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27 /// \file G4EmDNAChemistry_option3_Extended.cc
28 /// \brief Implementation of the G4EmDNAChemistry_option3_Extended class
29
30 #include "G4EmDNAChemistry_option3_Extended.hh"
31
32 #include "G4DNAMolecule.hh"
33 #include "G4MoleculeTable.hh"
34
35 // particles
36 #include "G4H2O.hh"
37 #include "G4H2.hh"
38 #include "G4Hydrogen.hh"
39 #include "G4OH.hh"
40 #include "G4H3O.hh"
41 #include "G4Electron_aq.hh"
42
43 #include "G4H2O2.hh"
44 #include "G4O2.hh"
45 #include "G4HO2.hh"
46
47 #include "G4PhysicalConstants.hh"
48 #include "G4SystemOfUnits.hh"
49 #include "G4DNAIndependentReactionTimeModel.hh"
50 #include "G4DNAMolecularReactionTable.hh"
51
52 #include "G4ChemicalMoleculeFinder.hh"
53 // factory
54 #include "G4PhysicsConstructorFactory.hh"
55
56 G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistry_option3_Extended);
57
58 void G4EmDNAChemistry_option3_Extended::ConstructParticle()
59 {
60 ConstructMolecule(); //from G4EmDNAChemistry_option3
61 //dna molecules
62 G4Deoxyribose::Definition();
63 G4Phosphate::Definition();
64 G4Adenine::Definition();
65 G4Guanine::Definition();
66 G4Thymine::Definition();
67 G4Cytosine::Definition();
68 G4Histone::Definition();
69 //damaged molecules
70 G4DamagedDeoxyribose::Definition();
71 G4DamagedAdenine::Definition();
72 G4DamagedGuanine::Definition();
73 G4DamagedThymine::Definition();
74 G4DamagedCytosine::Definition();
75 G4ModifiedHistone::Definition();
76 //________________DNA_______________________________________________
77 auto table = G4MoleculeTable::Instance();
78 table->CreateConfiguration("Deoxyribose",G4Deoxyribose::Definition());
79 table->CreateConfiguration("Phosphate",G4Phosphate::Definition());
80 table->CreateConfiguration("Adenine",G4Adenine::Definition());
81 table->CreateConfiguration("Thymine",G4Thymine::Definition());
82 table->CreateConfiguration("Guanine",G4Guanine::Definition());
83 table->CreateConfiguration("Cytosine",G4Cytosine::Definition());
84 table->CreateConfiguration("Histone",G4Histone::Definition());
85
86 //damaged DNAElement Configuration
87
88 table->CreateConfiguration("Damaged_Deoxyribose",
89 G4DamagedDeoxyribose::Definition());
90 table->CreateConfiguration("Damaged_Adenine",
91 G4DamagedAdenine::Definition());
92 table->CreateConfiguration("Damaged_Thymine",
93 G4DamagedThymine::Definition());
94 table->CreateConfiguration("Damaged_Guanine",
95 G4DamagedGuanine::Definition());
96 table->CreateConfiguration("Damaged_Cytosine",
97 G4DamagedCytosine::Definition());
98 }
99
100 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
101
102 void G4EmDNAChemistry_option3_Extended::ConstructReactionTable(
103 G4DNAMolecularReactionTable* theReactionTable)
104 {
105 G4EmDNAChemistry_option3::ConstructReactionTable(theReactionTable);//from G4EmDNAChemistry_option3
106
107 //Get the molecular configuration
108 auto table = G4MoleculeTable::Instance();
109 G4MolecularConfiguration* OH = table->GetConfiguration("°OH");
110 G4MolecularConfiguration* OHm = table->GetConfiguration("OHm");
111 G4MolecularConfiguration* e_aq = table->GetConfiguration("e_aq");
112 G4MolecularConfiguration* H2 = table->GetConfiguration("H2");
113 G4MolecularConfiguration* H3Op = table->GetConfiguration("H3Op");
114 G4MolecularConfiguration* H = table->GetConfiguration("H");
115 G4MolecularConfiguration* H2O2 = table->GetConfiguration("H2O2");
116
117 // DNA additions--------------------------------------------------
118 G4MolecularConfiguration* deoxyribose = table->GetConfiguration("Deoxyribose");
119 G4MolecularConfiguration* adenine = table->GetConfiguration("Adenine");
