Japanese Journal of Applied

Physics

ACCEPTED MANUSCRIPT

Cross sections, stopping power and Bragg peak range calculation of

proton collisions with the DNA base adenine
To cite this article before publication: Mustapha krim et al 2019 Jpn. J. Appl. Phys. in press https://doi.org/10.7567/1347-4065/ab35b0

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Page 1 of 19 AUTHOR SUBMITTED MANUSCRIPT - JJAP-101417.R3

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2 Japanese Journal of Applied Physics REGULAR PAPER
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4
5
6 Cross sections, Stopping power and Bragg peak range calculation
7
8 of proton collisions with the DNA base adenine

pt
9
10 1, 2 ∗
11 Mustapha Krim , Jamal Inchaouh2 , Noura Harakat2 , Abdenbi Khouaja2 , Meriem Fiak2 ,
12 Mohammed Reda Mesradi1 , Ahmed Fathi2, 3 , Omar Jdair2 and Redouane Elbaydaoui1
13

cri
14 1
15 Laboratory instrumentation and medical physics, Higher Institute of Health Sciences (ISSS), Hassan I
16 Settat University, Morocco
17 2
Subatomic Research and Applications Team, Department of Physics, LPMC-ERSA, Faculty of Sciences
18
19 Ben M’Sik, Hassan II Casablanca University, Morocco
20 3
Polydisciplinary Faculty of Khouribga, Hassan I Settat University, Morocco

us
21
22
23
24 Passage of ionizing radiation into the biological medium plays an important role in a variety of chemical
25 modifications, directly or indirectly of the four DNA bases. However, up to now proton collisions on DNA
26
27
28
29
an
bases remain experimentally approached and a theoretical model for total cross section, stopping cross
section and Bragg peak calculation are poorly characterized. In this current work, we restricted our study
on the interaction of energetic ion proton beams with DNA base adenine (C5H5N5). The total cross
30
31 section produced by high-energy impact of protons are here analytically investigated via a novel model
32 combining two methods – the Rudd semi-empirical formulas to calculate the ionization and the analytic
dM
33 method based on the similitude between the electron energy-loss in adenine and liquid water to calculate
34
35 the excitation and charge-transfer – these cross sections used to describe the total stopping cross section
36 of adenine molecule by protons including the nuclear stopping powers. We give in this work an estimation
37 of the Bragg peak profile and position with impact energies ranging from 1 MeV/amu to 20 MeV/amu.
38
39 The results are compared to the available experimental, theoretical and Monte-Carlo (MC) results, and
40 reasonable agreements are generally observed especially for the ionization. The proposed method is useful
41 as an alternative to traditional approaches, and is useful for studies of various radiation effects in other
42
43 biological material.
pte

44
45
46
47
48
49 1. Introduction
50
In the last few years, there has been a growing interest in the physic mechanisms re-
51
ce

52 sponsible for cellular damage. Particularly the role played by the ionization, excitation,
53
54 and charge-transfer processes. The cross section and stopping power (SP) calculation
55
of these processes of biological materials for proton beams are a subject of great im-
56
Ac

57 portance in many fields of fundamental and application researches, such as radiation

58
59
60 ∗
E-mail: mustapha.krim@uhp.ac.ma

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 AUTHOR SUBMITTED MANUSCRIPT - JJAP-101417.R3 Page 2 of 19

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2 Jpn. J. Appl. Phys. REGULAR PAPER
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5 biology and radiotherapy. A review of differential cross sections of excitation, ionization,
6 charge-transfer, elastic and inelastic scattering processes mainly dominates the energy
7
8 loss per unit length of traveling protons through the matter.

pt
9
10 We restricted our study on the interaction of energetic ion proton beams with DNA
11 base adenine. A new paramerization for total proton cross section has been developed.
12
13 Firstly it’s based on the Rudd26, 30) semi-empirical formula to find the total ioniza-

cri
14
15 tion cross section in adenine. We consider here all 35 sub-shell characteristics (Binding
16 energy, number of occupation), these features are calculated using a Molden software
17
18 package. Secondly, the absence of model calculate excitation and charge-transfer cross
19
20 sections leads us to adopt the Laverne and Pimblott18) work, we postulate that the ra-

us
21 tios between the cross section of ionization and excitation, and between the ionization
22
23 and charge-transfer in adenine and liquid water are the same. These ratios in liquid
24
25 water were calculated using our previous work,1, 20, 24) and analytical fitting expression
26
27
28
29
an
found via the adjustment, is used to summarize the relationship of these ratios and
energy incident. Starting this way allows one to calculate rather easily the excitation

30 and charge-transfer cross sections in adenine by solving proportions. We also investigate

31 implicit effects of ionization, excitation and charge-transfer processes on the electronic
32
dM
33 stopping power and we compute nuclear stopping powers for a large variety of proton
34
35 beams ranging the energy of 1 - 20 MeV , and in some cases we apply the relativistic
36 corrections to those existing semi-empirical models. In our analytical approach, the inci-
37
38 dent beam is treated event by event and the target medium is discretisized, incremented,
39
40 and divided into layers. The thickness of each layer is selected randomly from a distri-
41 bution weighted by the values of the total interaction cross section. Our calculated total
42
43 cross section and stopping power agrees with the available experimental data,14, 15, 33)
pte

