| Geant4 Cross Reference |
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26
27 #include "ChemistryList.hh"
28
29 #include "G4DNAChemistryManager.hh"
30 #include "G4DNAWaterDissociationDisplacer.hh"
31 #include "G4DNAWaterExcitationStructure.hh"
32 #include "G4PhysicalConstants.hh"
33 #include "G4ProcessManager.hh"
34 #include "G4SystemOfUnits.hh"
35 // *** Processes and models for Geant4-DNA
36 #include "DetectorConstruction.hh"
37 #include "IRTDamageReactionModel.hh"
38
39 #include "G4ChemicalMoleculeFinder.hh"
40 #include "G4DNABrownianTransportation.hh"
41 #include "G4DNAElectronHoleRecombination.hh"
42 #include "G4DNAElectronSolvation.hh"
43 #include "G4DNAIndependentReactionTimeModel.hh"
44 #include "G4DNAMolecularDissociation.hh"
45 #include "G4DNAMolecularReactionTable.hh"
46 #include "G4DNAMoleculeEncounterStepper.hh"
47 #include "G4DNAPolyNucleotideReactionProcess.hh"
48 #include "G4DNASancheExcitationModel.hh"
49 #include "G4DNAUeharaScreenedRutherfordElasticModel.hh"
50 #include "G4DNAVibExcitation.hh"
51 #include "G4Electron.hh"
52 #include "G4Electron_aq.hh"
53 #include "G4H2.hh"
54 #include "G4H2O.hh"
55 #include "G4H2O2.hh"
56 #include "G4H3O.hh"
57 #include "G4HO2.hh"
58 #include "G4Hydrogen.hh"
59 #include "G4MolecularConfiguration.hh"
60 #include "G4MoleculeTable.hh"
61 #include "G4O2.hh"
62 #include "G4O3.hh"
63 #include "G4OH.hh"
64 #include "G4Oxygen.hh"
65 #include "G4PhysicsListHelper.hh"
66 #include "G4ProcessTable.hh"
67 #include "G4RunManager.hh"
68 #include "G4VDNAHitModel.hh"
69 #include "G4VDNAReactionModel.hh"
70 #include "G4ChemDissociationChannels_option1.hh"
71
72 ChemistryList::ChemistryList() : G4VUserChemistryList(true)
73 {
74 G4DNAChemistryManager::Instance()->SetChemistryList(this);
75 }
76
77 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
78
79 void ChemistryList::ConstructMolecule()
80 {
81 //-----------------------------------
82 // Create the definition
83
84 G4H2O::Definition();
85 G4Hydrogen::Definition();
86 G4H3O::Definition();
87 G4OH::Definition();
88 G4Electron_aq::Definition();
89 G4H2O2::Definition();
90 G4H2::Definition();
91
92 G4O2::Definition();
93 G4HO2::Definition();
94 G4Oxygen::Definition();
95 G4O3::Definition();
96
97 auto G4OHm = new G4MoleculeDefinition("OH",/*mass*/ 17.00734 * g / Avogadro * c_squared,
98 2.8e-9 * (m * m / s), -1,
99 5, 0.958 * angstrom, // radius
100 2 // number of atoms
101 );
102
103 auto G4HO2m = new G4MoleculeDefinition("HO_2", 33.0034 * g / Avogadro * c_squared,
104 2.3e-9 * (m * m / s), -1, 0,
105 2.1 * angstrom, 3);
106 //____________________________________________________________________________
107
108 G4MoleculeTable::Instance()->CreateConfiguration("H3Op", G4H3O::Definition());
109 G4MolecularConfiguration* OHm =
110 G4MoleculeTable::Instance()->CreateConfiguration("OHm", // just a tag to store and retrieve
111 // from G4MoleculeTable
112 G4OHm,
113 -1, // charge
114 5.0e-9 * (m2 / s));
115 OHm->SetMass(17.0079 * g / Avogadro * c_squared);
116 G4MoleculeTable::Instance()->CreateConfiguration("°OH", G4OH::Definition());
117 G4MoleculeTable::Instance()->CreateConfiguration("e_aq", G4Electron_aq::Definition());
118 G4MoleculeTable::Instance()->CreateConfiguration("H", G4Hydrogen::Definition());
119 G4MoleculeTable::Instance()->CreateConfiguration("H2", G4H2::Definition());
120 G4MoleculeTable::Instance()->CreateConfiguration("H2O2", G4H2O2::Definition());
121
122 // molecules extension (RITRACKS)
123
124 G4MoleculeTable::Instance()->CreateConfiguration("HO2°", G4HO2::Definition());
125 G4MoleculeTable::Instance()->GetConfiguration("HO2°")->SetVanDerVaalsRadius(0.21 * nm);
126
127 G4MolecularConfiguration* HO2m =
128 G4MoleculeTable::Instance()->CreateConfiguration("HO2m", // just a tag to store and retrieve
