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Review of Geant4-DNA Applications for Micro and Nanoscale Simulations S Review of Geant4-DNA applications for micro and nanoscale simulations S. Incerti, M. Douglass, S. Penfold, S. Guatelli, E. Bezak To cite this version: S. Incerti, M. Douglass, S. Penfold, S. Guatelli, E. Bezak. Review of Geant4-DNA applica- tions for micro and nanoscale simulations. Physica Medica, Elsevier, 2016, 32 (10), pp.1187-1200. 10.1016/j.ejmp.2016.09.007. hal-03319740 HAL Id: hal-03319740 https://hal.archives-ouvertes.fr/hal-03319740 Submitted on 12 Aug 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. *Manuscript Click here to view linked References 1 Review of Geant4-DNA applications for micro and nanoscale simulations 2 1,2 3, 4 3, 4 5,6 4,7,8 3 S Incerti , M Douglass , S Penfold , S Guatelli , E Bezak 4 1Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France 5 2 6 CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France 7 3 Department of Medical Physics, Royal Adelaide Hospital, Adelaide, SA, Australia 8 4School of Physical Sciences, University of Adelaide, Adelaide, SA, Australia 9 5Centre for Medical Radiation Physics, University of Wollongong, NSW, Australia 10 6 11 Illawarra Health and Medical Research Institute, University of Wollongong, NSW, Australia 7 12 International Centre for Allied Health Evidence, University of South Australia, Adelaide, 13 SA, Australia 14 8Sansom Institute for Health Research, University of South Australia, Adelaide, SA, 15 16 Australia 17 18 19 Keywords: Geant4-DNA, radiation, Monte Carlo method, nanoscale simulations 20 21 Corresponding Author: Eva Bezak 22 23 Address: School of Health Sciences, University of South Australia 24 City East Campus 25 GPO Box 2471 26 Adelaide SA 5001 27 28 Australia 29 Email: [email protected] 30 31 32 33 Abstract 34 35 Emerging radiotherapy treatments including targeted particle therapy, hadron therapy or 36 37 radiosensitisation of cells by high-Z nanoparticles demand the theoretical determination of 38 radiation track structure at the nanoscale. This is essential in order to evaluate radiation 39 damage at the cellular and DNA level. Since 2007, Geant4 offers physics models to describe 40 41 particle interactions in liquid water at the nanometre level through the Geant4-DNA Package. 42 This package currently provides a complete set of models describing the event-by-event 43 electromagnetic interactions of particles with liquid water, as well as developments for the 44 45 modelling of water radiolysis. 46 47 Since its release, Geant4-DNA has been adopted as an investigational tool in kV and MV 48 external beam radiotherapy, hadron therapies using protons and heavy ions, targeted therapies 49 and radiobiology studies. It has been benchmarked with respect to other track structure Monte 50 51 Carlo codes and, where available, against reference experimental measurements. 52 53 While Geant4-DNA physics models and radiolysis modelling functionalities have already 54 been described in detail in the literature, this review paper summarises and discusses a 55 selection of representative papers with the aim of providing an overview of a) geometrical 56 57 descriptions of biological targets down to the DNA size, and b) the full spectrum of current 58 micro- and nano-scale applications of Geant4-DNA. 59 60 61 62 1 63 64 65 1. Introduction 1 Mathematical and computational models describing the complex biophysical processes 2 associated with radiation induced cell death have been used since the early 1960s. In 1973 3 Chadwick [1] first presented a mathematical formula which accurately fitted experimental 4 5 data of cell survival as a function of absorbed dose. It was the first model that attempted to 6 consolidate theories of macroscopic dose deposition and micro/nanoscopic damages caused 7 by ionising radiation. In macroscopic radiobiological models (such as Chadwick’s), small 8 9 scale behaviour is consolidated into a set of analytical equations representing the large scale 10 behaviour of the system. While these models are fast in terms of computation time, they are 11 not robust enough to predict outcomes for a wide range of input parameters. As physical, 12 13 chemical and biological interactions of radiation within an organic medium are stochastic 14 processes, a stochastic type model is required for a more accurate description. As a result, 15 with improvements to the speed and general availability of computer hardware, a transition is 16 17 occurring from simple analytical models to more physically realistic stochastic (i.e. Monte 18 Carlo) models. 