Geant4-11
G4EmDNAChemistry_option2.cc
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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 "G4DNAMolecularDissociation.hh"
40#include "G4DNABrownianTransportation.hh"
41#include "G4DNAMolecularReactionTable.hh"
42#include "G4DNAMolecularStepByStepModel.hh"
43#include "G4DNAElectronHoleRecombination.hh"
44#include "G4Electron.hh"
45#include "G4MoleculeTable.hh"
46#include "G4H2O.hh"
47#include "G4H2.hh"
48#include "G4Hydrogen.hh"
49#include "G4OH.hh"
50#include "G4H3O.hh"
51#include "G4Electron_aq.hh"
52#include "G4H2O2.hh"
53#include "G4PhysicsListHelper.hh"
54#include "G4ProcessTable.hh"
55#include "G4MolecularConfiguration.hh"
56#include "G4PhysicsConstructorFactory.hh"
57#include "G4VDNAReactionModel.hh"
58
59G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistry_option2);
60
61//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
62
63G4EmDNAChemistry_option2::G4EmDNAChemistry_option2()
64 : G4VUserChemistryList(true)
65{
66 G4DNAChemistryManager::Instance()->SetChemistryList(this);
67}
68
69//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
70
71G4EmDNAChemistry_option2::~G4EmDNAChemistry_option2()
72{}
73
74//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
75
76void G4EmDNAChemistry_option2::ConstructMolecule()
77{
78 //-----------------------------------
79 G4Electron::Definition(); // safety
80 //-----------------------------------
81 G4H2O::Definition();
82 G4Hydrogen::Definition();
83 G4H3O::Definition();
84 G4OH::Definition();
85 G4Electron_aq::Definition();
86 G4H2O2::Definition();
87 G4H2::Definition();
88 G4Deoxyribose::Definition();
89 G4Phosphate::Definition();
90 G4Adenine::Definition();
91 G4Guanine::Definition();
92 G4Thymine::Definition();
93 G4Cytosine::Definition();
94 G4Histone::Definition();
95//damaged molecules
96 G4DamagedDeoxyribose::Definition();
97 G4DamagedAdenine::Definition();
98 G4DamagedGuanine::Definition();
99 G4DamagedThymine::Definition();
100 G4DamagedCytosine::Definition();
101 G4ModifiedHistone::Definition();
102
103//_________________species___________________________________________________________
104
105 G4MoleculeTable::Instance()->
106 CreateConfiguration("H3Op", G4H3O::Definition());
107 G4MolecularConfiguration* OHm = G4MoleculeTable::Instance()->
108 CreateConfiguration("OHm",
109 G4OH::Definition(),
110 -1, // charge
111 5.0e-9 * (m2 / s));
112 OHm->SetMass(17.0079 * g / Avogadro * c_squared);
113 G4MoleculeTable::Instance()->
114 CreateConfiguration("OH", G4OH::Definition());
115 G4MoleculeTable::Instance()->
116 CreateConfiguration("e_aq",G4Electron_aq::Definition());
117 G4MoleculeTable::Instance()->
118 CreateConfiguration("H",G4Hydrogen::Definition());
119 G4MoleculeTable::Instance()->
120 CreateConfiguration("H2", G4H2::Definition());
121 G4MoleculeTable::Instance()->
122 CreateConfiguration("H2O2", G4H2O2::Definition());
123
124//________________DNA_______________________________________________
125
126 G4MoleculeTable::Instance()->
127 CreateConfiguration("Deoxyribose",G4Deoxyribose::Definition());
128 G4MoleculeTable::Instance()->
129 CreateConfiguration("Phosphate",G4Phosphate::Definition());
130 G4MoleculeTable::Instance()->
131 CreateConfiguration("Adenine",G4Adenine::Definition());
132 G4MoleculeTable::Instance()->
133 CreateConfiguration("Thymine",G4Thymine::Definition());
134 G4MoleculeTable::Instance()->
135 CreateConfiguration("Guanine",G4Guanine::Definition());
136 G4MoleculeTable::Instance()->
137 CreateConfiguration("Cytosine",G4Cytosine::Definition());
138 G4MoleculeTable::Instance()->
139 CreateConfiguration("Histone",G4Histone::Definition());
140
141//damaged DNAElement Configuration
142
143 G4MoleculeTable::Instance()->
144 CreateConfiguration("Damaged_Deoxyribose",
145 G4DamagedDeoxyribose::Definition());
146 G4MoleculeTable::Instance()->
147 CreateConfiguration("Damaged_Adenine",
148 G4DamagedAdenine::Definition());
149 G4MoleculeTable::Instance()->
150 CreateConfiguration("Damaged_Thymine",
151 G4DamagedThymine::Definition());
152 G4MoleculeTable::Instance()->
153 CreateConfiguration("Damaged_Guanine",
154 G4DamagedGuanine::Definition());
155 G4MoleculeTable::Instance()->
156 CreateConfiguration("Damaged_Cytosine",
157 G4DamagedCytosine::Definition());
158}
159
160//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
161
