2015
Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endpoints
Polster L, Schuemann J, Rinaldi I, Burigo L, McNamara AL, Stewart RD, Attili A, Carlson DJ, Sato T, Méndez J, Faddegon B, Perl J, Paganetti H. Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endpoints. Physics In Medicine And Biology 2015, 60: 5053-5070. PMID: 26061666, PMCID: PMC4511084, DOI: 10.1088/0031-9155/60/13/5053.Peer-Reviewed Original ResearchConceptsFrequency-mean specific energyProton linear energy transferProton radiation effectsMonte Carlo toolLinear energy transferDelta electronsLineal energyProton RBEBragg peakPhysics parametersRadiobiological experimentsExperimental arrangementEnergy transferTOPASRadiation effectsTrack structureBiological input parametersProton therapyExperimental dataDouble-strand break inductionDNA double-strand break inductionEnergyRBEElectronsSpecific geometry
2013
A molecular dynamics simulation of DNA damage induction by ionizing radiation
Abolfath RM, Carlson DJ, Chen ZJ, Nath R. A molecular dynamics simulation of DNA damage induction by ionizing radiation. Physics In Medicine And Biology 2013, 58: 7143-7157. PMID: 24052159, DOI: 10.1088/0031-9155/58/20/7143.Peer-Reviewed Original ResearchConceptsMolecular dynamics simulationsChemical reactionsDynamics simulationsChemical bond breaksWater moleculesMolecular dynamics softwareHydrogen abstractionHydroxyl free radicalsBond breaksChemical eventsCollection of ionsSingle protonRadicalsLow-energy electronsDNA moleculesProtonsBackbone damageFree radicalsMulti-scale simulationsIonsMoleculesReactionElectronsBroken bondsEnergy electronsTH‐F‐105‐02: Molecular Dynamics Simulation of DNA Damage Induction by Ionizing Radiation
Abolfath R, Carlson D, Chen Z, Nath R. TH‐F‐105‐02: Molecular Dynamics Simulation of DNA Damage Induction by Ionizing Radiation. Medical Physics 2013, 40: 552-552. DOI: 10.1118/1.4815815.Peer-Reviewed Original ResearchWater moleculesOH radicalsMD simulationsChemical reactionsMolecular dynamicsReaxFF molecular dynamicsHydrogen bond disruptionDynamics of OHMolecular dynamics simulationsChemical pathwaysPair of ionsResult of ionizationSuch computational approachesBond disruptionDynamics simulationsSingle protonMoleculesProtonsBeam of electronsIon distributionOHReactionElectronsIonizationComputational approach