120 G4MolecularConfiguration* guanine = table->GetConfiguration("Guanine");
121 G4MolecularConfiguration* thymine = table->GetConfiguration("Thymine");
122 G4MolecularConfiguration* cytosine = table->GetConfiguration("Cytosine");
123 G4MolecularConfiguration* histone = table->GetConfiguration("Histone");
124
125 G4MolecularConfiguration* damage_deoxyribose = table->GetConfiguration("Damaged_Deoxyribose");
126 G4MolecularConfiguration* damage_adenine = table->GetConfiguration("Damaged_Adenine");
127 G4MolecularConfiguration* damage_guanine = table->GetConfiguration("Damaged_Guanine");
128 G4MolecularConfiguration* damage_thymine = table->GetConfiguration("Damaged_Thymine");
129 G4MolecularConfiguration* damage_cytosine = table->GetConfiguration("Damaged_Cytosine");
130
131
132 // OH and DNA
133
134 // 2-Deoxyribose + OH -> damagedDeoxyribose
135 G4DNAMolecularReactionData* reactionData = new G4DNAMolecularReactionData(
136 1.80e9*(1e-3*m3/(mole*s)), deoxyribose, OH);
137 reactionData->AddProduct(damage_deoxyribose);
138 reactionData->SetReactionType(1);
139 theReactionTable->SetReaction(reactionData);
140
141 // adenine + OH -> ...
142 reactionData = new G4DNAMolecularReactionData(
143 6.10e9*(1e-3*m3/(mole*s)), adenine, OH);
144 reactionData->AddProduct(damage_adenine);
145 reactionData->SetReactionType(1);
146 theReactionTable->SetReaction(reactionData);
147
148 // guanine + OH -> ...
149 reactionData = new G4DNAMolecularReactionData(
150 9.20e9*(1e-3*m3/(mole*s)), guanine, OH);
151 reactionData->AddProduct(damage_guanine);
152 reactionData->SetReactionType(1);
153 theReactionTable->SetReaction(reactionData);
154
155 // thymine + OH -> ...
156 reactionData = new G4DNAMolecularReactionData(
157 6.40e9*(1e-3*m3/(mole*s)), thymine, OH);
158 reactionData->AddProduct(damage_thymine);
159 reactionData->SetReactionType(1);
160 theReactionTable->SetReaction(reactionData);
161
162 // cytosine + OH -> ...
163 reactionData = new G4DNAMolecularReactionData(
164 6.10e9*(1e-3*m3/(mole*s)), cytosine, OH);
165 reactionData->AddProduct(damage_cytosine);
166 reactionData->SetReactionType(1);
167 theReactionTable->SetReaction(reactionData);
168
169 // Hydrated e- and DNA
170
171 // Deoxyribose + Hydrated e- -> ...
172 reactionData = new G4DNAMolecularReactionData(
173 0.01e9*(1e-3*m3/(mole*s)), deoxyribose, e_aq);
174 reactionData->AddProduct(damage_deoxyribose);
175 reactionData->SetReactionType(1);
176 theReactionTable->SetReaction(reactionData);
177
178 // adenine + Hydrated e- -> ...
179 reactionData = new G4DNAMolecularReactionData(
180 9e9*(1e-3*m3/(mole*s)), adenine, e_aq);
181 reactionData->AddProduct(damage_adenine);
182 reactionData->SetReactionType(1);
183 theReactionTable->SetReaction(reactionData);
184
185 // guanine + Hydrated e- -> ...
186 reactionData = new G4DNAMolecularReactionData(
187 14e9*(1e-3*m3/(mole*s)), guanine, e_aq);
188 reactionData->AddProduct(damage_guanine);
189 reactionData->SetReactionType(1);
190 theReactionTable->SetReaction(reactionData);
191
192 // thymine + Hydrated e- -> ...
193 reactionData = new G4DNAMolecularReactionData(
194 18e9*(1e-3*m3/(mole*s)), thymine, e_aq);
195 reactionData->AddProduct(damage_thymine);
196 reactionData->SetReactionType(1);
197 theReactionTable->SetReaction(reactionData);
198
199 // cytosine + Hydrated e- -> ...
200 reactionData = new G4DNAMolecularReactionData(
201 13e9*(1e-3*m3/(mole*s)), cytosine, e_aq);
202 reactionData->AddProduct(damage_cytosine);
203 reactionData->SetReactionType(1);
204 theReactionTable->SetReaction(reactionData);
205
206 // Radical H and DNA
207
208 // Deoxyribose + Radical H -> ...