162void G4EmDNAChemistry_option2::ConstructDissociationChannels()
163{
164//-----------------------------------
165//Get the molecular configuration
166 G4MolecularConfiguration* OH =
167 G4MoleculeTable::Instance()->GetConfiguration("OH");
168 G4MolecularConfiguration* OHm =
169 G4MoleculeTable::Instance()->GetConfiguration("OHm");
170 G4MolecularConfiguration* e_aq =
171 G4MoleculeTable::Instance()->GetConfiguration("e_aq");
172 G4MolecularConfiguration* H2 =
173 G4MoleculeTable::Instance()->GetConfiguration("H2");
174 G4MolecularConfiguration* H3O =
175 G4MoleculeTable::Instance()->GetConfiguration("H3Op");
176 G4MolecularConfiguration* H =
177 G4MoleculeTable::Instance()->GetConfiguration("H");
178
179//-------------------------------------
180//Define the decay channels
181 G4MoleculeDefinition* water = G4H2O::Definition();
182 G4MolecularDissociationChannel* decCh1;
183 G4MolecularDissociationChannel* decCh2;
184
185 G4ElectronOccupancy* occ = new G4ElectronOccupancy(
186 *(water->GetGroundStateElectronOccupancy()));
187
189// EXCITATIONS //
191 G4DNAWaterExcitationStructure waterExcitation;
192//--------------------------------------------------------
193//---------------Excitation on the fifth layer------------
194
195 decCh1 = new G4MolecularDissociationChannel(
196 "A^1B_1_Relaxation");
197 decCh2 = new G4MolecularDissociationChannel(
198 "A^1B_1_DissociativeDecay");
199
200//Decay 1 : OH + H
201 decCh1->SetEnergy(waterExcitation.ExcitationEnergy(0));
202 decCh1->SetProbability(0.35);
203 decCh1->SetDisplacementType(
204 G4DNAWaterDissociationDisplacer::NoDisplacement);
205
206 decCh2->AddProduct(OH);
207 decCh2->AddProduct(H);
208 decCh2->SetProbability(0.65);
209 decCh2->SetDisplacementType(
210 G4DNAWaterDissociationDisplacer::A1B1_DissociationDecay);
211
212// water->AddExcitedState("A^1B_1");
213// this is the transition form ground state to
214 occ->RemoveElectron(4, 1);
215// the first unoccupied orbital: A^1B_1
216 occ->AddElectron(5, 1);
217
218 water->NewConfigurationWithElectronOccupancy("A^1B_1", *occ);
219 water->AddDecayChannel("A^1B_1", decCh1);
220 water->AddDecayChannel("A^1B_1", decCh2);
221
222//--------------------------------------------------------
223//---------------Excitation on the fourth layer-----------
224 decCh1 = new G4MolecularDissociationChannel(
225 "B^1A_1_Relaxation_Channel");
226 decCh2 = new G4MolecularDissociationChannel(
227 "B^1A_1_DissociativeDecay");
228 G4MolecularDissociationChannel* decCh3 =
229 new G4MolecularDissociationChannel("B^1A_1_AutoIonisation_Channel");
230
231//Decay 1 : energy
232 decCh1->SetEnergy(waterExcitation.ExcitationEnergy(1));
233 decCh1->SetProbability(0.3);
234
235//Decay 2 : 2OH + H_2
236 decCh2->AddProduct(H2);
237 decCh2->AddProduct(OH);
238 decCh2->AddProduct(OH);
239 decCh2->SetProbability(0.15);
240 decCh2->SetDisplacementType(
241 G4DNAWaterDissociationDisplacer::B1A1_DissociationDecay);
242
243//Decay 3 : OH + H_3Op + e_aq
244 decCh3->AddProduct(OH);
245 decCh3->AddProduct(H3O);
246 decCh3->AddProduct(e_aq);
247 decCh3->SetProbability(0.55);
248 decCh3->SetDisplacementType(
249 G4DNAWaterDissociationDisplacer::AutoIonisation);
250
251 *occ = *(water->GetGroundStateElectronOccupancy());
252 occ->RemoveElectron(3); // this is the transition form ground state to
253 occ->AddElectron(5, 1); // the first unoccupied orbital: B^1A_1
254
255 water->NewConfigurationWithElectronOccupancy("B^1A_1", *occ);
256 water->AddDecayChannel("B^1A_1", decCh1);
257 water->AddDecayChannel("B^1A_1", decCh2);
258 water->AddDecayChannel("B^1A_1", decCh3);
259
260//-------------------------------------------------------
261//-------------------Excitation of 3rd layer-----------------
262 decCh1 = new G4MolecularDissociationChannel(
263 "Excitation3rdLayer_AutoIonisation_Channel");
264 decCh2 = new G4MolecularDissociationChannel(
265 "Excitation3rdLayer_Relaxation_Channel");
266
267//Decay channel 1 : : OH + H_3Op + e_aq
268 decCh1->AddProduct(OH);
269 decCh1->AddProduct(H3O);
270 decCh1->AddProduct(e_aq);
271
272 decCh1->SetProbability(0.5);
273 decCh1->SetDisplacementType(
274 G4DNAWaterDissociationDisplacer::AutoIonisation);
275
276//Decay channel 2 : energy
277 decCh2->SetEnergy(waterExcitation.ExcitationEnergy(2));
278 decCh2->SetProbability(0.5);
279
280//Electronic configuration of this decay
