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José Ramos-Méndez, MS, PhD

Assistant Professor in Residence
Division of Physics
Department of Radiation Oncology

Meet Dr. Ramos-Méndez

I am proud to embark with the UCSF team on a journey to uncover innovative radiotherapy techniques and refine existing treatment approaches that hold the potential to heal and transform lives.

Research Center

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Dr. Ramos-Méndez received his PhD in Applied Physics from Benemérita Universidad Autónoma de Puebla, México, in 2014. From 2014 to 2021, he held appointments as a Postdoctoral Employee and Assistant Researcher at UCSF. He graduated from the UCLA CAMPEP Certificate Program and received his clinical training from the UCSF Medical Physics Residency Program. 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, and TOPAS-nBio. Those frameworks facilitate the simulations for radiation therapy research and investigate the connection between physics and biology at the cell and sub-cellular scale. Dr. Ramos-Méndez enjoys digging into the fundamental physics of radiotherapy but his biggest love is Family Time.

Education

2021-2023	University of California, San Francisco	Medical Physics Residency	Radiation Oncology
2021	University of California, Los Angeles	CAMPEP	Accredited Certificate Program
2013	Benemérita Universidad Autónoma de Puebla	PhD	Applied Physics
2010	Benemérita Universidad Autónoma de Puebla	MS	Applied Physics
2008	Benemérita Universidad Autónoma de Puebla	BS	Applied Physics

Professional Experience

2023-present	Assistant Professor in Residence	University of California, San Francisco	Department of Radiation Oncology
2018-2021	Assistant Professional Researcher	University of California, San Francisco	Department of Radiation Oncology
2014-2018	Postdoctoral Employee	University of California, San Francisco	Department of Radiation Oncology

Awards & Honors

2022	First place in talk	Northern California of the American Association of Physicists in Medicine’s: The Young Investigation Symposium. Category: Residents.
2022	Third place in SLAM talk	Northern California of the American Association of Physicists in Medicine
2021	Scholar-In-Training Feature of the Month	Radiation Research Society
2021	Annual Meeting’s Featured Lectures	Radiation Research Society
2020	Third Place video contest for imaging	NCI/ITCR 2020 Virtual Annual PI meeting
2018	Editor’s pick and front cover	Journal of Radiation Research Vol. 191, No. 2, 2018
2018	Featured article and front cover	International Journal of Medical Physics Vol. 44, No. 1, 2017
2017	Member of the Mexican Research National System (SNI)	Level I, 2018
2016	Member of the Mexican Research National System (SNI)	Level C, 2016
2010-2013	National fellow	CONACyT Mexico
2008-2010	National fellow	CONACyT Mexico

Publications

https://www.ncbi.nlm.nih.gov/myncbi/1dQUhFRaVNDQQ/bibliography/public/

https://orcid.org/0000-0002-8106-5142

D-Kondo J N, Garcia-Garcia O R, LaVerne J A, Faddegon B, Schuemann J, Shin W-G and Ramos-Méndez J 2023 An integrated Monte Carlo track-structure simulation framework for modeling inter and intra-track effects on homogenous chemistry Phys. Med. Biol. 68 125008

Han Y, Geng C, D-Kondo J N, Li M, Ramos-Méndez J, Altieri S, Liu Y and Tang X 2023 Microdosimetric analysis for boron neutron capture therapy via Monte Carlo track structure simulation with modified lithium cross-sections Radiation Physics and Chemistry 209 110956

von der Linden J, Ramos-Méndez J, Faddegon B, Massin D, Fiksel G, Holder J P, Willingale L, Peebles J, Edwards M R and Chen H 2021 Dispersion calibration for the National Ignition Facility electron–positron–proton spectrometers for intense laser matter interactions Review of Scientific Instruments 92 033516

Nanni E, Tantawi S, Loo B, Snively E, Schulte R, Faddegon B, Pankuch M, Li Z, Dolgashev V and Ramos J 2022 FLASH Modalities Track (Oral Presentations) 3D HIGH SPEED RF BEAM SCANNER FOR HADRON THERAPY OF CANCER Physica Medica 94 S45–6

Ramos-Mendez J 2023 Dosimetric characterization of single- and dual-port temporary tissue expanders for postmastectomy radiotherapy using Monte Carlo methods Frontiers in Oncology

Ramos-Mendez J A, LaVerne J A, Domínguez-Kondo J N, Milligan J, Stepan V, Stefanová K, Perrot Y, Villagrasa C, Shin W-G, Incerti S, McNamara A L, Paganetti H, Perl J, Schuemann J and Faddegon B A 2021 TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation Phys. Med. Biol. Online: https://iopscience.iop.org/article/10.1088/1361-6560/ac1f39

