Mechanistic DNA damage simulations in Geant4-DNA Part 2: Electron and proton damage in a bacterial cell

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.

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.

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.

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.

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.

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.

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.

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.

Effects of Differing Underlying Assumptions in In Silico Models on Predictions of DNA Damage and Repair

The induction and repair of DNA double-strand breaks (DSBs) are critical factors in the treatment of cancer by radiotherapy. To investigate the relationship between incident radiation and cell death through DSB induction many in silico models have been developed. These models produce and use custom formats of data, specific to the investigative aims of the researchers, and often focus on particular pairings of damage and repair models. In this work we use a standard format for reporting DNA damage to evaluate combinations of different, independently developed, models. We demonstrate the capacity of such inter-comparison to determine the sensitivity of models to both known and implicit assumptions. Specifically, we report on the impact of differences in assumptions regarding patterns of DNA damage induction on predicted initial DSB yield, and the subsequent effects this has on derived DNA repair models. The observed differences highlight the importance of considering initial DNA damage on the scale of nanometres rather than micrometres. We show that the differences in DNA damage models result in subsequent repair models assuming significantly different rates of random DSB end diffusion to compensate. This in turn leads to disagreement on the mechanisms responsible for different biological endpoints, particularly when different damage and repair models are combined, demonstrating the importance of inter-model comparisons to explore underlying model assumptions.

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.

Geant4-DNA simulation of human cancer cells irradiation with helium ion beams

PURPOSE

This study aimed to develop a computational environment for the accurate simulation of human cancer cell irradiation using Geant4-DNA. New cell geometrical models were developed and irradiated by alpha particle beams to induce DNA damage. The proposed approach may help further investigation of the benefits of external alpha irradiation therapy.

METHODS

The Geant4-DNA Monte Carlo (MC) toolkit allows the simulation of cancer cell geometries that can be combined with accurate modelling of physical, physicochemical and chemical stages of liquid water irradiation, including radiolytic processes. Geant4-DNA is used to calculate direct and non-direct DNA damage yields, such as single and double strand breaks, produced by the deposition of energy or by the interaction of DNA with free radicals.

RESULTS

In this study, the "molecularDNA" example application of Geant4-DNA was used to quantify early DNA damage in human cancer cells upon irradiation with alpha particle beams, as a function of linear energy transfer (LET). The MC simulation results are compared to experimental data, as well as previously published simulation data. The simulation results agree well with the experimental data on DSB yields in the lower LET range, while the experimental data on DSB yields are lower than the results obtained with the "molecularDNA" example in the higher LET range.

CONCLUSION

This study explored and demonstrated the possibilities of the Geant4-DNA toolkit together with the "molecularDNA" example to simulate the helium beam irradiation of cancer cell lines, to quantify the early DNA damage, or even the following DNA damage response.

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.

Simulation of DNA damage using Geant4-DNA: an overview of the "molecularDNA" example application

Purpose

The scientific community shows great interest in the study of DNA damage induction, DNA damage repair, and the biological effects on cells and cellular systems after exposure to ionizing radiation. Several in silico methods have been proposed so far to study these mechanisms using Monte Carlo simulations. This study outlines a Geant4-DNA example application, named "molecularDNA", publicly released in the 11.1 version of Geant4 (December 2022).

Methods

It was developed for novice Geant4 users and requires only a basic understanding of scripting languages to get started. The example includes two different DNA-scale geometries of biological targets, namely "cylinders" and "human cell". This public version is based on a previous prototype and includes new features, such as: the adoption of a new approach for the modeling of the chemical stage, the use of the standard DNA damage format to describe radiation-induced DNA damage, and upgraded computational tools to estimate DNA damage response.

Results

Simulation data in terms of single-strand break and double-strand break yields were produced using each of the available geometries. The results were compared with the literature, to validate the example, producing less than 5% difference in all cases. Conclusion: "molecularDNA" is a prototype tool that can be applied in a wide variety of radiobiology studies, providing the scientific community with an open-access base for DNA damage quantification calculations. New DNA and cell geometries for the "molecularDNA" example will be included in future versions of Geant4-DNA.

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.

Application of a simple DNA damage model developed for electrons to proton irradiation

Proton beam therapy allows irradiating tumor volumes with reduced side effects on normal tissues with respect to conventional x-ray radiotherapy. Biological effects such as cell killing after proton beam irradiations depend on the proton kinetic energy, which is intrinsically related to early DNA damage induction. As such, DNA damage estimation based on Monte Carlo simulations is a research topic of worldwide interest. Such simulation is a mean of investigating the mechanisms of DNA strand break formations. However, past modellings considering chemical processes and DNA structures require long calculation times. Particle and heavy ion transport system (PHITS) is one of the general-purpose Monte Carlo codes that can simulate track structure of protons, meanwhile cannot handle radical dynamics simulation in liquid water. It also includes a simple model enabling the efficient estimation of DNA damage yields only from the spatial distribution of ionizations and excitations without DNA geometry, which was originally developed for electron track-structure simulations. In this study, we investigated the potential application of the model to protons without any modification. The yields of single-strand breaks, double-strand breaks (DSBs) and the complex DSBs were assessed as functions of the proton kinetic energy. The PHITS-based estimation showed that the DSB yields increased as the linear energy transfer (LET) increased, and reproduced the experimental and simulated yields of various DNA damage types induced by protons with LET up to about 30 keV μm−1. These results suggest that the current DNA damage model implemented in PHITS is sufficient for estimating DNA lesion yields induced after protons irradiation except at very low energies (below 1 MeV). This model contributes to evaluating early biological impacts in radiation therapy.

