This study presents new parameters for proton ionisation cross sections in guanine, adenine, thymine, and cytosine based upon the semi-empirical Rudd model. The same model was used to find differential electron cross sections considering a speed scaling procedure. To accelerate computation, the total electron cross sections were obtained using the binary-encounter-Bethe approximation instead of the integrated Rudd formula. The cross sections were implemented in the Geant4 simulation toolkit as Geant4-DNA processes, and simulations were carried out measuring protons lineal energies in spherical micrometric volumes filled with water, adenine, thymine, guanine, and cytosine. Large differences were seen in the lineal energies evaluated for the different materials, with the lineal energy measured in guanine being sometimes twice that of water. This suggests that the cross sections developed here should be considered in biological simulations where cellular substructures are modelled, in contrast to the current approach which approximates these volumes as consisting of liquid water.
References
1.
Agostinelli
, S.
, Allison
, J.
, Amako
, K.
, Apostolakis
, J.
, Araujo
, H.
et al., “Geant4-a simulation toolkit
,” Nucl. Instrum. Methods Phys. Res., Sect. A
506
, 250
–303
(2003
).2.
Akar
, A.
and Gümüş
, H.
, “Electron stopping power in biological compounds for low and intermediate energies with the generalized oscillator strength (GOS) model
,” Radiat. Phys. Chem.
73
, 196
–203
(2005
).3.
Akkerman
, A.
and Akkerman
, E.
, “Characteristics of electron inelastic interactions in organic compounds and water over the energy range 20–10 000 eV
,” J. Appl. Phys.
86
, 5809
–5816
(1999
).4.
Allison
, J.
, Amako
, K.
, Apostolakis
, J.
, Araujo
, H.
, Dubois
, P. A
. et al., “Geant4 developments and applications
,” IEEE Trans. Nucl. Sci.
53
, 270
–278
(2006
).5.
Allison
, J.
, Amako
, K.
, Apostolakis
, J.
, Arce
, P.
, Asai
, M.
et al., “Recent developments in Geant4
,” Nucl. Instrum. Methods Phys. Res., Sect. A
835
, 186
–225
(2016
).6.
Baro
, J.
, Sempau
, J.
, Fernández-Varea
, J. M.
, and Salvat
, F.
, “PENELOPE: An algorithm for Monte Carlo simulation of the penetration and energy loss of electrons and positrons in matter
,” Nucl. Instrum. Methods Phys. Res., Sect. B
100
, 31
–46
(1995
).7.
Bazin
, M.
, Michaud
, M.
, and Sanche
, L.
, “Absolute cross sections for electronic excitations of cytosine by low energy electron impact
,” J. Chem. Phys.
133
, 155104
(2010
).8.
Bernal
, M. A.
, Bordage
, M. C.
, Brown
, J. M. C.
, Davídková
, M.
, Delage
, E.
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
,” Phys. Med.
31
, 861
–874
(2015a
).9.
Bernal
, M. A.
, DeAlmeida
, C. E.
, Incerti
, S.
, Champion
, C.
, Ivanchenko
, V
. et al., “The influence of DNA configuration on the direct strand break yield
,” Comput. Math. Methods Med.
2015
, 417501
(2015b
).10.
Bernal
, M. A.
, Sikansi
, D.
, Cavalcante
, F.
, Incerti
, S.
, Champion
, C
. et al., “An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations
,” Comput. Phys. Commun.
184
, 2840
–2847
(2013
).11.
Bernhardt
, P.
and Paretzke
, H. G.
, “Calculation of electron impact ionization cross sections of DNA using the Deutsch-Märk and Binary-Encounter-Bethe formalisms
,” Int. J. Mass Spectrom.
223–224
, 599
–611
(2003
).12.
Boudaiffa
, B.
, Cloutier
, P.
, Hunting
, D.
, Huels
, M.
, and Sanche
, L.
, “Resonnant formation of DNA strand breaks by low-energy (3 to 20 eV) electrons
,” Science
287
, 1658
–1660
(2000
).13.
Bousis
, C.
, Emfietzoglou
, D.
, Hadjidoukas
, P.
, and Nikjoo
, H.
, “A Monte Carlo study of absorbed dose distributions in both the vapor and liquid phases of water by intermediate energy electrons based on different condensed-history transport schemes
,” Phys. Med. Biol.
