| Geant4 Cross Reference |
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4 Geant4 - an Object-Oriented Toolkit for S
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7 moleculardna
8 ------------
9
10 A Geant4-DNA application for simulating DNA da
11
12 AUTHORS (alphabetical order)
13
14 J.M.C. Brown, K. Chatzipapas, P. Dondero, M. D
15 N. Lampe, D. Sakata, W.G. Shin, R. Stanzani, H
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17 (*) contact: tran@lp2ib.in2p3.fr
18
19 Dedicated website:
20 http://moleculardna.org
21 or
22 https://geant4-dna.github.io/molecular-docs/
23
24 This example is provided by the Geant4-DNA col
25 (http://geant4-dna.org)
26
27 These two PhD theses describe the chain:
28 W.-G. Shin (2020): https://tel.archives-ouvert
29 N. Lampe (2017): http://www.theses.fr/2017CLFA
30
31 Any report or published results obtained using
32 shall cite the following Geant4-DNA collaborat
33 Med. Phys. (2024) in press (https://doi.org/10
34 Med. Phys. 45 (2018) e722-e739
35 Phys. Med. 31 (2015) 861-874
36 Med. Phys. 37 (2010) 4692-4708
37 Int. J. Model. Simul. Sci. Comput. 1 (2010) 15
38
39 Related publications can be found at:
40 http://geant4-dna.org
41
42 0 - INTRODUCTION
43
44 This example shows how to simulate physics
45 chemistry processes in DNA geometries to p
46
47 A more detailed description is available a
48
49 To build the example:
50 mkdir build
51 cd build
52 cmake ../pathToExamples/moleculardna
53 make
54
55 To run the example:
56 ./molecular -m cylinders.mac -t 2 -p 2
57 # -m : macro file
58 # -t : number of threads to run
59 # -p : physics list option
60
61 Macro files can control every aspect of th
62 https://geant4-dna.github.io/molecular-doc
63
64 The macro commands of this example are lis
65 https://geant4-dna.github.io/molecular-doc
66
67 1 - GEOMETRY DEFINITION
68
69 The geometry is built from text files for
70 ecoli (ecoli.mac) and human cell (human_ce
71
72 - cylinders.mac: to build a 3 μm sphere f
73 long straight DNA segments in a 100×30Ã
74 This is a geometry used for parameter (o
75
76 - plasmid.mac: to model a cube of liquid w
77 10 000 plasmids (pBR322, 4367 base pairs
78
79 - ecoli.mac: to demonstrate a simple model
80 large scale fractal ‘Hilbert curve’
81
82 - human_cell.mac, human_cell_HTB177.mac an
83 three different cell geometries, as deta
84 be used to produce data that serve as in
85
86 - human_cell_chromosomes.mac: to model the
87 as detailed in [4].
88
89 More geometry information can be found in
90
91 To construct other DNA geometries, see htt
92
93 To construct chromosomal or other complex
94
95 Macro commands can be used to control the
96
97 # Commands for world and cell dimensions
98 /world/worldSize 10200 nm
99 /cell/radiusSize 3 3 3 um
100
101 # Command to select the chemistry model (o
102 /process/chem/TimeStepModel IRT_syn
103
104 # End time of chemistry simulation
105 /scheduler/endTime 1 us
106
107 # Set voxel optimisation
108 /dnageom/setSmartVoxels 1
109
110 # Check overlaps in DNA geometry region
111 /dnageom/checkOverlaps false
112
113 # Distance from base pairs at which radica
114 /dnageom/radicalKillDistance 9 nm
115
116 # Deposited energy accumulation range limi
117 /dnageom/interactionDirectRange 7 angstrom
118
119 # Side length for each placement (x, y, z)
120 /dnageom/placementSize 30 30 100 nm
121
122 # Scaling of XYZ in fractal definition fil
123 /dnageom/fractalScaling 1 1 1 nm
124
125 # Path to file that defines placement loca
126 /dnageom/definitionFile geometries/prisms2
127
128 # Set a placement volume [format] [name pa
129 /dnageom/placementVolume prism geometries/
130
131 # Take the angles in the voxel placement f
132 # E.g. set to true if the angle 0.5 should
133 /dnageom/setVoxelPlacementAnglesAsMultiple
134
135 # The molecule size columns are optional,
136 # fall back onto the default sizes or be s
137 # used default moleculeSize (as belows)