Impact of DNA Geometry and Scoring on Monte Carlo Track-Structure Simulations of Initial Radiation-Induced Damage

Track structure Monte Carlo simulations are a useful tool to investigate the damage induced to DNA by ionizing radiation. These simulations usually rely on simplified geometrical representations of the DNA subcomponents. DNA damage is determined by the physical and physicochemical processes occurring within these volumes. In particular, damage to the DNA backbone is generally assumed to result in strand breaks. DNA damage can be categorized as direct (ionization of an atom part of the DNA molecule) or indirect (damage from reactive chemical species following water radiolysis). We also consider quasi-direct effects, i.e., damage originated by charge transfers after ionization of the hydration shell surrounding the DNA. DNA geometries are needed to account for the damage induced by ionizing radiation, and different geometry models can be used for speed or accuracy reasons. In this work, we use the Monte Carlo track structure tool TOPAS-nBio, built on top of Geant4-DNA, for simulation at the nanometer scale to evaluate differences among three DNA geometrical models in an entire cell nucleus, including a sphere/spheroid model specifically designed for this work. In addition to strand breaks, we explicitly consider the direct, quasi-direct, and indirect damage induced to DNA base moieties. We use results from the literature to determine the best values for the relevant parameters. For example, the proportion of hydroxyl radical reactions between base moieties was 80%, and between backbone, moieties was 20%, the proportion of radical attacks leading to a strand break was 11%, and the expected ratio of base damages and strand breaks was 2.5-3. Our results show that failure to update parameters for new geometric models can lead to significant differences in predicted damage yields.

TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields

Current Monte Carlo simulations of DNA damage have been reported only at ambient temperature. The aim of this work is to use TOPAS-nBio to simulate the yields of DNA single-strand breaks (SSBs) and double-strand breaks (DSBs) produced in plasmids under low-LET irradiation incorporating the effect of the temperature changes in the environment. A new feature was implemented in TOPAS-nBio to incorporate reaction rates used in the simulation of the chemical stage of water radiolysis as a function of temperature. The implemented feature was verified by simulating temperature-dependent G-values of chemical species in liquid water from 20 °C to 90 °C. For radiobiology applications, temperature dependent SSB and DSB yields were calculated from 0 °C to 42 °C, the range of available published measured data. For that, supercoiled DNA plasmids dissolved in aerated solutions containing EDTA irradiated by Cobalt-60 gamma-rays were simulated. TOPAS-nBio well reproduced published temperature-dependent G-values in liquid water and the yields of SSB and DSB for the temperature range considered. For strand break simulations, the model shows that the yield of SSB and DSB increased linearly with the temperature at a rate of (2.94 ± 0.17) × 10−10 Gy–1 Da–1 °C–1 (R 2 = 0.99) and (0.13 ± 0.01) × 10−10 Gy–1 Da–1 °C–1 (R 2 = 0.99), respectively. The extended capability of TOPAS-nBio is a complementary tool to simulate realistic conditions for a large range of environmental temperatures, allowing refined investigations of the biological effects of radiation.

New damage model for simulating radiation-induced direct damage to biomolecular systems and experimental validation using pBR322 plasmid

In this work, we proposed a new damage model for estimating radiation-induced direct damage to biomolecular systems and validated its the effectiveness for pBR322 plasmids. The proposed model estimates radiation-induced damage to biomolecular systems by: (1) simulation geometry modeling using the coarse-grained (CG) technique to replace the minimum repeating units of a molecule with a single bead, (2) approximation of the threshold energy for radiation damage through CG potential calculation, (3) calculation of cumulative absorption energy for each radiation event in microscopic regions of CG models using the Monte Carlo track structure (MCTS) code, and (4) estimation of direct radiation damage to biomolecular systems by comparing CG potentials and absorption energy. The proposed model replicated measured data with an average error of approximately 14.2% in the estimation of radiation damage to pBR322 plasmids using the common MCTS code Geant4-DNA. This is similar to the results of previous simulation studies. However, in existing damage models, parameters are adjusted based on experimental data to increase the reliability of simulation results, whereas in the proposed model, they can be determined without using empirical data. Because the proposed model proposed is applicable to DNA and various biomolecular systems with minimal experimental data, it provides a new method that is convenient and effective for predicting damage in living organisms caused by radiation exposure.

A double-strand-break model for the relative biological effectiveness of electrons based on ionization clustering

BACKGROUND

The effectiveness of ionizing radiation regarding DNA damage induction depends on its spatial energy deposition pattern. For electrons an increased effectiveness is observed at low kinetic energies due to the enhanced density of energy deposition events at electron track ends.

PURPOSE

A model is presented, which enables the calculation of the double-strand-break (DSB) yield and the relative biological effectiveness (RBE) for DSB induction of electrons.

METHODS

The model applies the mean free path between two ionizations and the assumption that two ionizations within a certain threshold distance are necessary to potentially lead to a DSB. Next to an expression for the electron RBE according to its common definition, a local RBE is determined, which describes the electrons' local effectiveness at a defined point on their track.

RESULTS

This local RBE allows a better understanding of microscopic processes resulting from radiation and can be used, for instance, to describe the mean effectiveness of the mixed electron radiation field as a function of the radial distance to the center of an ion track.