53
, 3739
–3761
(2008a
).14.
Bousis
, C.
, Emfietzoglou
, D.
, Hadjidoukas
, P.
, Nikjoo
, H.
, and Pathak
, A.
, “Electron ionization cross-section calculations for liquid water at high impact energies
,” Nucl. Instrum. Methods Phys. Res., Sect. B
266
, 1185
–1192
(2008b
).15.
Briesmeister
, J. F.
, “MCNP—A general Monte Carlo N-particle transport code
,” Report No. LA-13709-M
(2000
).16.
Chmelevsky
, D.
and Kellerer
, A. M.
, “Computation of microdosimetric distributions for small sites
,” Radiat. Environ. Biophys.
14
, 123
–136
(1977
).17.
Dingfelder
, M.
, Hantke
, D.
, Inokuti
, M.
, and Paretzke
, H. G.
, “Electron inelastic scattering cross sections in liquid water
,” Radiat. Phys. Chem.
53
, 1
–18
(1998
).18.
Dingfelder
, M.
, Inokuti
, M.
, and Paretzke
, H. G.
, “Inelastic-collision cross-section of liquid water for interactions of energetic protons
,” Radiat. Phys. Chem.
59
, 255
–275
(2000
).19.
Dingfelder
, M.
, Ritchie
, R. H.
, Turner
, J. E.
, Friedland
, W.
, Paretzke
, H. G.
et al., “Comparisons of calculations with PARTRAC and NOREC: Transport of electrons in liquid water
,” Radiat. Res.
169
, 584
–594
(2008
).20.
Dingfelder
, M.
, Toburen
, L. H.
, and Paretzke
, H. G.
, in The Monte Carlo Method: Versatility Unbounded in a Dynamic Computing World
, Tennessee, 17–21 April 2005 (American Nuclear Society
, LaGrange Park
, 2005
).21.
Emerson
, L. C.
, Williams
, M. W.
, Tang
, I.
, Hamm
, R. N.
, and Arakawa
, E. T.
, “Optical properties of guanine from 2 to 82 eV
,” Radiat. Res.
63
, 235
–244
(1975
).22.
Emfietzoglou
, D.
, Karava
, K.
, Papamichael
, G.
, and Moscovitch
, M.
, “Monte Carlo simulation of the energy loss of low-energy electrons in liquid water
,” Phys. Med. Biol.
48
, 2355
–2371
(2003a
).23.
Emfietzoglou
, D.
, Moscovitch
, M.
, and Pathak
, A.
, “Inelastic cross-sections of energetic protons in liquid water calculated by model dielectric functions and optical data
,” Nucl. Instrum. Methods Phys. Res., Sect. B
212
, 101
–109
(2003b
).24.
Emfietzoglou
, D.
, Papamichael
, G.
, Pathak
, A.
, Fotopoulos
, A.
, and Nikjoo
, H.
, “Monte-Carlo study of energy deposition by heavy charged particles in sub-cellular volumes
,” Radiat. Prot. Dosim.
126
, 457
–462
(2007
).25.
ESTAR
, see http://physics.nist.gov/PhysRefData/Star/Text/ESTAR.html for stopping power and range tables for electrons, 2003
.26.
Fernandez-Varea
, J. M.
, Mayol
, R.
, Liljequist
, D.
, and Salvat
, F.
, “Inelastic scattering of electrons in solids from a generalized oscillator strength model using optical and photoelectric data
,” J. Phys.: Condens. Matter
5
, 3593
(1993
).27.
Francis
, Z.
, Incerti
, S.
, Capra
, R.
, Mascialino
, B.
, Montarou
, G
. et al., “Molecular scale track structure simulations in liquid water using the Geant4-DNA Monte-Carlo processes
,” Appl. Radiat. Isot.
69
, 220
–226
(2011a
).28.
Francis
, Z.
, Incerti
, S.
, Karamitros
, M.
, Tran
, H. N.
, and Villagrasa
, C.
, “Stopping power and ranges of electrons, protons and alpha particles in liquid water using the Geant4-DNA package
,” Nucl. Instrum. Methods Phys. Res., Sect. B
269
, 2307
–2311
(2011b
).29.
Francis
, Z.
, Villagrasa
, C.
, and Clairand
, I.
