Accelerated Monte Carlo simulation on the chemical stage in water radiolysis using GPU

摘要

The accurate simulation of water radiolysis is an important step to understand the mechanisms of radiobiology and quantitatively test some hypotheses regarding radiobiological effects. However, the simulation of water radiolysis is highly time consuming, taking hours or even days to be completed by a conventional CPU processor. This time limitation hinders cell-level simulations for a number of research studies. We recently initiated efforts to develop gMicroMC, a GPU-based fast microscopic MC simulation package for water radiolysis. The first step of this project focused on accelerating the simulation of the chemical stage, the most time consuming stage in the entire water radiolysis process. A GPU-friendly parallelization strategy was designed to address the highly correlated many-body simulation problem caused by the mutual competitive chemical reactions between the radiolytic molecules. Two cases were tested, using a 750 keV electron and a 5 MeV proton incident in pure water, respectively. The time-dependent yields of all the radiolytic species during the chemical stage were used to evaluate the accuracy of the simulation. The relative differences between our simulation and the Geant4-DNA simulation were on average 5.3% and 4.4% for the two cases. Our package, executed on an Nvidia Titan black GPU card, successfully completed the chemical stage simulation of the two cases within 599.2 s and 489.0 s. As compared with Geant4-DNA that was executed on an Intel i7-5500U CPU processor and needed 28.6 h and 26.8 h for the two cases using a single CPU core, our package achieved a speed-up factor of 171.1-197.2.