CONCLUSIONS

The presented model reflects the experimentally observed increased effectiveness of low-energetic electrons. It will be used in a future work to improve RBE predictions for ions performed with the local effect model.

DNA damage and microdosimetry for carbon ions: Track structure simulations as the key to quantitative modeling of radiation-induced damage

PURPOSE

Dose distribution in carbon-ion irradiations is generally envisaged to have therapeutic advantages over protons, primarily due to the carbon-ion's comparatively higher relative biological effectiveness (RBE) in the tumor than in the encompassing healthy tissues. The objective of this work was to simulate the overall physical and chemical reactions of primary carbon ions impinging on liquid water and, as such, to investigate the DNA-damage yields in the form of strand breaks (SBs) and in connection with the expected microdosimetric quantities.

MATERIALS AND METHODS

Using a B-DNA model and Geant4-DNA, we simulated the primary and secondary interactions in a spherical medium of water. Subsequently, we categorized DNA damages based on their complexity utilizing the concept of μ-randomness. We assumed a threshold of 17.5 eV for a direct SB and a probability of 0.13 for an indirect SB triggered by chemical reactions of hydroxyl radicals. Microdosimetric quantities were extracted for three cylindrical volumes representing typical sub-cellular organisms.

RESULTS

For fully-ionized carbons of 8 to 256 MeV/u, the yield results appeared to be considerably influenced by the chemical reactions - indicating the important role of secondary electrons in inflicting damage. However, it was mostly the direct-damage spectrum that determined the overall shape of the damage spectrum. At all primary energies, it was more probable to break each DNA strand at one point - the two points being less than 10 bp apart - than to break only one strand at two random points. Unlike proton's mean-specific-energy results, which showed more sensitivity to the volume increase of the smallest cylinder than of the larger ones, carbon-ion results showed no such sensitivity.

CONCLUSION

The growth of the yield ratio of the single- and double-strand breaks (SSB and DSB) with the particle energy was estimated for protons to be about two times that of alphas and 92 times that of carbon ions. Unlike the proton results, which suggested significant correlations between the DSB yields and mean specific (and lineal) energies, carbon ions exhibited no such correlations. This article is protected by copyright. All rights reserved.

Review of the Geant4-DNA Simulation Toolkit for Radiobiological Applications at the Cellular and DNA Level

Simple Summary

A brief description of the methodologies to simulate ionizing radiation transport in biologically relevant matter is presented. Emphasis is given to the physical, chemical, and biological models of Geant4-DNA that enable mechanistic radiobiological modeling at the cellular and DNA level, important to improve the efficacy of existing and novel radiotherapeutic modalities for the treatment of cancer.

Abstract

The Geant4-DNA low energy extension of the Geant4 Monte Carlo (MC) toolkit is a continuously evolving MC simulation code permitting mechanistic studies of cellular radiobiological effects. Geant4-DNA considers the physical, chemical, and biological stages of the action of ionizing radiation (in the form of x- and γ-ray photons, electrons and β^±-rays, hadrons, α-particles, and a set of heavier ions) in living cells towards a variety of applications ranging from predicting radiotherapy outcomes to radiation protection both on earth and in space. In this work, we provide a brief, yet concise, overview of the progress that has been achieved so far concerning the different physical, physicochemical, chemical, and biological models implemented into Geant4-DNA, highlighting the latest developments. Specifically, the “dnadamage1” and “molecularDNA” applications which enable, for the first time within an open-source platform, quantitative predictions of early DNA damage in terms of single-strand-breaks (SSBs), double-strand-breaks (DSBs), and more complex clustered lesions for different DNA structures ranging from the nucleotide level to the entire genome. These developments are critically presented and discussed along with key benchmarking results. The Geant4-DNA toolkit, through its different set of models and functionalities, offers unique capabilities for elucidating the problem of radiation quality or the relative biological effectiveness (RBE) of different ionizing radiations which underlines nearly the whole spectrum of radiotherapeutic modalities, from external high-energy hadron beams to internal low-energy gamma and beta emitters that are used in brachytherapy sources and radiopharmaceuticals, respectively.

DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions

The chemical stage of the Monte Carlo track-structure (MCTS) code Geant4-DNA was extended for its use in DNA strand break (SB) simulations and compared against published experimental data. Geant4-DNA simulations were performed using pUC19 plasmids (2686 base pairs) in a buffered solution of DMSO irradiated by⁶⁰Co or¹³⁷Csγ-rays. A comprehensive evaluation of SSB yields was performed considering DMSO, DNA concentration, dose and plasmid supercoiling. The latter was measured using the super helix density value used in a Brownian dynamics plasmid generation algorithm. The Geant4-DNA implementation of the independent reaction times method (IRT), developed to simulate the reaction kinetics of radiochemical species, allowed to score the fraction of supercoiled, relaxed and linearized plasmid fractions as a function of the absorbed dose. The percentage of the number of SB after •OH + DNA and H• + DNA reactions, referred as SSB efficiency, obtained using MCTS were 13.77% and 0.74% respectively. This is in reasonable agreement with published values of 12% and 0.8%. The SSB yields as a function of DMSO concentration, DNA concentration and super helix density recreated the expected published experimental behaviors within 5%, one standard deviation. The dose response of SSB and DSB yields agreed with published measurements within 5%, one standard deviation. We demonstrated that the developed extension of IRT in Geant4-DNA, facilitated the reproduction of experimental conditions. Furthermore, its calculations were strongly in agreement with experimental data. These two facts will facilitate the use of this extension in future radiobiological applications, aiding the study of DNA damage mechanisms with a high level of detail.