129 // from G4MoleculeTable
130 G4HO2m,
131 -1, // charge
132 1.4e-9 * (m2 / s));
133 HO2m->SetMass(33.00396 * g / Avogadro * c_squared);
134 HO2m->SetVanDerVaalsRadius(0.25 * nm);
135
136 G4MoleculeTable::Instance()->CreateConfiguration("Oxy", G4Oxygen::Definition());
137 G4MoleculeTable::Instance()->GetConfiguration("Oxy")->SetVanDerVaalsRadius(0.20 * nm);
138
139 G4MolecularConfiguration* Om =
140 G4MoleculeTable::Instance()->CreateConfiguration("Om", // just a tag to store and retrieve from
141 // G4MoleculeTable
142 G4Oxygen::Definition(),
143 -1, // charge
144 2.0e-9 * (m2 / s));
145 Om->SetMass(15.99829 * g / Avogadro * c_squared);
146 Om->SetVanDerVaalsRadius(0.25 * nm);
147
148 G4MoleculeTable::Instance()->CreateConfiguration("O2", G4O2::Definition());
149 G4MoleculeTable::Instance()->GetConfiguration("O2")->SetVanDerVaalsRadius(0.17 * nm);
150
151 G4MolecularConfiguration* O2m =
152 G4MoleculeTable::Instance()->CreateConfiguration("O2m", // just a tag to store and retrieve
153 // from G4MoleculeTable
154 G4O2::Definition(),
155 -1, // charge
156 1.75e-9 * (m2 / s));
157 O2m->SetMass(31.99602 * g / Avogadro * c_squared);
158 O2m->SetVanDerVaalsRadius(0.22 * nm);
159
160 G4MoleculeTable::Instance()->CreateConfiguration("O3", G4O3::Definition());
161 G4MoleculeTable::Instance()->GetConfiguration("O3")->SetVanDerVaalsRadius(0.20 * nm);
162
163 G4MolecularConfiguration* O3m =
164 G4MoleculeTable::Instance()->CreateConfiguration("O3m", // just a tag to store and retrieve
165 // from G4MoleculeTable
166 G4O3::Definition(),
167 -1, // charge
168 2.0e-9 * (m2 / s));
169 O3m->SetMass(47.99375 * g / Avogadro * c_squared);
170 O3m->SetVanDerVaalsRadius(0.20 * nm);
171
172 G4MoleculeDefinition* A = G4MoleculeTable::Instance()->CreateMoleculeDefinition("ADENINE", 0);
173 G4MoleculeTable::Instance()->CreateConfiguration("A", A);
174
175 G4MoleculeDefinition* T = G4MoleculeTable::Instance()->CreateMoleculeDefinition("THYMINE", 0);
176 G4MoleculeTable::Instance()->CreateConfiguration("T", T);
177
178 G4MoleculeDefinition* G = G4MoleculeTable::Instance()->CreateMoleculeDefinition("GUANINE", 0);
179 G4MoleculeTable::Instance()->CreateConfiguration("G", G);
180
181 G4MoleculeDefinition* C = G4MoleculeTable::Instance()->CreateMoleculeDefinition("CYTOSINE", 0);
182 G4MoleculeTable::Instance()->CreateConfiguration("C", C);
183
184 G4MoleculeDefinition* S = G4MoleculeTable::Instance()->CreateMoleculeDefinition("SUGAR", 0);
185 G4MoleculeTable::Instance()->CreateConfiguration("Sugar", S);
186
187 G4DNAMolecularMaterial* molMaterialManager = G4DNAMolecularMaterial::Instance();
188
189 molMaterialManager->SetMolecularConfiguration(G4Material::GetMaterial("G4_DNA_DEOXYRIBOSE"),
190 "Sugar");
191 molMaterialManager->SetMolecularConfiguration("G4_DNA_PHOSPHATE", "Sugar");
192 molMaterialManager->SetMolecularConfiguration(G4Material::GetMaterial("G4_DNA_ADENINE"), "A");
193 molMaterialManager->SetMolecularConfiguration(G4Material::GetMaterial("G4_DNA_THYMINE"), "T");
194 molMaterialManager->SetMolecularConfiguration(G4Material::GetMaterial("G4_DNA_GUANINE"), "G");
195 molMaterialManager->SetMolecularConfiguration(G4Material::GetMaterial("G4_DNA_CYTOSINE"), "C");
196 }
197
198 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
199
200 void ChemistryList::ConstructDissociationChannels()
201 {
202 G4ChemDissociationChannels_option1::ConstructDissociationChannels();
203 }
204
205 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
206
207 void ChemistryList::ConstructReactionTable(G4DNAMolecularReactionTable* theReactionTable)
208 {
209 //-----------------------------------
210 // Get the molecular configuration
211 G4MolecularConfiguration* OH = G4MoleculeTable::Instance()->GetConfiguration("°OH");
