Development of a computational system for the simulation of the interaction of ionizing radiations with the human genetic material

• Grant number: 11/51594-2
• Support Opportunities: Research Grants - Young Investigators Grants
• Start date: March 01, 2012
• End date: February 29, 2016
• Field of knowledge: Physical Sciences and Mathematics - Physics
• Principal Investigator: Mario Antonio Bernal Rodriguez
• Grantee: Mario Antonio Bernal Rodriguez
• Host Institution: Instituto de Física Gleb Wataghin (IFGW). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• City of the host institution: Campinas
• Associated research grant(s): 18/15316-7 - Study of the interaction of heavy charged particles with DNA using computational methods, AP.JP2

Abstract

The interaction of ionizing radiation with human beings leads to DNA damage. This damage is closely related to the origin of cancer as well as with its treatment through the radiation therapy. The Radiobiology is the branch of the science that studies the biological effects produced by ionizing radiations. There are two main approaches to study this kind of effects, experiments and simulations. The former is based on the use of in vitro cellular cultures exposed to ionizing radiations. The latter is based on the combination of biophysical models with Monte Carlo codes for the radiation transport simulation. Experiments present limitations to reproduce arbitrary combinations of irradiation setups and DNA configurations, among other parameters. Biophysical simulations allow to make a wide range of parameter combination and to discriminate between the influences of many factors, much of them impossible to be resolved in vitro experiments. However, experiments and simulations are complementary, as in many branchs of science. The GEANT4-DNA european project is intended to develop a computational package to simulate the transport of ns and electrons down to very low energies (~0.025 for electrons). This package would be used for nanodosimetry in Radiobiology. Our role into this project is to create biophysical models to validate the GEANT4-DNA package in Radiobiology. The scope of the proposed project is to develop a geometrical model of the human genetic material, accounting for six (6) organization levels for the three main DNA configurations (A, Band Z). In addition, a new biophysical model to simulate the DNA damage due to the impact of ionizing particles (direct damage) or water-derived chemical species (indirect damage) will be developed. The main scope of this project is to build up a computational tool to predict the relative biological effectiveness of photon, electron, and ion beams used in Radiation Therapy and Diagnostic. (AU)

Scientific publications

(41)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

BERNAL, M. A.; DEALMEIDA, C. E.; INCERTI, S.; CHAMPION, C.; IVANCHENKO, V.; FRANCIS, Z.. The Influence of DNA Configuration on the Direct Strand Break Yield. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, 2015. (11/51594-2)

INCERTI, S.; CHAMPION, C.; TRAN, H. N.; KARAMITROS, M.; BERNAL, M.; FRANCIS, Z.; IVANCHENKO, V.; MANTERO, A.; COLLABORATION, GEANT4-DNA. Energy deposition in small-scale targets of liquid water using the very low energy electromagnetic physics processes of the Geant4 toolkit. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIO, v. 306, p. 158-164, JUL 1 2013. (11/51594-2)

ROSALES, LISET DE LA FUENTE; INCERTI, SEBASTIEN; FRANCIS, ZIAD; BERNAL, MARIO A.. Accounting for radiation-induced indirect damage on DNA with the Geant 4-DNA code. PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS, v. 51, p. 108-116, JUL 2018. (15/21873-8, 11/51594-2)

FRANCIS, Z.; SEIF, E.; INCERTI, S.; CHAMPION, C.; KARAMITROS, M.; BERNAL, M. A.; IVANCHENKO, V. N.; MANTERO, A.; TRAN, H. N.; EL BITAR, Z.. Carbon ion fragmentation effects on the nanometric level behind the Bragg peak depth. Physics in Medicine and Biology, v. 59, n. 24, p. 7691-7702, DEC 21 2014. (11/51594-2)

TRAN, H. N.; EL BITAR, Z.; CHAMPION, C.; KARAMITROS, M.; BERNAL, M. A.; FRANCIS, Z.; IVANTCHENKO, V.; LEE, S. B.; SHIN, J. I.; INCERTI, S.; et al. Modeling proton and alpha elastic scattering in liquid water in Geant4-DNA. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIO, v. 343, p. 132-137, JAN 15 2015. (11/51594-2)

TRAN, H. N.; KARAMITROS, M.; IVANCHENKO, V. N.; GUATELLI, S.; MCKINNON, S.; MURAKAMI, K.; SASAKI, T.; OKADA, S.; BORDAGE, M. C.; FRANCIS, Z.; et al. Geant4 Monte Carlo simulation of absorbed dose and radiolysis yields enhancement from a gold nanoparticle under MeV proton irradiation. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIO, v. 373, p. 126-139, APR 15 2016. (11/51594-2)