Performance Evaluation for Repair of HSGc-C5 Carcinoma Cell Using Geant4-DNA

Track-structure Monte Carlo simulations are useful tools to evaluate initial DNA damage induced by irradiation. In the previous study, we have developed a Gean4-DNA-based application to estimate the cell surviving fraction of V79 cells after irradiation, bridging the gap between the initial DNA damage and the DNA rejoining kinetics by means of the two-lesion kinetics (TLK) model. However, since the DNA repair performance depends on cell line, the same model parameters cannot be used for different cell lines. Thus, we extended the Geant4-DNA application with a TLK model for the evaluation of DNA damage repair performance in HSGc-C5 carcinoma cells which are typically used for evaluating proton/carbon radiation treatment effects. For this evaluation, we also performed experimental measurements for cell surviving fractions and DNA rejoining kinetics of the HSGc-C5 cells irradiated by 70 MeV protons at the cyclotron facility at the National Institutes for Quantum and Radiological Science and Technology (QST). Concerning fast- and slow-DNA rejoining, the TLK model parameters were adequately optimized with the simulated initial DNA damage. The optimized DNA rejoining speeds were reasonably agreed with the experimental DNA rejoining speeds. Using the optimized TLK model, the Geant4-DNA simulation is now able to predict cell survival and DNA-rejoining kinetics for HSGc-C5 cells.

Towards the characterization of neutron carcinogenesis through direct action simulations of clustered DNA damage

Neutron exposure poses a unique radiation protection concern because neutrons have a large, energy-dependent relative biological effectiveness (RBE) for stochastic effects. Recent computational studies on the microdosimetric properties of neutron dose deposition have implicated clustered DNA damage as a likely contributor to this marked energy dependence. So far, publications have focused solely on neutron RBE for inducing clusters of DNA damage containing two or more DNA double strand breaks (DSBs). In this study, we have conducted a novel assessment of neutron RBE for inducing all types of clustered DNA damage that contain two or more lesions, stratified by whether the clusters contain DSBs (complex DSB clusters) or not (non-DSB clusters). This assessment was conducted for eighteen initial neutron energies between 1 eV and 10 MeV as well as a reference radiation of 250 keV x-rays. We also examined the energy dependence of cluster length and cluster complexity because these factors are believed to impact the DNA repair process. To carry out our investigation, we developed a user-friendly TOPAS-nBio application that includes a custom nuclear DNA model and a novel algorithm for recording clustered DNA damage. We found that neutron RBE for inducing complex DSB clusters exhibited similar energy dependence to the canonical neutron RBE for stochastic radiobiological effects, at multiple depths in human tissue. Qualitatively similar results were obtained for non-DSB clusters, although the quantitative agreement was lower. Additionally we identified a significant neutron energy dependence in the average length and complexity of clustered lesions. These results support the idea that many types of clustered DNA damage contribute to the energy dependence of neutron RBE for stochastic radiobiological effects and imply that the size and constituent lesions of individual clusters should be taken into account when modeling DNA repair. Our results were qualitatively consistent for (i) multiple radiation doses (including a low-dose 0.1 Gy irradiation), (ii) variations in the maximal lesion separation distance used to define a cluster, and (iii) two distinct collections of physics models used to govern particle transport. Our complete TOPAS-nBio application has been released under an open-source license to enable others to independently validate our work and to expand upon it.

A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast

Simple Summary

DNA damage caused by ionizing radiation in a human fibroblast cell evaluated by the Geant4-DNA Monte Carlo toolkit is presented. A validation study using a computational geometric human DNA model was then carried out, and the calculated DNA damage as a function of particle type and energy is presented. The results of this work showed a significant improvement on past work and were consistent with recent radiobiological experimental data, such as damage yields. This work and the developed methodology could impact a broad number of research fields in which the understanding of radiation effects is crucial, such as cancer radiotherapy, space science, and medical physics.

Abstract

Accurately modeling the radiobiological mechanisms responsible for the induction of DNA damage remains a major scientific challenge, particularly for understanding the effects of low doses of ionizing radiation on living beings, such as the induction of carcinogenesis. A computational approach based on the Monte Carlo technique to simulate track structures in a biological medium is currently the most reliable method for calculating the early effects induced by ionizing radiation on DNA, the primary cellular target of such effects. The Geant4-DNA Monte Carlo toolkit can simulate not only the physical, but also the physico-chemical and chemical stages of water radiolysis. These stages can be combined with simplified geometric models of biological targets, such as DNA, to assess direct and indirect early DNA damage. In this study, DNA damage induced in a human fibroblast cell was evaluated using Geant4-DNA as a function of incident particle type (gammas, protons, and alphas) and energy. The resulting double-strand break yields as a function of linear energy transfer closely reproduced recent experimental data. Other quantities, such as fragment length distribution, scavengeable damage fraction, and time evolution of damage within an analytical repair model also supported the plausibility of predicting DNA damage using Geant4-DNA.The complete simulation chain application “molecularDNA”, an example for users of Geant4-DNA, will soon be distributed through Geant4.