44
45 Monte-Carlo method,2, 6, 7, 13, 39) and theoretical method.34) This paper is organized as
46 follows. In section II, we present the semi-empirical and new parametrization of proton
47
48 impact cross section (Ionization, Excitation and Charge-transfer process). In section
49
50
III, we compute the electronic and nuclear stopping powers for a large variety of proton
51
ce

beams ranging the energy of 1 - 20 MeV. We discuss in the last section the deposited
52
53 energy of a proton beam in adenine as a function of the depth, so called the range (R),
54
55
and we present the possibility of using our parameterization approach in substitution
56 of alternative methods to describe the Bragg peak position.
Ac

57
58
59
60

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5 2. PROTON IMPACT CROSS SECTIONS
6
2.1 Semi-empirical approache for describing the direct ionization process
7
8 The direct ionization by protons in the molecule of adenine (p + C5 H5 N5 → p +

pt
9
10 C5 H5 N5+ + e− ) is the dominant process contributing to the overall energy loss; sev-
11
12
eral empirical models exist in the literature to estimate the singly differentiated cross
13 section with respect to the energy, W , of the ejected electrons and to estimate indirectly

cri
14
15 the ionization total cross section of atoms or molecules by ion impact. The derived dif-
16
17
ferential ionization cross section, taking into account 35 molecular orbitals of adenine
18 molecule, is given by semi-empirical Rudd’s expression:26, 30)
19
dσion (W, E0 ) ∑
35
20 F1 (νi ) + F2 (νi )ωi

us
21 = Si α(ω −ω max )
(1)
dW (1 + ωi )3 (1 + exp i i )
22 i νi
23 2
2 4πa0 Ni
24 Where Si = z Ii
( IRi )2 , and i is the index of the sub-shell in the isolated molecule
25
of adenine, R = 13.6 eV presents the Rydberg energy, a0 = 0.0529 nm is the Bohr
26
27
28
29
an
radius, Ii is the binding energy of the electron in the sub-shell i of molecule of adenine,
Ni is the shell occupancy, we used the Molden package from the Ab Initio packages and
30 the semi-empirical packages Mopac/Ampac to find the binding energy values of electron
31
32 in the sub-shell i and the shell occupancy (see table I). Wj is the energy transfer in a
dM
33 Wi
34 single collision, ωi = is the dimensionless normalized kinetic energy of the ejected
Ii √
35 electron, νi the dimensionless normalized velocity νi = Ei
, Ei is the energy of an
36 Ii
37 electron of mass m which would have the same velocity as a proton of mass M of the
38
39 same energy Ei = E0 (m/M ), E0 is the energy of the incident proton, ωimax is the scaled
40 cutoff energy ωimax = 4νi2 − 2νi − (R/4Ii ), and α is a numerical parameter related to
41
42 the relative size of the target molecule.
43
pte

44 F1 (ν) and F1 (ν) are empirical expressions given by:

45

 L1 (ν) = C1 ν(DD1
46 1+E1 ν 1 +4)
47 F1 (ν) = L1 (ν) + H1 (ν) ⇒ 2) (2)
 H1 (ν) = A1 ln(1+ν
2 B1
48 ν +
ν2
49 
50  L (ν) = C ν D2
51 L2 (ν)H2 (ν)
ce

2 2
F2 (ν) = ⇒ (3)
52 L2 (ν) + H2 (ν)  H2(ν) = A22 + B42
ν ν
53
54 The parameters Aj , Bj , Cj , Dj (j = 1, 2) depends the target ionized. The parame-
55
56 ters used in this work for isolated molecule of adenine are taking from Rudd’s model
Ac

57
58
(Abdallah and Francis, private communication) (see table II).38) Total ionization cross
59 sections were finally simply deduced by numerical integration of equation 1 for each
60

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5 Table I. Molecular Orbitals of isolated molecule of adenine.
6
Inner Shells : Outer Shells :
7
8 i Ii Ni i Ii Ni

pt
9 1 409.9 2.00 11 32.16 2.00
10
11 2 409.9 2.00 12 30.48 2.00
12 3 409.9 2.00 13 29.42 2.00
13 4 409.9 2.00 14 27.55 2.00

cri
14
15 5 409.9 2.00 15 26.90 2.00
16 6 284.2 2.00 16 24.06 2.00
17 7 284.2 2.00 17 20.21 2.00
18
19 8 284.2 2.00 18 19.61 2.00
20 9 284.2 2.00 19 19.91 2.00

us
21 10 284.2 2.00 20 16.92 2.00
22
23 21 16.52 2.00
24 22 16.20 2.00
25 23 15.73 2.00
26
27
28
29
an 24
25
15.44
15.06
2.00
2.00
26 15.01 2.00
30
27 14.55 2.00
31
32 28 14.52 2.00
dM
33 29 14.34 2.00
34
30 13.78 2.00
35
36 31 13.60 2.00
37 32 13.30 2.00
38
33 13.16 2.00
39
40 34 12.28 2.00
41 35 11.97 2.00
42
43
pte

44
45
46
47
48
49
50
orbital over the kinetic energy transfers Ei , the latter ranging from a minimum value
51 (Wi )min ∼
ce

= 0 to a maximum value (Wi )max = 4m Ei . M

52
53
54 35 ∫
∑ (Wi )max i
55
dσion
(σion )Ad = ( )dW (4)
56 j (Wi )min dW
Ac

57
58 To extend this formulation to a higher energy range, i.e., for proton energies greater
59
60
than about 10 MeVν 2 is replaced by (Ianik and Cucinotta, 200810) ):

