermore," "Standard" and "Standard and Geant4-DNA mixed" models for electrons and protons, as well as PHITS with "EGS" mode for electrons and radioisotopes. Multiple mesh-type real human cellular models can be applied to Monte Carlo codes directly without voxelization when combined with certain necessary surface reduction. Relative deviations between different cell types were observed among various irradiation scenarios. The relative deviation of nucleus S value reaches up to 85.65% between L-02 and GES-1 cells by 3H for the "nucleus-nucleus" combination, while that of 293T and FHs74Int nucleus dose for external beams at a 5.12 cm depth of water is 106.99%. Nucleus with smaller volume is far more affected by physical codes. There is a considerable deviation for dose within BEAS-2B at the nanoscale. The multiple mesh-type real cell models were more versatile than voxel models and mathematical models. The present study provided several models which can easily be extended to other cell types and irradiation scenarios for RBE estimations and biological effect predictions, including radiation biological experiments, radiotherapy and radiation protection.

Monte Carlo study of the free radical yields in minibeam radiation therapy

BACKGROUND

Minibeam radiation therapy (MBRT) is a novel technique which has been shown to widen the therapeutic window through significant normal tissue sparing. Despite the heterogeneous dose distributions, tumor control is still ensured. Nevertheless the exact radiobiological mechanisms responsible for MBRT efficacy are not fully understood.

PURPOSE

Reactive oxygen species (ROS) resulting from water radiolysis were investigated given their implications not only on targeted DNA damage, but also for their role in the immune response and non-targeted cell signalling effects: two potential drivers of MBRT efficacy.

METHODS

Monte Carlo simulations were performed using TOPAS-nBio to carry out the irradiation of a water phantom with beams of protons (pMBRT), photons (xMBRT), 4 He ions (HeMBRT), and 12 C ions (CMBRT). Primary yields at the end of the chemical stage were calculated in spheres of 20 μm diameter, located in the peaks and valleys at various depths up to the Bragg peak. The chemical stage was limited to 1 ns to approximate biological scavenging, and the yield of · OH, H2 O2 , ande aq - ${\rm e}^{-}_{\rm aq}$ was recorded.

RESULTS

Beyond 10 mm, there were no substantial differences in the primary yields between peaks and valleys of the pMBRT and HeMBRT modalities. For xMBRT, there was a lower primary yield of the radical species · OH ande aq - ${\rm e}^{-}_{\rm aq}$ at all depths in the valleys compared to the peaks, and a higher primary yield of H2 O2 . Compared to the peaks, the valleys of the CMBRT modality were subject to a higher · OH ande aq - ${\rm e}^{-}_{\rm aq}$ yield, and lower H2 O2 yield. This difference between peaks and valleys became more severe in depth. Near the Bragg peak, the increase in the primary yield of the valleys over the peaks was 6% and 4% for · OH ande aq - ${\rm e}^{-}_{\rm aq}$ respectively, while there was a decrease in the yield of H2 O2 by 16%. Given the similar ROS primary yields in the peaks and valleys of pMBRT and HeMBRT, the level of indirect DNA damage is expected to be directly proportional to the peak to valley dose ratio (PVDR). The difference in the primary yields implicates a lower level of indirect DNA damage in the valleys compared to the peaks than what would be suggested by the PVDR for xMBRT, and a higher level for CMBRT.

CONCLUSIONS

These results highlight the notion that depending on the particle chosen, one can expect different levels of ROS in the peaks and valley that goes beyond what would be expected by the macroscopic PVDR. The combination of MBRT with heavier ions is shown to be particularly interesting as the primary yield in the valleys progressively diverges from the level observed in the peaks as the LET increases. While differences in the reported · OH yields of this work implicated the indirect DNA damage, H2 O2 yields particularly implicate non-targeted cell signalling effects, and therefore this work provides a point of reference for future simulations in which the distribution of this species at more biologically relevant timescales could be investigated.

The complexity of DNA damage by radiation follows a Gamma distribution: insights from the Microdosimetric Gamma Model

Introduction

DNA damage is the main predictor of response to radiation therapy for cancer. Its Q8 quantification and characterization are paramount for treatment optimization, particularly in advanced modalities such as proton and alpha-targeted therapy.

