People Directory

Jan Schuemann, PhD

Associate Director of Physics Research & Head of the Multi-Scale Monte Carlo Modeling Lab
Associate Professor
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Rm. 3206, 125 Nashua St.
617 724 4183


  • Visiting student at the University of Calgary (1998), Research Topic: Applications of knot theory to quantum gravity
  • Diplom (MS) degree (2000) at the University of Hamburg, Germany, Title: Inelastic J/ψ-Photoproduction at HERA and the Color Evaporation Model (at H1, DESY, Germany)
  • Ph.D. (2005) degree at National Taiwan University, Taipei, Thesis title: Rare B meson decays with an η’ in the final state


Previous work experience

  • Postdoctorate position at the National United University, Taiwan (stationed at NTU, Taiwan, and Belle, KEK, Japan)

  • Research-Fellow of the Japanese Society for the Promotion of Science (JSPS) and Feodor Lynen Research Fellow (Alexander v. Humboldt Foundation) at Belle, KEK, Japan, related work: DAQ expert, B→ hadron hadron analysis

  • Project Researcher at the Institute for the Physics and Mathematics of the Universe, Tokyo University, Japan, Topic: Upgrading the Super-Kamiokande neutrino detector

  • Research Fellow, Massachusetts General Hospital and  Harvard Medical School, Topic: Creating an easy to use Tool for Particle Simulations for medical physics and particle therapy


 Honors and Scholarships

  • Winner of the “Jugend forscht” (Youth research) competition, Hamburg,Germany, Topic: Strange planetoid orbits in double star systems

  • Scholarship of the Friedrich-Ebert Foundation (FES, Germany)

  • Scholarship of the Deutscher Akademischer Austausch-Dienst (DAAD, German academic exchange office, Germany)

  • Ministry of Education Scholarship to outstanding  Foreign Students (Taiwan)

  • Fellowship from the Japanese Society for the Promotion of Science (JSPS) and Feodor Lynen research fellowship from the Alexander v. Humboldt Foundation

  • Poster Prize for Best Poster in the category of Physics, 52nd Annual Conference of the Particle Therapy Co-Operative Group (PTCOG)

  • Best in Physics Prize and ASTRO (American Society for Radiation Oncology) in 2014 & 2015 and Travel Grant for the ASTRO annual meeting (2014)
  • Early Career Investigator Conference Award from the Radiation Research Society
  • Michael Fry Research Award, Radiation Research Society (2018)
  • Damon Runyon-Rachleff Innovation Award (2019)


