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26 //
27 // G4EmDNAChemistryForPlasmids.cc
28 //
29 // Created on: Feb 10, 2021
30 // Authors: J. Naoki D. Kondo
31 // W. G. Shin, J. Ramos-Mendez a
32 //
33 /// \file G4EmDNAChemistryForPlasmids.cc
34 /// \brief Implementation of the Chemistry par
35
36 #include "G4EmDNAChemistryForPlasmids.hh"
37
38 #include "G4DNAChemistryManager.hh"
39 #include "G4DNAGenericIonsManager.hh"
40 #include "G4DNAWaterDissociationDisplacer.hh"
41 #include "G4DNAWaterExcitationStructure.hh"
42 #include "G4PhysicalConstants.hh"
43 #include "G4ProcessManager.hh"
44 #include "G4SystemOfUnits.hh"
45
46 // *** Processes and models for Geant4-DNA
47
48 #include "G4DNABrownianTransportation.hh"
49 #include "G4DNAElectronHoleRecombination.hh"
50 #include "G4DNAElectronSolvation.hh"
51 #include "G4DNAIRT.hh"
52 #include "G4DNAMolecularDissociation.hh"
53 #include "G4DNAMolecularIRTModel.hh"
54 #include "G4DNAMolecularReactionTable.hh"
55 #include "G4DNASancheExcitationModel.hh"
56 #include "G4DNAVibExcitation.hh"
57 #include "G4VDNAReactionModel.hh"
58
59 // particles
60
61 #include "PlasmidMolecules.hh"
62 #include "ScavengerMolecules.hh"
63
64 #include "G4BuilderType.hh"
65 #include "G4Electron.hh"
66 #include "G4Electron_aq.hh"
67 #include "G4FakeMolecule.hh"
68 #include "G4GenericIon.hh"
69 #include "G4H2.hh"
70 #include "G4H2O.hh"
71 #include "G4H2O2.hh"
72 #include "G4H3O.hh"
73 #include "G4HO2.hh"
74 #include "G4Hydrogen.hh"
75 #include "G4MoleculeTable.hh"
76 #include "G4O2.hh"
77 #include "G4O3.hh"
78 #include "G4OH.hh"
79 #include "G4Oxygen.hh"
80 #include "G4PhysicsListHelper.hh"
81 #include "G4Proton.hh"
82
83 /****/
84 #include "G4DNAMoleculeEncounterStepper.hh"
85 #include "G4MolecularConfiguration.hh"
86 #include "G4ProcessTable.hh"
87 /****/
88 // factory
89 #include "G4PhysicsConstructorFactory.hh"
90 #include "G4ChemDissociationChannels_option1.h
91 G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistry
92
93 //....oooOO0OOooo........oooOO0OOooo........oo
94
95 G4EmDNAChemistryForPlasmids::G4EmDNAChemistryF
96 {
97 G4DNAChemistryManager::Instance()->SetChemis
98
99 fDMSO = 0;
100 fOxygen = 0;
101 }
102
103 //....oooOO0OOooo........oooOO0OOooo........oo
104
105 G4EmDNAChemistryForPlasmids::G4EmDNAChemistryF
106 : G4VUserChemistryList(true)
107 {
108 G4DNAChemistryManager::Instance()->SetChemis
109
110 fDMSO = dmso;
111 fOxygen = oxygen;
112 }
113
114 //....oooOO0OOooo........oooOO0OOooo........oo
115
116 void G4EmDNAChemistryForPlasmids::ConstructMol
117 {
118 G4ChemDissociationChannels_option1::Construc
