Geant4-DNA simulation of the pre-chemical stage of water radiolysis and its impact on initial radiochemical yields

This paper demonstrates the impact of the pre-chemical stage, especially the dissociation scheme and the associated probabilities, on water radiolysis simulation using the Geant4-DNA Monte Carlo track structure simulation toolkit. The models and parameters provided by TRACs have been collected and implemented into Geant4-DNA. In order to evaluate their influence on water radiolysis simulation, the radiochemical yields (G-values) are evaluated as a function of time and LET using the “chem6” Geant4-DNA example, and they are compared with published experimental and calculated data. The new pre-chemical models lead to a better agreement with literature data than the default pre-chemical models of Geant4-DNA, especially for OH radicals and H₂O₂. The revised chemistry constructor “G4EmDNAChemistry_option3” is available in Geant4-DNA version 10.7.     

Comparison and assessment of electron cross sections for Monte Carlo track structure codes.

The purpose of this study was to make an intercomparison and assessment of cross sections for electrons in water used in electron track structure codes. This study is intended to shed light on the extent to which the differences between the input data and physical and chemical assumptions influence the outcome in biophysical modeling of radiation effects. Ionization cross sections and spectra of secondary electrons were calculated by various theories. The analyses were carried out for water vapor cross sections, as these are more abundant and readily available. All suitable published experimental total ionization cross sections were fitted by an appropriate function and used for generation of electron tracks. Three sets of compiled data were used for comparison of total excitation cross sections and mean excitation energy. The tracks generated by a Monte Carlo track code, using various combinations of cross sections, were compared in terms of radial distributions of interactions and point kernels. The spectrum of secondary electrons emitted by the ionization process was found to be the factor that has the most influence on these quantities. A different set of cross sections for excitation and elastic scattering did not affect the electron track structure as much as did ionization cross sections. It is concluded that all codes, using different cross sections and in different phase, currently used for biophysical modeling exhibit close similarities for energy deposition in larger size targets while appreciable differences are observed in B-DNA-size targets. We recommend fitted functions to all available suitable experimental data for the total ionization and elastic cross sections. We conclude that most codes produce tracks in reasonable agreement with the macroscopic quantities such as total stopping power and total yield of strand breaks. However, we predict differences in frequencies of clustering in tracks from the different models.     

Monte Carlo transport of swift protons and light ions in water: The influence of excitation cross sections,relativistic effects,and Auger electron emission in w-values

PurposeTo develop a particle transport code to compute w-values and stopping power of swift ions in liquid water and gases of interest for reference dosimetry in hadrontherapy. To analyze the relevance of inelastic and post-collisional processes considered.MethodsThe Monte Carlo code MDM was extended to the case of swift ion impact on liquid water (MDM-Ion). Relativistic corrections in the inelastic cross sections and the post-collisional Auger emission were considered. The effects of introducing different electronic excitation cross sections were also studied.ResultsThe stopping power of swift ions on liquid water, calculated with MDM-Ion, are in excellent agreement with recommended data. The w-values show a strong dependence on the electronic excitation cross sections and on the Auger electron emission. Comparisons with other Monte Carlo codes show the relevance of both the processes considered and of the cross sections employed. W and w-values for swift electron, proton, and carbon ions calculated with the MDM and MDM-Ion codes are in very close agreement with each other and with the 20.8 eV experimental value.ConclusionWe found that w-values in liquid water are independent of ion charge and energy, as assumed in reference dosimetry for hadrontherapy from sparse experimental results for electron and ion impact on gases. Excitation cross sections and Auger emission included in Monte Carlo codes are critical in w-values calculations. The computation of this physical parameter should be used as a benchmark for micro-dosimetry investigations, to assess the reliability of the cross sections employed.     

