MPEXS-DNA, a new GPU-based Monte Carlo simulator for track structures and radiation chemistry at subcellular scale

Abstract

Purpose: Track structure simulation codes can accurately reproduce the stochastic nature of particle-matter interactions in order to evaluate quantitatively radiation damage in biological cells such as DNA strand breaks and base damage. Such simulations handle large numbers of secondary charged particles and molecular species created in the irradiated medium. Every particle and molecular species are tracked step-by-step using a Monte Carlo method to calculate energy loss patterns and spatial distributions of molecular species inside a cell nucleus with high spatial accuracy. The Geant4-DNA extension of the Geant4 general-purpose Monte Carlo simulation toolkit allows for such track structure simulations and can be run on CPUs. However, long execution times have been observed for the simulation of DNA damage in cells. We present in this work an improvement of the computing performance of such simulations using ultraparallel processing on a graphical processing unit (GPU).

Methods: A new Monte Carlo simulator named MPEXS-DNA, allowing high computing performance by using a GPU, has been developed for track structure and radiolysis simulations at the subcellular scale. MPEXS-DNA physics and chemical processes are based on Geant4-DNA processes available in Geant4 version 10.02 p03. We have reimplemented the Geant4-DNA process codes of the physics stage (electromagnetic processes of charged particles) and the chemical stage (diffusion and chemical reactions for molecular species) for microdosimetry simulation by using the CUDA language. MPEXS-DNA can calculate a distribution of energy loss in the irradiated medium caused by charged particles and also simulate production, diffusion, and chemical interactions of molecular species from water radiolysis to quantitatively assess initial damage to DNA. The validation of MPEXS-DNA physics and chemical simulations was performed by comparing various types of distributions, namely the radial dose distributions for the physics stage, and the G-value profiles for each chemical product and their linear energy transfer dependency for the chemical stage, to existing experimental data and simulation results obtained by other simulation codes, including PARTRAC.

Results: For physics validation, radial dose distributions calculated by MPEXS-DNA are consistent with experimental data and numerical simulations. For chemistry validation, MPEXS-DNA can also reproduce G-value profiles for each molecular species with the same tendency as existing experimental data. MPEXS-DNA also agrees with simulations by PARTRAC reasonably well. However, we have confirmed that there are slight discrepancies in G-value profiles calculated by MPEXS-DNA for molecular species such as H₂ and H₂ O₂ when compared to experimental data and PARTRAC simulations. The differences in G-value profiles between MPEXS-DNA and PARTRAC are caused by the different chemical reactions considered. MPEXS-DNA can drastically boost the computing performance of track structure and radiolysis simulations. By using NVIDIA's GPU devices adopting the Volta architecture, MPEXS-DNA has achieved speedup factors up to 2900 against Geant4-DNA simulations with a single CPU core.

Conclusion: The MPEXS-DNA Monte Carlo simulation achieves similar accuracy to Monte Carlo simulations performed using other codes such as Geant4-DNA and PARTRAC, and its predictions are consistent with experimental data. Notably, MPEXS-DNA allows calculations that are, at maximum, 2900 times faster than conventional simulations using a CPU.

Keywords: CUDA; GPGPU; Geant4-DNA; Monte Carlo simulation; microdosimetry.

Figure 1

The diagram of parallel particle tracking in MPEXS simulation.

Figure 2

The process flow diagram of the MPEXS‐DNA chemical stage.

Figure 3

Comparison of radial dose between Geant4‐DNA 10.02 p03 (solid black line) and MPEXS‐DNA (filled red circle) for protons (a) and alpha particles (b) with kinetic energy 3 MeV, and 2.57 MeV/u oxygen ions (c). The bottom of each plot shows the residual of radial dose between Geant4‐DNA and MPEXS‐DNA.

Figure 4

Comparison of G‐value time profiles for each molecular species induced by electrons with kinetic energy 750 keV. $·\text{OH}$ radicals, H₃O⁺ ions, and hydrated electrons are shown in (a). OH⁻ ions, $\mathrm{H}·$ radicals, H₂ and H₂O₂ molecules are shown in (b). Each color denotes a molecular species. Solid lines are Geant4‐DNA 10.02 p03 results and filled circles are MPEXS‐DNA values.

Figure 5

Comparison of G‐value time profiles for each molecular species induced by 20 MeV protons. $·\text{OH}$ radicals, H₃O⁺ ions, and hydrated electrons are shown in (a). OH⁻ ions, $\mathrm{H}·$ radicals, H₂, and H₂O₂ molecules are shown in (b). Each color indicates a molecular species. Solid line and filled circle plots are simulation results by Geant4‐DNA 10.02 p03 and MPEXS‐DNA, respectively.

Figure 6

Comparison of radial dose between Monte Carlo simulation by MPEXS‐DNA (solid red line), numerical calculations by the Waligórski (dashed blue line)22 and Chunxiang et al. (dotted green line)21 models, and experiment data (filled circle19 and filled square20). Three types of initial particles are considered: 3 MeV protons (a) and alpha particles (b), 2.57 MeV/u oxygen ions (c).

Figure 7

Diffusion and reactions of molecular species induced by 10 keV electrons simulated by MPEXS‐DNA.

Figure 8

Comparison of G‐value time profiles of $·\text{OH}$ radicals (top left), hydrated electrons (top right), H₂ molecules (bottom left), and H₂O₂ molecules (bottom right) induced by electrons with kinetic energy 750 keV in liquid water. MPEXS‐DNA is represented by filled red circles with vertical bars representing the standard deviation. Geant4‐DNA 10.02 p03 and PARTRAC23 are soild blue and black lines, respectively. The other points are experimental and theoretical calculation results (Experimental data: open circles,28 filled squares,29 open triangles,30 filled triangles,31 calculations : filled diamonds,32 open diamonds,33 open squares34).

Figure 9

G‐value time profile for $·\text{OH}$ radicals (top left), hydrated electrons (top right), H₂ (bottom left), and H₂O₂ molecules (bottom right) induced by 5 MeV protons. MPEXS‐DNA is represented by filled red circles with vertical bars representing the standard deviation. Solid blue and black lines are Geant4‐DNA 10.02 p03 and PARTRAC23 results, respectively. Filled squares are Monte Carlo simulation results by Frongillo et al.44

Figure 10

G‐value time profile of $·\text{OH}$ radicals induced by 20 MeV proton in liquid water. Filled red circles are MPEXS‐DNA simulation results with vertical bars representing the standard deviation. Soild blue line is Geant4‐DNA 10.02 p03. Filled triangle is measured data.45

Figure 11

G‐value dependency on LET at 1 μs after irradiation for $·\text{OH}$ radicals, hydrated electrons, H₂, and H₂O₂ molecules. Comparison between simulations irradiating a water target with 500 keV–100 MeV protons and experiments. Filled circles represent MPEXS‐DNA simulations with vertical bars for the standard deviation of G‐value. Solid lines and dashed lines with open circles show the PARTRAC23 and Monte Carlo code developed by Frongillo, et al.,44 respectively. The other plots are experiment results (filled square,46 filled triangle,47 and filled inverted triangle48).