Jose Ramos-Mendez, PhD
Assistant Professor
Radiation Oncology
School of Medicine

Dr. Ramos-Méndez is an internationally recognized researcher in the field of Monte Carlo for radiation therapy. His research focuses on the development of the Monte Carlo simulation frameworks Geant4, TOPAS, TOPAS-nBio and TOPAS-tissue. Those frameworks facilitate the simulations for radiation therapy research and investigate the connection between physics and biology at the sub-cellular, cellular and multi-cellular scale.

• Lithium inelastic cross-sections and their impact on micro and nano dosimetry of boron neutron capture.
  Physics in medicine and biology 2024 D-Kondo N, Ortiz R, Faddegon B, Incerti S, Tran HN, Francis Z, Moreno Barbosa E, Schuemann J, Ramos-Méndez J
• Review of chemical models and applications in Geant4-DNA: Report from the ESA BioRad III Project.
  Medical physics 2024 Tran HN, Archer J, Baldacchino G, Brown JMC, Chappuis F, Cirrone GAP, Desorgher L, Dominguez N, Fattori S, Guatelli S, Ivantchenko V, Méndez JR, Nieminen P, Perrot Y, Sakata D, Santin G, Shin WG, …
• Corrigendum to "Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA" [Phys. Med. 105 (2023) 102508].
  Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) 2024 Sakata D, Hirayama R, Shin WG, Belli M, Tabocchini MA, Stewart RD, Belov O, Bernal MA, Bordage MC, Brown JMC, Dordevic M, Emfietzoglou D, Francis Z, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, …
• TOPAS simulation of photoneutrons in radiotherapy: accuracy and speed with variance reduction.
  Physics in medicine and biology 2024 Ramos-Mendez J, Ortiz CR, Schuemann J, Paganetti H, Faddegon B
• A digital male pelvis phantom series showing anatomical variations over the course of fractionated radiotherapy treatment.
  Medical physics 2023 Faddegon B, Descovich M, Chen K, Ramos-Méndez J, Iii MR, Wahl N, Taylor P, Griffin K, Lee C
• Cellular lethal damage of 64Cu incorporated in mammalian genome evaluated with Monte Carlo methods.
  Frontiers in medicine 2023 Carrasco-Hernandez J, Ramos-Méndez J, Padilla-Rodal E, Avila-Rodriguez MA
• Ionization detail parameters and cluster dose: a mathematical model for selection of nanodosimetric quantities for use in treatment planning in charged particle radiotherapy.
  Physics in medicine and biology 2023 Faddegon B, Blakely EA, Burigo L, Censor Y, Dokic I, Domínguez Kondo N, Ortiz R, Ramos Méndez J, Rucinski A, Schubert K, Wahl N, Schulte R
• GEANT4-DNA simulation of temperature-dependent and pH-dependent yields of chemical radiolytic species.
  Physics in medicine and biology 2023 Bian J, Duran J, Shin WG, Ramos-Méndez J, Sankey JC, Childress L, Seuntjens J, Enger SA
• An integrated Monte Carlo track-structure simulation framework for modeling inter and intra-track effects on homogenous chemistry.
  Physics in medicine and biology 2023 D-Kondo JN, Garcia-Garcia OR, LaVerne JA, Faddegon B, Schuemann J, Shin WG, Ramos-Méndez J
• Dosimetric characterization of single- and dual-port temporary tissue expanders for postmastectomy radiotherapy using Monte Carlo methods.
  Frontiers in oncology 2023 Ramos-Méndez J, Park C, Sharma M
• Microdosimetric Analysis for Boron Neutron Capture Therapy via Monte Carlo Track Structure Simulation with Modified Lithium Cross-sections.
  Radiation physics and chemistry (Oxford, England : 1993) 2023 Han Y, Geng C, D-Kondo JN, Li M, Ramos-Méndez J, Altieri S, Liu Y, Tang X
• TOPAS-imaging: extensions to the TOPAS simulation toolkit for medical imaging systems.
  Physics in medicine and biology 2023 Lee H, Cheon BW, Feld JW, Grogg K, Perl J, Ramos-Méndez JA, Faddegon B, Min CH, Paganetti H, Schuemann J
• Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA.
  Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) 2022 Sakata D, Hirayama R, Shin WG, Belli M, Tabocchini MA, Stewart RD, Belov O, Bernal MA, Bordage MC, Brown JMC, Dordevic M, Emfietzoglou D, Francis Z, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, …
• Impact of DNA Geometry and Scoring on Monte Carlo Track-Structure Simulations of Initial Radiation-Induced Damage.
  Radiation research 2022 Bertolet A, Ramos-Méndez J, McNamara A, Yoo D, Ingram S, Henthorn N, Warmenhoven JW, Faddegon B, Merchant M, McMahon SJ, Paganetti H, Schuemann J
• TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields.
  Physics in medicine and biology 2022 Ramos-Méndez J, García-García O, Domínguez-Kondo J, LaVerne JA, Schuemann J, Moreno-Barbosa E, Faddegon B
• DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions.
  Physics in medicine and biology 2021 D-Kondo N, Moreno-Barbosa E, Štephán V, Stefanová K, Perrot Y, Villagrasa C, Incerti S, De Celis Alonso B, Schuemann J, Faddegon B, Ramos-Méndez J
• TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation.
  Physics in medicine and biology 2021 Ramos-Méndez J, LaVerne JA, Domínguez-Kondo N, Milligan J, Štepán V, Stefanová K, Perrot Y, Villagrasa C, Shin WG, Incerti S, McNamara A, Paganetti H, Perl J, Schuemann J, Faddegon B
• The relation between microdosimetry and induction of direct damage to DNA by alpha particles.
  Physics in medicine and biology 2021 Bertolet A, Ramos-Méndez J, Paganetti H, Schuemann J
• Geant4-DNA simulation of the pre-chemical stage of water radiolysis and its impact on initial radiochemical yields.
  Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) 2021 Shin WG, Ramos-Mendez J, Tran NH, Okada S, Perrot Y, Villagrasa C, Incerti S
• Development of Ultra-High Dose-Rate (FLASH) Particle Therapy.
  IEEE transactions on radiation and plasma medical sciences 2021 Kim MM, Darafsheh A, Schuemann J, Dokic I, Lundh O, Zhao T, Ramos-Méndez J, Dong L, Petersson K
• Publisher's Note: "Dispersion calibration for the National Ignition Facility electron-positron-proton spectrometers for intense laser matter interactions" [Rev. Sci. Instrum. 92, 033516 (2021)].
  The Review of scientific instruments 2021 von der Linden J, Ramos-Mendez J, Faddegon B, Massin D, Fiksel G, Holder JP, Willingale L, Peebles J, Edwards MR, Chen H
• On the Equivalence of the Biological Effect Induced by Irradiation of Clusters of Heavy Atom Nanoparticles and Homogeneous Heavy Atom-Water Mixtures.
  Cancers 2021 Villagomez-Bernabe B, Ramos-Méndez J, Currell FJ
• Validation of the TOPAS Monte Carlo toolkit for HDR brachytherapy simulations.
  Brachytherapy 2021 Berumen F, Ma Y, Ramos-Méndez J, Perl J, Beaulieu L
• Boronated Condensed DNA as a Heterochromatic Radiation Target Model.
  Biomacromolecules 2021 Perry CC, Ramos-Méndez J, Milligan JR
• Dispersion calibration for the National Ignition Facility electron-positron-proton spectrometers for intense laser matter interactions.
  The Review of scientific instruments 2021 von der Linden J, Ramos-Méndez J, Faddegon B, Massin D, Fiksel G, Holder JP, Willingale L, Peebles J, Edwards MR, Chen H
• Assessment of DNA damage with an adapted independent reaction time approach implemented in Geant4-DNA for the simulation of diffusion-controlled reactions between radio-induced reactive species and a chromatin fiber.
  Medical physics 2020 Tran HN, Ramos-Méndez J, Shin WG, Perrot Y, Faddegon B, Okada S, Karamitros M, Davídková M, Štepán V, Incerti S, Villagrasa C
• Report on G4-Med, a Geant4 benchmarking system for medical physics applications developed by the Geant4 Medical Simulation Benchmarking Group.