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2 Jpn. J. Appl. Phys. REGULAR PAPER
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4
5 Table II. Rudd model parameters used for the ionization cross section calculation for isolated
6 molecule of adenine for classical energy range proton impact and relativistic energy range.38)
7
8 Inner shells Outer shells Inner shells Outer shells

pt
9
A1 1.25 1.18 A2 1.10 0.90
10
11 B1 0.50 14.00 B2 1.30 4.30
12 C1 1.00 0.36 C2 1.00 1.80
13
D1 1.00 0.52 D2 0.00 1.40

cri
14
15 E1 3.00 3.00 α 0.66 0.61
16
17
18
19
20

us
21 [ ]
22 mc2 1
23 ν = 2
1− (5)
2Ii 1 + Ei /mc2
24
25 (Wi )max is replaced by the relativistic expression (Turner, 200735) ):
26
27
28
29 Wmax =
an
2mc2 (γ 2 − 1)
(6)
30
1 + 2γ(m/M ) + (m/M )2
31 Where γ is expressed as a function of the energy of the incident proton E0 , γ = (1 −
32
dM
33 β 2 )−1/2 The total ionization cross section curve is obtained by numerically integrating
34
(equation 4) over W using the parameters for bioorganic adenine. Figure 1 shows that
35
36 the contribution of the inner shells of ionization process are not neglected (≈ 1%), so
37
38 we take into consideration all the shells. It should be noted that the total ionization
39
cross section for proton impact presents a maximum (peak) for proton energies around
40
41 70 keV . We compare our ionization cross sections calculations to the rare existing
42
43 experimental data, namely, the measurements provided by Tabet et al.33) for 80 keV -
pte

44
protons and those recently reported by Iriki et al.14, 15) for three higher energies, 500 keV ,
45
46 1 M eV and 2 M eV . However, at very low energy (90 eV ) the cross section of the positive
47
48 ion production of adenine C5 H5 N5+ (direct ionization) by proton remains very low
49 (0.02×10−16 cm2 ) compared with that found by the impact of electrons (7×10−16 cm2 ).3)
50
51
ce

2.2 Proposed analytical model for proton excitation and charge-transfer cross
52
53 section:
54
55
The incident protons mainly lose their energy by coulomb interactions with the outer
56 shell electrons of adenine molecules causing the ionization (calculated in paragraph
Ac

57
58 A) or excitation processes. At the end of range, the incident proton causes maximum
59
60
interactions with outer electrons of adenine molecules. For residual energy E0 less than

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2 Jpn. J. Appl. Phys. REGULAR PAPER
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4 3
5 10

cm 2)
6
7 -16 102 Work (All shells)

8 Work (Inner shells)

Total Ionization Cross section (10

pt
Experimental Data [28]

9
Experimental Data [13, 14]

10 10
11
12 1
13

cri
14
15 10−1
16
17 10−2
18
19
−3
20 10 3 5 6

us
102 10 104 10 10 107
21 Energy (eV)
22
23
24 Fig. 1. Ionization cross sections of protons in Adenine for inner shells (red dashed line) and all
25 shells (blue solid line) compared to existing experimental data of Iriki et al.14, 15) (solid triangle),
26
27
28
29
Tabet et al.33) (solid rectangle) and to the CTMC predictions4, 19) (open circles)
an
30
31
80 keV , the incident protons can capture or exchange electrons with hydrogen atoms
32
dM
33 of adenine molecules. Thereafter, we explain the different steps used to calculate the
34
35 excitation and charge-transfer cross section.
36
2.2.1 Approximation model Laverne and Pimblott18) work has shown that the en-
37
38 ergy losses (per unit mass) of electrons in liquid water and in DNA are relatively close
39
40 in a wide range of energy.
41
42
43
pte

44 (ρ · λ)DN A = (ρ · λ)W (7)

45
46 Since the average free path is the inverse of the attenuation coefficient, we deduce:
47
48 ( ) ( )
49 µ µ
50 = (8)
ρ DN A ρ W
51
ce

µ
52 However, the attenuation mass coefficient ρ
depends on the molar mass A and the
53
54
total interaction cross section σ of the considered material:
55
56
µ NA
Ac

57 = σ (9)
58 ρ A
59
60
Where ρ is density, µ is the attenuation coefficient, A is the molar mass, λ is the

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4
5 average free path, NA is the number of Avogadro, and σ is the total cross section.
6 hence:
7
8

pt
9 (σ) (σ) ADN A
10 = and σDN A = σW · (10)
11 A DN A A W AW
12 The total cross section of the DNA can therefore be deduced from that of the water.
13

cri
14 Similarly, considering each base of the DNA as an independent molecule:
15
16
17 AB
18 σB = σW · (11)
19
AW
20 Using this last equation for each process (ionization, excitation, and charge-transfer):

us
21
22
23 AB
24 σprocess )B = σprocess )W · (12)
25
AW
26 We replace the electron by proton and DNA by Adenine (the same mass damage
27
28
29
an
surface (g · cm−2 )). The equation 12 corresponding cross section relationship between
DNA base and liquid water for various energy ranges allows to approximate that the
30
31 ratios of ionization/excitation and ionization/charge-transfer are similar in liquid water
32
dM
33 and adenine:
34
35 ( ) ( )
36 σion σion
= (13)
37 σex σex
Ad W
38
39
( ) ( )
σion σion
40 = (14)
41 σct Ad σct W
42 In addition, other experimental studies have shown that the relative cross sections
43
pte

