| Geant4 Cross Reference |
1 //
2 // ********************************************************************
3 // * License and Disclaimer *
4 // * *
5 // * The Geant4 software is copyright of the Copyright Holders of *
6 // * the Geant4 Collaboration. It is provided under the terms and *
7 // * conditions of the Geant4 Software License, included in the file *
8 // * LICENSE and available at http://cern.ch/geant4/license . These *
9 // * include a list of copyright holders. *
10 // * *
11 // * Neither the authors of this software system, nor their employing *
12 // * institutes,nor the agencies providing financial support for this *
13 // * work make any representation or warranty, express or implied, *
14 // * regarding this software system or assume any liability for its *
15 // * use. Please see the license in the file LICENSE and URL above *
16 // * for the full disclaimer and the limitation of liability. *
17 // * *
18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboration. *
20 // * By using, copying, modifying or distributing the software (or *
21 // * any work based on the software) you agree to acknowledge its *
22 // * use in resulting scientific publications, and indicate your *
23 // * acceptance of all terms of the Geant4 Software license. *
24 // ********************************************************************
25 //
26 //
27 // G4EmDNAChemistryForPlasmids.cc
28 //
29 // Created on: Feb 10, 2021
30 // Authors: J. Naoki D. Kondo
31 // W. G. Shin, J. Ramos-Mendez and B. Faddegon
32 //
33 /// \file G4EmDNAChemistryForPlasmids.cc
34 /// \brief Implementation of the Chemistry parameters with DNA reactions
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.hh"
91 G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistryForPlasmids);
92
93 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
94
95 G4EmDNAChemistryForPlasmids::G4EmDNAChemistryForPlasmids() : G4VUserChemistryList(true)
96 {
97 G4DNAChemistryManager::Instance()->SetChemistryList(this);
98
99 fDMSO = 0;
100 fOxygen = 0;
101 }
102
103 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
104
105 G4EmDNAChemistryForPlasmids::G4EmDNAChemistryForPlasmids(G4double dmso, G4double oxygen)
106 : G4VUserChemistryList(true)
107 {
108 G4DNAChemistryManager::Instance()->SetChemistryList(this);
109
110 fDMSO = dmso;
111 fOxygen = oxygen;
112 }
113
114 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
115
116 void G4EmDNAChemistryForPlasmids::ConstructMolecule()
117 {
118 G4ChemDissociationChannels_option1::ConstructMolecule();
119 auto molTab = G4MoleculeTable::Instance();
120
121 molTab->CreateConfiguration("DMSO", G4DMSO::Definition(), 0, 0 * (m2 / s));
122
123 molTab->CreateConfiguration("O2", G4O2::Definition());
124 molTab->GetConfiguration("O2")->SetVanDerVaalsRadius(0.17 * nm);
125 molTab->CreateConfiguration("Oxygen", G4OxygenB::Definition(), 0,
126 0 * (m2 / s));
127 molTab->CreateConfiguration("Deoxyribose", G4DNA_Deoxyribose::Definition(),
128 0, 1E-150 * (m2 / s));
129 molTab->CreateConfiguration(
130 "Damaged_DeoxyriboseOH", G4DNA_DamagedDeoxyriboseOH::Definition(), 0, 1E-150 * (m2 / s));
131 molTab->CreateConfiguration(
132 "Damaged_DeoxyriboseH", G4DNA_DamagedDeoxyriboseH::Definition(), 0, 1E-150 * (m2 / s));
133 molTab->CreateConfiguration(
134 "Damaged_DeoxyriboseEAQ", G4DNA_DamagedDeoxyriboseEAQ::Definition(), 0, 1E-150 * (m2 / s));
135 }
136
137 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
138
139 void G4EmDNAChemistryForPlasmids::ConstructDissociationChannels()
140 {
141 G4ChemDissociationChannels_option1::ConstructDissociationChannels();
142 }
143
144 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
145
146 void G4EmDNAChemistryForPlasmids::ConstructReactionTable(
147 G4DNAMolecularReactionTable* theReactionTable)
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 * (1e-3 * m3 / (mole * s)), e_aq, OH);
169 reactionData->AddProduct(OHm);
170 reactionData->SetReactionType(1);
171 theReactionTable->SetReaction(reactionData);
172 //----------------------------------------------------------------//
173 // e_aq + H2O2 -> OH- + *OH prob: 0.11
174 reactionData = new G4DNAMolecularReactionData(1.10e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
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 G4DNAMolecularReactionData(1.55e10 * (1e-3 * m3 / (mole * s)), OH, H);