119 auto molTab = G4MoleculeTable::Instance();
120
121 molTab->CreateConfiguration("DMSO", G4DMSO::
122
123 molTab->CreateConfiguration("O2", G4O2::Defi
124 molTab->GetConfiguration("O2")->SetVanDerVaa
125 molTab->CreateConfiguration("Oxygen", G4Oxyg
126
127 molTab->CreateConfiguration("Deoxyribose", G
128
129 molTab->CreateConfiguration(
130 "Damaged_DeoxyriboseOH", G4DNA_DamagedDeox
131 molTab->CreateConfiguration(
132 "Damaged_DeoxyriboseH", G4DNA_DamagedDeoxy
133 molTab->CreateConfiguration(
134 "Damaged_DeoxyriboseEAQ", G4DNA_DamagedDeo
135 }
136
137 //....oooOO0OOooo........oooOO0OOooo........oo
138
139 void G4EmDNAChemistryForPlasmids::ConstructDis
140 {
141 G4ChemDissociationChannels_option1::Construc
142 }
143
144 //....oooOO0OOooo........oooOO0OOooo........oo
145
146 void G4EmDNAChemistryForPlasmids::ConstructRea
147 G4DNAMolecularReactionTable* theReactionTabl
148 {
149 // fReactionTable = theReactionTable;
150
151 //-----------------------------------
152 // Get the molecular configuration
153 auto molTab = G4MoleculeTable::Instance();
154
155 auto OH = molTab->GetConfiguration("°OH");
156 auto OHm = molTab->GetConfiguration("OHm");
157 auto e_aq = molTab->GetConfiguration("e_aq")
158 auto H2 = molTab->GetConfiguration("H2");
159 auto H3Op = molTab->GetConfiguration("H3Op")
160 auto H = molTab->GetConfiguration("H");
161 auto H2O2 = molTab->GetConfiguration("H2O2")
162
163 //------------------------------------------
164 // Type II
165 //------------------------------------------
166 // e_aq + *OH -> OH- prob: 0.49
167 auto reactionData =
168 new G4DNAMolecularReactionData(2.95e10 * (
169 reactionData->AddProduct(OHm);
170 reactionData->SetReactionType(1);
171 theReactionTable->SetReaction(reactionData);
172 //------------------------------------------
173 // e_aq + H2O2 -> OH- + *OH prob: 0.1
174 reactionData = new G4DNAMolecularReactionDat
175 reactionData->AddProduct(OHm);
176 reactionData->AddProduct(OH);
177 reactionData->SetReactionType(1);
178 theReactionTable->SetReaction(reactionData);
179 //------------------------------------------
180 // *OH + *H -> H2O prob: 0.33
181 reactionData = new G4DNAMolecularReactionDat
182 reactionData->SetReactionType(1);
183 theReactionTable->SetReaction(reactionData);
184 //------------------------------------------
185 // H + H2O2 -> OH prob: 0.00
186 reactionData = new G4DNAMolecularReactionDat
187 reactionData->AddProduct(OH);
188 reactionData->SetReactionType(1);
189 theReactionTable->SetReaction(reactionData);
190 //------------------------------------------
191 // *OH + *OH -> H2O2 prob: 0.
