Technical Note: Integrating an open source Monte Carlo code “MCsquare” for clinical use in intensity-modulated proton therapy

Wei Deng, James E. Younkin, Kevin Souris, Sheng Huang, Kurt Augustine, Mirek Fatyga, Xiaoning Ding, Marie Cohilis, Martin Bues, Jie Shan, Joshua Stoker, Liyong Lin, Jiajian Shen, Wei Liu

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Purpose: To commission an open source Monte Carlo (MC) dose engine, “MCsquare” for a synchrotron-based proton machine, integrate it into our in-house C++-based I/O user interface and our web-based software platform, expand its functionalities, and improve calculation efficiency for intensity-modulated proton therapy (IMPT). Methods: We commissioned MCsquare using a double Gaussian beam model based on in-air lateral profiles, integrated depth dose of 97 beam energies, and measurements of various spread-out Bragg peaks (SOBPs). Then we integrated MCsquare into our C++-based dose calculation code and web-based second check platform “DOSeCHECK.” We validated the commissioned MCsquare based on 12 different patient geometries and compared the dose calculation with a well-benchmarked GPU-accelerated MC (gMC) dose engine. We further improved the MCsquare efficiency by employing the computed tomography (CT) resampling approach. We also expanded its functionality by adding a linear energy transfer (LET)-related model-dependent biological dose calculation. Results: Differences between MCsquare calculations and SOBP measurements were <2.5% (<1.5% for ~85% of measurements) in water. The dose distributions calculated using MCsquare agreed well with the results calculated using gMC in patient geometries. The average 3D gamma analysis (2%/2 mm) passing rates comparing MCsquare and gMC calculations in the 12 patient geometries were 98.0 ± 1.0%. The computation time to calculate one IMPT plan in patients’ geometries using an inexpensive CPU workstation (Intel Xeon E5-2680 2.50 GHz) was 2.3 ± 1.8 min after the variable resolution technique was adopted. All calculations except for one craniospinal patient were finished within 3.5 min. Conclusions: MCsquare was successfully commissioned for a synchrotron-based proton beam therapy delivery system and integrated into our web-based second check platform. After adopting CT resampling and implementing LET model-dependent biological dose calculation capabilities, MCsquare will be sufficiently efficient and powerful to achieve Monte Carlo-based and LET-guided robust optimization in IMPT, which will be done in the future studies.

Original languageEnglish (US)
Pages (from-to)2558-2574
Number of pages17
JournalMedical physics
Issue number6
StatePublished - Jun 1 2020


  • Mcsquare
  • Monte Carlo method
  • dose calculation
  • intensity-modulated proton therapy (IMPT)
  • robust optimization

ASJC Scopus subject areas

  • Biophysics
  • Radiology Nuclear Medicine and imaging


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