Radiation-Inactivated S. gallinarum Vaccine Provides a High Protective Immune Response by Activating Both Humoral and Cellular Immunity

Salmonella enterica subsp. enterica serovar Gallinarum (SG) is a common pathogen in chickens, and causes an acute systemic disease that leads to high mortality. The live attenuated vaccine 9R is able to successfully protect chickens older than six weeks by activating a robust cell-mediated immune response, but its safety and efficacy in young chickens remains controversial. An inactivated SG vaccine is being used as an alternative, but because of its low cellular immune response, it cannot be used as a replacement for live attenuated 9R vaccine. In this study, we employed gamma irradiation instead of formalin as an inactivation method to increase the efficacy of the inactivated SG vaccine. Humoral, cellular, and protective immune responses were compared in both mouse and chicken models. The radiation-inactivated SG vaccine (r-SG) induced production of significantly higher levels of IgG2b and IgG3 antibodies than the formalin-inactivated vaccine (f-SG), and provided a homogeneous functional antibody response against group D, but not group B Salmonella. Moreover, we found that r-SG vaccination could provide a higher protective immune response than f-SG by inducing higher Th17 activation. These results indicate that r-SG can provide a protective immune response similar to the live attenuated 9R vaccine by activating a higher humoral immunity and a lower, but still protective, cellular immune response. Therefore, we expect that the radiation inactivation method might substitute for the 9R vaccine with little or no side effects in chickens younger than six weeks.

TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation

The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependentGvalues in pure liquid water for^·OH, e^-_aq, and H₂with published experimental data. For H₂O₂and H^·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by¹³⁷Csγ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependentGvalues and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for^·OH and H^·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.

Gamma irradiation-mediated inactivation of enveloped viruses with conservation of genome integrity: Potential application for SARS-CoV-2 inactivated vaccine development

Radiation inactivation of enveloped viruses occurs as the result of damages at the molecular level of their genome. The rapidly emerging and ongoing coronavirus disease 2019 (COVID-19) pneumonia pandemic prompted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is now a global health crisis and an economic devastation. The readiness of an active and safe vaccine against the COVID-19 has become a race against time in this unqualified global panic caused by this pandemic. In this review, which we hope will be helpful in the current situation of COVID-19, we analyze the potential use of γ-irradiation to inactivate this virus by damaging at the molecular level its genetic material. This inactivation is a vital step towards the design and development of an urgently needed, effective vaccine against this disease.

Fast neutron energy based modelling of biological effectiveness with implications for proton and ion beams

A practical neutron energy dependent RBE model has been developed, based on the relationship between a mono-energetic neutron energy and its likely recoil proton energy. Essentially, the linear energy transfer (LET) values of the most appropriate recoil proton energies are then used to modify the linear quadratic model radiosensitivities (α and β) from their reference LET radiation values to provide the RBE estimates. Experimental neutron studies published by Hall (including some mono-energetic beams ranging from 0.2 to 15 MeV), Broerse, Berry, and data from the Clatterbridge and Detroit clinical neutron beams, which all contain some data from a spectrum of neutron energies, are used to derive single effective neutron energies (NE_eff) for each spectral beam. These energies yield a recoil proton spectrum, but with an effective mean proton energy (being around 50% of NE_eff). The fractional increase in LET is given by the recoil proton LET divided by the proton (LET_U) value which provides the highest RBE. This ratio is then used to determine the change in the linear-quadratic model α and β parameters, from those of the reference radiation, to estimate the RBE. The predicted proton recoil RBE is then reasonably close to the experimental neutron RBE values found when taking into account the variation inherent in biological experiments. The work has some important consequences. The data of Hall et al (1975 Radiat. Res. 64 245-55) shows that the highest RBE values are found with neutron energies around 0.3-0.4 MeV, but this energy cannot possibly generate recoil proton energies which are higher, as necessary for a 0.68 MeV proton with a 30.5 keV μm^-1 LET_U (the LET value which provides the maximum obtainable RBE for a specified ion). For 0.4 MeV neutrons with proton recoil energies of around 0.2 MeV, the latter have a LET of around 62.88 keV μm^-1. This could have an impact on proton beam RBE modelling. However, this is compensated by finding that the maximum radiosensitivity for mono-energetic neutrons was around 1.7 times larger than previously suggested from experimental ion beam studies, probably due to the necessary spreading out of Bragg peaks for ion beam experimental purposes, sampling errors and particle range considerations. This semi-empirical model can be used with minimal computer support and could have applications in ionic beams and in radioprotection.

Assessment of DNA damage with an adapted independent reaction time approach implemented in Geant4-DNA for the simulation of diffusion-controlled reactions between radio-induced reactive species and a chromatin fiber

Purpose

Simulation of indirect damage originating from the attack of free radical species produced by ionizing radiation on biological molecules based on the independent pair approximation is investigated in this work. In addition, a new approach, relying on the independent pair approximation that is at the origin of the independent reaction time (IRT) method, is proposed in the chemical stage of Geant4‐DNA.

Methods

This new approach has been designed to respect the current Geant4‐DNA chemistry framework while proposing a variant IRT method. Based on the synchronous algorithm, this implementation allows us to access the information concerning the position of radicals and may make it more convenient for biological damage simulations. Estimates of the evolution of free species as well as biological hits in a segment of DNA chromatin fiber in Geant4‐DNA were compared for the dynamic time step approach of the step‐by‐step (SBS) method, currently used in Geant4‐DNA, and this newly implemented IRT.

Results

Results show a gain in computation time of a factor of 30 for high LET particle tracks with a better than 10% agreement on the number of DNA hits between the value obtained with the IRT method as implemented in this work and the SBS method currently available in Geant4‐DNA.

Conclusion

Offering in Geant4‐DNA more efficient methods for the chemical step based on the IRT method is a task in progress. For the calculation of biological damage, information on the position of chemical species is a crucial point. This can be achieved using the method presented in this paper.

Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio

The cellular response to ionizing radiation continues to be of significant research interest in cancer radiotherapy, and DNA is recognized as the critical target for most of the biologic effects of radiation. Incident particles can cause initial DNA damages through physical and chemical interactions within a short time scale. Initial DNA damages can undergo repair via different pathways available at different stages of the cell cycle. The misrepair of DNA damage results in genomic rearrangement and causes mutations and chromosome aberrations, which are drivers of cell death. This work presents an integrated study of simulating cell response after proton irradiation with energies of 0.5-500 MeV (LET of 60-0.2 keV/µm). A model of a whole nucleus with fractal DNA geometry was implemented in TOPAS-nBio for initial DNA damage simulations. The default physics and chemistry models in TOPAS-nBio were used to describe interactions of primary particles, secondary particles, and radiolysis products within the nucleus. The initial DNA double-strand break (DSB) yield was found to increase from 6.5 DSB/Gy/Gbp at low-linear energy transfer (LET) of 0.2 keV/µm to 21.2 DSB/Gy/Gbp at high LET of 60 keV/µm. A mechanistic repair model was applied to predict the characteristics of DNA damage repair and dose response of chromosome aberrations. It was found that more than 95% of the DSBs are repaired within the first 24 h and the misrepaired DSB fraction increases rapidly with LET and reaches 15.8% at 60 keV/µm with an estimated chromosome aberration detection threshold of 3 Mbp. The dicentric and acentric fragment yields and the dose response of micronuclei formation after proton irradiation were calculated and compared with experimental results.

Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA

Ionising radiation induced DNA damage and subsequent biological responses to it depend on the radiation’s track-structure and its energy loss distribution pattern. To investigate the underlying biological mechanisms involved in such complex system, there is need of predicting biological response by integrated Monte Carlo (MC) simulations across physics, chemistry and biology. Hence, in this work, we have developed an application using the open source Geant4-DNA toolkit to propose a realistic “fully integrated” MC simulation to calculate both early DNA damage and subsequent biological responses with time. We had previously developed an application allowing simulations of radiation induced early DNA damage on a naked cell nucleus model. In the new version presented in this work, we have developed three additional important features: (1) modeling of a realistic cell geometry, (2) inclusion of a biological repair model, (3) refinement of DNA damage parameters for direct damage and indirect damage scoring. The simulation results are validated with experimental data in terms of Single Strand Break (SSB) yields for plasmid and Double Strand Break (DSB) yields for plasmid/human cell. In addition, the yields of indirect DSBs are compatible with the experimental scavengeable damage fraction. The simulation application also demonstrates agreement with experimental data of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\gamma$$\end{document}γ-H2AX yields for gamma ray irradiation. Using this application, it is now possible to predict biological response along time through track-structure MC simulations.

Independent reaction times method in Geant4-DNA: Implementation and performance

PURPOSE

The simulation of individual particle tracks and the chemical stage following water radiolysis in biological tissue is an effective means of improving our knowledge of the physico-chemical contribution to the biological effect of ionizing radiation. However, the step-by-step simulation of the reaction kinetics of radiolytic species is the most time-consuming task in Monte Carlo track-structure simulations, with long simulation times that are an impediment to research. In this work, we present the implementation of the independent reaction times (IRT) method in Geant4-DNA Monte Carlo toolkit to improve the computational efficiency of calculating G-values, defined as the number of chemical species created or lost per 100 eV of deposited energy.

METHODS

The computational efficiency of IRT, as implemented, is compared to that from available Geant4-DNA step-by-step simulations for electrons, protons and alpha particles covering a wide range of linear energy transfer (LET). The accuracy of both methods is verified using published measured data from fast electron irradiations for ^• OH and e aq - for time-dependent G-values. For IRT, simulations in the presence of scavengers irradiated by cobalt-60 γ-ray and 2 MeV protons are compared with measured data for different scavenging capacities. In addition, a qualitative assessment comparing measured LET-dependent G-values with Geant4-DNA calculations in pure liquid water is presented.

RESULTS

The IRT improved the computational efficiency by three orders of magnitude relative to the step-by-step method while differences in G-values by 3.9% at 1 μs were found. At 7 ps, ^• OH and e aq - yields calculated with IRT differed from recent published measured data by 5% ± 4% and 2% ± 4%, respectively. At 1 μs, differences were 9% ± 5% and 6% ± 7% for ^• OH and e aq - , respectively. Uncertainties are one standard deviation. Finally, G-values at different scavenging capacities and LET-dependent G-values reproduced the behavior of measurements for all radiation qualities.

CONCLUSION

The comprehensive validation of the Geant4-DNA capabilities to accurately simulate the chemistry following water radiolysis is an ongoing work. The implementation presented in this work is a necessary step to facilitate performing such a task.

Simulation of Proton-Induced DNA Damage Patterns Using an Improved Clustering Algorithm

Simulations of deoxyribonucleic acid (DNA) molecular damage use the traversal algorithm that has the disadvantages of being time-consuming, slowly converging, and requiring high-performance computer clusters. This work presents an improved version of the algorithm, "density-based spatial clustering of applications with noise" (DBSCAN), using a KD-tree approach to find neighbors of each point for calculating clustered DNA damage. The resulting algorithm considers the spatial distributions for sites of energy deposition and hydroxyl radical attack, yielding the statistical probability of (single and double) DNA strand breaks. This work achieves high accuracy and high speed at calculating clustered DNA damage that has been induced by proton treatment at the molecular level while running on an i7 quad-core CPU. The simulations focus on the indirect effect generated by hydroxyl radical attack on DNA. The obtained results are consistent with those of other published experiments and simulations. Due to the array of chemical processes triggered by proton treatment, it is possible to predict the effects that different track structures of various energy protons produce on eliciting direct and indirect damage of DNA.