192 reactionData = new G4DNAMolecularReactionDat
193 reactionData->AddProduct(H2O2);
194 reactionData->SetReactionType(1);
195 theReactionTable->SetReaction(reactionData);
196 //------------------------------------------
197
198 //------------------------------------------
199 // Type III
200 //------------------------------------------
201 // e_aq + e_aq + 2H2O -> H2 + 2OH-
202 reactionData = new G4DNAMolecularReactionDat
203 reactionData->AddProduct(OHm);
204 reactionData->AddProduct(OHm);
205 reactionData->AddProduct(H2);
206 reactionData->SetReactionType(0);
207 theReactionTable->SetReaction(reactionData);
208 //------------------------------------------
209 // H3O+ + OH- -> 2H2O
210 reactionData = new G4DNAMolecularReactionDat
211 reactionData->SetReactionType(0);
212 theReactionTable->SetReaction(reactionData);
213 //------------------------------------------
214
215 //------------------------------------------
216 // Type IV
217 //------------------------------------------
218 // e_aq + H3O+ -> H* + H2O prob: 0.04
219 reactionData = new G4DNAMolecularReactionDat
220 reactionData->AddProduct(H);
221 reactionData->SetReactionType(1);
222 theReactionTable->SetReaction(reactionData);
223 //------------------------------------------
224
225 //------------------------------------------
226 // Type V
227 // First order reaction
228 //------------------------------------------
229 // e_aq + *H -> OH- + H2
230 reactionData = new G4DNAMolecularReactionDat
231 reactionData->AddProduct(OHm);
232 reactionData->AddProduct(H2);
233 reactionData->SetReactionType(0);
234 theReactionTable->SetReaction(reactionData);
235 //------------------------------------------
236 // *H + *H -> H2
237 reactionData = new G4DNAMolecularReactionDat
238 reactionData->AddProduct(H2);
239 reactionData->SetReactionType(0);
240 theReactionTable->SetReaction(reactionData);
241
242 if (fDMSO > 0) DeclareDMSOAndDNAReactions(th
243
244 if (fOxygen > 0) DeclareOxygenReactions(theR
245 }
246
247 //....oooOO0OOooo........oooOO0OOooo........oo
248
249 void G4EmDNAChemistryForPlasmids::ConstructPro
250 {
251 G4PhysicsListHelper* ph = G4PhysicsListHelpe
252
253 //==========================================
254 // Extend vibrational to low energy
255 // Anyway, solvation of electrons is taken i
256 // So below this threshold, for now, no accu
257 //
258 G4VProcess* process =
259 G4ProcessTable::GetProcessTable()->FindPro
260
261 if (process) {
262 G4DNAVibExcitation* vibExcitation = (G4DNA
263 G4VEmModel* model = vibExcitation->EmModel
264 G4DNASancheExcitationModel* sancheExcitati
265 dynamic_cast<G4DNASancheExcitationModel*
266 if (sancheExcitationMod) {
267 sancheExcitationMod->ExtendLowEnergyLimi
268 }
269 }
270
271 //==========================================
272 // *** Electron Solvatation ***
273 //
274 process = G4ProcessTable::GetProcessTable()-
275
276 if (process == 0) {
277 ph->RegisterProcess(new G4DNAElectronSolva
278 G4Electron::Definition
279 }
280
281 //==========================================
282 // Define processes for molecules
283 //
284 G4MoleculeTable* theMoleculeTable = G4Molecu
285 G4MoleculeDefinitionIterator iterator = theM
286 iterator.reset();
287 while (iterator()) {
288 G4MoleculeDefinition* moleculeDef = iterat
289
290 if (moleculeDef != G4H2O::Definition()) {
291 // G4cout << "Brownian motion added for:
292 // G4DNABrownianTransportation* bro
293 // ph->RegisterProcess(brown, molec
294 }
295 else {
296 moleculeDef->GetProcessManager()->AddRes
297 G4DNAMolecularDissociation* dissociation
298 new G4DNAMolecularDissociation("H2O_DN
299 dissociationProcess->SetDisplacer(molecu
300 dissociationProcess->SetVerboseLevel(3);
301
302 moleculeDef->GetProcessManager()->AddRes
303 }
304 /*
305 * Warning : end of particles and processe
306 * EM Physics builders
307 */
308 }
309
310 G4DNAChemistryManager::Instance()->Initializ
311 }
312
313 //....oooOO0OOooo........oooOO0OOooo........oo
314
