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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 
59 G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistry_option2);
60 
61 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
62 
63 G4EmDNAChemistry_option2::G4EmDNAChemistry_option2()
64  : G4VUserChemistryList(true)
65 {
66  G4DNAChemistryManager::Instance()->SetChemistryList(this);
67 }
68 
69 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
70 
71 G4EmDNAChemistry_option2::~G4EmDNAChemistry_option2()
72 {}
73 
74 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
75 
76 void 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 
162 void 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 
414  delete occ;
415 }
416 
417 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
418 
419 void G4EmDNAChemistry_option2::ConstructReactionTable(
420  G4DNAMolecularReactionTable* theReactionTable)
421 {
422 //-----------------------------------
423 //Get the molecular configuration
424  G4MolecularConfiguration* OH =
425  G4MoleculeTable::Instance()->GetConfiguration("OH");
426  G4MolecularConfiguration* OHm =
427  G4MoleculeTable::Instance()->GetConfiguration("OHm");
428  G4MolecularConfiguration* e_aq =
429  G4MoleculeTable::Instance()->GetConfiguration("e_aq");
430  G4MolecularConfiguration* H2 =
431  G4MoleculeTable::Instance()->GetConfiguration("H2");
432  G4MolecularConfiguration* H3Op =
433  G4MoleculeTable::Instance()->GetConfiguration("H3Op");
434  G4MolecularConfiguration* H =
435  G4MoleculeTable::Instance()->GetConfiguration("H");
436  G4MolecularConfiguration* H2O2 =
437  G4MoleculeTable::Instance()->GetConfiguration("H2O2");
438 
439  G4MolecularConfiguration* deoxyribose =
440  G4MoleculeTable::Instance()->GetConfiguration("Deoxyribose");
441  G4MolecularConfiguration* adenine =
442  G4MoleculeTable::Instance()->GetConfiguration("Adenine");
443  G4MolecularConfiguration* guanine =
444  G4MoleculeTable::Instance()->GetConfiguration("Guanine");
445  G4MolecularConfiguration* thymine =
446  G4MoleculeTable::Instance()->GetConfiguration("Thymine");
447  G4MolecularConfiguration* cytosine =
448  G4MoleculeTable::Instance()->GetConfiguration("Cytosine");
449  G4MolecularConfiguration* histone =
450  G4MoleculeTable::Instance()->GetConfiguration("Histone");
451 
452  G4MolecularConfiguration* damage_deoxyribose =
453  G4MoleculeTable::Instance()->GetConfiguration("Damaged_Deoxyribose");
454  G4MolecularConfiguration* damage_adenine =
455  G4MoleculeTable::Instance()->GetConfiguration("Damaged_Adenine");
456  G4MolecularConfiguration* damage_guanine =
457  G4MoleculeTable::Instance()->GetConfiguration("Damaged_Guanine");
458  G4MolecularConfiguration* damage_thymine =
459  G4MoleculeTable::Instance()->GetConfiguration("Damaged_Thymine");
460  G4MolecularConfiguration* damage_cytosine =
461  G4MoleculeTable::Instance()->GetConfiguration("Damaged_Cytosine");
462 
463 //------------------------------------------------------------------
464 // e_aq + e_aq + 2H2O -> H2 + 2OH-
465  G4DNAMolecularReactionData* reactionData =
466  new G4DNAMolecularReactionData(
467  0.5e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
468  reactionData->AddProduct(OHm);
469  reactionData->AddProduct(OHm);
470  reactionData->AddProduct(H2);
471  theReactionTable->SetReaction(reactionData);
472 //------------------------------------------------------------------
473 // e_aq + *OH -> OH-
474  reactionData = new G4DNAMolecularReactionData(
475  2.95e10 * (1e-3 * m3 / (mole * s)), e_aq, OH);
476  reactionData->AddProduct(OHm);
477  theReactionTable->SetReaction(reactionData);
478 //------------------------------------------------------------------
479 // e_aq + H* + H2O -> H2 + OH-
480  reactionData = new G4DNAMolecularReactionData(
481  2.65e10 * (1e-3 * m3 / (mole * s)), e_aq, H);
482  reactionData->AddProduct(OHm);
483  reactionData->AddProduct(H2);
484  theReactionTable->SetReaction(reactionData);
485 //------------------------------------------------------------------
486 // e_aq + H3O+ -> H* + H2O
487  reactionData = new G4DNAMolecularReactionData(
488  2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
489  reactionData->AddProduct(H);
490  theReactionTable->SetReaction(reactionData);
491 
492 //------------------------------------------------------------------
493 // e_aq + H2O2 -> OH- + *OH
494  reactionData = new G4DNAMolecularReactionData(
495  1.41e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
496  reactionData->AddProduct(OHm);
497  reactionData->AddProduct(OH);
498  theReactionTable->SetReaction(reactionData);
499 //------------------------------------------------------------------
500 // *OH + *OH -> H2O2
501  reactionData = new G4DNAMolecularReactionData(
502  0.44e10 * (1e-3 * m3 / (mole * s)), OH, OH);
503  reactionData->AddProduct(H2O2);
504  theReactionTable->SetReaction(reactionData);
505 //------------------------------------------------------------------
506 // *OH + *H -> H2O
507  theReactionTable->SetReaction(
508  1.44e10 * (1e-3 * m3 / (mole * s)), OH, H);
509 //------------------------------------------------------------------
510 // *H + *H -> H2
511  reactionData = new G4DNAMolecularReactionData(
512  1.20e10 * (1e-3 * m3 / (mole * s)), H, H);
513  reactionData->AddProduct(H2);
514  theReactionTable->SetReaction(reactionData);
515 //------------------------------------------------------------------
516 // H3O+ + OH- -> 2H2O
517  theReactionTable->SetReaction(
518  1.43e11 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
519 //------------------------------------------------------------------
520 
521 // DNA additions
522 
523 // OH and DNA
524 
525 // 2-Deoxyribose + OH -> damagedDeoxyribose
526  reactionData = new G4DNAMolecularReactionData(
527  1.80e9*(1e-3*m3/(mole*s)), deoxyribose, OH);
528  reactionData->AddProduct(damage_deoxyribose);
529  theReactionTable->SetReaction(reactionData);
530 
531  // adenine + OH -> ...