182 reactionData->SetReactionType(1);
183 theReactionTable->SetReaction(reactionData);
184 //----------------------------------------------------------------//
185 // H + H2O2 -> OH prob: 0.00
186 reactionData = new G4DNAMolecularReactionData(0.009e10 * (1e-3 * m3 / (mole * s)), H, H2O2);
187 reactionData->AddProduct(OH);
188 reactionData->SetReactionType(1);
189 theReactionTable->SetReaction(reactionData);
190 //----------------------------------------------------------------//
191 // *OH + *OH -> H2O2 prob: 0.55
192 reactionData = new G4DNAMolecularReactionData(0.55e10 * (1e-3 * m3 / (mole * s)), OH, OH);
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 G4DNAMolecularReactionData(0.636e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
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 G4DNAMolecularReactionData(11.3e10 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
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 G4DNAMolecularReactionData(2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
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 G4DNAMolecularReactionData(2.5e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
231 reactionData->AddProduct(OHm);
232 reactionData->AddProduct(H2);
233 reactionData->SetReactionType(0);
234 theReactionTable->SetReaction(reactionData);
235 //----------------------------------------------------------------//
236 // *H + *H -> H2
237 reactionData = new G4DNAMolecularReactionData(0.503e10 * (1e-3 * m3 / (mole * s)), H, H);
238 reactionData->AddProduct(H2);
239 reactionData->SetReactionType(0);
240 theReactionTable->SetReaction(reactionData);
241
242 if (fDMSO > 0) DeclareDMSOAndDNAReactions(theReactionTable);
243
244 if (fOxygen > 0) DeclareOxygenReactions(theReactionTable);
245 }
246
247 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
248
249 void G4EmDNAChemistryForPlasmids::ConstructProcess()
250 {
251 G4PhysicsListHelper* ph = G4PhysicsListHelper::GetPhysicsListHelper();
252
253 //===============================================================
254 // Extend vibrational to low energy
255 // Anyway, solvation of electrons is taken into account from 7.4 eV
256 // So below this threshold, for now, no accurate modeling is done
257 //
258 G4VProcess* process =
259 G4ProcessTable::GetProcessTable()->FindProcess("e-_G4DNAVibExcitation", "e-");
260
261 if (process) {
262 G4DNAVibExcitation* vibExcitation = (G4DNAVibExcitation*)process;
263 G4VEmModel* model = vibExcitation->EmModel();
264 G4DNASancheExcitationModel* sancheExcitationMod =
265 dynamic_cast<G4DNASancheExcitationModel*>(model);
266 if (sancheExcitationMod) {
267 sancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
268 }
269 }
270
271 //===============================================================
272 // *** Electron Solvatation ***
273 //
274 process = G4ProcessTable::GetProcessTable()->FindProcess("e-_G4DNAElectronSolvation", "e-");
275
276 if (process == 0) {
277 ph->RegisterProcess(new G4DNAElectronSolvation("e-_G4DNAElectronSolvation"),
278 G4Electron::Definition());
279 }
280
281 //===============================================================
282 // Define processes for molecules
283 //
284 G4MoleculeTable* theMoleculeTable = G4MoleculeTable::Instance();
285 G4MoleculeDefinitionIterator iterator = theMoleculeTable->GetDefintionIterator();
286 iterator.reset();
287 while (iterator()) {
288 G4MoleculeDefinition* moleculeDef = iterator.value();
289
290 if (moleculeDef != G4H2O::Definition()) {
291 // G4cout << "Brownian motion added for: "<< moleculeDef->GetName() << G4endl;
292 // G4DNABrownianTransportation* brown = new G4DNABrownianTransportation();
293 // ph->RegisterProcess(brown, moleculeDef);
294 }
295 else {
296 moleculeDef->GetProcessManager()->AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
297 G4DNAMolecularDissociation* dissociationProcess =
298 new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
299 dissociationProcess->SetDisplacer(moleculeDef, new G4DNAWaterDissociationDisplacer);
300 dissociationProcess->SetVerboseLevel(3);
301
302 moleculeDef->GetProcessManager()->AddRestProcess(dissociationProcess, 1);
303 }
304 /*
305 * Warning : end of particles and processes are needed by
306 * EM Physics builders
307 */
308 }
309
310 G4DNAChemistryManager::Instance()->Initialize();
