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Modeling Radiation Chemistry in the Geant4 Toolkit

Article · July 2011

DOI: 10.15669/pnst.2.503

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Joint International Conference on Supercomputing in Nuclear Applications and Monte Carlo 2010 (SNA + MC2010)
Hitotsubashi Memorial Hall, Tokyo, Japan, October 17-21, 2010

Modeling Radiation Chemistry and Biology in the Geant4 Toolkit

M. Karamitros1, A. Mantero2, S. Incerti1 *, G. Baldacchino3, P. Barberet1, M. Bernal4,5, R. Capra6, C. Champion7, Z. El Bitar8,
Z. Francis9, W. Friedland10, P. Guèye11, A. Ivanchenko1, V. Ivanchenko7,12, H. Kurashige13, B. Mascialino14, P. Moretto1,
P. Nieminen15, G. Santin15, H. Seznec1, H. N. Tran1, C. Villagrasa9 and C. Zacharatou16
1
Université Bordeaux 1, CNRS/IN2P3, Centre d’Etudes Nucléaires de Bordeaux Gradignan, CENBG, Chemin du Solarium, BP120, 33175
Gradignan, France
2
INFN Sezione di Genova,Via Dodecanneso 33,16146 Genova, Italy
3
CEA Saclay, IRAMIS, UMR 3299 CEA-CNRS SIS2M, Laboratoire de Radiolyse,
F-91191 Gif-sur-Yvette Cedex, France
4
Departamento de Física, Universidad Simón Bolívar, P.O. Box 89000, Caracas 1080-A, Venezuela
5
Laboratório de Ciências Radiológicas, Universidade do Estado do Rio de Janeiro, 20550-900, Brazil
6
Via Niella 12, 17100 Savona, Italy
7
Laboratoire de Physique Moléculaire et des Collisions, Université Paul Verlaine-Metz, 1 Boulevard Arago,
Technopôle 2000, 57078 Metz, France
8
Institut Pluridisciplinaire Hubert CURIEN, 23 rue du loess - BP28, 67037 Strasbourg cedex 2, France
9
IRSN, Institut de Radioprotection et de Sureté Nucléaire, BP17, 92262 Fontenay-aux-Roses, France
10
Institute of Radiation Protection, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter
Landstr. 1, 85764 Neuherberg, Germany
11
Department of Physics, Hampton University, Hampton, Virginia 23668, USA
12
Ecoanalytica, Moscow State University, Moscow, Russia
13
Kobe University, Japan
14
Karolinska Institutet, P.O. Box 260, S-171-76 Stockholm, Sweden
15
ESA-ESTEC, 2200 AG Noordwjik, The Netherlands
16
Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen, Denmark

On behalf of the Geant4 Standard and Low-Energy Electromagnetic Physics Working Groups.
The authors are members of the Geant4-DNA collaboration.

ABSTRACT

Simulation of biological effects of ionizing radiation at the DNA scale requires not only the modeling of direct
damages induced on DNA by the incident radiation and by secondary particles but also the modeling of indirect
effects of radiolytic products resulting from water radiolysis. They can provoke single and double strand breaks by
reacting with DNA. The Geant4 Monte Carlo toolkit is currently being extended for the simulation of biological
damages of ionizing radiation at the DNA scale in the framework of the “Geant4-DNA” project. Physics models for
the modeling of direct effects are already available in Geant4. In the present paper, an approach for the modeling of
radiation chemistry in pure liquid water within Geant4 is presented. In particular, this modeling includes Brownian
motion and chemical reactions between molecules following water radiolysis. First results on time-dependent
radiochemical yields1 from 1 picosecond up to 1 microsecond after irradiation are compared to published data and
discussed.

KEYWORDS: Geant4, Geant4-DNA, DNA, microdosimetry, liquid water, chemistry, radiolysis, biology,
radiation, damage

1
For a given molecular species, the time-dependent radiochemical yield G is defined as the number of molecules produced for a total
absorbed energy of 100 eV in the irradiated medium:


 ,

 
where N(t) is the number of molecules and E is the total energy deposit by the incident ionizing particle into the medium, expressed in eV.

