| Geant4 Cross Reference |
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27
28 #include "G4EmDNAChemistry_option2.hh"
29 #include "G4DNAMolecule.hh"
30 #include "G4DNAChemistryManager.hh"
31 #include "G4DNASmoluchowskiReactionModel.hh"
32 #include "G4PhysicalConstants.hh"
33 #include "G4SystemOfUnits.hh"
34 #include "G4DNAWaterDissociationDisplacer.hh"
35 #include "G4DNAWaterExcitationStructure.hh"
36 #include "G4ProcessManager.hh"
37 #include "G4DNAElectronSolvation.hh"
38 #include "G4DNAVibExcitation.hh"
39 #include "G4DNASancheExcitationModel.hh"
40 #include "G4DNAMolecularDissociation.hh"
41 #include "G4DNABrownianTransportation.hh"
42 #include "G4DNAMolecularReactionTable.hh"
43 #include "G4DNAMolecularStepByStepModel.hh"
44 #include "G4DNAElectronHoleRecombination.hh"
45 #include "G4Electron.hh"
46 #include "G4MoleculeTable.hh"
47 #include "G4H2O.hh"
48 #include "G4H2.hh"
49 #include "G4Hydrogen.hh"
50 #include "G4OH.hh"
51 #include "G4H3O.hh"
52 #include "G4Electron_aq.hh"
53 #include "G4H2O2.hh"
54 #include "G4PhysicsListHelper.hh"
55 #include "G4ProcessTable.hh"
56 #include "G4MolecularConfiguration.hh"
57 #include "G4PhysicsConstructorFactory.hh"
58 #include "G4VDNAReactionModel.hh"
59 #include "G4ChemDissociationChannels.hh"
60
61 G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistry_option2);
62
63 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
64
65 G4EmDNAChemistry_option2::G4EmDNAChemistry_option2()
66 : G4VUserChemistryList(true)
67 {
68 G4DNAChemistryManager::Instance()->SetChemistryList(this);
69 }
70
71 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
72
73 void G4EmDNAChemistry_option2::ConstructMolecule()
74 {
75 G4ChemDissociationChannels::ConstructMolecule();
76 //____________________________________________________________________________
77
78 G4Deoxyribose::Definition();
79 G4Phosphate::Definition();
80 G4Adenine::Definition();
81 G4Guanine::Definition();
82 G4Thymine::Definition();
83 G4Cytosine::Definition();
84 G4Histone::Definition();
85 //damaged molecules
86 G4DamagedDeoxyribose::Definition();
87 G4DamagedAdenine::Definition();
88 G4DamagedGuanine::Definition();
89 G4DamagedThymine::Definition();
90 G4DamagedCytosine::Definition();
91 G4ModifiedHistone::Definition();
92
93 //________________DNA_______________________________________________
94
95 G4MoleculeTable::Instance()->
96 CreateConfiguration("Deoxyribose",G4Deoxyribose::Definition());
97 G4MoleculeTable::Instance()->
98 CreateConfiguration("Phosphate",G4Phosphate::Definition());
99 G4MoleculeTable::Instance()->
100 CreateConfiguration("Adenine",G4Adenine::Definition());
101 G4MoleculeTable::Instance()->
102 CreateConfiguration("Thymine",G4Thymine::Definition());
103 G4MoleculeTable::Instance()->
104 CreateConfiguration("Guanine",G4Guanine::Definition());
105 G4MoleculeTable::Instance()->
106 CreateConfiguration("Cytosine",G4Cytosine::Definition());
107 G4MoleculeTable::Instance()->
108 CreateConfiguration("Histone",G4Histone::Definition());
109
110 //damaged DNAElement Configuration
111
112 G4MoleculeTable::Instance()->
113 CreateConfiguration("Damaged_Deoxyribose",
114 G4DamagedDeoxyribose::Definition());
115 G4MoleculeTable::Instance()->
116 CreateConfiguration("Damaged_Adenine",
117 G4DamagedAdenine::Definition());
118 G4MoleculeTable::Instance()->
119 CreateConfiguration("Damaged_Thymine",
120 G4DamagedThymine::Definition());
121 G4MoleculeTable::Instance()->
122 CreateConfiguration("Damaged_Guanine",