Methods

We present a novel approach called the Microdosimetric Gamma Model (MGM) to address this important issue. The MGM uses the theory of microdosimetry, specifically the mean energy imparted to small sites, as a predictor of DNA damage properties. MGM provides the number of DNA damage sites and their complexity, which were determined using Monte Carlo simulations with the TOPAS-nBio toolkit for monoenergetic protons and alpha particles. Complexity was used together with a illustrative and simplistic repair model to depict the differences between high and low LET radiations.

Results

DNA damage complexity distributions were were found to follow a Gamma distribution for all monoenergetic particles studied. The MGM functions allowed to predict number of DNA damage sites and their complexity for particles not simulated with microdosimetric measurements (yF) in the range of those studied.

Discussion

Compared to current methods, MGM allows for the characterization of DNA damage induced by beams composed of multi-energy components distributed over any time configuration and spatial distribution. The output can be plugged into ad hoc repair models that can predict cell killing, protein recruitment at repair sites, chromosome aberrations, and other biological effects, as opposed to current models solely focusing on cell survival. These features are particularly important in targeted alpha-therapy, for which biological effects remain largely uncertain. The MGM provides a flexible framework to study the energy, time, and spatial aspects of ionizing radiation and offers an excellent tool for studying and optimizing the biological effects of these radiotherapy modalities.

GEANT4-DNA simulation of temperature-dependent and pH-dependent yields of chemical radiolytic species

Objective.GEANT4-DNA can simulate radiation chemical yield (G-value) for radiolytic species such as the hydrated electron (eaq-) with the independent reaction times (IRT) method, however, only at room temperature and neutral pH. This work aims to modify the GEANT4-DNA source code to enable the calculation ofG-values for radiolytic species at different temperatures and pH values.Approach.In the GEANT4-DNA source code, values of chemical parameters such as reaction rate constant, diffusion coefficient, Onsager radius, and water density were replaced by corresponding temperature-dependent polynomials. The initial concentration of hydrogen ion (H+)/hydronium ion (H3O+) was scaled for a desired pH using the relationship pH = -log10[H+]. To validate our modifications, two sets of simulations were performed. (A) A water cube with 1.0 km sides and a pH of 7 was irradiated with an isotropic electron source of 1 MeV. The end time was 1μs. The temperatures varied from 25 °C to 150 °C. (B) The same setup as (A) was used, however, the temperature was set to 25 °C while the pH varied from 5 to 9. The results were compared with published experimental and simulated work.Main results.The IRT method in GEANT4-DNA was successfully modified to simulateG-values for radiolytic species at different temperatures and pH values. Our temperature-dependent results agreed with experimental data within 0.64%-9.79%, and with simulated data within 3.52%-12.47%. The pH-dependent results agreed well with experimental data within 0.52% to 3.19% except at a pH of 5 (15.99%) and with simulated data within 4.40%-5.53%. The uncertainties were below ±0.20%. Overall our results agreed better with experimental than simulation data.Significance.Modifications in the GEANT4-DNA code enabled the calculation ofG-values for radiolytic species at different temperatures and pH values.

The general-purpose Geant4 Monte Carlo toolkit and its Geant4-DNA extension to investigate mechanisms underlying the FLASH effect in radiotherapy: Current status and challenges

FLASH radiotherapy is a promising approach to cancer treatment that offers several advantages over conventional radiotherapy. With this novel technique, high doses of radiation are delivered in a short period of time, inducing the so-called FLASH effect - a phenomenon characterized by healthy tissue sparing without alteration of tumor control. The mechanisms behind the FLASH effect remain unknown. One way to approach this problem is to gain insight into the initial parameters that can distinguish FLASH from conventional irradiation by simulating particle transport in aqueous media using the general-purpose Geant4 Monte Carlo toolkit and its Geant4-DNA extension. This review article discusses the current status of Geant4 and Geant4-DNA simulations to investigate mechanisms underlying the FLASH effect, as well as the challenges faced in this research field. One of the primary challenges is to accurately simulate the experimental irradiation parameters. Another challenge is the temporal extension of the simulations. This review also focuses on two hypotheses to explain the FLASH effect - namely the oxygen depletion hypothesis and the inter-track interactions hypothesis - and discusses how the Geant4 toolkit can be used to investigate them. The aim of this review is to provide an overview of Geant4 and Geant4-DNA simulations for FLASH radiotherapy and to highlight the challenges that need to be overcome in order to better study the FLASH effect.