44 of fragment ion formation due to electron capture by Ar6+ ions form adenine and uracil
45
46
molecules give probabilities generally close to the probabilities of similar processes at
47 photoionization of molecules by electrons with energies falling into the range where the
48
49 cross section of molecule ionization by electron impact is maximal.36)
50
51 2.2.2 Fitted parameters for new model of excitation and charge-transfert cross
ce

52 section In last work,1, 20, 24) we have investigated different inelastic interactions of pro-
53
54 tons and neutral hydrogen atoms beams in liquid water. These interactions include not
55
56 only excitation and ionization processes of protons, but also charge-transfer and ion-
Ac

57 ization, excitation, and electron loss of moving neutral hydrogen atoms. Indeed, our
58
59 previous study have used different semi-empirical models to calculate the cross section
60

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2 Jpn. J. Appl. Phys. REGULAR PAPER
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4
5 for every interaction. Our calculations compare fairly well with available experimental
6 data and with different commonly used results. In present work, we use these results
7
8 to calculate the ratios of the total ionization/charge-transfer and ionization/excitation

pt
9
10 cross sections for each incident proton energy in liquid water, noted successively Rct
11 and Rex (See figure 2) with:
12
13
( )

cri
14
15
σion
Rct = (15)
16 σct W ater
17 ( )
18 σion
19 Rex = (16)
σex
20 W ater

us
21 In addition, we use the curve fitting for a series of cross section ratio values to find the
22
23 best fit curve , and we have segmented the fitting range for Rex in order to increase the
24 accuracy of the fit parameters (Figure 2). The produced equations are used to find the
25
26 continuous value of these ratios.
27
28
29
an
30 Rct = α0 · E α1 f or E ≤ 300 (17)
31
32

dM
33 
34 
 β0 + β1 · E + β2 · E 2 for E ≤ 0.0003


35 

 β3 · E
β4
36
 for 0.0003 < E ≤ 0.02

37 Rex = β5 · E β6 for 0.02 < E ≤ 0.6 (18)

38 



39  β7 + β8 · E + β9 · E 2
 for 0.6 < E ≤ 60


40  β +β ·E for E > 60
10 11
41
42 Where E is the kinetic energy in M eV , and αi et βi are the fitting parameters (see
43
pte

44 table III). The uncertainty in parameter values due to the fitting procedure was less
45
46
than 2% in all intervals.
47
48
49 The charge-transfer and excitation cross sections of DNA base adenine is approxi-
50
51
mated from that of liquid water, by:
ce

52
53
54 (σion )Ad
(σct )Ad = (19)
55 Rct
56
Ac

57 (σion )Ad
58 (σex )Ad = (20)
Rex
59
60

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4 Changing the stopping power

1010
5

R ct
109
6 108
(a)
7 107

Cross section ratio :

106
8 105

pt
9 104
103
10 102
11 10
1
12 10− 1
13 10 −2

cri
14 10− 3
10− 4
15 10− 5
16
3 5 6 8
102 10 104 10 10 107 10
Energy (eV)
17
18
Cro ss section ratio : R ex

22
Electrons, theta = 21,80 degrees

19 20 (b)
20 18

us
21 16
22 14
23 12
24 10
25 8
26 6
27
28
29
4
2
0 3
an 5 6 8
102 10 104 10 10 107 10
30 Energy (eV)

31
32
dM
33
34 Fig. 2. Ionization/charge-transfer cross section ratio value Rct ploted with fitted function (a).
35 Ionization/excitation cross section ratio Rex ploted with differents fitted function (b).
36
37
38
39
Table III. Parameters fits values for the cross section ratio of the ionization-excitation and of the
40
41 ionization-electron capture in liquid water.
42
43 Fit parameters of Rct and Rex :
pte

44 α0 = 1.62357e-06 α1 = 1.86333
45
46 β0 = 18.3057 β1 = 0.0206156 β2 = -7.64765e-05
47 β3 = 313.027 β4 = -0.492267 β5 = 0.0654245
48 β6 = 0.38803 β7 = 11.1453 β8 = 5.03807e-09
49
50 β9 = -1.0893e-16 β10 = 10.2019 β11 = 1.06736e-08
51
ce

52
53
54
55
The (σion )Ad value found using equation 4 and the parameters values of the analyt-
56 ical model of equations 17 and 18 (Table III) allowed us to calculate charge-transfer
Ac

57
58 and excitation cross section. The total cross sections for the different interaction
59
60
processes for proton impact in adenine, ionisation, excitation and charge-transfer are

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4 Ionization (Work)

5 Excitation (Work)

Total Ionization Cross section (10 -16 cm2)

6 Electron-capture (Work)
102
7 Experimental Data [32]
8 Experimental Data [13, 14]

pt
9
10
11 10
12
13

cri
14
15 1
16
17
18 3 5 6
19 102 10 104 10 10 107
Energy (eV)
20

us
21
22 Fig. 3. Total cross sections of the considered inelastic processes of protons in Adenine.
23
24
25
26
27
28
29
ploted. Figure 3 shows that the excitation and ionization cross sections for protons
an
have the same shape and have a peak in the energy field of the Bragg peak. As we
30
31 can observe from the figure, the charge-transfer process is dominant at low energy till
32
dM
33 intermediate one of 100 keV.
34
35
36
37 3. Proton stopping cross section
38
39
3.1 Electronic stopping cross section
40 The literature on stopping cross section for heavier ions is vast, including measurements,
41
42 theory, evaluations and tabulations, and software algorithms and programs (ICRU,11, 12)
43
pte

