A new open-source GPU-based microscopic Monte Carlo simulation tool for the calculations of DNA damages caused by ionizing radiation --- Part I: Core algorithm and validation.

PURPOSE Monte Carlo (MC) simulation of radiation interactions with water medium at physical, physicochemical, and chemical stages, as well as the computation of biologically relevant quantities such as DNA damages, are of critical importance for the understanding of microscopic basis of radiation effects. Due to the large problem size and many-body simulation problem in the chemical stage, existing CPU-based computational packages encounter the problem of low computational efficiency. This paper reports our development on a GPU-based microscopic Monte Carlo simulation tool gMicroMC using advanced GPU-acceleration techniques. METHODS gMicroMC simulated electron transport in the physical stage using an interaction-by-interaction scheme to calculate the initial events generating radicals in water. After the physicochemical stage, initial positions of all radicals were determined. Simulation of radicals' diffusion and reactions in the chemical stage was achieved using a step-by-step model using GPU-accelerated parallelization together with a GPU-enabled box-sorting algorithm to reduce the computations of searching for interaction pairs and therefore improve efficiency. A multi-scale DNA model of the whole lymphocyte cell nucleus containing ~6.2 Gbp DNA was built. RESULTS Accuracy of physics stage simulation was demonstrated by computing stopping power and track length. The results agreed with published data and the data produced by GEANT4-DNA (version 10.3.3) simulations with 10~20% difference in most cases. Difference of yield values of major radiolytic species from GEANT4-DNA results was within 10%. We computed DNA damages caused by monoenergetic 662 keV photons, approximately representing 137 Cs decay. Single-strand break (SSB) and double-strand break (DSB) yields were 196 ± 8 SSB/Gy/Gbp and 7.3 ± 0.7 DSB/Gy/Gbp, respectively, which agreed with the result of 188 SSB/Gy/Gbp and 8.4 DSB/Gy/Gbp computed by Hsiao et al. Comparing to computation using a single CPU, gMicroMC achieved a speedup factor of ~540x using a NVidia TITAN Xp GPU card. CONCLUSION The achieved accuracy and efficiency made gMicroMC can facilitate research on microscopic radiation transport simulation and DNA damage calculation. gMicroMC is an open-source package available to the research community.

[1]  T. Goulet,et al.  Monte Carlo simulation of fast electron and proton tracks in liquid water -- I. physical and physicochemical aspects , 1998 .

[2]  Steve B. Jiang,et al.  Fast Monte Carlo simulation for patient-specific CT/CBCT imaging dose calculation , 2011, Physics in medicine and biology.

[3]  Petteri Nieminen,et al.  Modeling Radiation Chemistry in the Geant4 Toolkit , 2011 .

[4]  R. Stewart,et al.  Monte Carlo simulation of DNA damage induction by x-rays and selected radioisotopes , 2008, Physics in medicine and biology.

[5]  D. Emfietzoglou.  Inelastic cross-sections for electron transport in liquid water: a comparison of dielectric models , 2003 .

[6]  Peter Jacob,et al.  Track structures, DNA targets and radiation effects in the biophysical Monte Carlo simulation code PARTRAC. , 2011, Mutation research.

[7]  A. Beaudré,et al.  Simulation of Space and Time Evolution of Radiolytic Species Induced by Electrons in Water , 1990 .

[8]  M. Zaider,et al.  A computationally convenient parameterisation of experimental angular distributions of low energy electrons elastically scattered off water vapour , 1984 .

[9]  H. Paretzke,et al.  Time- and space-resolved Monte Carlo study of water radiolysis for photon, electron and ion irradiation , 2009, Radiation and environmental biophysics.

[10]  Z. Tan,et al.  A new calculation on spectrum of direct DNA damage induced by low-energy electrons , 2010, Radiation and environmental biophysics.

[11]  Ianik Plante,et al.  A Monte–Carlo step-by-step simulation code of the non-homogeneous chemistry of the radiolysis of water and aqueous solutions. Part I: theoretical framework and implementation , 2011, Radiation and environmental biophysics.

[12]  L. Sanche,et al.  Cross Sections for Low-Energy (1–100 eV) Electron Elastic and Inelastic Scattering in Amorphous Ice , 2003, Radiation research.

[13]  J. Olivero,et al.  Electron deposition in water vapor, with atmospheric applications , 1972 .

[14]  Ianik Plante,et al.  A Monte-Carlo step-by-step simulation code of the non-homogeneous chemistry of the radiolysis of water and aqueous solutions—Part II: calculation of radiolytic yields under different conditions of LET, pH, and temperature , 2011, Radiation and environmental biophysics.