ANDRE, T.; MORINI, F.; KARAMITROS, M.; DELORME, R.; LE LOIREC, C.; CAMPOS, L.; CHAMPION, C.; GROETZ, J. -E.; FROMM, M.; BORDAGE, M. -C.; et al. Comparison of Geant4-DNA simulation of S-values with other Monte Carlo codes. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIO, v. 319, p. 87-94, JAN 15 2014. (11/51594-2)

FRANCIS, Z.; EL BAST, M.; EL HADDAD, R.; MANTERO, A.; INCERTI, S.; IVANCHENKO, V.; EL BITAR, Z.; CHAMPION, C.; BERNAL, M. A.; ROUMIE, M.. A comparison between Geant4 PIXE simulations and experimental data for standard reference samples. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIO, v. 316, p. 1-5, DEC 1 2013. (11/51594-2)

PATER, PIOTR; SEUNTJENS, JAN; EL NAQA, ISSAM; BERNAL, MARIO A.. On the consistency of Monte Carlo track structure DNA damage simulations. Medical Physics, v. 41, n. 12, DEC 2014. (11/51594-2)

INCERTI, S.; SUERFU, B.; XU, J.; IVANTCHENKO, V.; MANTERO, A.; BROWN, J. M. C.; BERNAL, M. A.; FRANCIS, Z.; KARAMITROS, M.; TRAN, H. N.. Simulation of Auger electron emission from nanometer-size gold targets using the Geant4 Monte Carlo simulation toolkit. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIO, v. 372, p. 91-101, APR 1 2016. (11/51594-2)

LI, WEI BO; STANGL, STEFAN; KLAPPROTH, ALEXANDER; SHEVTSOV, MAXIM; HERNANDEZ, ALICIA; KIMM, MELANIE A.; SCHUEMANN, JAN; QIU, RUI; MICHALKE, BERNHARD; BERNAL, MARIO A.; et al. Application of High-Z Gold Nanoparticles in Targeted Cancer Radiotherapy-Pharmacokinetic Modeling, Monte Carlo Simulation and Radiobiological Effect Modeling. CANCERS, v. 13, n. 21, NOV 2021. (15/21873-8, 20/08647-7, 11/51594-2, 18/15316-7)

FRANCIS, Z.; MONTAROU, G.; INCERTI, S.; BERNAL, M.; ZEIN, S. A.. A simulation study of gold nanoparticles localisation effects on radiation enhancement at the mitochondrion scale. PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS, v. 67, p. 148-154, NOV 2019. (11/51594-2, 18/15316-7, 15/21873-8)

MAGALHAES, D. P.; RINKEL, J.; TOMAL, A.. Radiation damage impact on hybrid-pixel detectors data. Radiation Physics and Chemistry, v. 160, p. 63-67, JUL 2019. (15/21873-8, 11/51594-2)

BERNAL, MARIO A.; LIENDO, JACINTO A.; INCERTI, SEBASTIEN; FRANCIS, ZIAD; TRAN, HOANG N.. Experimental cross sections for water ionization due to the impact of light ions-A review. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIO, v. 517, p. 10-pg., 2022-04-15. (11/51594-2, 18/15316-7, 15/21873-8, 20/08647-7)

MAGALHAES, D. P.; TOMAL, A.. Monte Carlo simulation of hybrid pixel detectors. Radiation Physics and Chemistry, v. 167, FEB 2020. (11/51594-2, 15/21873-8)

DE FARIA, JHAISON C.; PAUPITZ, RICARDO; VAN DUIN, ADRI C. T.; BERNAL, MARIO A.. Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 18, n. 11, p. 9-pg., 2022-11-08. (11/51594-2, 18/15316-7, 15/21873-8, 20/08647-7)

SHIN, WOOK-GEUN; SAKATA, DOUSATSU; LAMPE, NATHANAEL; BELOV, OLEG; TRAN, NGOC HOANG; PETROVIC, IVAN; RISTIC-FIRA, ALEKSANDRA; DORDEVIC, MILOS; BERNAL, MARIO A.; BORDAGE, MARIE-CLAUDE; et al. A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast. CANCERS, v. 13, n. 19, OCT 2021. (18/15316-7, 15/21873-8, 11/51594-2, 20/08647-7)

DE FARIA, JHAISON C.; PAUPITZ, RICARDO; VAN DUIN, ADRI C. T.; BERNAL, MARIO A.. Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. N/A, p. 9-pg., 2022-10-28. (15/21873-8, 20/08647-7, 18/15316-7, 11/51594-2)

ZABIHI, AZAM; INCERTI, SEBASTIEN; FRANCIS, ZIAD; FOROZANI, GHASEM; SEMSARHA, FARID; MOSLEHI, AMIR; REZAEIAN, PEIMAN; BERNAL, MARIO A.. Computational approach to determine the relative biological effectiveness of fast neutrons using the Geant4-DNA toolkit and a DNA atomic model from the Protein Data Bank. Physical Review E, v. 99, n. 5, MAY 10 2019. (11/51594-2)