Cellular S values in spindle-shaped cells: a dosimetry study on more realistic cell geometries using Geant4-DNA Monte Carlo simulation toolkit

OBJECTIVE

Cellular dosimetry plays a crucial role in radiobiology and evaluation of the relative merits of radiopharmaceuticals used for targeted radionuclide therapy. The present study aims to investigate the effects of various cell geometries on dosimetric characteristics of several Auger emitters distributed in different subcellular compartments using Monte Carlo simulation.

METHODS

The Geant4-DNA extension of the Geant4 Monte Carlo simulation toolkit was employed to calculate the mean absorbed dose per unit cumulated activity (S value) for different subcellular distributions of several Auger electron-emitting theranostic radionuclides including ^99mTc, ¹¹¹In, ¹²³I, ¹²⁵I, and ²⁰¹Tl. The simulations were carried out in various single-cell models of liquid water including spherical, ellipsoidal, spherical spindle, and ellipsoidal spindle cell models. The latter two models which are generalized from the first two models were inspired by the morphologies of spindle-shaped (fusiform) cells, and were developed to provide more realistic modeling of this common geometry observed in many healthy and cancerous cells.

RESULTS

Evaluation of the S values calculated for the examined cell models reveals that the differences are small (less than 9%) for the cell ← cell, cell ← cell surface, and nucleus ← nucleus source-target combinations. However, moderate discrepancies are seen (up to 28%) when the nucleus is considered as the target, as well as the radioactivity is either internalized into the cytoplasm or bound to the cell membrane.

CONCLUSIONS

The findings of the present work suggest that the assumption of spherical cell geometry may provide reasonably accurate estimates of the cellular/nuclear dose for the considered Auger emitters, even for spindle-shaped cells. Of course, this approximation should be used with caution for the nucleus ← cytoplasm and nucleus ← cell surface configurations, since the S-value sensitivity to the cell geometry is somewhat significant in these cases.

A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio

Monte Carlo (MC) track structure simulation tools are commonly used for predicting radiation induced DNA damage by modeling the physical and chemical reactions at the nanometer scale. However, the outcome of these MC simulations is particularly sensitive to the adopted parameters which vary significantly across studies. In this study, a previously developed full model of nuclear DNA was used to describe the DNA geometry. The TOPAS-nBio MC toolkit was used to investigate the impact of physics and chemistry models as well as three key parameters (the energy threshold for direct damage, the chemical stage time length, and the probability of damage between hydroxyl radical reactions with DNA) on the induction of DNA damage. Our results show that the difference in physics and chemistry models alone can cause differences up to 34% and 16% in the DNA double strand break (DSB) yield, respectively. Additionally, changing the direct damage threshold, chemical stage length, and hydroxyl damage probability can cause differences of up to 28%, 51%, and 71% in predicted DSB yields, respectively, for the configurations in this study.

A microdosimetric analysis of the interactions of mono-energetic neutrons with human tissue

Nuclear reactions induced during high-energy radiotherapy produce secondary neutrons that, due to their carcinogenic potential, constitute an important risk for the development of iatrogenic cancer. Experimental and epidemiological findings indicate a marked energy dependence of neutron relative biological effectiveness (RBE) for carcinogenesis, but little is reported on its physical basis. While the exact mechanism of radiation carcinogenesis is yet to be fully elucidated, numerical microdosimetry can be used to predict the biological consequences of a given irradiation based on its microscopic pattern of energy depositions. Building on recent studies, this work investigated the physics underlying neutron RBE by using the microdosimetric quantity dose-mean lineal energy (y‾_D) as a proxy. A simulation pipeline was constructed to explicitly calculate the y‾_D of radiation fields that consisted of (i) the open source Monte Carlo toolkit Geant4, (ii) its radiobiological extension Geant4-DNA, and (iii) a weighted track-sampling algorithm. This approach was used to study mono-energetic neutrons with initial kinetic energies between 1 eV and 10 MeV at multiple depths in a tissue-equivalent phantom. Spherical sampling volumes with diameters between 2 nm and 1 μm were considered. To obtain a measure of RBE, the neutron y‾_D values were divided by those of 250 keV X-rays that were calculated in the same way. Qualitative agreement was found with published radiation protection factors and simulation data, allowing for the dependencies of neutron RBE on depth and energy to be discussed in the context of the neutron interaction cross sections and secondary particle distributions in human tissue.

Ionizing Radiation and Complex DNA Damage: Quantifying the Radiobiological Damage Using Monte Carlo Simulations

Ionizing radiation is a common tool in medical procedures. Monte Carlo (MC) techniques are widely used when dosimetry is the matter of investigation. The scientific community has invested, over the last 20 years, a lot of effort into improving the knowledge of radiation biology. The present article aims to summarize the understanding of the field of DNA damage response (DDR) to ionizing radiation by providing an overview on MC simulation studies that try to explain several aspects of radiation biology. The need for accurate techniques for the quantification of DNA damage is crucial, as it becomes a clinical need to evaluate the outcome of various applications including both low- and high-energy radiation medical procedures. Understanding DNA repair processes would improve radiation therapy procedures. Monte Carlo simulations are a promising tool in radiobiology studies, as there are clear prospects for more advanced tools that could be used in multidisciplinary studies, in the fields of physics, medicine, biology and chemistry. Still, lot of effort is needed to evolve MC simulation tools and apply them in multiscale studies starting from small DNA segments and reaching a population of cells.

