Jose Ramos-Mendez, PhD

Assistant Professor in Residence
Department of Radiation Oncology

Head Research Lab

Publications: 

Effect of FLASH dose-rate and oxygen concentration in the production of H2O2in cellular-like media versus water: a Monte Carlo track-structure study.

Physics in medicine and biology

D-Kondo JN, Borys D, Rucinski A, Brzozowska B, Masilela TAM, Grochowska-Tatarczak M, Wegrzyn M, Ramos-Mendez JA

Investigation of hydrogen peroxide yields and oxygen consumption in high dose rate irradiation: a TOPAS-nBio Monte Carlo study.

Physics in medicine and biology

Shin WG, D-Kondo JN, Ramos-Mendez JA, LaVerne JA, Rothwell BC, Bertolet A, McNamara A, Faddegon BA, Paganetti H, Schuemann J

Modeling the oxygen effect in DNA strand break induced by gamma-rays with TOPAS-nBio.

Physics in medicine and biology

D-Kondo JN, Masilela TAM, Shin WG, Faddegon BA, LaVerne JA, Schuemann J, Ramos-Mendez JA

TOPAS-Tissue: A Framework for the Simulation of the Biological Response to Ionizing Radiation at the Multi-Cellular Level.

International journal of molecular sciences

García García OR, Ortiz R, Moreno-Barbosa E, D-Kondo N, Faddegon B, Ramos-Méndez J

An interface tool to parametrize treatment plans for the TrueBeam radiotherapy system into TOPAS parameter control files for Monte Carlo simulation.

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)

Ortiz R, Sawkey D, Faddegon B, D-Kondo N, Ramos-Méndez J

Lithium inelastic cross-sections and their impact on micro and nano dosimetry of boron neutron capture.

Physics in medicine and biology

D-Kondo JN, Ortiz R, Faddegon BA, Incerti S, Tran HN, Francis Z, Moreno-Barbosa E, Schuemann J, Ramos-Mendez JA

Review of chemical models and applications in Geant4-DNA: Report from the ESA BioRad III Project.

Medical physics

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, Villagrasa C, Zein S, Incerti S

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)

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, 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 HN, Villagrasa C, Incerti S

TOPAS simulation of photoneutrons in radiotherapy: accuracy and speed with variance reduction.

Physics in medicine and biology

Ramos-Mendez JA, Ortiz R, Schuemann J, Paganetti H, Faddegon BA

A digital male pelvis phantom series showing anatomical variations over the course of fractionated radiotherapy treatment.

Medical physics

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

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

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

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

D-Kondo JN, Garcia-Garcia OR, LaVerne JA, Faddegon B, Schuemann J, Shin WG, Ramos-Méndez J

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)

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

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)

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, 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 HN, Villagrasa C, Incerti S

Impact of DNA Geometry and Scoring on Monte Carlo Track-Structure Simulations of Initial Radiation-Induced Damage.

Radiation research

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

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

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

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

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)

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

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

von der Linden J, Ramos-Mendez J, Faddegon B, Massin D, Fiksel G, Holder JP, Willingale L, Peebles J, Edwards MR, Chen H

Validation of the TOPAS Monte Carlo toolkit for HDR brachytherapy simulations.

Brachytherapy

Berumen F, Ma Y, Ramos-Méndez J, Perl J, Beaulieu L

Boronated Condensed DNA as a Heterochromatic Radiation Target Model.

Biomacromolecules

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

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

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

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, Kyriakou I, Latyshev G, Le A, Mancini-Terracciano C, Maire M, Mantero A, Novak M, Omachi C, Pandola L, Perales A, Perrot Y, Petringa G, Quesada JM, Ramos-Méndez J, Romano F, Rosenfeld AB, Sarmiento LG, Sakata D, Sasaki T, Sechopoulos I, Simpson EC, Toshito T, Wright DH

Independent reaction times method in Geant4-DNA: Implementation and performance.

Medical physics

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

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

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

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

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

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

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)

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)

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

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. Lee and S. Incerti

Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams.

Physics in medicine and biology

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

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

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

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

Ramos-Méndez J, Burigo LN, Schulte R, Chuang C, Faddegon B

A New Standard DNA Damage (SDD) Data Format.

Radiation research

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, Friedland W, Kundrát P, Ottolenghi A, Baiocco G, Barbieri S, Dingfelder M, Incerti S, Villagrasa C, Bueno M, Bernal MA, Guatelli S, Sakata D, Brown JMC, Francis Z, Kyriakou I, Lampe N, Ballarini F, Carante MP, Davídková M, Štepán V, Jia X, Cucinotta FA, Schulte R, Stewart RD, Carlson DJ, Galer S, Kuncic Z, Lacombe S, Milligan J, Cho SH, Sawakuchi G, Inaniwa T, Sato T, Li W, Solov'yov AV, Surdutovich E, Durante M, Prise KM, McMahon SJ

Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit.

Physics in medicine and biology

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

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

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

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

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)

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

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

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

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

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

J Ramos Méndez, J Perl, J Schümann, J Shin, H Paganetti, B Faddegon