[15]  Gert Moliere,et al.  Theorie der Streuung schneller geladener Teilchen II Mehrfach-und Vielfachstreuung , 1948 .

[16]  L Maigne,et al.  Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit. , 2015, Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics.

[17]  E. Huttel,et al.  Screening corrections to the Rutherford cross section , 1985 .

[18]  G. Kraft,et al.  Calculations of heavy-ion track structure. , 1995, Radiation and environmental biophysics.

[19]  D. Goodhead,et al.  Track structure analysis of ultrasoft X-rays compared to high- and low-LET radiations. , 1989, International journal of radiation biology.

[20]  H. Paretzke,et al.  Modeling of ultrasoft X-ray induced DNA damage using structured higher order DNA targets , 2003 .

[21]  C Cremer,et al.  Radial arrangement of chromosome territories in human cell nuclei: a computer model approach based on gene density indicates a probabilistic global positioning code. , 2004, Biophysical journal.

[22]  K. Sharma,et al.  Mechanisms of Direct Radiation Damage in DNA, Based on a Study of the Yields of Base Damage, Deoxyribose Damage, and Trapped Radicals in d(GCACGCGTGC)2 , 2007, Radiation research.

[23]  Sébastien Incerti,et al.  Mechanistic DNA damage simulations in Geant4-DNA part 1: A parameter study in a simplified geometry. , 2018, Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics.

[24]  S. Incerti,et al.  Implementation of new physics models for low energy electrons in liquid water in Geant4-DNA. , 2016, Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics.

[25]  P O'Neill,et al.  Computational modelling of low-energy electron-induced DNA damage by early physical and chemical events. , 1997, International journal of radiation biology.

[26]  Steve B. Jiang,et al.  Accelerated Monte Carlo simulation on the chemical stage in water radiolysis using GPU , 2017, Physics in medicine and biology.

[27]  N. F. Sir Mott,et al.  The theory of atomic collisions , 1933 .

[28]  M. Dingfelder.  Track structure: time evolution from physics to chemistry. , 2006, Radiation protection dosimetry.

[29]  Rudd,et al.  Binary-encounter-dipole model for electron-impact ionization. , 1994, Physical review. A, Atomic, molecular, and optical physics.

[30]  Herwig G. Paretzke,et al.  Electron inelastic-scattering cross sections in liquid water , 1999 .

[31]  Sébastien Incerti,et al.  Simulation of early DNA damage after the irradiation of a fibroblast cell nucleus using Geant4-DNA , 2017, Scientific Reports.

[32]  The effect of ion-induced shock waves on the transport of reacting species around energetic ion tracks , 2017, 1703.09150.

[33]  N. Mason,et al.  Simulation of the ion-induced shock waves effects on the transport of chemically reactive species in ion tracks , 2017, The European Physical Journal D.

[34]  V. Ivanchenko,et al.  The Influence of DNA Configuration on the Direct Strand Break Yield , 2015, Comput. Math. Methods Medicine.

[35]  Francis A. Cucinotta,et al.  Track-structure codes in radiation research , 2006 .

[36]  D. Alloni,et al.  Heavy-ion effects: from track structure to DNA and chromosome damage , 2008 .

[37]  C Villagrasa,et al.  Comparison of GEANT4 very low energy cross section models with experimental data in water. , 2010, Medical physics.

[38]  Sandrine Edel.  Modélisation du transport des photons et des électrons dans l'ADN plasmide , 2006 .

[39]  Sébastien Incerti,et al.  The Geant4-DNA Project , 2010, Int. J. Model. Simul. Sci. Comput..

[40]  Marco Durante,et al.  TRAX-CHEM: A pre-chemical and chemical stage extension of the particle track structure code TRAX in water targets , 2018 .

[41]  J. Santos,et al.  Cross sections for K-shell ionization of atoms by electron impact , 2003 .

[42]  C. E. Melton.  Principles of mass spectrometry and negative ions , 1970 .

[43]  M. Beuve,et al.  Radiolysis of Water Confined in Porous Silica: A Simulation Study of the Physicochemical Yields , 2010, 1612.08720.

[44]  Yong-ki Kim,et al.  Extension of the binary-encounter-dipole model to relativistic incident electrons , 2000 .

[45]  V. Ivanchenko,et al.  Diffusion-controlled reactions modeling in Geant4-DNA , 2014, J. Comput. Phys..