311 }
312
313 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
314
315 void G4EmDNAChemistryForPlasmids::ConstructTimeStepModel(G4DNAMolecularReactionTable*
316 /*reactionTable*/)
317 {
318 RegisterTimeStepModel(new G4DNAMolecularIRTModel(), 0);
319 }
320
321 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
322
323 void G4EmDNAChemistryForPlasmids::DeclareDMSOAndDNAReactions(
324 G4DNAMolecularReactionTable* theReactionTable)
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_DeoxyriboseOH");
335 auto damage_deoxyribose_H =
336 molTab->GetConfiguration("Damaged_DeoxyriboseH");
337 auto damage_deoxyribose_eaq =
338 molTab->GetConfiguration("Damaged_DeoxyriboseEAQ");
339
340 G4double DNA_OH_Rate = 1.32E7 * std::pow(fDMSO * 7.1E9, 0.29);
341
342 // DMSO Reactions
343 // OH + DMSO
344 auto reactionData = new G4DNAMolecularReactionData(fDMSO * 7.1E9 / s, OH, DMSO);
345 theReactionTable->SetReaction(reactionData);
346 //----------------------------------------------------------------//
347 // H + DMSO
348 reactionData = new G4DNAMolecularReactionData(fDMSO * 2.7E7 / s, H, DMSO);
349 theReactionTable->SetReaction(reactionData);
350 //----------------------------------------------------------------//
351 // e-_aq + DMSO
352 reactionData = new G4DNAMolecularReactionData(fDMSO * 3.8E6 / s, e_aq, DMSO);
353 theReactionTable->SetReaction(reactionData);
354 //----------------------------------------------------------------//
355
356 //----------------------------------------------------------------//
357 // DNA Type //
358 //----------------------------------------------------------------//
359 // DNA + OH -> Damage
360 reactionData =
361 new G4DNAMolecularReactionData(DNA_OH_Rate * (1e-3 * m3 / (mole * s)), deoxyribose, OH);
362 reactionData->AddProduct(damage_deoxyribose_OH);
363 theReactionTable->SetReaction(reactionData);
364 //----------------------------------------------------------------//
365 // DNA + H
366 reactionData = new G4DNAMolecularReactionData(0.03e9 * (1e-3 * m3 / (mole * s)), deoxyribose, H);
367 reactionData->AddProduct(damage_deoxyribose_H);
368 theReactionTable->SetReaction(reactionData);
369 //----------------------------------------------------------------//
370 // DNA + e-_aq
371 reactionData =
372 new G4DNAMolecularReactionData(0.01e9 * (1e-3 * m3 / (mole * s)), deoxyribose, e_aq);
373 reactionData->AddProduct(damage_deoxyribose_eaq);
374 theReactionTable->SetReaction(reactionData);
375 //----------------------------------------------------------------//
376 }
377
378 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
379
380 void G4EmDNAChemistryForPlasmids::DeclareOxygenReactions(
381 G4DNAMolecularReactionTable* theReactionTable)
382 {
383 auto molTab = G4MoleculeTable::Instance();
384 auto Oxygen = molTab->GetConfiguration("Oxygen");
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 * 1.9E10) / s, e_aq, Oxygen);
396 reactionData->AddProduct(O2m);
397 theReactionTable->SetReaction(reactionData);
398 //------------------------------------------------------------------
399 // H + O2B
400 reactionData = new G4DNAMolecularReactionData((fOxygen * 2.1E10) / s, H, Oxygen);
401 reactionData->AddProduct(HO2);
402 theReactionTable->SetReaction(reactionData);
403 //------------------------------------------------------------------
404 // e_aq + O2
405 reactionData = new G4DNAMolecularReactionData(1.9E10 * (1e-3 * m3 / (mole * s)), e_aq, O2);
406 reactionData->AddProduct(O2m);
407 reactionData->SetReactionType(1);
408 theReactionTable->SetReaction(reactionData);
409 //------------------------------------------------------------------
410 // H + O2
411 reactionData = new G4DNAMolecularReactionData(2.1E10 * (1e-3 * m3 / (mole * s)), H, O2);
412 reactionData->AddProduct(HO2);
413 reactionData->SetReactionType(1);
414 theReactionTable->SetReaction(reactionData);
415 //------------------------------------------------------------------
416 // OH + HO2
417 reactionData = new G4DNAMolecularReactionData(7.9E9 * (1e-3 * m3 / (mole * s)), OH, HO2);
418 reactionData->AddProduct(O2);
419 reactionData->SetReactionType(1);
420 theReactionTable->SetReaction(reactionData);
421 //------------------------------------------------------------------
422 }
423
424 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
425