Recent publication of importance to the field

  1. Akagi R, Aso T, Faddegon B, Kimura A, Matsufuji N, Nishio T, Omachi C, Paganetti H, Perl J, Sasaki T, Sawkey D, Schuemann J, Shin J, Toshito T, Yamashita T, Yoshida H. The PTSim and TOPAS Projects, bringing Geant4 to the Particle Therapy Clinic. Progress in Nuclear Science and Technology. 2011;(2):912-917.
  2. Schuemann J, Paganetti H, Shin J, Faddegon B, Perl J. Efficient voxel navigation for proton therapy dose calculation in TOPAS and Geant4. Phys Med Biol. 2012;57(11):3281-3293. PMID: 22572154. PMCID: PMC3367506.
  3. Shin J, Perl J, Schuemann J, Paganetti H, Faddegon B. A modular method to handle multiple time-dependent quantities in Monte Carlo simulations. Phys Med Biol. 2012;57(11):3295-3308. PMID: 22572201. PMCID: PMC4477630.
  4. Carabe A, Moteabbed M, Depauw N, Schuemann J, Paganetti H. Range uncertainty in proton therapy due to variable biological effectiveness. Phys Med Biol. 2012;57(5):1159-1172. PMID: 22330133. DOI: 1088/0031-9155/57/5/1159.
  5. Butterworth KT, McGarry CK, Clasie B, Carabe-Fernandez A, Schuemann J, Depauw N, Tang S, McMahon SJ, Schettino G, O'Sullivan JM, Lu HM, Kooy H, Paganetti H, Hounsell AR, Held KD, Prise KM. Relative biological effectiveness (RBE) and out-of-field cell survival responses to passive scattering and pencil beam scanning proton beam deliveries. Phys Med Biol. 2012;57(20):6671-6680. PMID: 23022765. DOI: 1088/0031-9155/57/20/6671.
  6. Perl J, Shin J, Schuemann J, Faddegon B, Paganetti H. TOPAS: an innovative proton Monte Carlo platform for research and clinical applications. Med Phys. 2012;39(11):6818-6837. PMID: 23127075. PMCID: PMC3493036.
  7. Jia X, Schuemann J, Paganetti H, Jiang SB. GPU-based fast Monte Carlo dose calculation for proton therapy. Phys Med Biol. 2012;57(23):7783-7797. PMID: 23128424. PMCID: PMC4474737.
  8. Ramos-Méndez J, Perl J, Faddegon B, Schumann J, Paganetti H. Geometrical splitting technique to improve the computational efficiency in Monte Carlo calculations for proton therapy. Med Phys. 2013;40(4):041718. PMID: 23556888.
  9. Bueno M, Paganetti H, Duch MA, Schuemann J. An algorithm to assess the need for clinical Monte Carlo dose calculation for small proton therapy fields based on quantification of tissue heterogeneity. Med Phys. 2013;40(8):081704. PMID: 23927301. PMCID: PMC3618101.
  10. Testa M*, Schumann J*, Lu HM, Shin J, Faddegon B, Perl J, Paganetti H. Experimental validation of the TOPAS Monte Carlo system for passive scattering proton therapy. Med Phys. 2013;40(12):121719. PMID: 24320505. PMCID: PMC4109425. *both authors contributed equally
  11. Schuemann J, Dowdell S, Grassberger C, Min CH, Paganetti H, Site-specific range uncertainties caused by dose calculation algorithms for proton therapy. Phys Med Biol. 2014;59(15):4007-4031. PMID: 24990623. PMCID: PMC4136435.
  12. Testa M, Min CH, Verburg J, Schuemann J, Lu HM, Paganetti H. Range verification of passively scattered proton beams based on prompt gamma time patterns. Phys Med Biol. 2014;59(15):4181-4195. PMID: 25004257.DOI: 1088/0031-9155/59/15/4181.
  13. Lin Y, McMahon SJ, Scarpelli M, Paganetti H, Schuemann J. Comparing gold nano-particle enhanced radiotherapy with protons, megavoltage photons and kilovoltage photons: a Monte Carlo simulation. Phys Med Biol. 2014;59(24):7675-7689. PMID: 25415297. DOI: 1088/0031-9155/59/24/7675.