123 G4DamagedGuanine::Definition());
124 G4MoleculeTable::Instance()->
125 CreateConfiguration("Damaged_Cytosine",
126 G4DamagedCytosine::Definition());
127 }
128
129 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
130
131 void G4EmDNAChemistry_option2::ConstructDissociationChannels()
132 {
133 G4ChemDissociationChannels::ConstructDissociationChannels();
134 }
135
136 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
137
138 void G4EmDNAChemistry_option2::ConstructReactionTable(
139 G4DNAMolecularReactionTable* theReactionTable)
140 {
141 //-----------------------------------
142 //Get the molecular configuration
143 G4MolecularConfiguration* OH =
144 G4MoleculeTable::Instance()->GetConfiguration("°OH");
145 G4MolecularConfiguration* OHm =
146 G4MoleculeTable::Instance()->GetConfiguration("OHm");
147 G4MolecularConfiguration* e_aq =
148 G4MoleculeTable::Instance()->GetConfiguration("e_aq");
149 G4MolecularConfiguration* H2 =
150 G4MoleculeTable::Instance()->GetConfiguration("H2");
151 G4MolecularConfiguration* H3Op =
152 G4MoleculeTable::Instance()->GetConfiguration("H3Op");
153 G4MolecularConfiguration* H =
154 G4MoleculeTable::Instance()->GetConfiguration("H");
155 G4MolecularConfiguration* H2O2 =
156 G4MoleculeTable::Instance()->GetConfiguration("H2O2");
157
158 G4MolecularConfiguration* deoxyribose =
159 G4MoleculeTable::Instance()->GetConfiguration("Deoxyribose");
160 G4MolecularConfiguration* adenine =
161 G4MoleculeTable::Instance()->GetConfiguration("Adenine");
162 G4MolecularConfiguration* guanine =
163 G4MoleculeTable::Instance()->GetConfiguration("Guanine");
164 G4MolecularConfiguration* thymine =
165 G4MoleculeTable::Instance()->GetConfiguration("Thymine");
166 G4MolecularConfiguration* cytosine =
167 G4MoleculeTable::Instance()->GetConfiguration("Cytosine");
168 G4MolecularConfiguration* histone =
169 G4MoleculeTable::Instance()->GetConfiguration("Histone");
170
171 G4MolecularConfiguration* damage_deoxyribose =
172 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Deoxyribose");
173 G4MolecularConfiguration* damage_adenine =
174 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Adenine");
175 G4MolecularConfiguration* damage_guanine =
176 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Guanine");
177 G4MolecularConfiguration* damage_thymine =
178 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Thymine");
179 G4MolecularConfiguration* damage_cytosine =
180 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Cytosine");
181
182 //------------------------------------------------------------------
183 // e_aq + e_aq + 2H2O -> H2 + 2OH-
184 G4DNAMolecularReactionData* reactionData =
185 new G4DNAMolecularReactionData(
186 0.5e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
187 reactionData->AddProduct(OHm);
188 reactionData->AddProduct(OHm);
189 reactionData->AddProduct(H2);
190 theReactionTable->SetReaction(reactionData);
191 //------------------------------------------------------------------
192 // e_aq + *OH -> OH-
193 reactionData = new G4DNAMolecularReactionData(
194 2.95e10 * (1e-3 * m3 / (mole * s)), e_aq, OH);
195 reactionData->AddProduct(OHm);
196 theReactionTable->SetReaction(reactionData);
197 //------------------------------------------------------------------
198 // e_aq + H* + H2O -> H2 + OH-
199 reactionData = new G4DNAMolecularReactionData(
200 2.65e10 * (1e-3 * m3 / (mole * s)), e_aq, H);
201 reactionData->AddProduct(OHm);