Quantification of damage to plasmid DNA from 35 MeV electrons, 228 MeV protons and 300 kVp X-rays in varying hydroxyl radical scavenging environments

The pBR322 plasmid DNA was irradiated with 35 MeV electrons, 228 MeV protons and 300 kVp X-rays to quantify DNA damage and make comparisons of DNA damage between radiation modalities. Plasmid was irradiated in a medium containing hydroxyl radical scavengers in varying concentrations. This altered the amount of indirect hydroxyl-mediated DNA damage, to create an environment that is more closely associated with a biological cell. We show that increasing hydroxyl scavenger concentration significantly reduced post-irradiation DNA damage to pBR322 plasmid DNA consistently and equally with three radiation modalities. At low scavenging capacities, irradiation with both 35 MeV electrons and 228 MeV protons resulted in increased DNA damage per dose compared with 300 kVp X-rays. We quantify both single-strand break (SSB) and double-strand break (DSB) induction between the modalities as a ratio of yields relative to X-rays, referred to as relative biological effectiveness (RBE). RBESSB values of 1.16 ± 0.15 and 1.18 ± 0.08 were calculated for protons and electrons, respectively, in a low hydroxyl scavenging environment containing 1 mM Tris-HCl for SSB induction. In higher hydroxyl scavenging capacity environments (above 1.1 × 106 s-1), no significant differences in DNA damage induction were found between radiation modalities when using SSB induction as a measure of RBE. Considering DSB induction, significant differences were only found between X-rays and 35 MeV electrons, with an RBEDSB of 1.72 ± 0.91 for 35 MeV electrons, indicating that electrons result in significantly more SSBs and DSBs per unit of dose than 300 kVp X-rays.

State-of-the-art and potential of experimental microdosimetry in ion-beam therapy

In radiotherapy, radiation-quality should be an expression of the biological and physical characteristics of ionizing radiation such as spatial distribution of ionization or energy deposition. Linear energy transfer (LET) and lineal energy (y) are two descriptors used to quantify the radiation quality. These two quantities are connected and exhibit similar features. In ion-beam therapy (IBT), lineal energy can be measured with microdosimeters, which are specifically designed to cope with the high fluence of particles in clinical beams, while the quantification of LET is generally based on calculations. In pre-clinical studies, microdosimetric spectra are used for the indirect determination of relative biological effectiveness (RBE), e.g., using the microdosimetric kinetic model (MKM) or biophysical response functions. In this context it is important to consider saturation effects, which occur when the highest values of y become less biologically relevant compared to the relative contribution they make to the physical dose. Recent clinical data suggests that local tumor control and normal tissue effects can be linked to macroscopic and microscopic dosimetry parameters. In particular, positive clinical outcomes have been correlated to the highest LET values in the density distribution, and there is no evident link to the saturation discussed above. A systematic collection of microdosimetric information in combination with clinical data in retrospective studies may clarify the role of radiation quality at the highest LET. In the clinical setting, microdosimetry is not widely used yet, despite its potential to be linked with LET by experimentally-determined y values. Through this connection, both play an important role in complex therapy techniques such as intensity modulated particle therapy (IMPT), LET-painting and multi-ion optimization. This review summarizes the current state of microdosimetry for IBT and its potential, as well as research and development needed to make experimental microdosimetry a mature procedure in a clinical context.

Sub-keV corrections to binary encounter cross section models for electron ionization of liquid water with application to the Geant4-DNA Monte Carlo code

INTRODUCTION

The electron ionization cross section of water is one of the most important input in Monte Carlo studies of cellular radiobiological effects. Analytical cross section models of the binary-encounter type have the potential of reducing simulation time and facilitate application to a variety of biological materials (other than water). The Binary-Encounter-Bethe (BEB) and Binary-Encounter-Dipole (BED) models of NIST are perhaps the most popular of such models giving reliable results for atoms and molecules in the gas-phase over a wide energy range. However, the use of such models to sub-keV electron energies in liquid water raises concerns due to the neglect of condensed phase effects that leads to a significant overestimation when compared to medium-specific dielectric models.