  14. Moteabbed M, Schuemann J, Paganetti H. Dosimetric feasibility of real-time MRI-guided proton therapy. Med Phys. 2014;41(11):111713. PMID: 25370627. PMCID: PMC4209014.
  15. Giantsoudi D*, Schuemann J*, Jia X, Dowdell S, Jiang S, Paganetti H. Validation of a GPU-based Monte Carlo code (gPMC) for proton radiation therapy: clinical cases study. Phys Med Biol. 2015;60(6):2257-2269. PMID: 25715661. DOI: 1088/0031-9155/60/6/2257. *both authors contributed equally
  16. Lin Y, McMahon SJ, Paganetti H, Schuemann J. Biological modeling of gold nanoparticle enhanced radiotherapy for proton therapy. Phys Med Biol. 2015;60(10):4149-4168. PMID: 25953956. DOI: 1088/0031-9155/60/10/4149.
  17. Polster L, Schuemann J, Rinaldi I, Burigo L, McNamara AL, Stewart RD, Attili A, Carlson DJ, Sato T, Ramos Méndez J, Faddegon B, Perl J, Paganetti H. Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endpoints. Phys Med Biol. 2015;60(13):5053-5070. PMID: 26061666.PMCID: PMC4511084.
  18. Méndez JR, Perl J, Schuemann J, Shin J, Paganetti H, Faddegon B. Improved efficiency in Monte Carlo simulation for passive-scattering proton therapy. Phys Med Biol. 2015;60(13):5019-5035. PMID: 26061457.PMCID: PMC4498399
  19. Ramos-Méndez J, Perl J, Schuemann J, Shin J, Paganetti H, Faddegon B. A framework for implementation of organ effect models in TOPAS with benchmarks extended to proton therapy. Phys Med Biol. 2015;60(13):5037-5052. PMID: 26061583.
  20. Schuemann J*, Giantsoudi D*, Grassberger C, Moteabbed M, Min CH, Paganetti H. Assessing the clinical impact of approximations in analytical dose calculations for proton therapy. Int J Radiat Oncol Biol Phys. 2015;92(5):1157-1164. PMID: 26025779. PMCID: PMC4498397. *both authors contributed equally
  21. Verburg J, Grassberger C, Dowdell S, Schuemann J, Seco J, Paganetti H. Automated Monte Carlo simulation of proton therapy treatment plans. Technol Cancer Res Treat. 2016;15(6):NP35-NP46. PMID: 26596915.
  22. Lin YT, Paganetti H, McMahon S, Schuemann J. Gold nanoparticle induced vasculature damage in radiotherapy: Comparing protons, megavoltage photons, and kilovoltage photons. Med Phys. 2015;42(10):5890-5902. PMID: 26429263. DOI: 1177/1533034615614139.
  23. McNamara A, Schuemann J, Paganetti H. A phenomenological relative biological effectiveness (RBE) model for proton therapy based on all published in vitro cell survival data. Phys Med Biol. 2015;60(21):8399-8416. PMID: 26459756. PMCID: PMC4634882.
  24. Geng C, Moteabbed M, Xie Y, Schuemann J, Yock T, Paganetti H. Assessing the radiation-induced second cancer risk in proton therapy for pediatric brain tumors: the impact of employing a patient-specific aperture in pencil beam scanning. Phys Med Biol. 2016;61(1):12-22. PMID: 26605679. DOI: 1088/0031-9155/61/1/12.
  25. McNamara AL, Kam WWY, Scales N, McMahon SJ, Bennett JW, Byrne HL, Schuemann J, Paganetti H, Banati R, Kuncic Z. Dose enhancement effects to the nucleus and mitochondria from gold nanoparticles in the cytosol. Phys Med Biol. 2016;61(16):5993-6010. PMID: 27435339. PMCID: PMC4993038.
  26. Qin N, Botas P, Giantsoudi D, Schuemann J, Tian Z, Jiang SB, Paganetti H, Jia X. Recent developments and comprehensive evaluations of a GPU-based Monte Carlo package for proton therapy. Phys Med Biol. 2016;61(20):7347-7362. PMID: 27694712. PMCID: PMC5378691.