*Corresponding Author, E-mail:incerti@cenbg.in2p3.fr

I. Introduction
The accurate modeling of interactions of ionizing
radiation with biological matter remains a challenge in
radiobiology. Monte Carlo simulation techniques can
provide solutions allowing for example the prediction of
biological DNA damages, such as DNA single and double
strand breaks yields, which can be measured experimentally.
The Geant4 Monte Carlo simulation toolkit, an open source
set of libraries developed for modeling the passage of
particles through matter, covers a large variety of application
domains, ranging from high energy physics to space and
medical applications. In particular, the Geant4-DNA
project1,2), an activity of the Geant4 collaboration, aims at
providing Geant4 with new open source capabilities specific
to radiobiology applications, including the modeling of
elementary physical interactions down to the
sub-electronVolt scale, water radiolysis and radiation
chemistry. Applications are foreseen for long duration
manned space exploration programs as well as for the use of
radiation in the medical domain (e.g., particle therapy) where
radiation effects at the cellular level are of concern. This
work presents prototype developments for radiation
chemistry modeling in the Geant4 toolkit in the framework
of the Geant4-DNA project.
II. Principle of radiation chemistry simulation
One of the potential applications of radiation chemistry
simulations for cellular radiobiology is to evaluate the ratio
between DNA strand breaks created by primary and
secondary ionizing particles directly on the DNA molecule
(the so-called “direct effects”) and those provoked by
reactive oxygen species (the so-called “indirect effects”)
produced through water radiolysis by incident ionizing
radiation on the biological medium, mainly liquid water.
After ionization or excitation by a primary or secondary
particle, a water molecule can dissociate into new molecules.
These new molecular species can either interact amongst
themselves, producing other molecules, or can react with the
DNA molecule and finally induce strand breaks.
Consequently, after the physical irradiation, the number of
molecules of a given species in liquid water changes with
time.
In order to validate such a simulation, the time-evolution
of the number of molecules in liquid water (without
simulating explicitly the DNA molecule itself) can be
compared with experimental data. Additionally, these
numbers can be compared for verification to other
theoretical predictions and simulation results. For a given
molecular species, this evolution depends on the molecules’
capacity to move inside the medium (pure liquid water in our
case) and depends also on the proximity of the molecules
with their respective potential reactants.
III. Scenario of radiation chemistry in liquid water
The stochastic Monte Carlo simulation of early biological
damages on the DNA molecule from ionizing radiation
follows several identified consecutive stages, as explained
globally in references3,4,5).
(1) The physical stage
The first stage following cellular irradiation is the
so-called physical stage. In this stage, all physical
interactions take place. Thus, for electrons all the elastic and
inelastic interactions are simulated with Geant4-DNA,
namely, the elastic scattering, the ionization and the
excitation modes (electronic and vibrational).
(2) The physico-chemical stage
From 1 femtosecond (fs) to 1 picosecond (ps), the
physico-chemical stage encompasses the very fast events
(mainly electronic), such as thermalisation and solvation of
sub-excitation electrons, electronic hole migration and fast
electronic recombination that leads to chemical bond breaks.
This stage is not precisely described in the literature. For the
prototype development reported in this paper, we follow the
approach proposed by PARTRAC3), where branching ratios
and thermalization distances are the same for any incoming
particle and energy.
Excited water molecules are assumed to decay at 100 fs
after irradiation5).
The electronic holes of ionized water molecules quickly
migrate from a molecule to another following the chemical
reaction:
H 2O + + H 2O → H 2 O + H 2O +
The process lasts about 0.5 fs6,7).
At 10 fs after the electron removal8), a proton transfer
occurs between the final ionized water molecule and a
nearby water molecule to give birth to H3O+ and °OH
molecules from the reaction: H2O + + H2O → H3O+ + °OH.
The secondary electrons issued from the physical stage
get thermalized within a characteristic time of 110 fs through
vibrational excitation of water and they become solvated
within a characteristic time of 250 fs9). In our simulation, the
electrons can undergo vibrational excitation process until
they reach 0.025 eV. Afterwards, we consider them as
solvated and they start to diffuse through Brownian motion.
The hot dissociation fragments of water molecules are
assumed to get all thermalized within 1 ps. At 1 ps, the
placement of the fragments from the hit mother water
molecule can drastically affect the simulated radiochemical
yields. If, for example in the case of a water molecule in the
A1B1 excitation state, the dissociation fragments H°
and °OH are placed too close from each other, they would
rapidly recombine into H2O.
In the case of incident electrons, the following processes
for the physical and physico-chemical stages are simulated
with Geant4-DNA: elastic scattering, ionization, excitation,
vibrational electronic excitation and dissociative attachment.
These processes are expected to be fully available in the next
public release of the Geant4 toolkit (December 2010).
(3) The chemical stage approach followed by the state-of-the-art Monte Carlo
From 1 ps to 1 microsecond (µs), the so-called chemical PARTRAC software, which is precisely described by their
stage, the molecular species can diffuse through the medium authors in the literature3). Consequently, in this work we pay
and interact with each other or with the DNA molecule. The a particular attention to the time-dependent radiochemical
diffusion process and mutual interactions are described in yields calculated with PARTRAC.
more details in section V. With the present software prototype, the chemical stage
can be simulated up to 1 µs after irradiation. The simulation
(4) The biological stage starts with the positions of radiolytic products of the water
DNA damages such as single strand breaks and double molecules at 1 ps after the physical irradiation, using the
strand breaks may directly impact on the cell cancerization, branching ratios adjusted by PARTRAC3).
quiescence or death. The hot products have reached a so-called “thermalization
From about 1 µs, the cell starts to repair itself. It is the distance” from the hit mother water molecule before starting
biological stage which involves complex biological repair a Brownian motion. The method adopted to simulate the
mechanisms. The modeling of these processes is currently thermalization process in this work can be found in3). The
out of scope of the Geant4-DNA project, which focuses flexibility of the prototype software allows the user to easily
primarily on early DNA damages. implement his/her own thermalization distance computation
for each decay channel.
IV. Software Requirements Brownian diffusion of radiolytic products uses a random
change of direction after a time step ∆t corresponding to a
In order to simulate radiation chemistry of liquid water
geometrical step of size given by:
in Geant4, the software should fulfill the following five
  √6. . ∆
requirements (SR):
where D is the diffusion coefficient. The diffusion
− SR#1: description and management of molecules,
coefficient depends on the molecular species and on its
including some of their static (name, number of
excited state, while the time step can be adapted to the
atoms, ground state configuration, decay table…)
required accuracy as a function of physical time.
and dynamic (electronic configuration, diffusion
The criterion for the chemical reactions to occur is the
coefficient…) properties, as Geant4 does not
physical distance between two molecules. If two molecules
include any class for the handling of molecules;
are closer than a reaction radius10), related to the chemical
− SR#2: identification of the electronic state of
reaction rate, a reaction is assumed to happen, using a
excited and ionized water molecules from
jump-through correction10).
corresponding Geant4-DNA physics models;
− SR#3: decay process for molecules following VI. Simulation parameters
excitation and ionization, including thermalization;
− SR#4: diffusion process for molecules according to The default branching ratios (Table 1), diffusion
Brownian motion; coefficients (Table 2), reaction rates (Table 3) and time
− SR#5: chemical interaction process between steps (∆t) (Table 4) of this prototype software are those
diffusing molecules; proposed by PARTRAC3), but the user still has the
This is the first time that Geant4 is extended for the possibility to easily input his/her own parameters.
modeling of mutual interactions between tracks. Note that 3)
the prototype software described in this work is compatible Table 1 Branching ratios of a water molecule at 1 ps taken from
with Geant4 9.3 release and will be delivered with default
input parameters. Electronic state Decay Channel Fraction (%)
+
All ionizations states H3O + °OH 100
V. Molecular species and chemical processes
Excitation state °OH + H° 65
Under ionizing radiation, excited and ionized water A1B1:
(1b1) → (4a1/3s) H2O + ∆E 35
molecules may decay and dissociate into new molecules
(eaq2, H2, H°, °OH, H3O+) which can diffuse and interact Excitation state H3O + + °OH + e-aq 55
mutually to produce other molecules (OH-, H2O2). These eaq, B1A1:
(3a1) → (4a1/3s) °OH + °OH + H2 15
H°, °OH and H2O2 species can also directly interact with
DNA components. H2O + ∆E 30
New prototype processes for water radiolysis and the Excitation state: +
H3O + °OH + e aq-
50
resulting chemistry have been developed for Geant4 in the Rydberg, diffusion
framework of the Geant4-DNA project. We have adopted the bands H2O + ∆E 50