Ramos-Méndez J, García-García O, Domínguez-Kondo J, LaVerne J A, Schuemann J, Moreno-Barbosa E and Faddegon B 2022 TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields Phys. Med. Biol. 67 145007

Sakata D, Hirayama R, Shin W-G, Belli M, Tabocchini M A, Stewart R D, Belov O, Bernal M A, Bordage M-C, Brown J M C, Dordevic M, Emfietzoglou D, Francis Z, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, Kyriakou I, Lampe N, Li Z, Meylan S, Michelet C, Nieminen P, Perrot Y, Petrovic I, Ramos-Mendez J, Ristic-Fira A, Santin G, Schuemann J, Tran H N, Villagrasa C and Incerti S 2023 Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA Physica Medica 105 102508

Shin W-G 2021 Geant4-DNA simulation of the pre-chemical stage of water radiolysis and its impact on initial radiochemical yields Physica Medica 5

Tran H N, Ramos‐Méndez J, Shin W, Perrot Y, Faddegon B, Okada S, Karamitros M, Davídková M, Štěpán V, Incerti S and Villagrasa C 2021 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 48 890–901

Villagomez-Bernabe B, Ramos-Méndez J and Currell F J 2021 On the Equivalence of the Biological Effect Induced by Irradiation of Clusters of Heavy Atom Nanoparticles and Homogeneous Heavy Atom-Water Mixtures Cancers 13 2034

Perry CC, Ramos-Méndez J, Milligan JR. Boronated Condensed DNA as a Heterochromatic Radiation Target Model. Biomacromolecules. March 2021:acs.biomac.1c00106. doi:10.1021/acs.biomac.1c00106

von der Linden J, Ramos-Méndez J, Faddegon B, et al. Dispersion calibration for the National Ignition Facility electron–positron–proton spectrometers for intense laser matter interactions. Rev Sci Instrum. 2021;92(3):033516. doi:10.1063/5.0040624

Berumen F, Ma Y, Ramos-Méndez J, et al., “Validation of the TOPAS Monte Carlo toolkit for HDR Brachytherapy Simulations” Brachytherapy. In Press. 2021.

Tran HN, Ramos‐Méndez J, Shin W, et al. 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. Med Phys. 2021;48(2):890-901. doi:10.1002/mp.14612

Ramos‐Méndez J, Shin W, Karamitros M, et al. Independent reaction times method in Geant4‐DNA: Implementation and performance. Med Phys. 2020;47(11):5919-5930. doi:10.1002/mp.14490

Ramos-Méndez J, Domínguez-Kondo N, Schuemann J, McNamara A, Moreno-Barbosa E, Faddegon B. LET-Dependent Intertrack Yields in Proton Irradiation at Ultra-High Dose Rates Relevant for FLASH Therapy. Radiat Res. 2020;194(4):5-7. doi:10.1667/RADE-20-00084.1

Moreno-Barbosa F, de Celis-Alonso B, Moreno-Barbosa E, Hernández-López JM, Geoghegan T, Ramos-Méndez J. Monte Carlo simulation of the effect of magnetic fields on brachytherapy dose distributions in lung tissue material. Zhang R, ed. PLoS One. 2020;15(10):e0238704. doi:10.1371/journal.pone.0238704

Faddegon, B., Ramos-Méndez, J., Schuemann, J., McNamara, A., Shin, J., Perl, J., Paganetti, H., 2020. The TOPAS tool for particle simulation, a Monte Carlo simulation tool for physics, biology and clinical research. Phys. Medica 72, 114–121. https://doi.org/10.1016/j.ejmp.2020.03.019

Carrasco-Hernández J, Ramos-Méndez J, Faddegon B, Jalilian AR, Moranchel M, Ávila-Rodríguez MA. Monte Carlo track-structure for the radionuclide Copper-64: characterization of S-values, nanodosimetry and quantification of direct damage to DNA. Phys Med Biol. 2020;65(15):155005. doi:10.1088/1361-6560/ab8aaa

Arce P, Bolst D, Bordage M, Ramos-Méndez J, et al. Report on G4‐Med, a Geant4 benchmarking system for medical physics applications developed by the Geant4 Medical Simulation Benchmarking Group. Med Phys. 2021;48(1):19-56. doi:10.1002/mp.14226

Zhu H, McNamara AL, McMahon SJ, Ramos-Méndez J, et al. Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio. Radiat Res. 2020;194(1):9. doi:10.1667/RR15531.1

Zhu, H., McNamara, A.L., Ramos-Méndez, J., McMahon, S.J., Henthorn, N.T., Faddegon, B., Held, K.D., Perl, J., Li, J., Paganetti, H., Schuemann, J., 2020. A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio. Phys. Med. Biol. 65, 085015.