PURPOSE

To modify the BEB and BED models towards better agreement with the recommended low-energy dielectric model of Geant4-DNA (Option 4). To implement the new modifications to the existing BEB model of the Option 6 physics constructor of Geant4-DNA and re-evaluate fundamental transport quantities for sub-keV electrons.

METHODS

In analogy to a Yukawa potential a simple, yet physically-motivated, modification of the Burgess correction term is proposed to account for the reduction of the Coulomb interaction due to the polarizability of the target. The magnitude of the correction is guided by the dielectric-based ionization cross section implemented in Option 4.

RESULTS

Differential, total and stopping ionization cross sections for low-energy electrons in liquid water are presented. When combined with the Vriens correction (which is not included in Option 6), the proposed modification to the BEB and BED models brings the ionization and stopping cross sections in much better agreement against those used in the Option 4 dielectric model of Geant4-DNA, with up to 30% and 10% deviation, respectively. Implementation of the new correction to the Option 6 constructor of Geant4-DNA and re-evaluation of fundamental transport quantities, such as electron penetration ranges and dose-point-kernels, reduced the discrepancies from Option 4 at sub-keV energies from 20 to 100% (or more) to well below 10% in most cases.

CONCLUSIONS

A simple modification to the BEB and BED analytic models was found to improve their performance for sub-keV electrons in liquid water medium. Implementation of the new modification to the Option 6 constructor of Geant4-DNA significantly improved the agreement with the recommended low-energy Option 4 constructor for a variety of fundamental quantities related to electron transport.

Time-Dependent Density-Functional Theory for Determining the Electron-Capture Cross Section for Protons Impacting on Atoms and Molecules

The use of the Time-Dependent Density-Functional Theory (TDDFT) has increased in the atomic collision field. Calculating the electron-capture cross section (ECCS) for protons is an important question in hadrontherapy and plasma physics, among other areas. In previous studies, it was shown that the approach based on the Local Density Approximation (LDA) fails in the 1-50 keV region, requiring the use of the Optimized Effective Potential (OEP) method. In this work, the ECCS values for 1-50 keV protons impacting on isolated hydrogen, carbon, nitrogen, oxygen, and nitrogenous atoms were determined using the TDDFT. It is shown that adding the Self Interaction Correction to the LDA (LDA-Sic) allows obtaining results close to those provided by the OEP and experiments, with the advantage that the LDA-Sic consumes less computational time. In addition, it was demonstrated that it is imperative to include the spin correction for the specific helium and oxygen cases, in order to get good results for the ECCS using the TDDFT. Theoretical results obtained in this work show excellent agreement with experimental values.

Modeling of scavenging systems in water radiolysis with Geant4-DNA

PURPOSE

This paper presents the capabilities of the Geant4-DNA Monte Carlo toolkit to simulate water radiolysis with scavengers using the step-by-step (SBS) or the independent reaction times (IRT) methods. It features two examples of application areas: (1) computing the escape yield of H₂O₂ following a ⁶⁰Co γ-irradiation and (2) computing the oxygen depletion in water irradiated with 1 MeV electrons.

METHODS

To ease the implementation of the chemical stage in Geant4-DNA, we developed a user interface that helps define the chemical reactions and set the concentration of scavengers. The first application area example required two computational steps to perform water radiolysis using NO₂^- and NO₃^- as scavengers and a ⁶⁰Co irradiation. The oxygen depletion computation technique for the second application area example consisted of simulating track segments of 1 MeV electrons and determining the radio-induced loss and gain of oxygen molecules.

RESULTS

The production of H₂O₂ under variable scavenging levels is consistent with the literature; the mean relative difference between the SBS and IRT methods is 7.2 % ± 0.5 %. For the oxygen depletion 1 µs post-irradiation, the mean relative difference between both methods is equal to 9.8 % ± 0.3 %. The results in the microsecond scale depend on the initial partial pressure of oxygen in water. In addition, the computed oxygen depletions agree well with the literature.

CONCLUSIONS

The Geant4-DNA toolkit makes it possible to simulate water radiolysis in the presence of scavengers. This feature offers perspectives in radiobiology, with the possibility of simulating cell-relevant scavenging mechanisms.