A new open-source GPU-based microscopic Monte Carlo simulation tool for the calculations of DNA damages caused by ionizing radiation - Part II: sensitivity and uncertainty analysis

PURPOSE

Calculations of deoxyribonucleic acid (DNA) damages involve many parameters in the computation process. As these parameters are often subject to uncertainties, it is of central importance to comprehensively quantify their impacts on DNA single-strand break (SSB) and double-strand break (DSB) yields. This has been a challenging task due to the required large number of simulations and the relatively low computational efficiency using CPU-based MC packages. In this study, we present comprehensive evaluations on sensitivities and uncertainties of DNA SSB and DSB yields on 12 parameters using our GPU-based MC tool, gMicroMC.

METHODS

We sampled one electron at a time in a water sphere containing a human lymphocyte nucleus and transport the electrons and generated radicals until 2 Gy dose was accumulated in the nucleus. We computed DNA damages caused by electron energy deposition events in the physical stage and the hydroxyl radicals at the end of the chemical stage. We repeated the computations by varying 12 parameters: (a) physics cross section, (b) cutoff energy for electron transport, (c)-(e) three branching ratios of hydroxyl radicals in the de-excitation of excited water molecules, (f) temporal length of the chemical stage, (g)-(h) reaction radii for direct and indirect damages, (i) threshold energy defining the threshold damage model to generate a physics damage, (j)-(k) minimum and maximum energy values defining the linear-probability damage model to generate a physics damage, and (l) probability to generate a damage by a radical. We quantified sensitivity of SSB and DSB yields with respect to these parameters for cases with 1.0 and 4.5 keV electrons. We further estimated uncertainty of SSB and DSB yields caused by uncertainties of these parameters.

RESULTS

Using a threshold of 10% uncertainty as a criterion, threshold energy in the threshold damage model, maximum energy in the linear-probability damage model, and probability for a radical to generate a damage were found to cause large uncertainties in both SSB and DSB yields. The scaling factor of the cross section, cutoff energy, physics reaction radius, and minimum energy in the linear-probability damage model were found to generate large uncertainties in DSB yields.

CONCLUSIONS

We identified parameters that can generate large uncertainties in the calculations of SSB and DSB yields. Our study could serve as a guidance to reduce uncertainties of parameters and hence uncertainties of the simulation results.

Microdosimetric calculations of the direct DNA damage induced by low energy electrons using the Geant4-DNA Monte Carlo code

To calculate the yield of direct DNA damage induced by low energy electrons using Monte Carlo generated microdosimetric spectra at the nanometer scale and examine the influence of various simulation inputs. The potential of classical microdosimetry to offer a viable and simpler alternative to more elaborate mechanistic approaches for practical applications is discussed. Track-structure simulations with the Geant4-DNA low-energy extension of the Geant4 Monte Carlo toolkit were used for calculating lineal energy spectra in spherical volumes with dimensions relevant to double-strand-break (DSB) induction. The microdosimetric spectra were then used to calculate the yield of simple and clustered DSB based on literature values of the threshold energy of DNA damage. The influence of the different implementations of the dielectric function of liquid water available in Geant4-DNA (Option 2 and Option 4 constructors), as well as the effect of particle tracking cutoff energy and target size are examined. Frequency- and dose-mean lineal energies in liquid-water spheres of 2, 2.3, 2.6, and 3.4 nm diameter, as well as, number of simple and clustered DSB/Gy/cell are presented for electrons over the 100 eV to 100 keV energy range. Results are presented for both the 'default' (Option 2) and 'Ioannina' (Option 4) physics models of Geant4-DNA applying several commonly used tracking cutoff energies (10, 20, 50, 100 eV). Overall, the choice of the physics model and target diameter has a moderate effect (up to ~10%-30%) on the DSB yield whereas the effect of the tracking cutoff energy may be significant (>100%). Importantly, the yield of both simple and clustered DSB was found to vary significantly (by a factor of 2 or more) with electron energy over the examined range. The yields of electron-induced simple and clustered DSB exhibit a strong energy dependence over the 100 eV-100 keV range with implications to radiation quality issues. It is shown that a classical microdosimetry approach for the calculation of DNA damage based on lineal energy spectra in nanometer-size targets predicts comparable results to computationally intensive mechanistic approaches which use detailed atomistic DNA geometries, thus, offering a relatively simple and robust alternative for some practical applications.

Reducing the ionizing radiation background does not significantly affect the evolution of Escherichia coli populations over 500 generations

Over millennia, life has been exposed to ionizing radiation from cosmic rays and natural radioisotopes. Biological experiments in underground laboratories have recently demonstrated that the contemporary terrestrial radiation background impacts the physiology of living organisms, yet the evolutionary consequences of this biological stress have not been investigated. Explaining the mechanisms that give rise to the results of underground biological experiments remains difficult, and it has been speculated that hereditary mechanisms may be involved. Here, we have used evolution experiments in standard and very low-radiation backgrounds to demonstrate that environmental ionizing radiation does not significantly impact the evolutionary trajectories of E. coli bacterial populations in a 500 generations evolution experiment.