CPOP: An open source C++ cell POPulation modeler for radiation biology applications

PurposeMulticellular tumor spheroids are realistic in-vitro systems used in radiation biology research to study the effect of anticancer drugs or to evaluate the resistance of cancer cells under specific conditions. When combining the modeling of spheroids together with the simulation of radiation using Monte Carlo methods, one could estimate cell and DNA damage to be compared with experimental data. We developed a Cell Population (CPOP) modeler combined to Geant4 simulations in order to tackle how energy depositions are allocated to cells, especially when enhancing radiation outcomes using high-Z nanoparticles. CPOP manages to model large three-dimensional cell populations with independent deformable cells described with their nucleus, cytoplasm and membranes together with force law systems to manage cell–cell interactions.MethodsCPOP is an opensource platform written in C++. It is divided into two main libraries: a “Modeler” library, for cell geometry modeling using meshes, and a Multi Agent System (MAS) library, simulating all agent (cell) interactions among the population. CPOP is fully interfaced with the Geant4 Monte Carlo toolkit and is able to directly launch Geant4 simulations after compilation.We modeled a full and realistic 3D cell population from SK-MEL28 melanoma cell population cultured experimentally. The spheroid diameter of 550 ± 40 µm corresponds to a population of approximately 1000 cells having a diameter of 17.2 ± 2.5 µm and a nucleus diameter of 11.2 ± 2.0 µm. We decided to reproduce cell irradiations performed with a X-RAD 320 Biological Irradiator (Precision XRay Inc., North Branford, CT).ResultsWe simulated the energy spectrum of secondary particles generated in the vicinity of the spheroid and plotted the different energy spectra recovered internally to the spheroid. We evaluated also the impact of AGuIX (Gadolinium) nanoparticles modeled into the spheroid with their corresponding secondary energy spectra.ConclusionsWe succeeded into modeling cell populations and combined them with Geant4 simulations. The next step will be to integrate DNA geometrical models into cell nuclei and to use the Geant4-DNA physics and radiolysis modeling capabilities in order to evaluate early strand breaks induced on DNA.     

Low-energy electron penetration range in liquid water

Monte Carlo simulations of electron tracks in liquid water are performed to calculate the energy dependence of the electron penetration range at initial electron energies between 0.2 eV and 150 keV, including the subexcitation electron region (<7.3 eV). Our calculated electron penetration distances are compared with available experimental data and earlier calculations as well as with the results of simulations using newly reported amorphous ice electron scattering cross sections in the range approximately 1-100 eV.     

Measurement of depth-dose of linear accelerator and simulation by use of Geant4 computer code

Radiation therapy is an established method of cancer treatment. New technologies in cancer radiotherapy need a more accurate computation of the dose delivered in the radiotherapy treatment plan. This study presents some results of a Geant4-based application for simulation of the absorbed dose distribution given by a medical linear accelerator (LINAC). The LINAC geometry is accurately described in the Monte Carlo code with use of the accelerator manufacturer''s specifications. The capability of the software for evaluating the dose distribution has been verified by comparisons with measurements in a water phantom; the comparisons were performed for percentage depth dose (PDD) and profiles for various field sizes and depths, for a 6-MV electron beam. Experimental and calculated dose values were in good agreement both in PDD and in transverse sections of the water phantom.     

Calculation of the proximity function of electrons

A new semianalytical method to calculate the proximity function for electrons is proposed. An integral equation for the proximity function that can be solved by using information on the spatial dose distributions is obtained. The proximity function for electrons in the energy range from 10 eV to 10 keV is calculated by solving the equation numerically, using a set of electron collision cross sections for water vapor. The results are in good agreement with those obtained using the Monte Carlo method. The proposed method can be used for electrons of high energies much more efficiently than the Monte Carlo method.     

Validation of Monte carlo Geant4 multithreading code for a 6 MV photon beam of varian linac on the grid computing