202 reactionData->AddProduct(H2);
203 theReactionTable->SetReaction(reactionData);
204 //------------------------------------------------------------------
205 // e_aq + H3O+ -> H* + H2O
206 reactionData = new G4DNAMolecularReactionData(
207 2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
208 reactionData->AddProduct(H);
209 theReactionTable->SetReaction(reactionData);
210
211 //------------------------------------------------------------------
212 // e_aq + H2O2 -> OH- + *OH
213 reactionData = new G4DNAMolecularReactionData(
214 1.41e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
215 reactionData->AddProduct(OHm);
216 reactionData->AddProduct(OH);
217 theReactionTable->SetReaction(reactionData);
218 //------------------------------------------------------------------
219 // *OH + *OH -> H2O2
220 reactionData = new G4DNAMolecularReactionData(
221 0.44e10 * (1e-3 * m3 / (mole * s)), OH, OH);
222 reactionData->AddProduct(H2O2);
223 theReactionTable->SetReaction(reactionData);
224 //------------------------------------------------------------------
225 // *OH + *H -> H2O
226 theReactionTable->SetReaction(
227 1.44e10 * (1e-3 * m3 / (mole * s)), OH, H);
228 //------------------------------------------------------------------
229 // *H + *H -> H2
230 reactionData = new G4DNAMolecularReactionData(
231 1.20e10 * (1e-3 * m3 / (mole * s)), H, H);
232 reactionData->AddProduct(H2);
233 theReactionTable->SetReaction(reactionData);
234 //------------------------------------------------------------------
235 // H3O+ + OH- -> 2H2O
236 theReactionTable->SetReaction(
237 1.43e11 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
238 //------------------------------------------------------------------
239
240 // DNA additions
241
242 // OH and DNA
243
244 // 2-Deoxyribose + OH -> damagedDeoxyribose
245 reactionData = new G4DNAMolecularReactionData(
246 1.80e9*(1e-3*m3/(mole*s)), deoxyribose, OH);
247 reactionData->AddProduct(damage_deoxyribose);
248 theReactionTable->SetReaction(reactionData);
249
250 // adenine + OH -> ...
251 reactionData = new G4DNAMolecularReactionData(
252 6.10e9*(1e-3*m3/(mole*s)), adenine, OH);
253 reactionData->AddProduct(damage_adenine);
254 theReactionTable->SetReaction(reactionData);
255
256 // guanine + OH -> ...
257 reactionData = new G4DNAMolecularReactionData(
258 9.20e9*(1e-3*m3/(mole*s)), guanine, OH);
259 reactionData->AddProduct(damage_guanine);
260 theReactionTable->SetReaction(reactionData);
261
262 // thymine + OH -> ...
263 reactionData = new G4DNAMolecularReactionData(
264 6.40e9*(1e-3*m3/(mole*s)), thymine, OH);
265 reactionData->AddProduct(damage_thymine);
266 theReactionTable->SetReaction(reactionData);
267
268 // cytosine + OH -> ...
269 reactionData = new G4DNAMolecularReactionData(
270 6.10e9*(1e-3*m3/(mole*s)), cytosine, OH);
271 reactionData->AddProduct(damage_cytosine);
272 theReactionTable->SetReaction(reactionData);
273
274 // Hydrated e- and DNA
275
276 // Deoxyribose + Hydrated e- -> ...
277 reactionData = new G4DNAMolecularReactionData(
278 0.01e9*(1e-3*m3/(mole*s)), deoxyribose, e_aq);
279 reactionData->AddProduct(damage_deoxyribose);
280 theReactionTable->SetReaction(reactionData);
281
282 // adenine + Hydrated e- -> ...
283 reactionData = new G4DNAMolecularReactionData(
284 9e9*(1e-3*m3/(mole*s)), adenine, e_aq);
285 reactionData->AddProduct(damage_adenine);
286 theReactionTable->SetReaction(reactionData);
287
288 // guanine + Hydrated e- -> ...