Perry C C, Ramos-Méndez J and Milligan J R 2020 DNA condensation with a boron-containing cationic peptide for modeling boron neutron capture therapy. Radiat. Phys. Chem. 166 108521

Shin W-G, Ramos-Méndez J, Faddegon B, Tran H N, Villagrasa C, Perrot Y, Okada S, Karamitros M, Emfietzoglou D, Kyriakou I, Bordage M C, Sakata D, Guatelli S, Choi H J, Min C H, Lee S B and Incerti S 2019 Evaluation of the influence of physical and chemical parameters on water radiolysis simulations under MeV electron irradiation using Geant4-DNA. J. Appl. Phys. 126:114301

Rudek B, McNamara A, Ramos-Méndez J, Byrne H, Kuncic Z and Schuemann J 2019 Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams. Phys. Med. Biol. 64 175005

Moya-Sánchez E U, Maciel-Hernández A M, Niebla A S, Ramos-Méndez J and Carbajal-Espinosa O 2019 Monte Carlo Geometry Modeling for Particle Transport Using Conformal Geometric Algebra. Adv. Appl. Clifford Algebr. 29:26 http://link.springer.com/10.1007/s00006-019-0939-2

Burigo L N, Ramos-Méndez J, Bangert M, Schulte R W and Faddegon B 2019 Simultaneous optimization of RBE-weighted dose and nanometric ionization distributions in treatment planning with carbon ions. Phys. Med. Biol. 64 015015 https://doi.org/10.1088/1361-6560/aaf400

Schuemann J, McNamara A L, Ramos-Méndez J, Perl J, Held K D, Paganetti H, Incerti S and Faddegon B 2018 TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology. Radiat. Res. 191:125-138. http://www.rrjournal.org/doi/pdf/10.1667/RR15226.1

Ramos-Mendez J, Burigo L N, Schulte R W, Chuang C and Faddegon B 2018 Fast calculation of nanodosimetric quantities in treatment planning of proton and ion therapy Phys. Med. Biol. 63:1–25. http://iopscience.iop.org/article/10.1088/1361-6560/aaeeee

J. Schuemann and A. L. McNamara and J. W. Warmenhoven and N. T. Henthorn and K. Kirkby and M. J. Merchant and S. Ingram and H. Paganetti and K. D. Held and J. Ramos-Méndez et al., 2019 A New Standard DNA Damage (SDD) Data Format. Radiat Res. 191:76-92. https://doi.org/10.1667/RR15209.1

McNamara AL, Ramos-Méndez J, Perl J, et al. Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit. Phys Med Biol. 2018;63(17):175018. doi:10.1088/1361-6560/aad8eb

Piersimoni P, Faddegon B A, Ramos-Méndez J, Schulte R W, Volz L and Seco J 2018 Helium CT: Monte Carlo simulation results for an ideal source and detector with comparison to proton CT. Med. Phys. 45(7) 3264-3274

Ramos-Méndez J, Perl J, Schuemann J, McNamara A, Paganetti H and Faddegon B 2018 Monte Carlo simulation of chemistry following radiolysis with TOPAS-nBio. Phys. Med. Biol. 63(10) 105014-12pp

McNamara A, Geng C, Turner R, Ramos-Méndez J, Perl J, Held K, Faddegon B, Paganetti H and Schuemann J 2017 Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries. Phys. Medica 33 207–15

Piersimoni P, Ramos-Méndez J, Geoghegan T, Bashkirov V A, Schulte R W and Faddegon B A 2017 The effect of beam purity and scanner complexity on proton CT accuracy. Med. Phys. 44 284–98

Ramos-Méndez J, Schuemann J, Incerti S, Paganetti H, Schulte R and Faddegon B 2017 Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations. Phys. Med. Biol. 62 5908–25

Geng C, Moteabbed M, Seco J, Gao Y, George Xu X, Ramos-Méndez J, Faddegon B and Paganetti H 2016 Dose assessment for the fetus considering scattered and secondary radiation from photon and proton therapy when treating a brain tumor of the mother. Phys. Med. Biol. 61 683–95