281 *occ = *(water->GetGroundStateElectronOccupancy());
282 occ->RemoveElectron(2, 1);
283 occ->AddElectron(5, 1);
284
285//Configure the water molecule
286 water->NewConfigurationWithElectronOccupancy(
287 "Excitation3rdLayer", *occ);
288 water->AddDecayChannel("Excitation3rdLayer", decCh1);
289 water->AddDecayChannel("Excitation3rdLayer", decCh2);
290
291//-------------------------------------------------------
292//-------------------Excitation of 2nd layer-----------------
293 decCh1 = new G4MolecularDissociationChannel(
294 "Excitation2ndLayer_AutoIonisation_Channel");
295 decCh2 = new G4MolecularDissociationChannel(
296 "Excitation2ndLayer_Relaxation_Channel");
297
298//Decay Channel 1 : : OH + H_3Op + e_aq
299 decCh1->AddProduct(OH);
300 decCh1->AddProduct(H3O);
301 decCh1->AddProduct(e_aq);
302
303 decCh1->SetProbability(0.5);
304 decCh1->SetDisplacementType(
305 G4DNAWaterDissociationDisplacer::AutoIonisation);
306
307//Decay channel 2 : energy
308 decCh2->SetEnergy(waterExcitation.ExcitationEnergy(3));
309 decCh2->SetProbability(0.5);
310
311 *occ = *(water->GetGroundStateElectronOccupancy());
312 occ->RemoveElectron(1, 1);
313 occ->AddElectron(5, 1);
314
315 water->NewConfigurationWithElectronOccupancy(
316 "Excitation2ndLayer", *occ);
317 water->AddDecayChannel("Excitation2ndLayer", decCh1);
318 water->AddDecayChannel("Excitation2ndLayer", decCh2);
319
320//-------------------------------------------------------
321//-------------------Excitation of 1st layer-----------------
322 decCh1 = new G4MolecularDissociationChannel(
323 "Excitation1stLayer_AutoIonisation_Channel");
324 decCh2 = new G4MolecularDissociationChannel(
325 "Excitation1stLayer_Relaxation_Channel");
326
327 *occ = *(water->GetGroundStateElectronOccupancy());
328 occ->RemoveElectron(0, 1);
329 occ->AddElectron(5, 1);
330
331//Decay Channel 1 : : OH + H_3Op + e_aq
332 decCh1->AddProduct(OH);
333 decCh1->AddProduct(H3O);
334 decCh1->AddProduct(e_aq);
335 decCh1->SetProbability(0.5);
336 decCh1->SetDisplacementType(
337 G4DNAWaterDissociationDisplacer::AutoIonisation);
338
339//Decay channel 2 : energy
340 decCh2->SetEnergy(waterExcitation.ExcitationEnergy(4));
341 decCh2->SetProbability(0.5);
342
343 water->NewConfigurationWithElectronOccupancy(
344 "Excitation1stLayer", *occ);
345 water->AddDecayChannel("Excitation1stLayer", decCh1);
346 water->AddDecayChannel("Excitation1stLayer", decCh2);
347
349// IONISATION //
351//--------------------------------------------------------
352//------------------- Ionisation -------------------------
353
354 decCh1 = new G4MolecularDissociationChannel("Ionisation_Channel");
355
356//Decay Channel 1 : : OH + H_3Op
357 decCh1->AddProduct(H3O);
358 decCh1->AddProduct(OH);
359 decCh1->SetProbability(1);
360 decCh1->SetDisplacementType(
361 G4DNAWaterDissociationDisplacer::Ionisation_DissociationDecay);
362
363 *occ = *(water->GetGroundStateElectronOccupancy());
364 occ->RemoveElectron(4, 1);
365// this is a ionized h2O with a hole in its last orbital
366 water->NewConfigurationWithElectronOccupancy("Ionisation5", *occ);
367 water->AddDecayChannel("Ionisation5", decCh1);
368
369 *occ = *(water->GetGroundStateElectronOccupancy());
370 occ->RemoveElectron(3, 1);
371 water->NewConfigurationWithElectronOccupancy("Ionisation4", *occ);
372 water->AddDecayChannel("Ionisation4",
373 new G4MolecularDissociationChannel(*decCh1));
374
375 *occ = *(water->GetGroundStateElectronOccupancy());
376 occ->RemoveElectron(2, 1);
377 water->NewConfigurationWithElectronOccupancy("Ionisation3", *occ);
378 water->AddDecayChannel("Ionisation3",
379 new G4MolecularDissociationChannel(*decCh1));
380
381 *occ = *(water->GetGroundStateElectronOccupancy());
382 occ->RemoveElectron(1, 1);
383 water->NewConfigurationWithElectronOccupancy("Ionisation2", *occ);
384 water->AddDecayChannel("Ionisation2",
385 new G4MolecularDissociationChannel(*decCh1));
386
387 *occ = *(water->GetGroundStateElectronOccupancy());
388 occ->RemoveElectron(0, 1);
389 water->NewConfigurationWithElectronOccupancy("Ionisation1", *occ);
390 water->AddDecayChannel("Ionisation1",
391 new G4MolecularDissociationChannel(*decCh1));
392
394// Dissociative Attachment //
396 decCh1 = new G4MolecularDissociationChannel(
397 "DissociativeAttachment");
398
399//Decay 1 : 2OH + H_2
400 decCh1->AddProduct(H2);
401 decCh1->AddProduct(OHm);