, “Simulation of DNA damage clustering after proton irradiation using an adapted DBSCAN algorithm
,” Comput. Methods Programs Biomed.
101
, 265
–270
(2011c
).30.
Francis
, Z.
, Incerti
, S.
, Ivanchenko
, V.
, Champion
, C.
, Karamitros
, M
. et al., “Monte Carlo simulation of energy-deposit clustering for ions of the same LET in liquid water
,” Phys. Med. Biol.
57
, 209
–224
(2012
).31.
Francis
, Z.
, Seif
, E.
, Incerti
, S.
, Champion
, C.
, Karamitros
, M
. et al., “Carbon ion fragmentation effects on the nanometric level behind the Bragg peak depth
,” Phys. Med. Biol.
59
, 7691
(2014
).32.
Francis
, Z.
and Stypczynska
, A.
, Data Mining: New Technologies, Benefits and Privacy Concerns
(Nova Science Publishers
, 2012
).33.
Galassi
, M. E.
, Champion
, C.
, Weck
, P. F.
, Rivarola
, R. D.
, Fojon
, O
. et al., “Quantum-mechanical predictions of DNA and RNA ionization by energetic proton beams
,” Phys. Med. Biol.
57
, 2081
–2099
(2012
).34.
Garty
, G.
, Schulte
, R.
, Shchemelinin
, S.
, Leloup
, C.
, Assaf
, G
. et al., “A nanodosimetric model of radiation-induced clustered DNA damage yields
,” Phys. Med. Biol.
55
, 761
–781
(2010
).35.
Gudowska
, I.
, Sobolevsky
, N.
, Andreo
, P.
, Belkic
, D.
, and Brahme
, A.
, “Ion beam transport in tissue-like media using the Monte Carlo code SHIELD-HIT
,” Phys. Med. Biol.
49
, 1933
–1958
(2004
).36.
Hayashi
, H.
, Watanabe
, N.
, and Udagawa
, Y.
, “Optical spectra of liquid water in vacuum UV region by means of inelastic X-ray scattering spectroscopy
,” J. Chem. Phys.
108
, 823
–825
(1998
).37.
Heller
, J. M.
, Hamm
, R. N.
, Birkhoff
, R. D.
, and Painter
, L. R.
, “Collective oscillation in liquid water
,” J. Chem. Phys.
60
, 3483
–3486
(1974
).38.
Henkner
, K.
, Sobolevsky
, N.
, Jakel
, O.
, and Paganetti
, H.
, “Test of the nuclear interaction model in SHIELD-HIT and comparison to energy distributions from GEANT4
,” Phys. Med. Biol.
54
, N509
–N517
(2009
).39.
Huels
, M.
, Boudaiffa
, B.
, Cloutier
, P.
, Hunting
, D.
, and Sanche
, L.
, “Single, double, and multiple double strand breaks induced in DNA by 3-100 eV electrons
,” J. Am. Chem. Soc.
125
, 4467
–4477
(2003
).40.
Hwang
, W.
, Kim
, Y. K.
, and Rudd
, M. E.
, “New model for electron‐impact ionization cross sections of molecules
,” J. Chem. Phys.
104
, 2956
–2966
(1996
).41.
Incerti
, S.
, Ivanchenko
, A.
, Karamitros
, M.
, Mantero
, A.
, Moretto
, P
. et al., “Comparison of GEANT4 very low energy cross section models with experimental data in water
,” Med. Phys.
37
, 4692
–4708
(2010
).42.
Iriki
, Y.
, Kikuchi
, Y.
, Imai
, M.
, and Itoh
, A.
, “Absolute doubly differential cross sections for ionization of adenine by 1.0-MeV protons
,” Phys. Rev. A
84
, 032704
(2011a
).43.
Iriki
, Y.
, Kikuchi
, Y.
, Imai
, M.
, and Itoh
, A.
, “Proton-impact ionization cross sections of adenine measured at 0.5 and 2.0 MeV by electron spectroscopy
,” Phys. Rev. A
84
, 052719
(2011b
).44.
Joy
, D. C.
, see http://web.utk.edu/∼srcutk/htm/interact.htm for a data-base of electron-solid interaction, 2001
.45.
Karamitros
, M.
, Luan
, S.
, Bernal
, M. A.
, Allison
, J.
, Baldacchino
, G
. et al., “Diffusion-controlled reactions modeling in Geant4-DNA
,” J. Comput. Phys.