AimTo evaluate the computation time efficiency of the multithreaded code (G4Linac-MT) in the dosimetry application, using the high performance of the HPC-Marwan grid to determine with high accuracy the initial parameters of the 6 MV photon beam of Varian CLINAC 2100C.BackgroundThe difficulty of Monte Carlo methods is the long computation time, this is one of the disadvantages of the Monte Carlo methods.Materials and methodsCalculations are performed by the multithreaded code G4Linac-MT and Geant4.10.04.p02 using the HPC-Marwan computing grid to evaluate the computing speed for each code. The multithreaded version is tested in several CPUs to evaluate the computing speed according to the number of CPUs used. The results were compared to the measurements using different types of comparisons, TPR_20.10, penumbra, mean dose error and gamma index.ResultsThe results obtained for this work indicate a much higher computing time saving for the G4Linac-MT version compared to the Geant4.10.04 version, the computing time decreases with the number of CPUs used, can reach about 12 times if 64CPUs are used. After optimization of the initial electron beam parameters, the results of the dose simulations obtained for this work are in very good agreement with the experimental measurements with a mean dose error of up to 0.41% on the PDDs and 1.79% on the lateral dose.ConclusionsThe gain in computation time leads us to perform Monte Carlo simulations with a large number of events which gives a high accuracy of the dosimetry results obtained in this work.     

Analysis of low-energy electron track structure in liquid water

An implementation is presented of interaction cross sections for non-relativistic electron track structure simulations. The model, incorporating liquid-phase cross sections for inelastic interactions and improved algorithms for elastic scattering, is applied to Monte Carlo simulation of the track structure of low-energy electrons. Benchmark distributions and mean values are presented for several measures of penetration distances that characterize the general physical extent of the track structure. The results indicate that, except for the last approximately 500 eV of energy loss, electron tracks have a quasi-linear character; this suggests that a major part of an electron track may be reasonably described by a lineal-energy-like characterization.     

Geant4 implementation of inter-atomic interference effect in small-angle coherent X-ray scattering for materials of medical interest

An extension to Geant4 Monte Carlo code was developed to take into account inter-atomic (molecular) interference effects in X-ray coherent scattering. Based on our previous works, the developed code introduces a set of form factors including interference effects for a selected variety of amorphous materials useful for medical applications, namely various tissues and plastics used to build phantoms. The code is easily upgradable in order to include new materials and offers the possibility to model a generic tissue as a combination of a set of four basic components. A dedicated Geant4 application for the simulation of X-ray diffraction experiments was created to validate the proposed upgrade of Rayleigh scattering model. A preliminary validation of the code obtained through a comparison with EGS4 and an experiment is presented, showing a satisfactory agreement.     

A Monte Carlo code for the simulation of heavy-ion tracks in water

TILDA, a new Monte Carlo track structure code for ions in gaseous water that is valid for both high-LET (approximately 10(4) keV/microm) and low-LET ions, is presented. It is specially designed for a comparison of the patterns of energy deposited by a large range of ions. Low-LET ions are described in a perturbative frame, whereas heavy ions with a very high stopping power are treated using the Lindhard local density approximation and the Russek and Meli statistical method. Ionization cross sections singly differential with energy compare well with the experiment. As an illustration of the non-perturbative interaction of high-LET ions, a comparison between the ion tracks of light and heavy ions with the same specific energy is presented (1.4 MeV/nucleon helium and uranium ions). The mean energy for ejected electrons was found to be approximately four times larger for uranium than for helium, leading to a much larger track radius in the first case. For electrons, except for the excitation cross sections that are deduced from experimental fits, cross sections are derived analytically. For any orientation of the target molecule, the code calculates multiple differential cross sections as a function of the ejection and scattering angles and of the energy transfer. The corresponding singly differential and total ionization cross sections are in good agreement with experimental data. The angular distribution of secondary electrons is shown to depend strongly on the orientation of the water molecule.     

Radial secondary electron dose profiles and biological effects in light-ion beams based on analytical and Monte Carlo calculations using distorted wave cross sections

