A new open-source GPU-based microscopic Monte Carlo simulation tool for the calculations of DNA damages caused by...

Area of Science:

• Computational physics and biophysics
• Radiation science and radiobiology
• High-performance computing

Background:

• Understanding radiation effects at the microscopic level is crucial for radiobiology.
• Accurate simulation of radiation transport and subsequent biological damage is computationally intensive.
• Existing CPU-based Monte Carlo (MC) methods face efficiency limitations due to large problem sizes and complex many-body interactions, particularly in the chemical stage of radiation effects.

Purpose of the Study:

• To develop a GPU-accelerated microscopic Monte Carlo (MC) simulation tool, named gMicroMC.
• To improve the computational efficiency of simulating radiation interactions in water and calculating biologically relevant quantities like DNA damage.
• To leverage advanced GPU-acceleration techniques for MC simulations.

Main Methods:

• gMicroMC simulates electron transport in the physical stage using an interaction-by-interaction scheme.
• The physicochemical stage determines the initial positions of radicals generated in water.
• The chemical stage employs a step-by-step model with GPU-accelerated parallelization and a GPU-enabled box-sorting algorithm for efficient simulation of radical diffusion and reactions.
• A multi-scale DNA model representing a lymphocyte cell nucleus (~6.2 Gbp) was integrated.

Main Results:

• Physical stage simulation accuracy was validated by computing stopping power and track length, showing 10-20% agreement with published data and GEANT4-DNA.
• Yields of major radiolytic species showed within 10% difference compared to GEANT4-DNA.
• Calculated DNA damage yields for 662 keV photons (¹³⁷Cs source) were 196 ± 8 SSB/Gy/Gbp and 7.3 ± 0.7 DSB/Gy/Gbp, consistent with prior studies.
• gMicroMC achieved a significant speedup factor of approximately 540x compared to single-CPU computations using an NVidia TITAN Xp GPU.

Conclusions:

• gMicroMC demonstrates high accuracy and efficiency in simulating microscopic radiation transport and DNA damage.
• The tool is capable of facilitating advanced research in radiobiology and radiation effects.
• gMicroMC is an open-source package, readily available for the scientific community.