Effects of incoming particle energy and cluster size on the G-value of hydrated electrons

In hydrated electron (e^-_aq) dosimetry, absorbed radiation dose to water is measured by monitoring the concentration of radiation-induced e^-_aq. However, to obtain accurate dose, the radiation chemical yield of e^-_aq, G(e^-_aq), is needed for the radiation quality/setup under investigation. The aim of this study was to investigate the time-evolution of the G-values for the main generated reactive species during water radiolysis using GEANT4-DNA. The effects of cluster size and linear energy transfer (LET) on G(e^-_aq) were examined. Validity of GEANT4-DNA for calculation of G(e^-_aq) for clinically relevant energies was studied. Three scenarios were investigated with different phantom sizes and incoming electron energies (1 keV to 1 MeV). The time evolution of G(e^-_aq) was in good agreement with published data and did not change with decreasing phantom size. The time-evolution of the G-values increases with increasing LET for all radiolytic species. The particle tracks formed with high-energy electrons are separated and the resulting reactive species develop independently in time. With decreasing energy, the mean separation distance between reactive species decreases. The particle tracks might not initially overlap but will overlap shortly thereafter due to diffusion of reactive species, increasing the probability of e^-_aq recombination with other species. This also explains the decrease of G(e^-_aq) with cluster size and LET. Finally, if all factors are kept constant, as the incoming electron energy increases to clinically relevant energies, G(e^-_aq) remains similar to its value at 1 MeV, hence GEANT4-DNA can be used for clinically relevant energies.

Modelling tissue specific RBE for different radiation qualities based on a multiscale characterization of energy deposition

PURPOSE

We present the nanoCluE model, which uses nano- and microdosimetric quantities to model RBE for protons and carbon ions. Under the hypothesis that nano- and microdosimetric quantities correlates with the generation of complex DNA double strand breakes, we wish to investigate whether an improved accuracy in predicting LQ parameters may be achieved, compared to some of the published RBE models.

METHODS

The model is based on experimental LQ data for protons and carbon ions. We generated a database of track structure data for a number of proton and carbon ion kinetic energies with the Geant4-DNA Monte Carlo code. These data were used to obtain both a nanodosimetric quantity and a set of microdosimetric quantities. The latter were tested with different parameterizations versus experimental LQ-data to select the variable and parametrization that yielded the best fit.

RESULTS

For protons, the nanoCluE model yielded, for the ratio of the linear LQ term versus the test data, a root mean square error (RMSE) of 1.57 compared to 1.31 and 1.30 for two earlier other published proton models. For carbon ions the RMSE was 2.26 compared to 3.24 and 5.24 for earlier published carbon ion models.

CONCLUSION

These results demonstrate the feasibility of the nanoCluE RBE model for carbon ions and protons. The increased accuracy for carbon ions as compared to two other considered models warrants further investigation.

Impact of secondary particles on the magnetic field generated by a proton pencil beam: a finite-element analysis based on Geant4-DNA simulations

PURPOSE

To investigate the static magnetic field generated by a proton pencil beam as a candidate for range verification by means of Monte Carlo simulations, thereby improving upon existing analytical calculations. We focus on the impact of statistical current fluctuations and secondary protons and electrons.

METHODS

We considered a pulsed beam (10 μ ${\umu}$ s pulse duration) during the duty cycle with a peak beam current of 0.2 μ $\umu$ A and an initial energy of 100 MeV. We ran Geant4-DNA Monte Carlo simulations of a proton pencil beam in water and extracted independent particle phase spaces. We calculated longitudinal and radial current density of protons and electrons, serving as an input for a magnetic field estimation based on a finite element analysis in a cylindrical geometry. We made sure to allow for non-solenoidal current densities as is the case of a stopping proton beam.