44 Ziegler,40) Sigmund31) ). Electronic stopping cross sections are typically calculated with
45 either the Bethe-Bloch equation or empirical functions, depending on the energy regime
46
47 of the ion. In this work, the total electronic stopping cross section σsp, total is defined as
48
49
the sum of the ionization, excitation, and charge-transfer stopping cross section of the
50 incident particle.
51
ce

52
53
54 σsp, total (Ei ) = σsp, ion (Ei ) + σsp, exe (Ei ) + σsp, cc (Ei ) (21)
55
56 Where σsp, ion is the ionization stopping cross section, σsp, exe is the excitation
Ac

57
58 stopping cross section and σsp, cc is the charge change stopping cross section.
59
60

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4
5 3.1.1 Ionization stopping cross section: The ionization stopping cross section for
6 the ith orbital can be calculated from the differential ionization cross section for this
7
8 orbital. The total ionization stopping cross section can be obtained as the sum of the

pt
9
10 ionization stopping cross section of all orbitals and is given by:28)
11
12 ∫
13 ∑
35
dσion

cri
14 (σsp, ion )Ad = Gj (W + Ij )( )dW (22)
dW
15 j
16 Where Gj is the partitioning factor to adjust the contribution of different sub-shells
17
18 j, and we take Gj = 1; W is the energy of the secondary electrons, and Ij is the
19
20 binding energy of the electron in the sub-shell j of the molecule of adenine.

us
21
22
23 3.1.2 Fitted parameters for new model of excitation and charge-transfert stop-
24
25 ping cross section: The preceding analysis of paragraph B.2 the section II was reit-
26
27
28
29
stopping cross section Rsp, ex ,
an
erated to take into consideration this time the ratio between ionization and excitation
and the ratio between ionization and charge-transfer
30 Rsp, ct in liquid water,1, 20, 24) are then:
31
32 ( )
dM
33 σsp, ion
34
Rsp, ex = (23)
σsp; exe W ater
35
36
( )
37 σsp, ion
38 Rsp, ct = (24)
39
σsp; ct W ater
40 We have optimized these ratios by a mathematical formalism using always the fit-
41
42 ting equation (figure 4 for ionization/excitation stopping cross section ratio). The ratio
43
pte

distribution can now be calculated simply by using these equations:

44
45
46 
47 
 b0 · E b 1 for E ≤ 0.12


48 

49 
 b2 + b3 · E for 0.12 < E ≤ 0.3

50  b · ln(E) + b · √E

for 0.3 < E ≤ 4
4 5
51 Rsp,
ce

ex = (25)
52 
 b6 + b7 · E for 4 < E ≤ 10


53 
 b + b · E + b · E2

 for 10 < E ≤ 110
54 

8 9 10
55 
b11 + b12 · E for E > 110
56
Ac

57
58
Rsp, ct = c0 · E −c1 f or E ≤ 80M eV (26)
59
60

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2 Jpn. J. Appl. Phys. REGULAR PAPER
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4
5 Table IV. Set of fit parameters for the ratio ionization and excitation stopping cross section for
6 liquid water.
7
8 Fit parameters of Rsp, exe (E) and Rsp, cc (E) :

pt
9
b0 = 192.57 b1 = -0.33377 b2 = 4.53621
10
11 b3 =0.000228672 b4 =4.67132 b5 = 0.0029771
12 b6 = 68.0967 b7 = 1.86912e-06 b8 = 87.1547
13
b9 = - 8.43648e-08 b10 = 9.06715e-16 b11 =77.2977

cri
14
15 b12 = 8.2359e-08 c0 = 1300.02 c1 = 0.718396
16
17
18
19 Where E is the kinetic energy. The ratios fit parameters of the analytical model
20

us
21 found are listed in table IV.
22
23
In our approach, we have always assumed that the Rsp, ex and Rsp, ct ratios are
24 similar in liquid water and adenine in range of energy (10 eV - 20 MeV), so we can
25
26 write:
27
28
29
an (σsp, ion )Ad
30 (σsp, ex )Ad = (27)
Rsp, ex
31
32
dM
33 (σsp, ion )Ad
34 (σsp, ct )Ad = (28)
35 Rsp, ct
36 Where (σsp, , Rsp, and Rsp,
ion )Ad ex , ct are calculated using equations 22, 25, and 26
37
38 and also using parameters fits values of table IV.
39
40 We show in figure 6, the stopping cross section calculated for the ionization, ex-
41 citation and charge-changing processes as function of incident energy. We note the
42
43 dominance of ionization process for proton at high energy. For low energy less than 20
pte

44
45 keV, the charge changing processes become more dominant than the ionization process.
46 In same figure our predictions model are compared to a series of theoretical calculations
47
48 and MC simulations in terms of ionization stopping power resulting in adenine for pro-
49
50
ton energies limited to the 40 keV–20 MeV range. As expected, the divergences between
51
ce

our model, theoretical and Monte carlo ones essentially appear for impact proton ener-
52
53 gies more than 20 MeV and less than 40 KeV. More precisely, agreement within ≃ 4%
54
55
is achieved between our calculation and systematic ones of Tan et al.,34) and ≃ 3% com-
56 pared to those found by SRIM and Geant4-DNA Monte-Carlo results, with in particular
Ac