402 decCh1->AddProduct(OH);
403 decCh1->SetProbability(1);
404 decCh1->SetDisplacementType(
405 G4DNAWaterDissociationDisplacer::DissociativeAttachment);
406
407 *occ = *(water->GetGroundStateElectronOccupancy());
408 occ->AddElectron(5, 1); // H_2O^-
409 water->NewConfigurationWithElectronOccupancy(
410 "DissociativeAttachment", *occ);
411 water->AddDecayChannel(
412 "DissociativeAttachment", decCh1);
413
415 // Electron-hole recombination //
417 decCh1 = new G4MolecularDissociationChannel("H2Ovib_DissociationDecay1");
418 decCh2 = new G4MolecularDissociationChannel("H2Ovib_DissociationDecay2");
419 decCh3 = new G4MolecularDissociationChannel("H2Ovib_DissociationDecay3");
420
421//Decay 1 : 2OH + H_2
422 decCh1->AddProduct(H2);
423 decCh1->AddProduct(OH);
424 decCh1->AddProduct(OH);
425 decCh1->SetProbability(0.15);
426 decCh1->SetDisplacementType(G4DNAWaterDissociationDisplacer::
427 B1A1_DissociationDecay);
428
429//Decay 2 : OH + H
430 decCh2->AddProduct(OH);
431 decCh2->AddProduct(H);
432 decCh2->SetProbability(0.55);
433 decCh2->SetDisplacementType(G4DNAWaterDissociationDisplacer::
434 A1B1_DissociationDecay);
435
436//Decay 3 : relaxation
437 decCh3->SetProbability(0.30);
438
439 const auto pH2Ovib = G4H2O::Definition()->NewConfiguration("H2Ovib");
440 assert(pH2Ovib != nullptr);
441
442 water->AddDecayChannel(pH2Ovib, decCh1);
443 water->AddDecayChannel(pH2Ovib, decCh2);
444 water->AddDecayChannel(pH2Ovib, decCh3);
445
446 delete occ;
447}
448
449//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
450
451void G4EmDNAChemistry_option2::ConstructReactionTable(
452 G4DNAMolecularReactionTable* theReactionTable)
453{
454//-----------------------------------
455//Get the molecular configuration
456 G4MolecularConfiguration* OH =
457 G4MoleculeTable::Instance()->GetConfiguration("OH");
458 G4MolecularConfiguration* OHm =
459 G4MoleculeTable::Instance()->GetConfiguration("OHm");
460 G4MolecularConfiguration* e_aq =
461 G4MoleculeTable::Instance()->GetConfiguration("e_aq");
462 G4MolecularConfiguration* H2 =
463 G4MoleculeTable::Instance()->GetConfiguration("H2");
464 G4MolecularConfiguration* H3Op =
465 G4MoleculeTable::Instance()->GetConfiguration("H3Op");
466 G4MolecularConfiguration* H =
467 G4MoleculeTable::Instance()->GetConfiguration("H");
468 G4MolecularConfiguration* H2O2 =
469 G4MoleculeTable::Instance()->GetConfiguration("H2O2");
470
471 G4MolecularConfiguration* deoxyribose =
472 G4MoleculeTable::Instance()->GetConfiguration("Deoxyribose");
473 G4MolecularConfiguration* adenine =
474 G4MoleculeTable::Instance()->GetConfiguration("Adenine");
475 G4MolecularConfiguration* guanine =
476 G4MoleculeTable::Instance()->GetConfiguration("Guanine");
477 G4MolecularConfiguration* thymine =
478 G4MoleculeTable::Instance()->GetConfiguration("Thymine");
479 G4MolecularConfiguration* cytosine =
480 G4MoleculeTable::Instance()->GetConfiguration("Cytosine");
481 G4MolecularConfiguration* histone =
482 G4MoleculeTable::Instance()->GetConfiguration("Histone");
483
484 G4MolecularConfiguration* damage_deoxyribose =
485 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Deoxyribose");
486 G4MolecularConfiguration* damage_adenine =
487 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Adenine");
488 G4MolecularConfiguration* damage_guanine =
489 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Guanine");
490 G4MolecularConfiguration* damage_thymine =
491 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Thymine");
492 G4MolecularConfiguration* damage_cytosine =
493 G4MoleculeTable::Instance()->GetConfiguration("Damaged_Cytosine");
494
495//------------------------------------------------------------------
496// e_aq + e_aq + 2H2O -> H2 + 2OH-
497 G4DNAMolecularReactionData* reactionData =
498 new G4DNAMolecularReactionData(
499 0.5e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
500 reactionData->AddProduct(OHm);
501 reactionData->AddProduct(OHm);
502 reactionData->AddProduct(H2);
503 theReactionTable->SetReaction(reactionData);
504//------------------------------------------------------------------
505// e_aq + *OH -> OH-
506 reactionData = new G4DNAMolecularReactionData(
507 2.95e10 * (1e-3 * m3 / (mole * s)), e_aq, OH);
508 reactionData->AddProduct(OHm);
509 theReactionTable->SetReaction(reactionData);
510//------------------------------------------------------------------