  Medical physics 2020 Arce P, Bolst D, Bordage MC, Brown JMC, Cirrone P, Cortés-Giraldo MA, Cutajar D, Cuttone G, Desorgher L, Dondero P, Dotti A, Faddegon B, Fedon C, Guatelli S, Incerti S, Ivanchenko V, Konstantinov D, …
• Independent reaction times method in Geant4-DNA: Implementation and performance.
  Medical physics 2020 Ramos-Méndez J, Shin WG, Karamitros M, Domínguez-Kondo J, Tran NH, Incerti S, Villagrasa C, Perrot Y, Štepán V, Okada S, Moreno-Barbosa E, Faddegon B
• Monte Carlo simulation of the effect of magnetic fields on brachytherapy dose distributions in lung tissue material.
  PloS one 2020 Moreno-Barbosa F, de Celis-Alonso B, Moreno-Barbosa E, Hernández-López JM, Geoghegan T, Ramos-Méndez J
• LET-Dependent Intertrack Yields in Proton Irradiation at Ultra-High Dose Rates Relevant for FLASH Therapy.
  Radiation research 2020 Ramos-Méndez J, Domínguez-Kondo N, Schuemann J, McNamara A, Moreno-Barbosa E, Faddegon B
• Monte Carlo track-structure for the radionuclide Copper-64: characterization of S-values, nanodosimetry and quantification of direct damage to DNA.
  Physics in medicine and biology 2020 Carrasco-Hernández J, Ramos-Méndez J, Faddegon B, Jalilian AR, Moranchel M, Ávila-Rodríguez MA
• Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio.
  Radiation research 2020 Zhu H, McNamara AL, McMahon SJ, Ramos-Mendez J, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J
• Report on G4‐Med, a Geant4 benchmarking system for medical physics applications developed by the Geant4 Medical Simulation Benchmarking Group
  Medical Physics 2020 Arce, P. Bolst, D. Cutajar, D. Guatelli, S. Le, A. Rosenfeld, A.B. Sakata, D. Bordage, M-C. Brown, J.M.C. Cirrone, P. Cuttone, G. Pandola, L. Petringa, G. Cort?s-Giraldo, M.A. Quesada, J.M. Desorgher, L. Dondero, P. Mantero, A. Dotti, A. Wright, D.H. Faddegon, B. Ramos-M?ndez, J. Fedon, C. Incerti, S. Ivanchenko, V. Konstantinov, D. Latyshev, G. Kyriakou, I. Mancini-Terracciano, C. Maire, M. Novak, M. Omachi, C. Toshito, T. Perales, A. Perrot, Y. Romano, F. Sarmiento, L.G. Sasaki, T. Sechopoulos, I. Simpson, E.C.
• A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio.
  Physics in medicine and biology 2020 Zhu H, McNamara AL, Ramos-Mendez J, McMahon SJ, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J
• The TOPAS tool for particle simulation, a Monte Carlo simulation tool for physics, biology and clinical research.
  Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) 2020 Faddegon B, Ramos-Méndez J, Schuemann J, McNamara A, Shin J, Perl J, Paganetti H
• DNA Condensation with a Boron-Containing Cationic Peptide for Modeling Boron Neutron Capture Therapy.
  Radiation physics and chemistry (Oxford, England : 1993) 2019 Perry CC, Ramos-Méndez J, Milligan JR
• Evaluation of the influence of physical and chemical parameters on water radiolysis simulations under MeV electron irradiation using Geant4-DNA
  Journal of Applied Physics 2019 W.-G. Shin, J. Ramos-Méndez, B. Faddegon, H. N. Tran, C. Villagrasa, Y. Perrot, S. Okada, M. Karamitros, D. Emfietzoglou, I. Kyriaku, M. C. Bordage, D. Sakata, S. Guatelli, H. J. Choi, C. H. Min, S. B…
• Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams.