  27. McMahon S, Schuemann J, Paganetti H, Prise K. Mechanistic modelling of DNA repair and cellular survival following radiation-induced DNA damage. Sci Rep. 2016;6:33290. PMID: 27624453. PMCID: PMC5022028.
  28. Geng C, Daartz J, Lam-Tin-Cheung K, Bussiere M, Shih HA, Paganetti H, Schuemann J. Limitations of analytical dose calculations for small field proton radiosurgery. Phys Med Biol. 2017;62(1):246-257. PMID: 27991438. DOI: 1088/1361-6560/62/1/246.
  29. McMahon SJ, McNamara AL, Schuemann J, Prise KM, Paganetti H. Mitochondria as a target for radiosensitisation by gold nanoparticles. Journal of Physics: Conference Series. 2016;777(1):
  30. McNamara A, Geng C, Turner R, Mendez JR, Perl J, Held K, Faddegon B, Paganetti H, Schuemann J. Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries. Phys Med. 2017; 33:207-215. PMID: 28017738. PMCID: PMC5292291.
  31. Underwood TSA, Sung W, McFadden CH, McMahon SJ, Hall DC, McNamara AL, Paganetti H, Sawakuchi G, Schuemann J. Comparing stochastic proton interactions simulated using TOPAS-nBio to experimental data from fluorescent nuclear track detectors. Phys Med Biol. 2017; 62(8):3237-3249. PMID: 28350546. DOI: 1088/1361-6560/aa6429.
  32. Sung W, Ye SJ, McNamara A, McMahon S, Hainfeld J, Shin J, Smilowitz H, Paganetti H, Schuemann J.Dependence of gold nanoparticle radiosensitization on cell geometry. Nanoscale. 2017;9(18):5843-5853. PMID: 28429022. PMCID: PMC5526329.
  33. Sung W, Ye SJ, McNamara A, McMahon S, Hainfeld J, Shin J, Smilowitz H, Paganetti H, Schuemann J.Correction: Dependence of gold nanoparticle radiosensitization on cell geometry. Nanoscale. 2017;9(18):11338. PMID: 28758663. DOI: 1039/c7nr90158e.
  34. Ramos-Mendez J, Schuemann J, Incerti S, Paganetti H, Schulte R, Faddegon B. Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations. Phys Med Biol. 2017;62(15):5908-5925. PMID: 28594336. PMCID: PMC5785278.
  35. McMahon SJ, McNamara AL, Schuemann J, Paganetti H, Prise KM. A general mechanistic model enables predictions of the biological effectiveness of different qualities of radiation. Sci Rep. 2017;7(1):10790. PMID: 28883414. PMCID: PMC5589818
  36. Meyer J, Stewart R, Smith D, Eagle J, Lee E, Cao N, Ford E, Hashemian R, Schuemann J, Saini J, Marsh S, Emery R, Dorman E, Schwartz J, Sandison G. Biological and dosimetric characterisation of spatially fractionated proton minibeams. Phys Med Biol. 2017; 62(24), 9260-9281. PMID: 29053105. DOI: 1088/1361-6560/aa950c.
  37. Toltz A, Hosl M, Schuemann J, Lu HM, Paganetti H, Seuntjes J. Time-resolved diode dosimetry calibration through Monte Carlo modeling for in vivo passive scattered proton therapy range verification. J Appl Clin Med Phys. 2017; 18(6): 200-205. PMID: 29082601. PMCID: PMC5689909.
  38. Ramos-Mendez J, Perl J, Schuemann J, McNamara A, Paganetti H, Faddegon B. Monte Carlo simulation of chemistry following radiolysis with TOPAS-nBio. Phys Med Biol. 2018; 63(10): 105014. PMID: 29697057. PMCID: PMC6027650.
  39. Yang C, Bromma K, Sung W, Schuemann J, Chithrani D. Determining the radiation enhancement effects of gold nanoparticles in cells in a combined treatment with Cisplatin and radiation at therapeutic megavoltage energies. Cancers(Basel). 2018; 10(5): 150. PMID: 29786642. PMCID: PMC5977123.
  40. Sung W, Schuemann J. Energy Optimization in Gold Nanoparticle Enhanced Radiation Therapy. Phys. Med. Biol. 2018; 63(13): 135001. PMID: 29873303, PMCID: PMC6040581.