511// e_aq + H* + H2O -> H2 + OH-
512 reactionData = new G4DNAMolecularReactionData(
513 2.65e10 * (1e-3 * m3 / (mole * s)), e_aq, H);
514 reactionData->AddProduct(OHm);
515 reactionData->AddProduct(H2);
516 theReactionTable->SetReaction(reactionData);
517//------------------------------------------------------------------
518// e_aq + H3O+ -> H* + H2O
519 reactionData = new G4DNAMolecularReactionData(
520 2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
521 reactionData->AddProduct(H);
522 theReactionTable->SetReaction(reactionData);
523
524//------------------------------------------------------------------
525// e_aq + H2O2 -> OH- + *OH
526 reactionData = new G4DNAMolecularReactionData(
527 1.41e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
528 reactionData->AddProduct(OHm);
529 reactionData->AddProduct(OH);
530 theReactionTable->SetReaction(reactionData);
531//------------------------------------------------------------------
532// *OH + *OH -> H2O2
533 reactionData = new G4DNAMolecularReactionData(
534 0.44e10 * (1e-3 * m3 / (mole * s)), OH, OH);
535 reactionData->AddProduct(H2O2);
536 theReactionTable->SetReaction(reactionData);
537//------------------------------------------------------------------
538// *OH + *H -> H2O
539 theReactionTable->SetReaction(
540 1.44e10 * (1e-3 * m3 / (mole * s)), OH, H);
541//------------------------------------------------------------------
542// *H + *H -> H2
543 reactionData = new G4DNAMolecularReactionData(
544 1.20e10 * (1e-3 * m3 / (mole * s)), H, H);
545 reactionData->AddProduct(H2);
546 theReactionTable->SetReaction(reactionData);
547//------------------------------------------------------------------
548// H3O+ + OH- -> 2H2O
549 theReactionTable->SetReaction(
550 1.43e11 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
551//------------------------------------------------------------------
552
553// DNA additions
554
555// OH and DNA
556
557// 2-Deoxyribose + OH -> damagedDeoxyribose
558 reactionData = new G4DNAMolecularReactionData(
559 1.80e9*(1e-3*m3/(mole*s)), deoxyribose, OH);
560 reactionData->AddProduct(damage_deoxyribose);
561 theReactionTable->SetReaction(reactionData);
562
563 // adenine + OH -> ...
564 reactionData = new G4DNAMolecularReactionData(
565 6.10e9*(1e-3*m3/(mole*s)), adenine, OH);
566 reactionData->AddProduct(damage_adenine);
567 theReactionTable->SetReaction(reactionData);
568
569 // guanine + OH -> ...
570 reactionData = new G4DNAMolecularReactionData(
571 9.20e9*(1e-3*m3/(mole*s)), guanine, OH);
572 reactionData->AddProduct(damage_guanine);
573 theReactionTable->SetReaction(reactionData);
574
575 // thymine + OH -> ...
576 reactionData = new G4DNAMolecularReactionData(
577 6.40e9*(1e-3*m3/(mole*s)), thymine, OH);
578 reactionData->AddProduct(damage_thymine);
579 theReactionTable->SetReaction(reactionData);
580
581 // cytosine + OH -> ...
582 reactionData = new G4DNAMolecularReactionData(
583 6.10e9*(1e-3*m3/(mole*s)), cytosine, OH);
584 reactionData->AddProduct(damage_cytosine);
585 theReactionTable->SetReaction(reactionData);
586
587 // Hydrated e- and DNA
588
589 // Deoxyribose + Hydrated e- -> ...
590 reactionData = new G4DNAMolecularReactionData(
591 0.01e9*(1e-3*m3/(mole*s)), deoxyribose, e_aq);
592 reactionData->AddProduct(damage_deoxyribose);
593 theReactionTable->SetReaction(reactionData);
594
595 // adenine + Hydrated e- -> ...
596 reactionData = new G4DNAMolecularReactionData(
597 9e9*(1e-3*m3/(mole*s)), adenine, e_aq);
598 reactionData->AddProduct(damage_adenine);
599 theReactionTable->SetReaction(reactionData);
600
601 // guanine + Hydrated e- -> ...
602 reactionData = new G4DNAMolecularReactionData(
603 14e9*(1e-3*m3/(mole*s)), guanine, e_aq);
604 reactionData->AddProduct(damage_guanine);
605 theReactionTable->SetReaction(reactionData);
606
607 // thymine + Hydrated e- -> ...
608 reactionData = new G4DNAMolecularReactionData(
609 18e9*(1e-3*m3/(mole*s)), thymine, e_aq);
610 reactionData->AddProduct(damage_thymine);
611 theReactionTable->SetReaction(reactionData);
612
613 // cytosine + Hydrated e- -> ...
614 reactionData = new G4DNAMolecularReactionData(
615 13e9*(1e-3*m3/(mole*s)), cytosine, e_aq);
616 reactionData->AddProduct(damage_cytosine);
617 theReactionTable->SetReaction(reactionData);
618
619 // Radical H and DNA
620
621 // Deoxyribose + Radical H -> ...