BERNAL, M. A.; SIKANSI, D.; CAVALCANTE, F.; INCERTI, S.; CHAMPION, C.; IVANCHENKO, V.; FRANCIS, Z.. An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations. COMPUTER PHYSICS COMMUNICATIONS, v. 184, n. 12, p. 2840-2847, DEC 2013. (11/51594-2)

INCERTI, S.; PSALTAKI, M.; GILLET, P.; BARBERET, PH.; BARDIES, M.; BERNAL, M. A.; BORDAGE, M. -C.; BRETON, V.; DAVIDKOVA, M.; DELAGE, E.; et al. Simulating radial dose of ion tracks in liquid water simulated with Geant4-DNA: A comparative study. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIO, v. 333, p. 92-98, AUG 15 2014. (11/51594-2)

KARAMITROS, M.; LUAN, S.; BERNAL, M. A.; ALLISON, J.; BALDACCHINO, G.; DAVIDKOVA, M.; FRANCIS, Z.; FRIEDLAND, W.; IVANTCHENKO, V.; IVANTCHENKO, A.; et al. Diffusion-controlled reactions modeling in Geant4-DNA. Journal of Computational Physics, v. 274, p. 841-882, OCT 1 2014. (11/51594-2)

TANG, NICOLAS; BUENO, MARTA; MEYLAN, SYLVAIN; PERROT, YANN; TRAN, HOANG N.; FRENEAU, AMELIE; DOS SANTOS, MORGANE; VAURIJOUX, AURELIE; GRUEL, GAETAN; BERNAL, MARIO A.; et al. Assessment of Radio-Induced Damage in Endothelial Cells Irradiated with 40 kVp, 220 kVp, and 4 MV X-rays by Means of Micro and Nanodosimetric Calculations. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 20, n. 24, DEC 2019. (11/51594-2, 18/15316-7, 15/21873-8)

INCERTI, S.; BARBERET, PH.; DEVES, G.; MICHELET, C.; FRANCIS, Z.; IVANTCHENKO, V.; MANTERO, A.; EL BITAR, Z.; BERNAL, M. A.; TRAN, H. N.; et al. Comparison of experimental proton-induced fluorescence spectra for a selection of thin high-Z samples with Geant4 Monte Carlo simulations. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIO, v. 358, p. 210-222, SEP 1 2015. (11/51594-2)

INCERTI, S.; KYRIAKOU, I.; BERNAL, M. A.; BORDAGE, M. C.; FRANCIS, Z.; GUATELLI, S.; IVANCHENKO, V.; KARAMITROS, M.; LAMPE, N.; LEE, S. B.; et al. Geant4-DNA example applications for track structure simulations in liquid water: A report from the Geant4-DNA Project. Medical Physics, v. 45, n. 8, p. E722-E739, AUG 2018. (11/51594-2)

BERNAL, M. A.; BORDAGE, M. C.; BROWN, J. M. C.; DAVIDKOVA, M.; DELAGE, E.; EL BITAR, Z.; ENGER, S. A.; FRANCIS, Z.; GUATELLI, S.; IVANCHENKO, V. N.; et al. Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit. PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS, v. 31, n. 8, p. 861-874, DEC 2015. (11/51594-2)

TELLO, JOHN J.; INCERTI, SEBASTIEN; FRANCIS, ZIAD; TRAN, HOANG; BERNAL, M. A.. Numerical insight into the Dual Radiation Action Theory. PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS, v. 43, p. 120-126, NOV 2017. (11/51594-2)

AGUIRRE, E.; DAVID, M.; DEALMEIDA, C. E.; BERNAL, M. A.. Impact of photon cross section uncertainties on Monte Carlo-determined depth-dose distributions. PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS, v. 32, n. 9, p. 1065-1071, SEP 2016. (11/51594-2)

DE FARIA, JHAISON C.; SANTIAGO, JOAO; FRANCIS, ZIAD; BERNAL, MARIO A.. Time-Dependent Density-Functional Theory for Determining the Electron-Capture Cross Section for Protons Impacting on Atoms and Molecules. Journal of Physical Chemistry A, v. 127, n. 11, p. 7-pg., 2023-03-14. (15/21873-8, 18/15316-7, 11/51594-2, 20/08647-7)

SEIF, EDGARD; EL BITAR, ZIAD; INCERTI, SEBASTIEN; BERNAL, MARIO A.; FRANCIS, ZIAD. Electron tracks simulation in water: Performance comparison between GPU CPU and the EUMED grid installation. PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS, v. 104, p. 11-pg., 2022-11-08. (11/51594-2, 15/21873-8, 20/08647-7)