  41. McNamara A, Ramos Mendez J, Perl j, Held K, Dominguez N, Moreno E, Henthorn N, Kirkby K, Meylan S, Villagrasa, C, Incerti S, Faddegon B, Paganetti H, Schuemann J. Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit. Phys Med Biol. 2018; 63(17): 175018. PMID: 30088810. PMCID: PMC6176684.
  42. Schuemann J, McNamara AL, Warmenhoven J, et al. (55 authors). A new Standard DNA Damage (SDD) data format. Radiat. Res. 2019; 191(1):76. PMID: 30407901. PMCID: PMC6407706.
  43. Sung W, Jeong Y, Kim H, Jeong H, Grassberger C, Jung S, Ahn GO, Kim IH, Schuemann J, Lee K, Ye SJ. Computational Modeling and Clonogenic Assay for Radioenhancement of Gold Nanoparticles using 3D live cell images. Rad Res. 2018; 190(5): 558-564. PMID: 30142031. PMCID: PMC6258025.
  44. Schuemann J, Ramos-Méndez J, Perl J, Held KD, Paganetti H, Incerti S, Faddegon B. TOPAS-nBio – An extension to the TOPAS simulation toolkit for cellular and sub-cellular radiobiology. Rad. Res. 2019; 191(2): 125-138. PMID: 30609382. PMCID: PMC6377808.
  45. Newpower M, Schuemann J, Mohan R, Paganetti H, Titt U. Comparing 2 Monte Carlo Systems in Use for Proton Therapy Research. Int J Particle Ther. (2019);
  46. Bromma K, Rieck K, Kulkarni J, O’Sullivan C, Sung W, Cullis P, Schuemann J, Chithrani D. Use of a lipid nanoparticle system as a Trojan horse in delivery of gold nanoparticles to human breast cancer cells for improved outcomes in radiation therapy. Cancer Nanotechnology (2019); 10: 1.
  47. Abhyankar YS, Dev S, Sarun OS, Saxena A, Joshi R, Darbari H, Sajish C, Sonoavane UB, Gavane V, Deshpande A, Dixit T, Harsh R, Badwe R, Rath GK, Laskar S, Faddegon B, Perl J, Paganetti H, Schuemann J, Srivastava A, Obcemea C, Nath AK, Sharma A, Buchsbaum J. Monte Carlo Processing on a Chip (MCoaC) – preliminary experiments towards the realization of optimal-hardware for TOPAS/Geant4 to drive discovery. Physica Medica (2019); 64; 166.
  48. Zhu H, Chen Y, Sung W, McNamara A, Tran T, Burigo L, Rosenfeld A, Li J, Faddegon B, Schuemann J, Paganetti H. The microdosimetric extension in TOPAS: Development and comparison with published data. Phys. Med. Biol. (2019); 64(14); 145004. PMID: 31117056. PMCID: PMC7182072.
  49. Marteinsdottir M, Schuemann J, Paganetti H. Impact of uncertainties in range and RBE on small field proton therapy. Phys. Med. Biol. (2019); 64(20); 205005. PMID: 31519016. DOI: 1088/1361-6560/ab448f.
  50. Rudek B, McNamara A, Ramos-Méndez J, Byrne H, Kuncic Z, Schuemann J. Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams. Phys Med Biol. 2019; 64(17); 175005; PMID: 31295730. DOI: 1088/1361-6560/ab314c.
  51. Rieck K, Bromma K, Sung W, Bannister A, Schuemann J, Chithrani DB. Modulation of gold nanoparticle mediated radiation dose enhancement through synchronization of breast tumor cell population. Br J Radiol. 2019; 92(1100); 20190283. PMID:31219711. PMCID: PMC6724617.
  52. Li WB, Belchior A, Beuve M, Chen YZ, DiMaria S, Friedland W, Gervais B, Heide B, Hocine N, Ipatov A, Klapproth AP, Li CY, Li JL, Multhoff G, Poignant F, Qui R, Rabus H, Rudek B, Schuemann J, Stangl S, Testa E, Villagrasa C, Xie WZ, Zhang YB. Intercomparison of dose enhancement ratio and secondary electron spectra for gold nanoparticles irradiated by x-rays calculated using multiple Monte Carlo simulation codes; Phys. Med. 2020; 69; 147-63, PMID: 31918367. DOI: 1016/j.ejmp.2019.12.011.