289 reactionData = new G4DNAMolecularReactionData(
290 14e9*(1e-3*m3/(mole*s)), guanine, e_aq);
291 reactionData->AddProduct(damage_guanine);
292 theReactionTable->SetReaction(reactionData);
293
294 // thymine + Hydrated e- -> ...
295 reactionData = new G4DNAMolecularReactionData(
296 18e9*(1e-3*m3/(mole*s)), thymine, e_aq);
297 reactionData->AddProduct(damage_thymine);
298 theReactionTable->SetReaction(reactionData);
299
300 // cytosine + Hydrated e- -> ...
301 reactionData = new G4DNAMolecularReactionData(
302 13e9*(1e-3*m3/(mole*s)), cytosine, e_aq);
303 reactionData->AddProduct(damage_cytosine);
304 theReactionTable->SetReaction(reactionData);
305
306 // Radical H and DNA
307
308 // Deoxyribose + Radical H -> ...
309 reactionData = new G4DNAMolecularReactionData(
310 0.029e9*(1e-3*m3/(mole*s)), deoxyribose, H);
311 reactionData->AddProduct(damage_deoxyribose);
312 //eactionData->SetEffectiveReactionRadius(0);
313
314 theReactionTable->SetReaction(reactionData);
315
316 // adenine + Radical H -> ...
317 reactionData = new G4DNAMolecularReactionData(
318 0.10e9*(1e-3*m3/(mole*s)), adenine, H);
319 reactionData->AddProduct(damage_adenine);
320 theReactionTable->SetReaction(reactionData);
321
322 // thymine + Radical H -> ...
323 reactionData = new G4DNAMolecularReactionData(
324 0.57e9*(1e-3*m3/(mole*s)), thymine, H);
325 reactionData->AddProduct(damage_thymine);
326 theReactionTable->SetReaction(reactionData);
327
328 // cytosine + Radical H -> ...
329 reactionData = new G4DNAMolecularReactionData(
330 0.092e9*(1e-3*m3/(mole*s)), cytosine, H);
331 reactionData->AddProduct(damage_cytosine);
332 theReactionTable->SetReaction(reactionData);
333
334 //histone + all molecules -> modification(or "damage")
335
336 reactionData = new G4DNAMolecularReactionData(
337 0.0*(1e-3*m3/(mole*s)), histone, OH);
338 reactionData->AddProduct(histone);
339 reactionData->SetEffectiveReactionRadius(
340 2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
341 theReactionTable->SetReaction(reactionData);
342
343 reactionData = new G4DNAMolecularReactionData(
344 0.0*(1e-3*m3/(mole*s)), histone, OHm);
345 reactionData->AddProduct(histone);
346 reactionData->SetEffectiveReactionRadius(
347 2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
348 theReactionTable->SetReaction(reactionData);
349
350 reactionData = new G4DNAMolecularReactionData(
351 0.0*(1e-3*m3/(mole*s)), histone, e_aq);
352 reactionData->AddProduct(histone);
353 reactionData->SetEffectiveReactionRadius(
354 2.4*nm + G4Electron_aq::Definition()->GetVanDerVaalsRadius());
355 theReactionTable->SetReaction(reactionData);
356
357 reactionData = new G4DNAMolecularReactionData(
358 0.0*(1e-3*m3/(mole*s)), histone, H2);
359 reactionData->AddProduct(histone);
360 reactionData->SetEffectiveReactionRadius(
361 2.4*nm + G4H2::Definition()->GetVanDerVaalsRadius());
362 theReactionTable->SetReaction(reactionData);
363
364 reactionData = new G4DNAMolecularReactionData(
365 0.0*(1e-3*m3/(mole*s)), histone, H3Op);
366 reactionData->AddProduct(histone);
367 reactionData->SetEffectiveReactionRadius(
368 2.4*nm + G4H3O::Definition()->GetVanDerVaalsRadius());
369 theReactionTable->SetReaction(reactionData);
370
371 reactionData = new G4DNAMolecularReactionData(
372 0.0*(1e-3*m3/(mole*s)), histone, H);