212 G4MolecularConfiguration* OHm = G4MoleculeTable::Instance()->GetConfiguration("OHm");
213 G4MolecularConfiguration* e_aq = G4MoleculeTable::Instance()->GetConfiguration("e_aq");
214 G4MolecularConfiguration* H2 = G4MoleculeTable::Instance()->GetConfiguration("H2");
215 G4MolecularConfiguration* H3Op = G4MoleculeTable::Instance()->GetConfiguration("H3Op");
216 G4MolecularConfiguration* H = G4MoleculeTable::Instance()->GetConfiguration("H");
217 G4MolecularConfiguration* H2O2 = G4MoleculeTable::Instance()->GetConfiguration("H2O2");
218 G4MolecularConfiguration* HO2 = G4MoleculeTable::Instance()->GetConfiguration("HO2°");
219 G4MolecularConfiguration* HO2m = G4MoleculeTable::Instance()->GetConfiguration("HO2m");
220 G4MolecularConfiguration* O = G4MoleculeTable::Instance()->GetConfiguration("Oxy");
221 G4MolecularConfiguration* Om = G4MoleculeTable::Instance()->GetConfiguration("Om");
222 G4MolecularConfiguration* O2 = G4MoleculeTable::Instance()->GetConfiguration("O2");
223 G4MolecularConfiguration* O2m = G4MoleculeTable::Instance()->GetConfiguration("O2m");
224 G4MolecularConfiguration* O3 = G4MoleculeTable::Instance()->GetConfiguration("O3");
225 G4MolecularConfiguration* O3m = G4MoleculeTable::Instance()->GetConfiguration("O3m");
226
227 // Type I //
228 //------------------------------------------------------------------
229 // *H + *H -> H2
230 auto* reactionData = new G4DNAMolecularReactionData(0.503e10 * (1e-3 * m3 / (mole * s)), H, H);
231 reactionData->AddProduct(H2);
232 theReactionTable->SetReaction(reactionData);
233 //------------------------------------------------------------------
234 // e_aq + H* + H2O -> H2 + OH-
235 reactionData = new G4DNAMolecularReactionData(2.50e10 * (1e-3 * m3 / (mole * s)), e_aq, H);
236 reactionData->AddProduct(OHm);
237 reactionData->AddProduct(H2);
238 theReactionTable->SetReaction(reactionData);
239
240 // H + O(3p) -> OH
241 reactionData = new G4DNAMolecularReactionData(2.02e10 * (1e-3 * m3 / (mole * s)), H, O);
242 reactionData->AddProduct(OH);
243 theReactionTable->SetReaction(reactionData);
244 //------------------------------------------------------------------
245 // H + O- -> OH-
246 reactionData = new G4DNAMolecularReactionData(2.00e10 * (1e-3 * m3 / (mole * s)), H, Om);
247 reactionData->AddProduct(OHm);
248 theReactionTable->SetReaction(reactionData);
249 //------------------------------------------------------------------
250 // OH + O(3p) -> HO2
251 reactionData = new G4DNAMolecularReactionData(2.02e10 * (1e-3 * m3 / (mole * s)), OH, O);
252 reactionData->AddProduct(HO2);
253 theReactionTable->SetReaction(reactionData);
254 //------------------------------------------------------------------
255 // HO2 + O(3p) -> O2
256 reactionData = new G4DNAMolecularReactionData(2.02e10 * (1e-3 * m3 / (mole * s)), HO2, O);
257 reactionData->AddProduct(O2);
258 reactionData->AddProduct(OH);
259 theReactionTable->SetReaction(reactionData);
260 //------------------------------------------------------------------
261 // O(3p) + O(3p) -> O2
262 reactionData = new G4DNAMolecularReactionData(2.20e10 * (1e-3 * m3 / (mole * s)), O, O);
263 reactionData->AddProduct(O2);
264 theReactionTable->SetReaction(reactionData);
265
266 // Type III //
267 //------------------------------------------------------------------
268 // e_aq + e_aq + 2H2O -> H2 + 2OH-
269 reactionData = new G4DNAMolecularReactionData(0.636e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
270 reactionData->AddProduct(OHm);
271 reactionData->AddProduct(OHm);
272 reactionData->AddProduct(H2);
273 theReactionTable->SetReaction(reactionData);
274 //------------------------------------------------------------------
275 // H3O+ + OH- -> 2H2O
276 reactionData = new G4DNAMolecularReactionData(1.13e11 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