209 reactionData = new G4DNAMolecularReactionData(
210 0.029e9*(1e-3*m3/(mole*s)), deoxyribose, H);
211 reactionData->AddProduct(damage_deoxyribose);
212 reactionData->SetReactionType(1);
213 theReactionTable->SetReaction(reactionData);
214
215 // adenine + Radical H -> ...
216 reactionData = new G4DNAMolecularReactionData(
217 0.10e9*(1e-3*m3/(mole*s)), adenine, H);
218 reactionData->AddProduct(damage_adenine);
219 reactionData->SetReactionType(1);
220 theReactionTable->SetReaction(reactionData);
221
222 // thymine + Radical H -> ...
223 reactionData = new G4DNAMolecularReactionData(
224 0.57e9*(1e-3*m3/(mole*s)), thymine, H);
225 reactionData->AddProduct(damage_thymine);
226 reactionData->SetReactionType(1);
227 theReactionTable->SetReaction(reactionData);
228
229 // cytosine + Radical H -> ...
230 reactionData = new G4DNAMolecularReactionData(
231 0.092e9*(1e-3*m3/(mole*s)), cytosine, H);
232 reactionData->AddProduct(damage_cytosine);
233 reactionData->SetReactionType(1);
234 theReactionTable->SetReaction(reactionData);
235
236 //histone + all molecules -> modification(or "damage")
237
238 reactionData = new G4DNAMolecularReactionData(
239 0.0*(1e-3*m3/(mole*s)), histone, OH);
240 reactionData->AddProduct(histone);
241 reactionData->SetEffectiveReactionRadius(
242 2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
243 reactionData->SetReactionType(1);
244 theReactionTable->SetReaction(reactionData);
245
246 reactionData = new G4DNAMolecularReactionData(
247 0.0*(1e-3*m3/(mole*s)), histone, OHm);
248 reactionData->AddProduct(histone);
249 reactionData->SetEffectiveReactionRadius(
250 2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
251 reactionData->SetReactionType(1);
252 theReactionTable->SetReaction(reactionData);
253
254 reactionData = new G4DNAMolecularReactionData(
255 0.0*(1e-3*m3/(mole*s)), histone, e_aq);
256 reactionData->AddProduct(histone);
257 reactionData->SetEffectiveReactionRadius(
258 2.4*nm + G4Electron_aq::Definition()->GetVanDerVaalsRadius());
259 reactionData->SetReactionType(1);
260 theReactionTable->SetReaction(reactionData);
261
262 reactionData = new G4DNAMolecularReactionData(
263 0.0*(1e-3*m3/(mole*s)), histone, H2);
264 reactionData->AddProduct(histone);
265 reactionData->SetEffectiveReactionRadius(
266 2.4*nm + G4H2::Definition()->GetVanDerVaalsRadius());
267 reactionData->SetReactionType(1);
268 theReactionTable->SetReaction(reactionData);
269
270 reactionData = new G4DNAMolecularReactionData(
271 0.0*(1e-3*m3/(mole*s)), histone, H3Op);
272 reactionData->AddProduct(histone);
273 reactionData->SetEffectiveReactionRadius(
274 2.4*nm + G4H3O::Definition()->GetVanDerVaalsRadius());
275 reactionData->SetReactionType(1);
276 theReactionTable->SetReaction(reactionData);
277
278 reactionData = new G4DNAMolecularReactionData(
279 0.0*(1e-3*m3/(mole*s)), histone, H);
280 reactionData->AddProduct(histone);
281 reactionData->SetEffectiveReactionRadius(
282 2.4*nm + G4Hydrogen::Definition()->GetVanDerVaalsRadius());
283 reactionData->SetReactionType(1);
284 theReactionTable->SetReaction(reactionData);
285
286 reactionData = new G4DNAMolecularReactionData(
287 0.0*(1e-3*m3/(mole*s)), histone, H2O2);
288 reactionData->AddProduct(histone);
289 reactionData->SetEffectiveReactionRadius(
290 2.4*nm + G4H2O2::Definition()->GetVanDerVaalsRadius());
291 reactionData->SetReactionType(1);
292 theReactionTable->SetReaction(reactionData);
293 }
294
295