To speed up dose calculation, an analytical pencil-beam method has been developed to calculate the mean radial dose distributions due to secondary electrons that are set in motion by light ions in water. For comparison, radial dose profiles calculated using a Monte Carlo technique have also been determined. An accurate comparison of the resulting radial dose profiles of the Bragg peak for (1)H(+), (4)He(2+) and (6)Li(3+) ions has been performed. The double differential cross sections for secondary electron production were calculated using the continuous distorted wave-eikonal initial state method (CDW-EIS). For the secondary electrons that are generated, the radial dose distribution for the analytical case is based on the generalized Gaussian pencil-beam method and the central axis depth-dose distributions are calculated using the Monte Carlo code PENELOPE. In the Monte Carlo case, the PENELOPE code was used to calculate the whole radial dose profile based on CDW data. The present pencil-beam and Monte Carlo calculations agree well at all radii. A radial dose profile that is shallower at small radii and steeper at large radii than the conventional 1/r(2) is clearly seen with both the Monte Carlo and pencil-beam methods. As expected, since the projectile velocities are the same, the dose profiles of Bragg-peak ions of 0.5 MeV (1)H(+), 2 MeV (4)He(2+) and 3 MeV (6)Li(3+) are almost the same, with about 30% more delta electrons in the sub keV range from (4)He(2+)and (6)Li(3+) compared to (1)H(+). A similar behavior is also seen for 1 MeV (1)H(+), 4 MeV (4)He(2+) and 6 MeV (6)Li(3+), all classically expected to have the same secondary electron cross sections. The results are promising and indicate a fast and accurate way of calculating the mean radial dose profile.     

Mechanistic DNA damage simulations in Geant4-DNA part 1: A parameter study in a simplified geometry

Mechanistic modelling of DNA damage in Monte Carlo simulations is highly sensitive to the parameters that define DNA damage. In this work, we use a simple testing geometry to investigate how different choices of physics models and damage model parameters can change the estimation of DNA damage in a mechanistic DNA damage simulation built in Geant4-DNA. The choice of physics model can lead to variations by up to a factor of two in the yield of physically induced strand breaks, and the parameters that determine scavenging, and physical and chemical single strand break induction can have even larger consequences. Using low energy electrons as primary particles, a variety of parameters are tested in this geometry in order to arrive at a parameter set consistent with past simulation studies. We find that the modelling of scavenging can play an important role in determining results, and speculate that high-scavenging regimes, where only chemical radicals within 1 nm of DNA are simulated, could provide a good means of testing mechanistic DNA simulations.     

Comparison between an event-by-event Monte Carlo code,NOREC, and ETRAN for electron scaled point kernels between 20 keV and 1 MeV

An event-by-event Monte Carlo code called NOREC, a substantially improved version of the Oak Ridge electron transport code (OREC), was released in 2003, after a number of modifications to OREC. In spite of some earlier work, the characteristics of the code have not been clearly shown so far, especially for a wide range of electron energies. Therefore, NOREC was used in this study to generate one of the popular dosimetric quantities, the scaled point kernel, for a number of electron energies between 0.02 and 1.0 MeV. Calculated kernels were compared with the most well-known published kernels based on a condensed history Monte Carlo code, ETRAN, to show not only general agreement between the codes for the electron energy range considered but also possible differences between an event-by-event code and a condensed history code. There was general agreement between the kernels within about 5% up to 0.7 r/r ₀ for 100 keV and 1 MeV electrons. Note that r/r ₀ denotes the scaled distance, where r is the radial distance from the source to the dose point and r ₀ is the continuous slowing down approximation (CSDA) range of a mono-energetic electron. For the same range of scaled distances, the discrepancies for 20 and 500 keV electrons were up to 6 and 12%, respectively. Especially, there was more pronounced disagreement for 500 keV electrons than for 20 keV electrons. The degree of disagreement for 500 keV electrons decreased when NOREC results were compared with published EGS4/PRESTA results, producing similar agreement to other electron energies.     

Response of SOI microdosimeter in fast neutron beams: experiment and Monte Carlo simulations

In this study, Monte Carlo codes, Geant4 and MCNP6, were used to characterize the fast neutron therapeutic beam produced at iThemba LABS in South Africa. Experimental and simulation results were compared using the latest generation of Silicon on Insulator (SOI) microdosimeters from the Centre for Medical Radiation Physics (CMRP). Geant4 and MCNP6 were able to successfully model the neutron gantry and simulate the expected neutron energy spectrum produced from the reaction by protons bombarding a ⁹Be target. The neutron beam was simulated in a water phantom and its characteristics recorded by the silicon microdosimeters; bare and covered by a ¹⁰B enriched boron carbide converter, at different positions. The microdosimetric quantities calculated using Geant4 and MCNP6 are in agreement with experimental measurements. The thermal neutron sensitivity and production of ¹⁰B capture products in the p+ boron-implanted dopant regions of the Bridge microdosimeter is investigated. The obtained results are useful for the future development of dedicated SOI microdosimeters for Boron Neutron Capture Therapy (BNCT). This paper provides a benchmark comparison of Geant4 and MCNP6 capabilities in the context of further applications of these codes for neutron microdosimetry.     