277 theReactionTable->SetReaction(reactionData);
278 //------------------------------------------------------------------
279 // H3O+ + O3- -> OH + O2
280 reactionData = new G4DNAMolecularReactionData(9.0e10 * (1e-3 * m3 / (mole * s)), H3Op, O3m);
281 reactionData->AddProduct(OH);
282 reactionData->AddProduct(O2);
283 theReactionTable->SetReaction(reactionData);
284
285 // Type II //
286
287 //------------------------------------------------------------------
288 // *OH + *H -> H2O
289 reactionData = new G4DNAMolecularReactionData(1.55e10 * (1e-3 * m3 / (mole * s)), OH, H);
290 reactionData->SetReactionType(1);
291 theReactionTable->SetReaction(reactionData);
292 //------------------------------------------------------------------
293 // H + H2O2 -> OH
294 reactionData = new G4DNAMolecularReactionData(3.50e7 * (1e-3 * m3 / (mole * s)), H, H2O2);
295 reactionData->AddProduct(OH);
296 reactionData->SetReactionType(1);
297 theReactionTable->SetReaction(reactionData);
298 //------------------------------------------------------------------
299 // H + OH- -> eaq-
300 reactionData = new G4DNAMolecularReactionData(2.51e7 * (1e-3 * m3 / (mole * s)), H, OHm);
301 reactionData->AddProduct(e_aq);
302 reactionData->SetReactionType(1);
303 theReactionTable->SetReaction(reactionData);
304 //------------------------------------------------------------------
305 // H + O2 -> HO2
306 reactionData = new G4DNAMolecularReactionData(2.10e10 * (1e-3 * m3 / (mole * s)), H, O2);
307 reactionData->AddProduct(HO2);
308 reactionData->SetReactionType(1);
309 theReactionTable->SetReaction(reactionData);
310 //------------------------------------------------------------------
311 // H + HO2 -> H2O2
312 reactionData = new G4DNAMolecularReactionData(1.00e10 * (1e-3 * m3 / (mole * s)), H, HO2);
313 reactionData->AddProduct(H2O2);
314 reactionData->SetReactionType(1);
315 theReactionTable->SetReaction(reactionData);
316 //------------------------------------------------------------------
317 // H + O2- -> HO2-
318 reactionData = new G4DNAMolecularReactionData(1.00e10 * (1e-3 * m3 / (mole * s)), H, O2m);
319 reactionData->AddProduct(HO2m);
320 reactionData->SetReactionType(1);
321 theReactionTable->SetReaction(reactionData);
322 //------------------------------------------------------------------
323 // *OH + *OH -> H2O2
324 reactionData = new G4DNAMolecularReactionData(0.55e10 * (1e-3 * m3 / (mole * s)), OH, OH);
325 reactionData->AddProduct(H2O2);
326 reactionData->SetReactionType(1);
327 theReactionTable->SetReaction(reactionData);
328 //------------------------------------------------------------------
329 // OH + H2O2 -> HO2
330 reactionData = new G4DNAMolecularReactionData(2.88e7 * (1e-3 * m3 / (mole * s)), OH, H2O2);
331 reactionData->AddProduct(HO2);
332 reactionData->SetReactionType(1);
333 theReactionTable->SetReaction(reactionData);
334 //------------------------------------------------------------------
335 // OH + H2 -> H
336 reactionData = new G4DNAMolecularReactionData(3.28e7 * (1e-3 * m3 / (mole * s)), OH, H2);
337 reactionData->AddProduct(H);
338 reactionData->SetReactionType(1);
339 theReactionTable->SetReaction(reactionData);
340 //------------------------------------------------------------------
341 // e_aq + *OH -> OH-
342 reactionData = new G4DNAMolecularReactionData(2.95e10 * (1e-3 * m3 / (mole * s)), e_aq, OH);
343 reactionData->AddProduct(OHm);
344 reactionData->SetReactionType(1);
345 theReactionTable->SetReaction(reactionData);
346 //------------------------------------------------------------------
347 // OH + OH- -> O-
348 reactionData = new G4DNAMolecularReactionData(6.30e9 * (1e-3 * m3 / (mole * s)), OH, OHm);
349 reactionData->AddProduct(Om);
350 reactionData->SetReactionType(1);