622 reactionData = new G4DNAMolecularReactionData(
623 0.029e9*(1e-3*m3/(mole*s)), deoxyribose, H);
624 reactionData->AddProduct(damage_deoxyribose);
625 //eactionData->SetEffectiveReactionRadius(0);
626
627 theReactionTable->SetReaction(reactionData);
628
629 // adenine + Radical H -> ...
630 reactionData = new G4DNAMolecularReactionData(
631 0.10e9*(1e-3*m3/(mole*s)), adenine, H);
632 reactionData->AddProduct(damage_adenine);
633 theReactionTable->SetReaction(reactionData);
634
635 // thymine + Radical H -> ...
636 reactionData = new G4DNAMolecularReactionData(
637 0.57e9*(1e-3*m3/(mole*s)), thymine, H);
638 reactionData->AddProduct(damage_thymine);
639 theReactionTable->SetReaction(reactionData);
640
641 // cytosine + Radical H -> ...
642 reactionData = new G4DNAMolecularReactionData(
643 0.092e9*(1e-3*m3/(mole*s)), cytosine, H);
644 reactionData->AddProduct(damage_cytosine);
645 theReactionTable->SetReaction(reactionData);
646
647 //histone + all molecules -> modification(or "damage")
648
649 reactionData = new G4DNAMolecularReactionData(
650 0.0*(1e-3*m3/(mole*s)), histone, OH);
651 reactionData->AddProduct(histone);
652 reactionData->SetEffectiveReactionRadius(
653 2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
654 theReactionTable->SetReaction(reactionData);
655
656 reactionData = new G4DNAMolecularReactionData(
657 0.0*(1e-3*m3/(mole*s)), histone, OHm);
658 reactionData->AddProduct(histone);
659 reactionData->SetEffectiveReactionRadius(
660 2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
661 theReactionTable->SetReaction(reactionData);
662
663 reactionData = new G4DNAMolecularReactionData(
664 0.0*(1e-3*m3/(mole*s)), histone, e_aq);
665 reactionData->AddProduct(histone);
666 reactionData->SetEffectiveReactionRadius(
667 2.4*nm + G4Electron_aq::Definition()->GetVanDerVaalsRadius());
668 theReactionTable->SetReaction(reactionData);
669
670 reactionData = new G4DNAMolecularReactionData(
671 0.0*(1e-3*m3/(mole*s)), histone, H2);
672 reactionData->AddProduct(histone);
673 reactionData->SetEffectiveReactionRadius(
674 2.4*nm + G4H2::Definition()->GetVanDerVaalsRadius());
675 theReactionTable->SetReaction(reactionData);
676
677 reactionData = new G4DNAMolecularReactionData(
678 0.0*(1e-3*m3/(mole*s)), histone, H3Op);
679 reactionData->AddProduct(histone);
680 reactionData->SetEffectiveReactionRadius(
681 2.4*nm + G4H3O::Definition()->GetVanDerVaalsRadius());
682 theReactionTable->SetReaction(reactionData);
683
684 reactionData = new G4DNAMolecularReactionData(
685 0.0*(1e-3*m3/(mole*s)), histone, H);
686 reactionData->AddProduct(histone);
687 reactionData->SetEffectiveReactionRadius(
688 2.4*nm + G4Hydrogen::Definition()->GetVanDerVaalsRadius());
689 theReactionTable->SetReaction(reactionData);
690
691 reactionData = new G4DNAMolecularReactionData(
692 0.0*(1e-3*m3/(mole*s)), histone, H2O2);
693 reactionData->AddProduct(histone);
694 reactionData->SetEffectiveReactionRadius(
695 2.4*nm + G4H2O2::Definition()->GetVanDerVaalsRadius());
696 theReactionTable->SetReaction(reactionData);
697}
698
699//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
700
701void G4EmDNAChemistry_option2::ConstructProcess()
702{
703 auto pPhysicsListHelper =
704 G4PhysicsListHelper::GetPhysicsListHelper();
705 G4VProcess* pProcess =
706 G4ProcessTable::GetProcessTable()->
707 FindProcess("e-_G4DNAVibExcitation", "e-");
708
709 if (pProcess != nullptr)
710 {
711 G4DNAVibExcitation* pVibExcitation =
712 (G4DNAVibExcitation*) pProcess;
713 G4VEmModel* pModel = pVibExcitation->EmModel();
714 G4DNASancheExcitationModel* pSancheExcitationMod =
715 dynamic_cast<G4DNASancheExcitationModel*>(pModel);
716 if(pSancheExcitationMod != nullptr)
717 {
718 pSancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
719 }
720 }
721
722//===============================================================
723// Electron Solvatation
724//
725 pProcess = G4ProcessTable::GetProcessTable()->
726 FindProcess("e-_G4DNAElectronSolvation", "e-");
727
728 if (pProcess == nullptr)
729 {
730 pPhysicsListHelper->
731 RegisterProcess(new G4DNAElectronSolvation(
732 "e-_G4DNAElectronSolvation"), G4Electron::Definition());
733 }
734
735//===============================================================
736// Define processes for molecules
737//
