**5. Conclusions**

We successfully developed and validated two new features in gMicroMC, the transport of protons and heavy ions in the physical stage and the concurrent transport of DNA in the chemical stage. We implemented the two features on a GPU parallel computing platform, resulting in a remarkable time performance. The physical transport of 100 protons with an initial kinetic energy of 10 MeV could be finished in s. The chemical simulation with concurrent DNA transport was far more complex, but it still only took a few minutes to run a representative case. The two newly developed features in gMicroMC that had both high accuracy and efficiency gave gMicroMC the high promise of solving large-scale problems in active radiation research areas.

**Author Contributions:** Conceptualization, X.J. and Y.C.; methodology, X.J. and Y.C.; software, Y.L.; validation, Y.L. and Y.C.; formal analysis, Y.L. and Y.C.; investigation, Y.L.; resources, Y.C.; data curation, Y.L., X.J., and Y.C.; writing—original draft preparation, Y.L.; writing—review and editing, Y.L., X.J., and Y.C.; visualization, Y.L.; supervision, X.J. and Y.C.; project administration, X.J. and Y.C.; funding acquisition, X.J. and Y.C. All authors read and agreed to the published version of the manuscript.

**Funding:** This work was supported in part by the Cancer Prevention and Research Institute of Texas (CPRIT) Grant RP160661 and by the National Institutes of Health Grants R37CA214639 and R15CA256668.

**Institutional Review Board Statement:** Not applicable.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** Not applicable.

**Conflicts of Interest:** The authors declare no conflict of interest.