Faddegon B a., Shin J, Castenada C M, Ramos-Méndez J and Daftari I K 2015 Experimental depth dose curves of a 67.5 MeV proton beam for benchmarking and validation of Monte Carlo simulation. Med. Phys. 42 4199–210

Polster L, Schuemann J, Rinaldi I, Burigo L, McNamara A L, Stewart R D, Attili A, Carlson D J, Sato T, Ramos Méndez J, Faddegon B, Perl J and Paganetti H 2015 Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endpoints. Phys. Med. Biol. 60 5053–70

Ramos-Méndez J, Perl J, Schümann J, Shin J, Paganetti H and Faddegon B 2015 Improved efficiency in Monte Carlo simulation for passive-scattering proton therapy. Phys. Med. Biol. 60 5019–35

Ramos-Méndez J, Perl J, Schümann J, Shin J, Paganetti H and Faddegon B 2015 A framework for implementation of organ effect models in TOPAS with benchmarks extended to proton therapy. Phys. Med. Biol. 60 5037–52

Ramos-Méndez J, Perl J, Faddegon B, Schümann J and Paganetti H 2013 Geometrical splitting technique to improve the computational efficiency in Monte Carlo calculations for proton therapy. Med. Phys. 40 041718

J. Ramos-Mendez, J. Shin, J. Perl, H. Paganetti and B. Faddegon “Systematic error in discrete time sampling of 4D-Monte Carlo simulations for particle therapy” Proceedings to the 58th Annual Conference of the Particle Therapy Cooperative Group (PTCOG58). Int J Part Ther. 2020;6(4):45-491. doi:10.14338/IJPT.19-PTCOG-6.4

Perl J, Paganetti H, Schuemann A, Ramos-Méndez J, Shin J, Faddegon B “The TOPAS tool for particle simulation: Facilitating studies of creative ideas for Monte Carlo based research” Proceedings to the 58th Annual Conference of the Particle Therapy Cooperative Group (PTCOG58). Int J Part Ther. 2020;6(4):45-491. doi:10.14338/IJPT.19-PTCOG-6.4

Piersimoni P, Geoghegan T, Ramos-Méndez J, Bashkirov V, Schulte R, Faddegon B. “Proton CT Uncertainties Estimated with Measurement-Validated Monte Carlo Simulations” Proceedings to the 55 th Annual Meeting for the Particle Therapy Cooperative Group (PTCOG). Int J Part Ther. 2016;3(1):71-276. doi:10.14338/IJPT.16-PTCOG-1.1

A McNamara, J. Perl, P. Piersimoni, J. Ramos-Méndez, B. Faddegon, K. Held, H. Paganetti and J. Schuemann “WE-H-BRA-04: Biological Geometries for the Monte Carlo Simulation Toolkit TOPAS-nBio” Med. Phys. 43(6) 3843-3843, (2016)

J. Ramos-Méndez, J. Perl, J. Schümann, H. Paganetti and B. Faddegon “Implementation of An Extension Module for Dose Response Models in the TOPAS Monte Carlo Toolkit” SU-E-T-466. Med. Phys. 42(6), 3441 (2015)

J. Ramos-Méndez, H. Paganetti and B. Faddegon “Monte Carlo Calculation of Source Terms and Attenuation Lengths for Neutrons Produced by 50-200 MeV Protons On Brass”; SU-E-T-554. Med. Phys. 42(6), 3463 (2015)

T Dou, J Ramos-Méndez, P Piersimoni , V Giacometti , S Penfold, Y Censor, B Faddegon, D Low and R Schulte “Tools for Development of 4D Proton CT” SU-E-J-148. Med. Phys. 42(6), 3298, (2015)

J. Ramos-Méndez, H. Paganetti and B. Faddegon “Monte Carlo calculations of shielding parameters for neutrons produced by 50-200 MeV proton on brass target”. PTCOG 54th Annual Meeting (2015) May 21th-23th, San Diego, CA, USA.

J. Ramos-Méndez, J. Perl, J. Schuemann, J. Shin, B. Faddegon and H. Paganetti “Optimal Parameters for Variance Reduction in Monte Carlo Simulations for Proton Therapy” WE-C-108-07. Med. Phys. 40, 475 (2013)

J. Ramos-Méndez, J. Perl, B. Faddegon and H. Paganetti “Geometrical Splitting Technique to Improve the Computational Efficiency in Monte Carlo Calculations for Proton Therapy” SU-E-T-478, Med. Phys. 39(6), 3815 (2012)

Selected Abstracts