57
58 a maximum total stopping power of 1407 M eV /cm at Einc ≃ 100 keV for our work
59
60
and maximum stopping power of 1113 M eV /cm, 1320 M eV /cm and 1362 M eV /cm

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4 Electrons, theta = 21,80 degrees

σ sp,ion / σ sp,ex
6
7 160 σsp,ion / σ sp,ex (E ≤ 0.12MeV)
Liquid Water

8 σsp,ion / σ sp,ex (E ∈ [0.12; 0.3MeV])

pt
140
9 σsp,ion / σ sp,ex (E ∈ [0.3; 4MeV])

10 120
σsp,ion / σsp,ex (E ∈ [4; 10MeV])
σsp,ion / σsp,ex (E ∈ [10; 110MeV])
11
σ sp,ion / σsp,ex (E > 110MeV)
12 100
Fit Function
13

cri
14 80
15
60
16
17 40
18
19 20
20

us
21 0
102 103 104 105 106 107 108
22 Energy (eV)
23
24
25 Fig. 4. Stopping cross section ratio fitting at different intervals.
26
27
28
29
an Sp_Exc
Sp_C_change
Stopping Cross Section (MeV / cm)

Sp_Ioni
30 10
3 Sp_Total
Sp_Tan et al
31 Sp_SRIM
32 Sp_Geant4-DNA
dM
33
34 10
2

35
36
37
38 10
39
40
41 4 5 6 7
42 10 10 10 10
Energy (eV)
43
pte

44
45 Fig. 5. Total electronic stopping cross sections of the considered inelastic processes of protons in
46 Adenine compared to Tan et al.34) and Monte-Carlo methods SRIM (Ziegler et al 201239) ) and
47 Geant4-DNA2, 6, 7, 13)
48
49 .
50
51
ce

52
53 at same energy for theoretical calculates of Tan et al.,34) and Monte-Carlo calculates of
54 SRIM (Ziegler et al 201239) ) and Geant4-DNA.2, 6, 7, 13)
55
56 3.2 Nuclear stopping power
Ac

57
58 The nuclear stopping power is especially influential when the projectile is close to stop-
59
60
ping in the target. However, when the incident particle energy becomes high, the nuclear

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4
5 stopping is not important and can be safely neglected in the calculation of the total
6 stopping power.
7
8 The reduced energy considers the dependence of the nuclear stopping power on the

pt
9
10 masses (M1 and M2 ) and the charges (Z1 and Z2 ) of the atoms involved in the scatter-
11 ing process.17, 37) The nuclear stopping power in units of M eV · cm2 /g for proton with
12
13 the real ion energy Ep in units of keV is given by:

cri
14
15
16 8, 462 · 10−17 · Z1 · Z2 · M1
17 Sn (Ep ) = · Sn (ϵ) (29)
18 (M1 + M2 ) · (Z10,23 + Z20,23 )
19 The analytical approximation for Sn (ϵ) is given by:
20

us
21

22 
23
(ln(1+1,1383·ϵ)
2·(ϵ+0,01321·ϵ0,21226 +0,19593·ϵ0,5
for ϵ ≤ 30
24
Sn (ϵ) = (30)
 ln(ϵ)
for ϵ > 30
25 2·ϵ
26
27
28
29
with:
an
32, 53 · M2
30 ϵ= · Ep (31)
31 Z1 · Z2 · (M1 + M2 ) · (Z10,23 + Z20,23 )
32
dM
Figure 6 presents the curves of the electronic , and nuclear stopping power of proton
33
34 in liquid water, it shows the contribution of nuclear stopping power is low but not
35
36 negligible the contribution is dominant at low energy. A high energy contribution of
37
the electronic and significant and dominant stopping power, while the contribution of
38
39 nuclear stopping power is negligible.
40
41
42 4. Depth of Bragg peak calculation
43
pte

The total stopping cross section calculated from the interaction cross sections offers the
44
45 possibility to calculate the stopping power S, by using this given formula:32)
46
47
48
49 Se (Ep ) = N · σst, total (Ep ) (32)
50
51 Where N is the number of adenine molecules per unit of volume (= 7.13 · 1027 m−3 ).
ce

52
53 This numbre can be expressed in terms of their mass density ρm (in kg/m3 ) as N =
54 NA
ρ where NA = 6.022140857 · 1023 mol−1 is the Avogadro constant, M = 135.13 ·
M m
55
56 10 kg/m−3 is the molar mass and ρm = 1.6 · 103 kg · m−3 is the mass density. Ep is the
3
Ac

57
58 incident proton energy, σst, total is the total stopping cross section (equation 21).
59 The energy deposition per unit length that is to say, the stopping power increases very
60

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4

Stopping Cross Section (MeV.cm-2)