274
, 841
–882
(2014
).46.
Kellerer
, A. M.
and Chmelevsky
, D.
, “Concepts of microdosimetry I. Quantities
,” Radiat. Environ. Biophys.
12
, 61
–69
(1975a
).47.
Kellerer
, A. M.
and Chmelevsky
, D.
, “Concepts of microdosimetry II. Probability distributions of the microdosimetric variables
,” Radiat. Environ. Biophys.
12
, 205
–216
(1975b
).48.
Kellerer
, A. M.
and Chmelevsky
, D.
, “Concepts of microdosimetry III. Mean values of the microdosimetric distributions
,” Radiat. Environ. Biophys.
12
, 321
–335
(1975c
).49.
Kim
, Y. K.
and Rudd
, M. E.
, “Binary-encounter-dipole model for electron-impact ionization
,” Phys. Rev. A
50
, 3954
–3967
(1994
).50.
Kim
, Y.-K.
, Santos
, J. P.
, and Parente
, F.
, “Extension of the binary-encounter-dipole model to relativistic incident electrons
,” Phys. Rev. A
62
, 052710
(2000
).51.
Lindborg
, L.
and Nikjoo
, H.
, “Microdosimetry and radiation quality determinations in radiation protection and radiation therapy
,” Radiat. Prot. Dosim.
143
, 402
–408
(2011
).52.
Mozejko
, P.
and Sanche
, L.
, “Cross section calculations for electron scattering from DNA and RNA bases
,” Radiat. Environ. Biophys.
42
, 201
–211
(2003
).53.
Nikjoo
, H.
, O'Neill
, P.
, Wilson
, W. E.
, and Goodhead
, D. T.
, “Computational approach for determining the spectrum of DNA damage induced by ionizing radiation
,” Radiat. Res.
156
, 577
–583
(2001
).54.
Palajova
, Z.
, Spurny
, F.
, and Davıdkova
, M.
, “Microdosimetry distributions for 40-200 MeV protons
,” Radiat. Prot. Dosim.
121
, 376
–381
(2006
).55.
Palmans
, H.
, Rabus
, H.
, Belchior
, A. L.
, Bug
, M. U.
, Galer
, S
. et al., “Future development of biologically relevant dosimetry
,” Br. J. Radiol.
88
, 20140392
(2015
).56.
Plante
, I.
and Cucinotta
, F.
, “Ionization and excitation cross sections for the interaction of HZE particles in liquid water and application to Monte Carlo simulation of radiation tracks
,” New J. Phys.
10
, 125020
(2008
).57.
Ponomarev
, A. L.
and Sachs
, R. K.
, “Polymer chromosome models and Monte Carlo simulations of radiation breaking DNA
,” Bioinformatics
15
, 957
–964
(1999
).58.
Rudd
, M. E.
, “Cross sections for production of secondary electrons by charged particles
,” Radiat. Prot. Dosim.
31
, 17
–22
(1990
).59.
Rudd
, M. E.
, Kim
, Y. K.
, Madison
, D. H.
, and Gay
, T. J.
, “Electron production in proton collisions with atoms and molecules: Energy distributions
,” Rev. Mod. Phys.
64
, 441
–490
(1992
).60.
Sanche
, L.
, “Low energy electron-driven damage in biomolecules
,” Eur. Phys. J. D
35
, 367
–390
(2005
).61.
Stewart
, R. D.
, Wilson
, W. E.
, McDonald
, J. C.
, and Strom
, D. J.
, “Microdosimetric properties of ionizing electrons in water: A test of the PENELOPE code system
,” Phys. Med. Biol.
47
, 79
–88
(2002
).62.
Tan
, Z.
, Xia
, Y.
, Zhao
, M.
, and Liu
, X.
, “Proton stopping power in a group of bioorganic compounds over the energy range of 0.05-10 MeV
,” Nucl. Instrum. Methods Phys. Res., Sect. B
248
, 1
–6
(2006
).63.
Wilson
, W. E.
and Toburen
, L. H.
, “Electron emission from proton-hydrocarbon-molecule collisions at 0.3-2.0 MeV
,” Phys. Rev. A
11
, 1303
–1308
(1975
).© 2017 Author(s).
2017
Author(s)
You do not currently have access to this content.