738 G4MoleculeTable* pMoleculeTable =
739 G4MoleculeTable::Instance();
740 G4MoleculeDefinitionIterator iterator =
741 pMoleculeTable->GetDefintionIterator();
742 iterator.reset();
743 while (iterator())
744 {
745 G4MoleculeDefinition* pMoleculeDef = iterator.value();
746
747 if(pMoleculeDef != G4H2O::Definition())
748 {
749 G4DNABrownianTransportation* pBrownianTransport =
750 new G4DNABrownianTransportation();
751 pPhysicsListHelper->
752 RegisterProcess(pBrownianTransport, pMoleculeDef);
753 }
754 else
755 {
756 pMoleculeDef->GetProcessManager()->
757 AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
758 G4DNAMolecularDissociation* pDissociationProcess =
759 new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
760 pDissociationProcess->SetDisplacer(pMoleculeDef,
761 new G4DNAWaterDissociationDisplacer);
762 pDissociationProcess->SetVerboseLevel(1);
763
764 pMoleculeDef->GetProcessManager()->
765 AddRestProcess(pDissociationProcess, 1);
766 }
767 }
768 G4DNAChemistryManager::Instance()->Initialize();
769}
770
771
772//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
773
774void G4EmDNAChemistry_option2::ConstructTimeStepModel(
775G4DNAMolecularReactionTable* reactionTable)
776{
777 G4VDNAReactionModel* reactionRadiusComputer =
778 new G4DNASmoluchowskiReactionModel();
779 reactionTable->PrintTable(reactionRadiusComputer);
780
781 G4DNAMolecularStepByStepModel* stepByStep =
782 new G4DNAMolecularStepByStepModel();
783 stepByStep->SetReactionModel(reactionRadiusComputer);
784
785 RegisterTimeStepModel(stepByStep, 0);
786}
G4Electron_aq.hh
G4_DECLARE_PHYSCONSTR_FACTORY
G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistry_option2)
G4EmDNAChemistry_option2.hh
mole
static constexpr double mole
Definition: G4SIunits.hh:279
nm
static constexpr double nm
Definition: G4SIunits.hh:92
s
static constexpr double s
Definition: G4SIunits.hh:154
m3
static constexpr double m3
Definition: G4SIunits.hh:111
eV
static constexpr double eV
Definition: G4SIunits.hh:201
g
static constexpr double g
Definition: G4SIunits.hh:168
m2
static constexpr double m2
Definition: G4SIunits.hh:110
G4Adenine::Definition
static G4Adenine * Definition()
Definition: G4DNAMolecule.cc:225
G4Cytosine::Definition
static G4Cytosine * Definition()
Definition: G4DNAMolecule.cc:305
G4DNAChemistryManager::Instance
static G4DNAChemistryManager * Instance()
Definition: G4DNAChemistryManager.cc:132
G4DNAChemistryManager::SetChemistryList
void SetChemistryList(G4VUserChemistryList &)
Definition: G4DNAChemistryManager.cc:714
G4DNAMolecularDissociation::SetDisplacer
void SetDisplacer(Species *, Displacer *)
Definition: G4DNAMolecularDissociation.cc:285
G4DNAMolecularReactionData::SetEffectiveReactionRadius
void SetEffectiveReactionRadius(G4double radius)
Definition: G4DNAMolecularReactionTable.cc:250
G4DNAMolecularReactionTable::PrintTable
void PrintTable(G4VDNAReactionModel *=0)
Definition: G4DNAMolecularReactionTable.cc:424
G4DNAMolecularReactionTable::SetReaction
void SetReaction(G4double observedReactionRate, Reactant *reactive1, Reactant *reactive2)
Definition: G4DNAMolecularReactionTable.cc:414
G4DNAMolecularStepByStepModel::SetReactionModel
void SetReactionModel(G4VDNAReactionModel *)
Definition: G4DNAMolecularStepByStepModel.cc:87
G4DamagedAdenine::Definition
static G4DamagedAdenine * Definition()
Definition: G4DNAMolecule.cc:66
G4DamagedCytosine::Definition
static G4DamagedCytosine * Definition()
Definition: G4DNAMolecule.cc:146
G4DamagedDeoxyribose::Definition
static G4DamagedDeoxyribose * Definition()
Definition: G4DNAMolecule.cc:39
G4DamagedGuanine::Definition
static G4DamagedGuanine * Definition()
Definition: G4DNAMolecule.cc:93
G4DamagedThymine::Definition
static G4DamagedThymine * Definition()
Definition: G4DNAMolecule.cc:119
G4Deoxyribose::Definition
static G4Deoxyribose * Definition()
Definition: G4DNAMolecule.cc:173
G4ElectronOccupancy::AddElectron
G4int AddElectron(G4int orbit, G4int number=1)
Definition: G4ElectronOccupancy.cc:139
G4ElectronOccupancy::RemoveElectron
G4int RemoveElectron(G4int orbit, G4int number=1)
Definition: G4ElectronOccupancy.cc:161
G4Electron_aq::Definition
static G4Electron_aq * Definition()
Definition: G4Electron_aq.cc:45
G4Electron::Definition
static G4Electron * Definition()
Definition: G4Electron.cc:48