2
eaq : a solvated electron in water (also named aqueous solvated
electron) is a free electron in an aqueous solution surrounded by
water molecules.
Table 2 Diffusion coefficients for the diffusing species taken ionization and excitation which are available in Geant4
3)
from release 9.3 and are described in1). New processes for electron
dissociation attachment and vibrational excitation in water
Species Diffusion coefficient D (10-9 m2 s-1)
have been developed privately for the moment.
e-aq 4.9 The results of this prototype software are compared to
°OH 2.8 other reference data (theoretical calculations, simulation
H° 7.0 codes and experimental measurements) as done in
+
references3,4). They appear in global agreement. Still, early
H3O 9.0
yields seem slightly underestimated while later ones appear
H2 4.8 overestimated when compared to PARTRAC results. The
-
OH 5.0 use of different physics models between PARTRAC and
H2O2 2.3 Geant4-DNA could explain these differences. Besides, it is
difficult to draw firm conclusions regarding the comparison
3)
Table 3 Reaction rates taken from to the theoretical and experimental data shown since these
Reaction Reaction rate (1010 M-1 s-1) data are available for incident energies different from 750
- -
2.65 keV. They however reflect the time-evolution trend.
H° + e + H O→ OH + H
aq 2 2
H° + °OH → H O 1.44
2
H° + H° → H 1.20
2
H + °OH → H° + H O 4.17×10-3
2 2
- -
HO + e → OH + °OH 1.41
2 2 aq
+ -
HO + e → H° + H O 2.11
3 aq 2
+
HO + OH- → 2 H O 14.3
3 2
- -
°OH + e → OH 2.95
aq
°OH + °OH → H O 0.44
2 2
- - -
e +e + 2 H O→ 2 OH + H 0.50
aq aq 2 2