351 theReactionTable->SetReaction(reactionData);
352 //------------------------------------------------------------------
353 // OH + HO2 -> O2
354 reactionData = new G4DNAMolecularReactionData(7.90e9 * (1e-3 * m3 / (mole * s)), OH, HO2);
355 reactionData->AddProduct(O2);
356 reactionData->SetReactionType(1);
357 theReactionTable->SetReaction(reactionData);
358 //------------------------------------------------------------------
359 // OH + O2- -> O2 + OH-
360 reactionData = new G4DNAMolecularReactionData(1.07e10 * (1e-3 * m3 / (mole * s)), OH, O2m);
361 reactionData->AddProduct(O2);
362 reactionData->AddProduct(OHm);
363 reactionData->SetReactionType(1);
364 theReactionTable->SetReaction(reactionData);
365 //------------------------------------------------------------------
366 // OH + HO2- -> HO2 + OH-
367 reactionData = new G4DNAMolecularReactionData(8.32e9 * (1e-3 * m3 / (mole * s)), OH, HO2m);
368 reactionData->AddProduct(HO2);
369 reactionData->AddProduct(OHm);
370 reactionData->SetReactionType(1);
371 theReactionTable->SetReaction(reactionData);
372 //------------------------------------------------------------------
373 // OH + O- -> HO2-
374 reactionData = new G4DNAMolecularReactionData(1.00e9 * (1e-3 * m3 / (mole * s)), OH, Om);
375 reactionData->AddProduct(HO2m);
376 reactionData->SetReactionType(1);
377 theReactionTable->SetReaction(reactionData);
378 //------------------------------------------------------------------
379 // OH + O3- -> O2- + HO2
380 reactionData = new G4DNAMolecularReactionData(8.50e9 * (1e-3 * m3 / (mole * s)), OH, O3m);
381 reactionData->AddProduct(O2m);
382 reactionData->AddProduct(HO2);
383 reactionData->SetReactionType(1);
384 theReactionTable->SetReaction(reactionData);
385 //------------------------------------------------------------------
386 // e_aq + H2O2 -> OH- + *OH
387 reactionData = new G4DNAMolecularReactionData(1.10e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
388 reactionData->AddProduct(OHm);
389 reactionData->AddProduct(OH);
390 reactionData->SetReactionType(1);
391 theReactionTable->SetReaction(reactionData);
392 //------------------------------------------------------------------
393 // H2O2 + OH- -> HO2-
394 reactionData = new G4DNAMolecularReactionData(4.71e8 * (1e-3 * m3 / (mole * s)), H2O2, OHm);
395 reactionData->AddProduct(HO2m);
396 reactionData->SetReactionType(1);
397 theReactionTable->SetReaction(reactionData);
398 //------------------------------------------------------------------
399 // H2O2 + O(3p) -> HO2 + OH
400 reactionData = new G4DNAMolecularReactionData(1.60e9 * (1e-3 * m3 / (mole * s)), H2O2, O);
401 reactionData->AddProduct(HO2);
402 reactionData->AddProduct(OH);
403 reactionData->SetReactionType(1);
404 theReactionTable->SetReaction(reactionData);
405 //------------------------------------------------------------------
406 // H2O2 + O- -> HO2 + OH-
407 reactionData = new G4DNAMolecularReactionData(5.55e8 * (1e-3 * m3 / (mole * s)), H2O2, Om);
408 reactionData->AddProduct(HO2);
409 reactionData->AddProduct(OHm);
410 reactionData->SetReactionType(1);
411 theReactionTable->SetReaction(reactionData);
412 //------------------------------------------------------------------
413 // H2 + O(3p) -> H + OH
414 reactionData = new G4DNAMolecularReactionData(4.77e3 * (1e-3 * m3 / (mole * s)), H2, O);
415 reactionData->AddProduct(H);
416 reactionData->AddProduct(OH);
417 reactionData->SetReactionType(1);
418 theReactionTable->SetReaction(reactionData);
419 //------------------------------------------------------------------
420 // H2 + O- -> H + OH-
421 reactionData = new G4DNAMolecularReactionData(1.21e8 * (1e-3 * m3 / (mole * s)), H2, Om);
422 reactionData->AddProduct(H);
423 reactionData->AddProduct(OHm);
424 reactionData->SetReactionType(1);