Local dose enhancement of proton therapy by ceramic oxide nanoparticles investigated with Geant4 simulations

Nanoparticles (NPs) have been shown to enhance X-ray radiotherapy and proton therapy of cancer. The effectiveness of radiation damage is enhanced in the presence of high atomic number (high-Z) NPs due to increased production of low energy, higher linear energy transfer (LET) secondary electrons when NPs are selectively internalized by tumour cells. This work quantifies the local dose enhancement produced by the high-Z ceramic oxide NPs Ta₂O₅ and CeO₂, in the target tumour, for the first time in proton therapy, by means of Geant4 simulations. The dose enhancement produced by the ceramic oxides is compared against gold NPs. The energy deposition on a nanoscale around a single nanoparticle of 100 nm diameter is investigated using the Geant4-DNA extension to model particle interactions in the water medium. Enhancement of energy deposition in nano-sized shells of water, local to the NP boundary, ranging between 14% and 27% was observed for proton energies of 5 MeV and 50 MeV, depending on the NP material. Enhancement of electron production and energy deposition can be correlated to the direct DNA damage mechanism if the NP is in close proximity to the nucleus.     

Monte Carlo calculations of energy deposition distributions of electrons below 20 keV in protein

The distributions of energy depositions of electrons in semi-infinite bulk protein and the radial dose distributions of point-isotropic mono-energetic electron sources [i.e., the so-called dose point kernel (DPK)] in protein have been systematically calculated in the energy range below 20 keV, based on Monte Carlo methods. The ranges of electrons have been evaluated by extrapolating two calculated distributions, respectively, and the evaluated ranges of electrons are compared with the electron mean path length in protein which has been calculated by using electron inelastic cross sections described in this work in the continuous-slowing-down approximation. It has been found that for a given energy, the electron mean path length is smaller than the electron range evaluated from DPK, but it is large compared to the electron range obtained from the energy deposition distributions of electrons in semi-infinite bulk protein. The energy dependences of the extrapolated electron ranges based on the two investigated distributions are given, respectively, in a power-law form. In addition, the DPK in protein has also been compared with that in liquid water. An evident difference between the two DPKs is observed. The calculations presented in this work may be useful in studies of radiation effects on proteins.     

GEANT4 Monte Carlo simulations for virtual clinical trials in breast X-ray imaging: Proof of concept

Virtual clinical trials (VCT) are in-silico reproductions of medical examinations, which adopt digital models of patients and simulated devices. They are intended to produce clinically equivalent outcome data avoiding long execution times, ethical issues related to radiation induced risks and huge costs related to real clinical trials with a patient population. In this work, we present a platform for VCT in 2D and 3D X-ray breast imaging. The VCT platform uses Monte Carlo simulations based on the Geant4 toolkit and patient breast models derived from a cohort of high resolution dedicated breast CT (BCT) volume data sets. Projection images of the breast and three-dimensional glandular dose maps are generated for a given breast model, by simulating both 2D full-field digital mammography (DM) and 3D BCT examinations. Uncompressed voxelized breast models were derived from segmented patient images. Compressed versions of the digital breast phantoms for DM were generated using a previously published digital compression algorithm. The Monte Carlo simulation framework has the capability of generating and tracking ~10⁵ photons/s using a server equipped with 16-cores and 3.0 GHz clock speed. The VCT platform will provide a framework for scanner design optimization, comparison between different scanner designs and between different modalities or protocols on computational breast models, without the need for scanning actual patients as in conventional clinical trials.