  Physics in medicine and biology 2019 Rudek B, McNamara A, Ramos-Méndez J, Byrne H, Kuncic Z, Schuemann J
• Monte Carlo geometry modeling for particle transport using conformal geometric algebra
  Advances in Applied Clifford Algebras 2019 E. Ulises Moya-Sánchez, A. Moisés Maciel-Hernández, Adrian S. Niebla, José Ramos-Méndez and Oscar Carbajal-Espinosa
• Simultaneous optimization of RBE-weighted dose and nanometric ionization distributions in treatment planning with carbon ions.
  Physics in medicine and biology 2019 Burigo LN, Ramos-Méndez J, Bangert M, Schulte RW, Faddegon B
• TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology.
  Radiation research 2019 Schuemann J, McNamara AL, Ramos-Méndez J, Perl J, Held KD, Paganetti H, Incerti S, Faddegon B
• Fast calculation of nanodosimetric quantities in treatment planning of proton and ion therapy.
  Physics in medicine and biology 2018 Ramos-Méndez J, Burigo LN, Schulte R, Chuang C, Faddegon B
• A New Standard DNA Damage (SDD) Data Format.
  Radiation research 2018 Schuemann J, McNamara AL, Warmenhoven JW, Henthorn NT, Kirkby KJ, Merchant MJ, Ingram S, Paganetti H, Held KD, Ramos-Mendez J, Faddegon B, Perl J, Goodhead DT, Plante I, Rabus H, Nettelbeck H, …
• Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit.
  Physics in medicine and biology 2018 McNamara AL, Ramos-Méndez J, Perl J, Held K, Dominguez N, Moreno E, Henthorn NT, Kirkby KJ, Meylan S, Villagrasa C, Incerti S, Faddegon B, Paganetti H, Schuemann J
• Helium CT: Monte Carlo simulation results for an ideal source and detector with comparison to proton CT.
  Medical physics 2018 Piersimoni P, Faddegon BA, Méndez JR, Schulte RW, Volz L, Seco J
• Monte Carlo simulation of chemistry following radiolysis with TOPAS-nBio.
  Physics in medicine and biology 2018 Ramos-Méndez J, Perl J, Schuemann J, McNamara A, Paganetti H, Faddegon B
• Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations.
  Physics in medicine and biology 2017 Ramos-Méndez J, Schuemann J, Incerti S, Paganetti H, Schulte R, Faddegon B
• The effect of beam purity and scanner complexity on proton CT accuracy.
  Medical physics 2017 Piersimoni P, Ramos-Méndez J, Geoghegan T, Bashkirov VA, Schulte RW, Faddegon BA
• Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries.
  Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB) 2016 McNamara A, Geng C, Turner R, Mendez JR, Perl J, Held K, Faddegon B, Paganetti H, Schuemann J
• Dose assessment for the fetus considering scattered and secondary radiation from photon and proton therapy when treating a brain tumor of the mother.
  Physics in medicine and biology 2015 Geng C, Moteabbed M, Seco J, Gao Y, Xu XG, Ramos-Méndez J, Faddegon B, Paganetti H
• Experimental depth dose curves of a 67.5 MeV proton beam for benchmarking and validation of Monte Carlo simulation.
  Medical physics 2015 Faddegon BA, Shin J, Castenada CM, Ramos-Méndez J, Daftari IK
• A framework for implementation of organ effect models in TOPAS with benchmarks extended to proton therapy.
  Physics in medicine and biology 2015 Ramos-Méndez J, Perl J, Schümann J, Shin J, Paganetti H, Faddegon B
• Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endpoints.
  Physics in medicine and biology 2015 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
• Improved efficiency in Monte Carlo simulation for passive-scattering proton therapy
  Improved efficiency in Monte Carlo simulation for passive-scattering proton therapy 2015 J Ramos Méndez, J Perl, J Schümann, J Shin, H Paganetti, B Faddegon
• Geometrical splitting technique to improve the computational efficiency in Monte Carlo calculations for proton therapy.
  Medical physics 2013 Ramos-Méndez J, Perl J, Faddegon B, Schümann J, Paganetti H
• SU-E-T-478: Geometrical Splitting Technique to Improve the Computational Efficiency in Monte Carlo Calculations for Proton Therapy.
  Medical physics 2012 Ramos-Mendez J, Perl J, Faddegon B, Paganetti H