425 theReactionTable->SetReaction(reactionData);
426 //------------------------------------------------------------------
427 // eaq- + O2 -> O2-
428 reactionData = new G4DNAMolecularReactionData(1.74e10 * (1e-3 * m3 / (mole * s)), e_aq, O2);
429 reactionData->AddProduct(O2m);
430 reactionData->SetReactionType(1);
431 theReactionTable->SetReaction(reactionData);
432 //------------------------------------------------------------------
433 // eaq + HO2 -> HO2-
434 reactionData = new G4DNAMolecularReactionData(1.29e10 * (1e-3 * m3 / (mole * s)), e_aq, HO2);
435 reactionData->AddProduct(HO2m);
436 reactionData->SetReactionType(1);
437 theReactionTable->SetReaction(reactionData);
438 //------------------------------------------------------------------
439 // OH- + HO2 -> O2-
440 reactionData = new G4DNAMolecularReactionData(6.30e9 * (1e-3 * m3 / (mole * s)), OHm, HO2);
441 reactionData->AddProduct(O2m);
442 reactionData->SetReactionType(1);
443 theReactionTable->SetReaction(reactionData);
444 //------------------------------------------------------------------
445 // OH- + O(3p) -> HO2-
446 reactionData = new G4DNAMolecularReactionData(4.20e8 * (1e-3 * m3 / (mole * s)), OHm, O);
447 reactionData->AddProduct(HO2m);
448 reactionData->SetReactionType(1);
449 theReactionTable->SetReaction(reactionData);
450 //------------------------------------------------------------------
451 // O2 + O(3p) -> O3
452 reactionData = new G4DNAMolecularReactionData(4.00e9 * (1e-3 * m3 / (mole * s)), O2, O);
453 reactionData->AddProduct(O3);
454 reactionData->SetReactionType(1);
455 theReactionTable->SetReaction(reactionData);
456 //------------------------------------------------------------------
457 // O2 + O- -> O3-
458 reactionData = new G4DNAMolecularReactionData(3.70e9 * (1e-3 * m3 / (mole * s)), O2, Om);
459 reactionData->AddProduct(O3m);
460 reactionData->SetReactionType(1);
461 theReactionTable->SetReaction(reactionData);
462 //------------------------------------------------------------------
463 // HO2 + HO2 -> H2O2 + O2
464 reactionData = new G4DNAMolecularReactionData(9.80e5 * (1e-3 * m3 / (mole * s)), HO2, HO2);
465 reactionData->AddProduct(H2O2);
466 reactionData->AddProduct(O2);
467 reactionData->SetReactionType(1);
468 theReactionTable->SetReaction(reactionData);
469 //------------------------------------------------------------------
470 // HO2 + O2- -> HO2- + O2
471 reactionData = new G4DNAMolecularReactionData(9.70e7 * (1e-3 * m3 / (mole * s)), HO2, O2m);
472 reactionData->AddProduct(HO2m);
473 reactionData->AddProduct(O2);
474 reactionData->SetReactionType(1);
475 theReactionTable->SetReaction(reactionData);
476 //------------------------------------------------------------------
477 // HO2- + O(3p) -> O2- + OH
478 reactionData = new G4DNAMolecularReactionData(5.30e9 * (1e-3 * m3 / (mole * s)), HO2m, O);
479 reactionData->AddProduct(O2m);
480 reactionData->AddProduct(OH);
481 reactionData->SetReactionType(1);
482 theReactionTable->SetReaction(reactionData);
483
484 // Type IV //
485 //------------------------------------------------------------------
486 // e_aq + H3O+ -> H* + H2O
487 reactionData = new G4DNAMolecularReactionData(2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
488 reactionData->AddProduct(H);
489 reactionData->SetReactionType(1);
490 theReactionTable->SetReaction(reactionData);
491 //------------------------------------------------------------------
492 // e_aq + O2- -> H2O2 + OH- + OH-
493 reactionData = new G4DNAMolecularReactionData(1.29e10 * (1e-3 * m3 / (mole * s)), e_aq, O2m);
494 reactionData->AddProduct(H2O2);
495 reactionData->AddProduct(OHm);
496 reactionData->AddProduct(OHm);
497 reactionData->SetReactionType(1);
498 theReactionTable->SetReaction(reactionData);