5
103
6
7
8

pt
9
10 102

11
12 Sp_Total
13 Sp_Elec

cri
14 10 Sp_Nuc

15
16
17 3
10 104
5
10 10
6
107
18 Energy (eV)
19
20

us
21 Fig. 6. Stopping cross sections for nuclear and electronic processes of energetic protons passing
22 through a volume of adenine
23
24 .
25
26
27
28
29
an
gradually with greater depth and lower speed, suddenly rising to a peak when the proton
is ultimately stopped. The slowing down of proton to inferior limit of 100 eV can be
30
31 written with inelastic interaction alone by:
32
dM
33
34 ∑
i−1
35 Epi (X) = Ep0 − ST otal (Epj )Xj (33)
36 j=1
37
38 Where Ep0 is the initial incident proton energy, i is the number of collision, Epj is the
39 energy of proton traveled Xj distance. ST otal (Epj ) = Se (Epj ) + Sn (Epj ) is the electronic
40
41 and nuclear stopping power. Where Xj is the flight distance between two successive
42
43 collisions, which is given by (Date et al., 2007):5)
pte

44
45 ∫
46 −lnξ L ∑
i−1

47 Xj = j and XRange = dx = Xj (34)

48
σtot N 0 j=1
49
50
Where j
σtot , is the total collision cross section for Epj energy. N = 7.13 · 1027 m−3
51
ce

is the density of adenine molecules and ξ is a random number (0 < ξ ≤ 1), the total
52
53 collision cross section consists of ionization and excitation by proton . Xrange is the total
54
55
depth traveled by proton in molecule of adenine. In this study the Bragg peak range is
56 estimated by using the equation 33. The relation X = X(j), according to equation 34,
Ac

57
58 provides a tool to calculate E(X) and the stopping power S(X) = dE(X)/dX as a
59
60
function of the position X. Figure 7 show the evolution of E(X) and S(X) as function

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4
3
5 6000
×10
1800

Energy (eV)

SP (MeV / cm)
6
E(X)
7 5000
1600
8 E(X)/dX 1400

pt
9
10 4000 1200
11 1000
12 3000
13 800

cri
14
2000 600
15
16 400
17 1000
200
18
19 0 0
0 0.005 0.01 0.015 0.02 0.025
20 X (cm)

us
21
22
23 Fig. 7. Stopping powers, SP = −dE(X)/dX, and energy E, versus ranges, X(cm), of proton
24 incident energy 5 M eV .
25
26
27
28
29 Table V.
an
The Bragg peak range calculated by our analytical program comapared with estimation,
30 SRIM and Geant4 methods.
31
32 Bragg peak range method (mm):
dM
33 Energy (MeV) SRIM Geant4 Work
34
35 3 0.126 0.098 0.102
36 5 0.255 0.238 0.272
37 20 2.960 2.826 2.886
38
39
40
41
42 of the position X for proton energy of 5 M eV in adenine and also shows a maximum
43
pte

44 just before the end of the path translating a complete stop of the proton incident ”Bragg
45 peak” who is located at 0.0272 cm depth. In table V the obtained results compared
46
47 with the results from Monte-Carlo method using GEANT4-DNA and SRIM toolkits.
48
49 We notice that our results are in agreement with the others from Monte-Carlo method.
50
51
ce

5. Conclusion
52
53 This analytical study offers the possibility of simulating very complex setups in order
54
55
to better understand the role played by the ionization, excitation, and electron capture
56 processes as well as to improve depth of the Bragg peak calculation algorithms the
Ac

57
58 proton in molecule of adenine.
59
60
Based on the semi-emprical model of Rudd26, 30) and our analytic approach, the system-

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4
5 atic calculations of the cross section for protons (ionization, excitation, and electron
6 capture) in molecule of adenine have been performed, and we develope an analytical
7
8 expression for calculating stopping power and Bragg peak position. The results from

pt
9
10 our cross section calculation are consistent with those from Iriki14, 15) and Tabet33) and
11 using the theoretical model of Tan et al the maximum relative difference produced for
12
13 stopping power calculation was 16%. Finally, we developed a model to characterize the

cri
14
15 proton Bragg peak position in the adenine molecule and to measure the target thickness
16 traversed by the proton beam. We showed an agreement between our results and those
17
18 estimated by the use of liquid water and other MC methods SRIM and Geant4-DNA.
19
20 The proposed model is useful as an alternative to traditional approaches, and is useful

us
21 for studies of various radiation effects in all biological material (Gaunine, Thymine, and
22
23 Cytosine).
24
25
26
27
28
29
an
30
31
32
dM
33
34
35
36
37
38
39
40
41
42
43
pte

44
45
46
47
48
49
50
51
ce

52
53
54
55
56
Ac

57
58
59
60

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4
5 References
6
7 1) A. Marouane, J. Inchaouh, S. Ouaskit, and A. Fathi, Appl. Radiat. Isotopes 70,
8 1089 (2012).

pt
9
10 2) M. A. Bernal, M. C. Bordage, J. M. C. Brown, M. Davı̀dkovà, E. Delage et al.,
11
12 Phys. Med. 31, 861 (2015a).
13 3) B. F. Minaev et al., J. Chem. Phys. 140, 184303 (2014).

cri
14
15 4) C. Champion, H. Lekadir, M. E. Galassi, O. Fojon, R. D. Rivarola, and J. Hanssen,
16
17 Phys. Med. Biol. 55, 6053 (2010).
18 5) K. L. Date and H. Sutherland, Nucl. Instrum. Methods Phys. Res. B 265, 515
19
20 (2007).