ZABIHI, AZAM; INCERTI, SEBASTIEN; FRANCIS, ZIAD; FOROZANI, GHASEM; SEMSARHA, FARID; MOSLEHI, AMIR; REZAEIAN, PEIMAN; BERNAL, MARIO A.. Computational approach to determine the relative biological effectiveness of fast neutrons using the Geant4-DNA toolkit and a DNA atomic model from the Protein Data Bank. PHYSICAL REVIEW E, v. 99, n. 5, p. 8-pg., 2019-05-10. (11/51594-2)

BERNAL, M. A.; DEALMEIDA, C. E.; INCERTI, S.; CHAMPION, C.; IVANCHENKO, V.; FRANCIS, Z.. The Influence of DNA Configuration on the Direct Strand Break Yield. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, v. 2015, p. 8-pg., 2015-01-01. (11/51594-2)

SANTIAGO, JOAO; DE FARIA, JHAISON C.; SAN-MIGUEL, MIGUEL; BERNAL, MARIO A.. A TD-DFT-Based Study on the Attack of the OH center dot Radical on a Guanine Nucleotide. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 23, n. 17, p. 9-pg., 2022-09-01. (20/02348-8, 18/15316-7, 15/21873-8, 20/08647-7, 11/51594-2)

BERNAL, M. A.; SIKANSI, D.; CAVALCANTE, F.; INCERTI, S.; CHAMPION, C.; IVANCHENKO, V.; FRANCIS, Z.; KARAMITROS, M.; VAGENAS, EC; VLACHOS, DS. Performance of a new atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations. WAKE CONFERENCE 2021, v. 490, p. 4-pg., 2014-01-01. (11/51594-2)

MAGALHAES, D. P.; RINKEL, J.; TOMAL, A.. Radiation damage impact on hybrid-pixel detectors data (Reprinted from Radiation Physics and Chemistry, vol 160, pg 63-67, 2019). Radiation Physics and Chemistry, v. 167, p. 5-pg., 2020-02-01. (15/21873-8, 11/51594-2)

ZABIHI, AZAM; TELLO, JOHN; INCERTI, SEBASTIEN; FRANCIS, ZIAD; FOROZANI, GHASEM; SEMSARHA, FARID; MOSLEHI, AMIR; BERNAL, MARIO A.. Determination of fast neutron RBE using a fully mechanistic computational model. Applied Radiation and Isotopes, v. 156, FEB 2020. (11/51594-2, 18/15316-7, 15/21873-8)

SAKATA, DOUSATSU; HIRAYAMA, RYOICHI; SHIN, WOOK-GEUN; BELLI, MAURO; TABOCCHINI, MARIA A.; STEWART, ROBERT D.; BELOV, OLEG; BERNAL, MARIO A.; BORDAGE, MARIE-CLAUDE; BROWN, JEREMY M. C.; et al. Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA. PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS, v. 105, p. 9-pg., 2022-12-20. (18/15316-7, 15/21873-8, 20/08647-7, 11/51594-2)

BALLARINI, F.; CARANTE, M. P.; CAJIAO, J. J. TELLO; BERNAL, M. A.. Biophysical modelling of proximity effects in chromosome aberration production. NUOVO CIMENTO C-COLLOQUIA AND COMMUNICATIONS IN PHYSICS, v. 41, n. 6, NOV-DEC 2018. (11/51594-2, 15/21873-8)

SAKATA, DOUSATSU; LAMPE, NATHANAEL; KARAMITROS, MATHIEU; KYRIAKOU, IOANNA; BELOV, OLEG; BERNAL, MARIO A.; BOLST, DAVID; BORDAGE, MARIE-CLAUDE; BRETON, VINCENT; BROWN, JEREMY M. C.; et al. Evaluation of early radiation DNA damage in a fractal cell nucleus model using Geant4-DNA. PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS, v. 62, p. 152-157, JUN 2019. (15/21873-8, 11/51594-2)

SENIWAL, BALJEET; BERNAL, MARIO A.; FONSECA, TELMA C. F.. Microdosimetric calculations for radionuclides emitting beta and alpha particles and Auger electrons. Applied Radiation and Isotopes, v. 166, DEC 2020. (18/15316-7, 15/21873-8, 11/51594-2)

DE OLIVEIRA, LUCA A.; DE FARIAS, JHAISON C.; BERNAL, MARIO A.. Combination of the TD-DFT and the pixel counting method for determining electron capture cross sections for protons impacting on organic molecules. EUROPEAN PHYSICAL JOURNAL D, v. 78, n. 12, p. 11-pg., 2024-12-01. (15/21873-8, 18/15316-7, 11/51594-2, 20/08647-7)