G4EmDNAChemistry_option2
Definition: G4EmDNAChemistry_option2.hh:40
G4EmDNAChemistry_option2::~G4EmDNAChemistry_option2
virtual ~G4EmDNAChemistry_option2() override
Definition: G4EmDNAChemistry_option2.cc:71
G4EmDNAChemistry_option2::ConstructProcess
void ConstructProcess() override
Definition: G4EmDNAChemistry_option2.cc:701
G4EmDNAChemistry_option2::ConstructDissociationChannels
void ConstructDissociationChannels() override
Definition: G4EmDNAChemistry_option2.cc:162
G4EmDNAChemistry_option2::ConstructMolecule
void ConstructMolecule() override
Definition: G4EmDNAChemistry_option2.cc:76
G4EmDNAChemistry_option2::ConstructReactionTable
void ConstructReactionTable(G4DNAMolecularReactionTable *pTable) override
Definition: G4EmDNAChemistry_option2.cc:451
G4EmDNAChemistry_option2::ConstructTimeStepModel
void ConstructTimeStepModel(G4DNAMolecularReactionTable *pTable) override
Definition: G4EmDNAChemistry_option2.cc:774
G4EmDNAChemistry_option2::G4EmDNAChemistry_option2
G4EmDNAChemistry_option2()
Definition: G4EmDNAChemistry_option2.cc:63
G4Guanine::Definition
static G4Guanine * Definition()
Definition: G4DNAMolecule.cc:251
G4H2O2::Definition
static G4H2O2 * Definition()
Definition: G4H2O2.cc:45
G4H2O::Definition
static G4H2O * Definition()
Definition: G4H2O.cc:42
G4H2::Definition
static G4H2 * Definition()
Definition: G4H2.cc:45
G4H3O::Definition
static G4H3O * Definition()
Definition: G4H3O.cc:46
G4Histone::Definition
static G4Histone * Definition()
Definition: G4DNAMolecule.cc:358
G4Hydrogen::Definition
static G4Hydrogen * Definition()
Definition: G4Hydrogen.cc:45
G4ModifiedHistone::Definition
static G4ModifiedHistone * Definition()
Definition: G4DNAMolecule.cc:331
G4MolecularDissociationChannel::AddProduct
void AddProduct(Product *, G4double displacement=0.)
Definition: G4MolecularDissociationChannel.cc:60
G4MoleculeDefinition::GetGroundStateElectronOccupancy
const G4ElectronOccupancy * GetGroundStateElectronOccupancy() const
Definition: G4MoleculeDefinition.hh:240
G4MoleculeDefinition::AddDecayChannel
void AddDecayChannel(const G4MolecularConfiguration *molConf, const G4MolecularDissociationChannel *channel)
Definition: G4MoleculeDefinition.cc:223
G4MoleculeDefinition::NewConfiguration
G4MolecularConfiguration * NewConfiguration(const G4String &excitedStateLabel)
Definition: G4MoleculeDefinition.cc:147
G4MoleculeDefinition::NewConfigurationWithElectronOccupancy
G4MolecularConfiguration * NewConfigurationWithElectronOccupancy(const G4String &excitedStateLabel, const G4ElectronOccupancy &, double decayTime=0.)
Definition: G4MoleculeDefinition.cc:170
G4MoleculeTable::GetConfiguration
G4MolecularConfiguration * GetConfiguration(const G4String &, bool mustExist=true)
Definition: G4MoleculeTable.cc:105
G4MoleculeTable::GetDefintionIterator
G4MoleculeDefinitionIterator GetDefintionIterator()
Definition: G4MoleculeTable.hh:116
G4MoleculeTable::Instance
static G4MoleculeTable * Instance()
Definition: G4MoleculeTable.cc:53
G4OH::Definition
static G4OH * Definition()
Definition: G4OH.cc:45
G4ParticleDefinition::GetProcessManager
G4ProcessManager * GetProcessManager() const
Definition: G4ParticleDefinition.cc:238
G4Phosphate::Definition
static G4Phosphate * Definition()
Definition: G4DNAMolecule.cc:199
G4PhysicsListHelper::GetPhysicsListHelper
static G4PhysicsListHelper * GetPhysicsListHelper()
Definition: G4PhysicsListHelper.cc:89
G4ProcessTable::GetProcessTable
static G4ProcessTable * GetProcessTable()
Definition: G4ProcessTable.cc:108
G4Thymine::Definition
static G4Thymine * Definition()
Definition: G4DNAMolecule.cc:279
G4VEmProcess::EmModel
G4VEmModel * EmModel(size_t index=0) const
Definition: G4VEmProcess.hh:805
G4VPhysicsConstructor::RegisterProcess
G4bool RegisterProcess(G4VProcess *process, G4ParticleDefinition *particle)
Definition: G4VPhysicsConstructor.hh:206
G4VProcess::SetVerboseLevel
void SetVerboseLevel(G4int value)
Definition: G4VProcess.hh:412
G4VUserChemistryList::RegisterTimeStepModel
void RegisterTimeStepModel(G4VITStepModel *timeStepModel, double startingTime=0)
Definition: G4VUserChemistryList.cc:56
source.hepunit.Avogadro
float Avogadro
Definition: hepunit.py:252
source.hepunit.c_squared
float c_squared
Definition: hepunit.py:257
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