499 //------------------------------------------------------------------
500 // e_aq + HO2- -> O- + OH-
501 reactionData = new G4DNAMolecularReactionData(3.51e9 * (1e-3 * m3 / (mole * s)), e_aq, HO2m);
502 reactionData->AddProduct(Om);
503 reactionData->AddProduct(OHm);
504 reactionData->SetReactionType(1);
505 theReactionTable->SetReaction(reactionData);
506 //------------------------------------------------------------------
507 // e_aq + O- -> OH- + OH-
508 reactionData = new G4DNAMolecularReactionData(2.31e10 * (1e-3 * m3 / (mole * s)), e_aq, Om);
509 reactionData->AddProduct(OHm);
510 reactionData->AddProduct(OHm);
511 reactionData->SetReactionType(1);
512 theReactionTable->SetReaction(reactionData);
513 //------------------------------------------------------------------
514 // H3O+ + O2- -> HO2
515 reactionData = new G4DNAMolecularReactionData(4.78e10 * (1e-3 * m3 / (mole * s)), H3Op, O2m);
516 reactionData->AddProduct(HO2);
517 reactionData->SetReactionType(1);
518 theReactionTable->SetReaction(reactionData);
519 //------------------------------------------------------------------
520 // H3O+ + HO2- -> H2O2
521 reactionData = new G4DNAMolecularReactionData(5.00e10 * (1e-3 * m3 / (mole * s)), H3Op, HO2m);
522 reactionData->AddProduct(H2O2);
523 reactionData->SetReactionType(1);
524 theReactionTable->SetReaction(reactionData);
525 //------------------------------------------------------------------
526 // H3O+ + O- -> OH
527 reactionData = new G4DNAMolecularReactionData(4.78e10 * (1e-3 * m3 / (mole * s)), H3Op, Om);
528 reactionData->AddProduct(OH);
529 reactionData->SetReactionType(1);
530 theReactionTable->SetReaction(reactionData);
531 //------------------------------------------------------------------
532 // O2- + O- -> O2 + OH- + OH-
533 reactionData = new G4DNAMolecularReactionData(6.00e8 * (1e-3 * m3 / (mole * s)), O2m, Om);
534 reactionData->AddProduct(O2);
535 reactionData->AddProduct(OHm);
536 reactionData->AddProduct(OHm);
537 reactionData->SetReactionType(1);
538 theReactionTable->SetReaction(reactionData);
539 //------------------------------------------------------------------
540 // HO2- + O- -> O2- + OH-
541 reactionData = new G4DNAMolecularReactionData(3.50e8 * (1e-3 * m3 / (mole * s)), HO2m, Om);
542 reactionData->AddProduct(O2m);
543 reactionData->AddProduct(OHm);
544 reactionData->SetReactionType(1);
545 theReactionTable->SetReaction(reactionData);
546 //------------------------------------------------------------------
547 // O- + O- -> H2O2 + OH- + OH-
548 reactionData = new G4DNAMolecularReactionData(1.00e8 * (1e-3 * m3 / (mole * s)), Om, Om);
549 reactionData->AddProduct(H2O2);
550 reactionData->AddProduct(OHm);
551 reactionData->AddProduct(OHm);
552 reactionData->SetReactionType(1);
553 theReactionTable->SetReaction(reactionData);
554 //------------------------------------------------------------------
555 // O- + O3- -> O2- + O2-
556 reactionData = new G4DNAMolecularReactionData(7.00e8 * (1e-3 * m3 / (mole * s)), Om, O3m);
557 reactionData->AddProduct(O2m);
558 reactionData->AddProduct(O2m);
559 reactionData->SetReactionType(1);
560 theReactionTable->SetReaction(reactionData);
561
562 //------------------------------------------------------------------
563 // Get the DNA entites
564 G4MolecularConfiguration* A = G4MoleculeTable::Instance()->GetConfiguration("A");
565 G4MolecularConfiguration* T = G4MoleculeTable::Instance()->GetConfiguration("T");
566 G4MolecularConfiguration* G = G4MoleculeTable::Instance()->GetConfiguration("G");
567 G4MolecularConfiguration* C = G4MoleculeTable::Instance()->GetConfiguration("C");
568 G4MolecularConfiguration* Sugar = G4MoleculeTable::Instance()->GetConfiguration("Sugar");
569
570 // From Buxton et al., J. Phys. Chern. Ref. Data, Vol. 17, No.2, 1988.