us
21
22 6) Z. Francis et al., Appl. Radiat. Isot. 69, 220 (2011a).
23 7) Z. Francis, S. Incerti, M. Karamitros, H. N. Tran, and C. Villagrasa, Nucl.
24
25 Instrum. Methods Phys. Res., Sect. B 269, 2307 (2011b).
26
27
28
29
an
8) R. Garcia-Molina et al., Nucl. Instrum. Methods B 267, 2647 (2009).
9) S. Heredia-Avalos and R. Garcia-Molina, Nucl. Instrum. Methods B 193, 15 (2002).
30 10) P. Ianik, F. A Cucinotta, and A. Francis, 2008. N. J. Phys. 10, (2008).
31
32 11) ICRU 1993 Stopping Powers and Ranges for Protons and Alpha Particles
dM
33 (Bethesda, MD: ICRU)
34
35 12) ICRU 2005 Stopping of ions heavier than helium ICRU Report 73 ed R. Bimbot
36
37 et al.
38 13) S. Incerti et al., Med. Phys. 37, 4692 (2010).
39
40 14) Y. Iriki, Y. Kikuchi, M. Imai, and A. Itoh, Phys. Rev. A 84, 032704 (2011a).
41
42 15) Y. Iriki, Y. Kikuchi, M. Imai, and A. Itoh, Phys. Rev. A 84, 052719 (2011b).
43
pte

16) J. C. Ashley, Phys.: Condens. Matter 3, 2741 (1991).

44
45 17) S. Kalbitzer, Proceedings of the 1978 International Conference on Ion Beam
46
47 Modification of Materials, Hungarian Academy of Sciences, Budapest, Hungary
48 (1979), p. 3.
49
50 18) J. A. LaVerne and S. M. Pimblott, dry DNA. Radiat. Res. 141, 208 (1995).
51
ce

52
19) H. Lekadir, I. Abbas, C. Champion, O. Fojòn, R. Rivarola and J. Hanssen, Phys.
53 Rev. A 79, 062710 (2009).
54
55 20) A. Marouane, S. Ouaskit, and J. Inchaouh, Radiat. Meas. 46, 988 (2011).
56
21) M. Dingfelder, M. Inokuti, and H. G. Paretzke, Radiat. Phys. Chem. 59, 255
Ac

57
58 (2000).
59
60

18/19
Page 19 of 19 AUTHOR SUBMITTED MANUSCRIPT - JJAP-101417.R3

1
2 Jpn. J. Appl. Phys. REGULAR PAPER
3
4
5 22) M. Dingfelder, I. G. Jorjishvili, J. A. Gersh, and L. H. Toburen, Radiat. Prot.
6 Dosim. 122, 26 (2006).
7
8 23) J. H. Millera and A. E. S.Green, Radiat. Res. 54, 343 (1973).

pt
9
10 24) M. Krim, et al. 2017., International Journal of Scientific and Engineering Research
11 8(3), 728 (2107).
12
13 25) R. G. Molina, I. Abril, C. D. Denton, S. H. Avalos, I. Kyriakou, and D.

cri
14
15 Emfietzoglou, Nucl. Instrum. Methods: Phys. Res. B 267, 2647 (2009).
16 26) M. E. Rudd, Nucl. Tracks Radiat. Meas. 16, 213 (1989).
17
18 27) M. E. Rudd, T. V. Goffe, R. D. Dubois, and L. H. Toburen, Phys. Rev. A 31, 492
19
20 (1985a).

us
21 28) M. E. Rudd, T. V. Goffe, R. D. DuBois, and L. H. Toburen, Phys. Rev. A 31, 492
22
23 (1985b).
24
25 29) M. E. Rudd, Phys. Rev. A 38, 6129 (1988).
26
27
28
29
an
30) M. E. Rudd, Radiat. Prot. Dosim. 31, 17 (1990).
31) P. Sigmund, A. Schinner and H. Paul 2009 Errata, and addenda for ICRU Report

30 73, stopping of ions heavier than helium J. ICRU 51

31 32) S. Uehara, L. H. Toburen, W. E. Wilson, D. T. Goodhead, and H. Nikjoo, Radiat.
32
dM
33 Phys. Chem. 59, 1 (2000)
34
35 33) J. Tabet, S. Eden, S. Feil, H. Abdoul-Carime, B. Farizon, M. Farizon, S. Ouaskit,
36 and T. D. Mark, Phys. Rev. A 82, 022703 (2010)
37
38 34) Z. Tan, Y. Xia, M. Zhao, and X. Liu, Nucl. Instrum. Methods Phys. Res., Sect. B
39
40 248, 1 (2006).
41 35) J. Turner, Atoms, Radiations and Radiation Protection, 3rd ed., Wiley, New York
42
43 (2007) p. 112-113.
pte

44
45 36) V. V. Afrosimov et al., Technical Physics 57(5), 594 (2012).
46 37) W. K. Chu, Proceedings of the 1978 International Conference on Ion Beam
47
48 Modification of Materials, Hungarian Academy of Sciences, Budapest, Hungary
49
50
(1979), p. 179.
51
ce

38) Z. Francis et al., J. Appl. Phys. 122, 014701 (2017).

52
53 39) J. F. Ziegler, J. P. Biersack, and M. D. Ziegler SRIM: The Stopping and Range of
54
55
Ions in Matter, SRIM Co., Chester, MD (USA), 2008.
56 40) J. F. Ziegler, J. Appl. Phys. 85, 1249 (1999).
Ac

57
58
59
60

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