RESULTS

The rising proton charge density toward the range is not perturbed by energy straggling and only lowered through nuclear reactions by up to 15%, leading to an approximately constant longitudinal current. Their relative low density however (at most 0.37 protons/mm³ for the 0.2  μ ${\umu}$ A current and a beam cross-section of 2.5 mm), gives rise to considerable current density fluctuations. The radial proton current resulting from lateral scattering and being two orders of magnitude weaker than the longitudinal current is subject to even stronger fluctuations. Secondary electrons with energies above 10 eV, that far outnumber the primary protons, reduce the primary proton current by only 10% due to their largely isotropic flow. A small fraction of electrons (<1%), undergoing head-on collisions, constitutes the relevant electron current. In the far-field, both contributions to the magnetic field strength (longitudinal and lateral) are independent of the beam spot size. We also find that the nuclear reaction-related losses cause a shift of 1.3 mm to the magnetic field profile relative to the actual range, which is further enlarged to 2.4 mm by the electron current (at a distance of ρ = 50 $\rho =50$  mm away from the central beam axis). For ρ > 45 $\rho &gt;45$  mm, the shift increases linearly. While the current density variations cause significant magnetic field uncertainty close to the central beam axis with a relative standard deviation (RSD) close to 100%, they average out at a distance of 10 cm, where the RSD of the total magnetic field drops below 2%.

CONCLUSIONS

With the small influence of the secondary electrons together with the low RSD, our analysis encourages an experimental detection of the magnetic field through sensitive instrumentation, such as optical magnetometry or SQUIDs.

MINAS TIRITH: a new tool for simulating radiation-induced DNA damage at the cell population level

Objective. The mechanisms of radiation-induced DNA damage can be understood via the fundamental acquisition of knowledge through a combination of experiments and modeling. Currently, most biological experiments are performed by irradiating an entire cell population, whereas modeling of radiation-induced effects is usually performed via Monte Carlo simulations with track structure codes coupled to realistic DNA geometries of a single-cell nucleus. However, the difference in scale between the two methods hinders a direct comparison because the dose distribution in the cell population is not necessarily uniform owing to the stochastic nature of the energy deposition. Thus, this study proposed the MINAS TIRITH tool to model the distribution of radiation-induced DNA damage in a cell population.Approach. The proposed method is based on precomputed databases of microdosimetric parameters and DNA damage distributions generated using the Geant4-DNA Monte Carlo Toolkit. First, a specific energyzwas assigned to each cell of an irradiated population for a particular absorbed doseDabs,following microdosimetric formalism. Then, each cell was assigned a realistic number of DNA damage events according to the specific energyz,respecting the stochastic character of its occurrence.Main results. This study validated the MINAS TIRITH tool by comparing its results with those obtained using the Geant4-DNA track structure code and a Geant4-DNA based simulation chain for DNA damage calculation. The different elements of comparison indicated consistency between MINAS TIRITH and the Monte Carlo simulation in case of the dose distribution in the population and the calculation of the amount of DNA damage.Significance. MINAS TIRITH is a new approach for the calculation of radiation-induced DNA damage at the cell population level that facilitates reasonable simulation times compared to those obtained with track structure codes. Moreover, this tool enables a more direct comparison between modeling and biological experimentation.

Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA

PURPOSE

Track structure Monte Carlo (MC) codes have achieved successful outcomes in the quantitative investigation of radiation-induced initial DNA damage. The aim of the present study is to extend a Geant4-DNA radiobiological application by incorporating a feature allowing for the prediction of DNA rejoining kinetics and corresponding cell surviving fraction along time after irradiation, for a Chinese hamster V79 cell line, which is one of the most popular and widely investigated cell lines in radiobiology.

METHODS

We implemented the Two-Lesion Kinetics (TLK) model, originally proposed by Stewart, which allows for simulations to calculate residual DNA damage and surviving fraction along time via the number of initial DNA damage and its complexity as inputs.

RESULTS

By optimizing the model parameters of the TLK model in accordance to the experimental data on V79, we were able to predict both DNA rejoining kinetics at low linear energy transfers (LET) and cell surviving fraction.

CONCLUSION

This is the first study to demonstrate the implementation of both the cell surviving fraction and the DNA rejoining kinetics with the estimated initial DNA damage, in a realistic cell geometrical model simulated by full track structure MC simulations at DNA level and for various LET. These simulation and model make the link between mechanistic physical/chemical damage processes and these two specific biological endpoints.

Electron tracks simulation in water: Performance comparison between GPU CPU and the EUMED grid installation

PURPOSE

We explored different technologies to minimize simulation time of the Monte-Carlo method for track generation following the Geant4-DNA processes for electrons in water.