315 void G4EmDNAChemistryForPlasmids::ConstructTim
316
317 {
318 RegisterTimeStepModel(new G4DNAMolecularIRTM
319 }
320
321 //....oooOO0OOooo........oooOO0OOooo........oo
322
323 void G4EmDNAChemistryForPlasmids::DeclareDMSOA
324 G4DNAMolecularReactionTable* theReactionTabl
325 {
326 auto molTab = G4MoleculeTable::Instance();
327 auto DMSO = molTab->GetConfiguration("DMSO")
328 auto OH = molTab->GetConfiguration("°OH");
329 auto H = molTab->GetConfiguration("H");
330 auto e_aq = molTab->GetConfiguration("e_aq")
331 auto deoxyribose =
332 molTab->GetConfiguration("Deoxyribose");
333 auto damage_deoxyribose_OH =
334 molTab->GetConfiguration("Damaged_Deoxyr
335 auto damage_deoxyribose_H =
336 molTab->GetConfiguration("Damaged_Deoxyr
337 auto damage_deoxyribose_eaq =
338 molTab->GetConfiguration("Damaged_Deoxyr
339
340 G4double DNA_OH_Rate = 1.32E7 * std::pow(fDM
341
342 // DMSO Reactions
343 // OH + DMSO
344 auto reactionData = new G4DNAMolecularReacti
345 theReactionTable->SetReaction(reactionData);
346 //------------------------------------------
347 // H + DMSO
348 reactionData = new G4DNAMolecularReactionDat
349 theReactionTable->SetReaction(reactionData);
350 //------------------------------------------
351 // e-_aq + DMSO
352 reactionData = new G4DNAMolecularReactionDat
353 theReactionTable->SetReaction(reactionData);
354 //------------------------------------------
355
356 //------------------------------------------
357 // DNA Type
358 //------------------------------------------
359 // DNA + OH -> Damage
360 reactionData =
361 new G4DNAMolecularReactionData(DNA_OH_Rate
362 reactionData->AddProduct(damage_deoxyribose_
363 theReactionTable->SetReaction(reactionData);
364 //------------------------------------------
365 // DNA + H
366 reactionData = new G4DNAMolecularReactionDat
367 reactionData->AddProduct(damage_deoxyribose_
368 theReactionTable->SetReaction(reactionData);
369 //------------------------------------------
370 // DNA + e-_aq
371 reactionData =
372 new G4DNAMolecularReactionData(0.01e9 * (1
373 reactionData->AddProduct(damage_deoxyribose_
374 theReactionTable->SetReaction(reactionData);
375 //------------------------------------------
376 }
377
378 //....oooOO0OOooo........oooOO0OOooo........oo
379
380 void G4EmDNAChemistryForPlasmids::DeclareOxyge
381 G4DNAMolecularReactionTable* theReactionTabl
382 {
383 auto molTab = G4MoleculeTable::Instance();
384 auto Oxygen = molTab->GetConfiguration("Oxyg
385 auto H = molTab->GetConfiguration("H");
386 auto e_aq = molTab->GetConfiguration("e_aq")
387 auto O2m = molTab->GetConfiguration("O2m");
388 auto HO2 = molTab->GetConfiguration("HO2°")
389 auto O2 = molTab->GetConfiguration("O2");
390 auto OH = molTab->GetConfiguration("°OH");
391
392 // Oxygen Reactions
393 // e_aq + O2B
394 auto reactionData =
395 new G4DNAMolecularReactionData((fOxygen *
396 reactionData->AddProduct(O2m);
397 theReactionTable->SetReaction(reactionData);
398 //------------------------------------------
399 // H + O2B
400 reactionData = new G4DNAMolecularReactionDat
401 reactionData->AddProduct(HO2);
402 theReactionTable->SetReaction(reactionData);
403 //------------------------------------------
404 // e_aq + O2
405 reactionData = new G4DNAMolecularReactionDat
406 reactionData->AddProduct(O2m);
407 reactionData->SetReactionType(1);
408 theReactionTable->SetReaction(reactionData);
409 //------------------------------------------
410 // H + O2
411 reactionData = new G4DNAMolecularReactionDat
412 reactionData->AddProduct(HO2);
413 reactionData->SetReactionType(1);
414 theReactionTable->SetReaction(reactionData);
415 //------------------------------------------
416 // OH + HO2
417 reactionData = new G4DNAMolecularReactionDat
418 reactionData->AddProduct(O2);
419 reactionData->SetReactionType(1);
420 theReactionTable->SetReaction(reactionData);
421 //------------------------------------------
422 }
423
424 //....oooOO0OOooo........oooOO0OOooo........oo
425