19 20 In Monte Carlo codes based on a condensed history approach [2], such as EGS [3], 21 PENELOPE [4], GEANT4 [5-7] and MCNP [8], a large number of collision processes are 22 23 grouped together or “condensed” to a single “step”. This approach made the Monte Carlo 24 simulation of charged particle transport computationally feasible, but it is intrinsically 25 inadequate to describe particle interactions at the nanometre scale. For more than twenty 26 years the ab-initio physical mechanism at the basis of radiation damage in biological 27 28 molecules has been investigated at the DNA and cellular level by means of other dedicated 29 Monte Carlo codes, referred to as track structure codes. 30 31 A variety of track structure codes, such as PTra [9], PARTRAC [10], KURBUC [11], TRAX 32 [12], RITRACKS [13] have been developed to calculate the energy deposition at the 33 34 nanometre scale, modelling particle tracks interaction-by-interaction (“event-by-event”), 35 typically in gaseous medium or liquid water, to approximate biological systems (this will be 36 discussed further in section 2). 37 38 The success of the track structure codes resulted from insights from the observation that the 39 40 micro and nano scale pattern of radiation track and associated energy deposition has a crucial 41 role in the determination of the probability of formation of critical biological lesions [14]. 42 The importance of modelling the electron interactions down to eV energies with nanoscale 43 44 resolution was shown by Nikjoo and Goodhead [15]. These authors estimated that 45 approximately 50% of all ionisations are produced by electrons with energy less than 1 keV 46 in the case of irradiation with a photon or a proton beam. These observations have a 47 48 significant impact in both radiation protection and radiotherapy studies. 49 50 More recently, emerging radiotherapy treatments demand theoretical determination of 51 radiation track structure at the nanoscale, and the radiation damage at the cellular and DNA 52 level. For example, in Targeted Particle (alpha, beta, Auger) Therapy, the calculation of 53 energy deposition at cellular level is necessary because of the short path length of particles 54 emitted by the radionuclide and the spatial distribution of the radionuclide relative to the 55 56 small target volumes [16, 17]. The investigation of high-Z nanoparticles (NP) as 57 radiosensitisers has demonstrated the need to investigate the effect of radiation at nanoscale 58 [18]. The Local Effect Model (LEM) calculates the survival of cells exposed to a carbon ion 59 beam based on the assumption that the cell response to a given microscopic dose deposited 60 61 62 2 63 64 65 by densely ionising radiation, such as carbon ions, is related to how the cell would respond to a uniform dose of sparsely ionising radiation, such as X-rays, in a particular nanoscale 1 domain. The LEM is used clinically in the carbon ion beam Treatment Planning System at the 2 Heidelberg Heavy Ion Therapy centre [19]. Alternatively, at the Heavy Ion Medical 3 Accelerator (HIMAC) of NIRS in Chiba, Japan, the RBE (RBE at 10% cell surviving 4 10 5 fraction in Human Salivary Gland tumour cells [20] was evaluated by means of the 6 Microdosimetric Kinetic Model (MKM), formulated by Hawkins [21, 22] which is based on 7 microdosimetric measurements. 8 9 Since its first release in 2007, the Geant4-DNA Package has been increasingly used for track 10 11 structure studies. The Geant4-DNA project, originally initiated by the European Space 12 Agency to study the effect of radiation in astronauts, was increasingly applied to other 13 application domains. 14 15 Figure 1 shows the number of published journal articles using Geant4-DNA as an 16 17 investigation tool between 2010 and 2015. As far as the authors of this paper are aware, the 18 total number of journal articles published in this period is approximately 70. The 19 bibliographic research was performed by means of the Scopus (www.scopus.com) database. 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 Figure 1. Number of journal articles published in the period between 2010-2015, using 45 Geant4-DNA as an investigation tool according to Scopus database. 46 47 48 49 Given the large number of papers published, this review paper summarises and discusses a 50 selection of representative papers with the aim of providing an overview of a) geometrical 51 52 descriptions of biological targets down to the DNA size, and b) the full spectrum of current 53 applications of Geant4-DNA. 54 55 56 57 2. Overview of physics and radiolysis modelling capabilities 58 59 2.1 Track structure codes 60 61 62 3 63 64 65 Track structure codes have been used for several decades in order to simulate mechanistically the physical interactions of ionising particles with biological matter at small scale and low 1 energy.
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