Table 4 Time steps ∆t with respect to the physical time, taken

3)
from
Time interval (s) ∆t (ps)
Until 10-11 0.1
10-11 – 10-10 1 Fig. 1 Preliminary results on radiochemical yield
10-10 – 10-9 3 (molecules/100 eV) from 750 keV incident electrons for °OH
10-9 – 10-8 10 with respect to time (ps). References: PARTRAC ,
3)

Above 10-8 100 4)

RADACK , Jonah et al. rescaled with factor 0.8
3,12)
, Stabin et
13) 14
al. , LaVerne et al. ), Tomita et al.15). All data are extracted
VII. Time-dependent radiochemical yields from reference3).
Experimental data on time-dependent chemical yields are
rare. Consequently, in order to verify our prototype software,
we compare our results with other simulation codes
(PARTRAC3) and RADACK4)). However, as Geant4-DNA
and PARTRAC3,11) physics models are not strictly identical,
the outcome of the physical stage will necessarily be
different.
Results shown here were obtained by shooting 25000
incident electrons of 750 keV onto a 2.5 µm–thick slide of
liquid water and using the above default parameters. The
resulting radiochemical yields for OH° and the solvated
electron are respectively shown in Figure 1 and Figure 2.
These preliminary results have been obtained using the
G4DNABornIonisationModel and
G4DNAEmfietzoglouExcitationModel models for electron

Fig. 2 Preliminary results on radiochemical yield
(molecules/100 eV) from 750 keV incident electrons for eaq
3)
with respect to time (ps). References: PARTRAC ,
4) 16) 17) 18)
RADACK , Jonah et al. , Buxton , Jonah et al. ,
19) 13) 14)
Shiraishi et al. , Stabin et al. , LaVerne et al. , Tomita
15) 3)
et al. . All data are extracted from reference .
VIII. Conclusion
A first prototype for simulating radiation chemistry within
Geant4 in the framework of the Geant4-DNA project has
been developed and compared to other simulations and some
existing experimental data. The described prototype software
is still under development. We expect to compare our results
to dedicated radiolysis experiments that will be performed in
the coming months at the Laboratoire de Radiolyse (CEA
Saclay, Gif-sur-Yvette, France) in order to measure
time-dependent °OH yields by using chemiluminescence
technics20).
Acknowledgment
We are grateful to Dr Marie Davidkova (Nuclear Physics
Institute AS CR, Praha, Czech Republic) for her advice and
suggestions and also for providing us with relevant
publications. We are also thankful to Dr Makoto Asai
(SLAC National Accelerator Laboratory, Menlo Parc, CA,
USA) for his technical advice. The Geant4-DNA project
receives funding from the French Agence Nationale de la
Recherche Contract No. ANR-09-BLAN-0135-01 and from
the European Space Agency under Contract No.
AO6041-22712/09/NL/AT.
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