373 reactionData->AddProduct(histone);
374 reactionData->SetEffectiveReactionRadius(
375 2.4*nm + G4Hydrogen::Definition()->GetVanDerVaalsRadius());
376 theReactionTable->SetReaction(reactionData);
377
378 reactionData = new G4DNAMolecularReactionData(
379 0.0*(1e-3*m3/(mole*s)), histone, H2O2);
380 reactionData->AddProduct(histone);
381 reactionData->SetEffectiveReactionRadius(
382 2.4*nm + G4H2O2::Definition()->GetVanDerVaalsRadius());
383 theReactionTable->SetReaction(reactionData);
384 }
385
386 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
387
388 void G4EmDNAChemistry_option2::ConstructProcess()
389 {
390 auto pPhysicsListHelper =
391 G4PhysicsListHelper::GetPhysicsListHelper();
392 G4VProcess* pProcess =
393 G4ProcessTable::GetProcessTable()->
394 FindProcess("e-_G4DNAVibExcitation", "e-");
395
396 if (pProcess != nullptr)
397 {
398 G4DNAVibExcitation* pVibExcitation =
399 (G4DNAVibExcitation*) pProcess;
400 G4VEmModel* pModel = pVibExcitation->EmModel();
401 G4DNASancheExcitationModel* pSancheExcitationMod =
402 dynamic_cast<G4DNASancheExcitationModel*>(pModel);
403 if(pSancheExcitationMod != nullptr)
404 {
405 pSancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
406 }
407 }
408
409 //===============================================================
410 // Electron Solvatation
411 //
412 pProcess = G4ProcessTable::GetProcessTable()->
413 FindProcess("e-_G4DNAElectronSolvation", "e-");
414
415 if (pProcess == nullptr)
416 {
417 pPhysicsListHelper->
418 RegisterProcess(new G4DNAElectronSolvation(
419 "e-_G4DNAElectronSolvation"), G4Electron::Definition());
420 }
421
422 //===============================================================
423 // Define processes for molecules
424 //
425 G4MoleculeTable* pMoleculeTable =
426 G4MoleculeTable::Instance();
427 G4MoleculeDefinitionIterator iterator =
428 pMoleculeTable->GetDefintionIterator();
429 iterator.reset();
430 while (iterator())
431 {
432 G4MoleculeDefinition* pMoleculeDef = iterator.value();
433
434 if(pMoleculeDef != G4H2O::Definition())
435 {
436 G4DNABrownianTransportation* pBrownianTransport =
437 new G4DNABrownianTransportation();
438 pPhysicsListHelper->
439 RegisterProcess(pBrownianTransport, pMoleculeDef);
440 }
441 else
442 {
443 pMoleculeDef->GetProcessManager()->
444 AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
445 G4DNAMolecularDissociation* pDissociationProcess =
446 new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
447 pDissociationProcess->SetDisplacer(pMoleculeDef,
448 new G4DNAWaterDissociationDisplacer);
449 pDissociationProcess->SetVerboseLevel(1);
450
451 pMoleculeDef->GetProcessManager()->
452 AddRestProcess(pDissociationProcess, 1);
453 }
454 }
455 G4DNAChemistryManager::Instance()->Initialize();
456 }
457
458
459 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
460
461 void G4EmDNAChemistry_option2::ConstructTimeStepModel(
462 G4DNAMolecularReactionTable* reactionTable)
463 {
464 G4VDNAReactionModel* reactionRadiusComputer =
465 new G4DNASmoluchowskiReactionModel();
466 reactionTable->PrintTable(reactionRadiusComputer);
467
468 G4DNAMolecularStepByStepModel* stepByStep =
469 new G4DNAMolecularStepByStepModel();
470 stepByStep->SetReactionModel(reactionRadiusComputer);
471
472 RegisterTimeStepModel(stepByStep, 0);
473 }
474