METHODS

A GPU software tool is developed for electron track simulations. A similar CPU version is also developed using the same collision models. CPU simulations were carried out on a single user desktop computer and on the computing grid France Grilles using 10 and 100 computing nodes. Computing time results for CPU, GPU, and grid simulations are compared with those using Geant4-DNA processes.

RESULTS

The CPU simulations better performs when the number of electrons is less than 10⁴ with 100 eV initial energy, this number decreases as the energy increases. The GPU simulations gives better results when the number of electrons is more than 10⁴ with initial energy of 100 eV, this number decreases to 10³ for electrons with 10KeV and increases back with higher energy. The use of the grid introduces an additional queuing time which slows down the overall simulation performance. Thus, the Grid gives better performance when the number of electrons is over 10⁵ with initial energy of 10KeV, and this number decreases as the energy increases.

CONCLUSIONS

The CPU is best suited for small numbers of primary incident electrons. The GPU is best suited when the number of primary incident particles occupies sufficient resources on GPU card in order to get an important computing power. The grid is best suited for simulations with high number of primary incident electrons with high initial energy.

Multiple levels of stochasticity accounted for in different radiation biophysical models: from physics to biology

PURPOSE

In the present paper we investigate how some stochastic effects are included in a class of radiobiological models with particular emphasis on how such randomnesses reflect into the predicted cell survival curve.

MATERIALS AND METHODS

We consider four different models, namely the Generalized Stochastic Microdosimetric Model GSM², in its original full form, the Dirac GSM² the Poisson GSM² and the Repair-Misrepair Model (RMR). While GSM² and the RMR models are known in literature, the Dirac and the Poisson GSM²  have been newly introduced in this work. We further numerically investigate via Monte Carlo simulation of four different particle beams, how the proposed stochastic approximations reflect into the predicted survival curves. To achieve these results, we consider different ion species at energies of interest for therapeutic applications, also including a mixed field scenario.

RESULTS

We show how the Dirac GSM², the Poisson GSM² and the RMR can be obtained from the GSM² under suitable approximations on the stochasticity considered. We analytically derive the cell survival curve predicted by the four models, characterizing rigorously the high and low dose limits. We further study how the theoretical findings emerge also using Monte Carlo numerical simulations.

CONCLUSIONS

We show how different models include different levels of stochasticity in the description of cellular response to radiation. This translates into different cell survival predictions depending on the radiation quality.

Nano-scale simulation of neuronal damage by galactic cosmic rays

The effects of realistic, deep space radiation environments on neuronal function remain largely unexplored.In silicomodeling studies of radiation-induced neuronal damage provide important quantitative information about physico-chemical processes that are not directly accessible through radiobiological experiments. Here, we present the first nano-scale computational analysis of broad-spectrum galactic cosmic ray irradiation in a realistic neuron geometry. We constructed thousands ofin silicorealizations of a CA1 pyramidal neuron, each with over 3500 stochastically generated dendritic spines. We simulated the entire 33 ion-energy beam spectrum currently in use at the NASA Space Radiation Laboratory galactic cosmic ray simulator (GCRSim) using the TOol for PArticle Simulation (TOPAS) and TOPAS-nBio Monte Carlo-based track structure simulation toolkits. We then assessed the resulting nano-scale dosimetry, physics processes, and fluence patterns. Additional comparisons were made to a simplified 6 ion-energy spectrum (SimGCRSim) also used in NASA experiments. For a neuronal absorbed dose of 0.5 Gy GCRSim, we report an average of 250 ± 10 ionizations per micrometer of dendritic length, and an additional 50 ± 10, 7 ± 2, and 4 ± 2 ionizations per mushroom, thin, and stubby spine, respectively. We show that neuronal energy deposition by proton andα-particle tracks declines approximately hyperbolically with increasing primary particle energy at mission-relevant energies. We demonstrate an inverted exponential relationship between dendritic segment irradiation probability and neuronal absorbed dose for each ion-energy beam. We also find that there are no significant differences in the average physical responses between the GCRSim and SimGCRSim spectra. To our knowledge, this is the first nano-scale simulation study of a realistic neuron geometry using the GCRSim and SimGCRSim spectra. These results may be used as inputs to theoretical models, aid in the interpretation of experimental results, and help guide future study designs.