  53. Bannister A, Bromma K, Sung W, Mesa M, Cicon L, Howard P, Chow B, Schuemann J, Chithrani DB. Modulation of nanoparticle uptake, intracellular distribution, and retention with docetaxel to enhance radiotherapy. Br J Radiol. 2019; 20190742, PMID: 31778316. PMCID: PMC7055427.
  54. Wang CC, McNamara AL, Shin J, Schuemann J, Grassberger C, Taghian AG, Jimenez RB, MacDonald SM, Paganetti H. End-of-Range Radiobiological Effect on Rib Fractures in Patients Receiving Proton Therapy for Breast Cancer, Int. J Radiat. Oncol. Biol. Phys, 2020,107(3):449-454, PMID:32240774. PMCID: PMC7293563.
  55. Schuemann J, Bagley A, Berbeco R, Bromma K, Butterworth KT, Byrne H, Chithrani DB, Cho SH, = Cook JR, Favaudon V, Gholami YH, Gargioni E, Hainfeld JF, Hespeels F, Heuskin AC, Ibeh UM, Kuncic Z, Kunjachan S, Lacombe S, Lucas S, Lux F, McMahon SJ, Nevozhay D, Ngwa W, Payne JD, Penninckx S, Porcel S, Prise KM, Rabus H, Ridwan SM, Rudek B, Sanche L, Singh B, Smilowitz HM, Konstantin V Sokolov, Srinivas Sridhar, Yaroslav Stanishevskiy, Wonmo Sung, Olivier Tillement, Virani NA, Yantasee W, Krishnan S, Roadmap for metal nanoparticles in radiation therapy: current status, translational challenges, and future directions, Phys. Med. Biol., 2020, (online ahead of print), PMID: DOI: 10.1088/1361-6560/ab9159.
  56. Zhu H, McNamara AL, McMahon SJ, Ramos-Mendez J, Henthorn NT, Faddegon BA, Held KD, Perl J, Li J, Paganetti H, Schuemann J. Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio. Rad. Res., 2020, 194(1): 9-21, PMID: DOI: 10.1667/RR15531.1.
  57. Zhu H, McNamara AL, Ramos-Mendez J, McMahon SJ, Henthorn NT, Faddegon BA, Held KD, Perl J, Li J, Paganetti H, Schuemann J. A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio. Phys. Med. Biol, 2020, 65(8): 085015, PMID: 32101803. DOI: 1088/1361-6560/ab7a6b.
  58. Ramos-Méndez J, Schuemann J, Domínguez-Kondo N, McNamara AL, Moreno-Barbosa E, Faddegon B. LET-Dependent Intertrack Yields in Proton Irradiation at Ultra-High Dose Rates Relevant for FLASH Therapy. Rad. Res., 2020, 194 (4): 351–362. PMID: DOI: 10.1667/RADE-20-00084.1.
  59. ZhangQZ, CascioE, LiCM, YangQY, GerweckL, HuangP, GottschalkB, FlanzJ, Schuemann J. FLASH investigations using protons: Design of delivery system, pre-clinical setup and confirmation of FLASH effect with protons in animal systems, Rad. Res., 2020, 194(6):656-664. PMID: DOI: 10.1667/RADE-20-00068.1.
  60. Niemierko A*, Schuemann J*, Niyazi M, Giantsoudi D, Maquilan G, Shih HA, Paganetti H. Brain Necrosis in Adult Patients After Proton Therapy: Is There Evidence for Dependency on Linear Energy Transfer? Int. J. Radiat. Oncol. Biol., 2021, 109(1):109-119, PMID:32911019, DOI: 1016/j.ijrobp.2020.08.058. *both authors contributed equally.
  61. Stainforth R, Schuemann J, McNamara AL, Wilkins RC, Chauhan V. Challenges in the quantification approach to a radiation relevant adverse outcome pathway for lung cancer. Int. J. Rad. Biol., 2021, 97(1): 85-101, PMID 32909875, DOI: 1080/09553002.2020.1820096.
  62. Faddegon B, Ramos-Mendez J, Schuemann J, McNamara A, Shin J, Perl J, Paganetti H. The TOPAS tool for particle simulation, a Monte Carlo simulation tool for physics, biology and clinical research. Phys. Med., 2020, 72:114-121. PMID: 32247964. PMCID: 7192305. DOI: 1016/j.ejmp.2020.03.019.
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