571 theReactionTable->SetReaction(0.61e10 * (1e-3 * m3 / (mole * s)), OH, A);
572 theReactionTable->SetReaction(0.64e10 * (1e-3 * m3 / (mole * s)), OH, T);
573 theReactionTable->SetReaction(0.92e10 * (1e-3 * m3 / (mole * s)), OH, G);
574 theReactionTable->SetReaction(0.61e10 * (1e-3 * m3 / (mole * s)), OH, C);
575 theReactionTable->SetReaction(0.18e10 * (1e-3 * m3 / (mole * s)), OH, Sugar);
576
577 theReactionTable->SetReaction(0.9e10 * (1e-3 * m3 / (mole * s)), e_aq, A);
578 theReactionTable->SetReaction(1.8e10 * (1e-3 * m3 / (mole * s)), e_aq, T);
579 theReactionTable->SetReaction(1.4e10 * (1e-3 * m3 / (mole * s)), e_aq, G);
580 theReactionTable->SetReaction(1.3e10 * (1e-3 * m3 / (mole * s)), e_aq, C);
581 theReactionTable->SetReaction(1.0e7 * (1e-3 * m3 / (mole * s)), e_aq, Sugar);
582
583 theReactionTable->SetReaction(1.0e8 * (1e-3 * m3 / (mole * s)), H, A);
584 theReactionTable->SetReaction(5.7e8 * (1e-3 * m3 / (mole * s)), H, T);
585 theReactionTable->SetReaction(9.2e7 * (1e-3 * m3 / (mole * s)), H, C);
586 theReactionTable->SetReaction(2.9e7 * (1e-3 * m3 / (mole * s)), H, Sugar);
587 }
588
589 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
590
591 void ChemistryList::ConstructProcess()
592 {
593 G4PhysicsListHelper* ph = G4PhysicsListHelper::GetPhysicsListHelper();
594
595 //===============================================================
596 // Extend vibrational to low energy
597 // Anyway, solvation of electrons is taken into account from 7.4 eV
598 // So below this threshold, for now, no accurate modeling is done
599 //
600 G4VProcess* process =
601 G4ProcessTable::GetProcessTable()->FindProcess("e-_G4DNAVibExcitation", "e-");
602
603 if (process != nullptr) {
604 auto* vibExcitation = (G4DNAVibExcitation*)process;
605 G4VEmModel* model = vibExcitation->EmModel();
606 auto* sancheExcitationMod = dynamic_cast<G4DNASancheExcitationModel*>(model);
607 if (sancheExcitationMod != nullptr) {
608 sancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
609 }
610 }
611
612 //===============================================================
613 // *** Electron Solvatation ***
614 //
615 process = G4ProcessTable::GetProcessTable()->FindProcess("e-_G4DNAElectronSolvation", "e-");
616
617 if (process == nullptr) {
618 ph->RegisterProcess(new G4DNAElectronSolvation("e-_G4DNAElectronSolvation"),
619 G4Electron::Definition());
620 }
621
622 //===============================================================
623 // Define processes for molecules
624 //
625 G4MoleculeTable* theMoleculeTable = G4MoleculeTable::Instance();
626 G4MoleculeDefinitionIterator iterator = theMoleculeTable->GetDefintionIterator();
627 iterator.reset();
628 while (iterator()) {
629 G4MoleculeDefinition* moleculeDef = iterator.value();
630
631 if (moleculeDef != G4H2O::Definition()) {
632 auto brown = new G4DNABrownianTransportation();
633 ph->RegisterProcess(brown, moleculeDef);
634
635 if (moleculeDef == G4Electron_aq::Definition() || moleculeDef == G4OH::Definition()
636 || moleculeDef == G4Hydrogen::Definition())
637 {
638 G4VDNAHitModel* pDamageModel = new IRTDamageReactionModel("IRTDamageReactionModel");
639 auto staticMoleculeReactionProcess =
640 new G4DNAPolyNucleotideReactionProcess("PolyNucleotideReactionProcess");
641 staticMoleculeReactionProcess->SetVerbose(1);
642 staticMoleculeReactionProcess->SetDNADamageReactionModel(pDamageModel);
643 ph->RegisterProcess(staticMoleculeReactionProcess, moleculeDef);
644 }
645 }
646 else {
647 moleculeDef->GetProcessManager()->AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
648 auto* dissociationProcess = new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
649 dissociationProcess->SetDisplacer(moleculeDef, new G4DNAWaterDissociationDisplacer);
650 dissociationProcess->SetVerboseLevel(3);
651
652 moleculeDef->GetProcessManager()->AddRestProcess(dissociationProcess, 1);
653 }
654 }
655 }
656
657 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
658
659 void ChemistryList::ConstructTimeStepModel(G4DNAMolecularReactionTable*
660 /*reactionTable*/)
661 {
662 auto model = G4EmParameters::Instance()->GetTimeStepModel();
663 if(model == G4ChemTimeStepModel::IRT_syn)
664 {
665 RegisterTimeStepModel(new G4DNAIndependentReactionTimeModel(), 0);
666 }else
667 {
668 G4ExceptionDescription exceptionDescription;
669 exceptionDescription << "This example uses only IRT_syn";
670 G4Exception(
671 "ChemistryList"
672 "ConstructTimeStepModel",
673 "ConstructTimeStepModel", FatalException, exceptionDescription);
674 }
675 }
676
677 void ChemistryList::ConstructParticle()
678 {
679 ConstructMolecule();
680 }
681