138 /dnageom/useCustomMoleculeSizes false # de
139 #/dnageom/moleculeSize
140
141 # Draw cell/chromosome volumes rather than
142 /dnageom/drawCellVolumes false # default
143
144 # Activate Histone scavenging function wit
145 /dnageom/activateHistoneScavenging true #
146
147 # DNA geometries are only ever placed in a
148 /chromosome/add cylinder sphere 3000 0 0 0
149
150 # For the visualisation of DNA geometries,
151 /control/execute vis.mac
152 # More specifically, start moleculardna us
153 # to open the Qt visualiser. Then use the
154 # /control/execute cylinders.mac
155 # For the visualization, large amount of R
156 # using cylinders DNA geometries, to visua
157 # are needed. For 2000 cylinders, ~11 GB a
158
159 The DNA parallel world can be activated us
160 in the PhysicsList.cc and DetectorConstruc
161 Setting "useParallelPhysicsWorld = false"
162 with the water volume. Energy deposition i
163 recorded using octree data structures asso
164
165 2 - PHYSICS LIST
166
167 The physics list can use the recommended G
168 G4EmDNAPhysics_option4 or
169 G4EmDNAPhysics_option6 constructors.
170
171 3 - PRIMARY GENERATOR
172
173 The source can be specified via General Pa
174 macro files.
175
176 4 - DNA DAMAGE MODEL
177
178 Mechanistic DNA simulations are dependent
179 DNA damage model to relate energy depositi
180 and chemical reactions with DNA, to actual
181
182 The following macro commands can be used t
183
184 # Direct damage threshold
185 /dnadamage/directDamageLower 17.5 eV
186 /dnadamage/directDamageUpper 17.5 eV
187
188 # Indirect damage probability to create a
189 # OH radical + DNA base
190 /dnadamage/indirectOHBaseChance 1.0
191 /dnadamage/indirectOHStrandChance 0.65
192 /dnadamage/inductionOHChance 0.0
193
194 # H radicals + DNA base
195 /dnadamage/indirectHBaseChance 1.0
196 /dnadamage/indirectHStrandChance 0.65
197 /dnadamage/inductionHChance 0.0
198
199 # e_aq radicals + base
200 /dnadamage/indirectEaqBaseChance 1.0
201 /dnadamage/indirectEaqStrandChance 0.65
202 /dnadamage/inductionEaqChance 0.0
203
204 5 - RESULTS
205
206 # Bool to set whether strands ought be sav
207 /analysisDNA/saveStrands false # default
208
209 # Directory to save DNA damage fragments
210 /analysisDNA/strandDir
211
212 # Gap between DNA fragments in base pairs
213 # Set to zero to score placement volumes i
214 /analysisDNA/fragmentGap 0
215
216 # To save the position of hits histos only
217 /analysisDNA/diagnosticChain
218
219 Several ROOT macro files are provided in t
220 - cylinders.C: to plot damage from cylinde
221 - ecoli.C: to plot damage from ecoli geome
222 - human_cell.C: to plot damage and fragmen
223 geometries. The human_cell_alphas.C macr
224 - plasmid.C: to plot damage and fragments
225 - human_cell_chromosomes.C: to plot damage
226 from human_cell_chromosomes geometries.
227
228 A python macro file is provided to modify
229 - createSDD.py: to use it, insert the com
230 If error with ROOT, simpl
231 source /path/to/root/bin/
232 do "pip install pyroot" a
233
234 A python macro file is provided to analyse
235 - human_cell_chromosomes.py: to use it, in
236
237
238 A python macro file to calculate repair ki
239 repair_survival_models. This script can be
240 file human_cell (10^5 primaries) to reprod
241 - molecularDNArepair.py: to use it, inser
242 The molecular-dn
243 the human-cell.m
244
245 A python macro file to calculate the survi
246 in the folder repair_survival_models. This
247 to fit any data.
248 - molecularDNAsurvival.py: to use it, ins
249 The molecular-
250 the human-cell
251
252 6 - PHASE SPACE READING
253
254 The example can read a phase space file as
255 defined in the csv format used by the GRAS
256 An example of phase space file and the mac
257 "/phase_space" subdirectory.
258 This simple phase space file only provides
259 45 keV on a randomly shaped surface based
260
261 7 - REFERENCES
262
263 [1] https://doi.org/10.1016/j.ejmp.2023.10
264 [2] https://doi.org/10.1667/RR15209.1
265 [3] https://doi.org/10.1002/pro6.1186
266 [4] https://doi.org/10.1016/j.ejmp.2024.10
267 [5] https://spitfire.estec.esa.int/trac/GR
268
269 An alternative example for DNA damage calculat