532  reactionData = new G4DNAMolecularReactionData(
533  6.10e9*(1e-3*m3/(mole*s)), adenine, OH);
534  reactionData->AddProduct(damage_adenine);
535  theReactionTable->SetReaction(reactionData);
536 
537  // guanine + OH -> ...
538  reactionData = new G4DNAMolecularReactionData(
539  9.20e9*(1e-3*m3/(mole*s)), guanine, OH);
540  reactionData->AddProduct(damage_guanine);
541  theReactionTable->SetReaction(reactionData);
542 
543  // thymine + OH -> ...
544  reactionData = new G4DNAMolecularReactionData(
545  6.40e9*(1e-3*m3/(mole*s)), thymine, OH);
546  reactionData->AddProduct(damage_thymine);
547  theReactionTable->SetReaction(reactionData);
548 
549  // cytosine + OH -> ...
550  reactionData = new G4DNAMolecularReactionData(
551  6.10e9*(1e-3*m3/(mole*s)), cytosine, OH);
552  reactionData->AddProduct(damage_cytosine);
553  theReactionTable->SetReaction(reactionData);
554 
555  // Hydrated e- and DNA
556 
557  // Deoxyribose + Hydrated e- -> ...
558  reactionData = new G4DNAMolecularReactionData(
559  0.01e9*(1e-3*m3/(mole*s)), deoxyribose, e_aq);
560  reactionData->AddProduct(damage_deoxyribose);
561  theReactionTable->SetReaction(reactionData);
562 
563  // adenine + Hydrated e- -> ...
564  reactionData = new G4DNAMolecularReactionData(
565  9e9*(1e-3*m3/(mole*s)), adenine, e_aq);
566  reactionData->AddProduct(damage_adenine);
567  theReactionTable->SetReaction(reactionData);
568 
569  // guanine + Hydrated e- -> ...
570  reactionData = new G4DNAMolecularReactionData(
571  14e9*(1e-3*m3/(mole*s)), guanine, e_aq);
572  reactionData->AddProduct(damage_guanine);
573  theReactionTable->SetReaction(reactionData);
574 
575  // thymine + Hydrated e- -> ...
576  reactionData = new G4DNAMolecularReactionData(
577  18e9*(1e-3*m3/(mole*s)), thymine, e_aq);
578  reactionData->AddProduct(damage_thymine);
579  theReactionTable->SetReaction(reactionData);
580 
581  // cytosine + Hydrated e- -> ...
582  reactionData = new G4DNAMolecularReactionData(
583  13e9*(1e-3*m3/(mole*s)), cytosine, e_aq);
584  reactionData->AddProduct(damage_cytosine);
585  theReactionTable->SetReaction(reactionData);
586 
587  // Radical H and DNA
588 
589  // Deoxyribose + Radical H -> ...
590  reactionData = new G4DNAMolecularReactionData(
591  0.029e9*(1e-3*m3/(mole*s)), deoxyribose, H);
592  reactionData->AddProduct(damage_deoxyribose);
593  //eactionData->SetEffectiveReactionRadius(0);
594 
595  theReactionTable->SetReaction(reactionData);
596 
597  // adenine + Radical H -> ...
598  reactionData = new G4DNAMolecularReactionData(
599  0.10e9*(1e-3*m3/(mole*s)), adenine, H);
600  reactionData->AddProduct(damage_adenine);
601  theReactionTable->SetReaction(reactionData);
602 
603  // thymine + Radical H -> ...
604  reactionData = new G4DNAMolecularReactionData(
605  0.57e9*(1e-3*m3/(mole*s)), thymine, H);
606  reactionData->AddProduct(damage_thymine);
607  theReactionTable->SetReaction(reactionData);
608 
609  // cytosine + Radical H -> ...
610  reactionData = new G4DNAMolecularReactionData(
611  0.092e9*(1e-3*m3/(mole*s)), cytosine, H);
612  reactionData->AddProduct(damage_cytosine);
613  theReactionTable->SetReaction(reactionData);
614 
615  //histone + all molecules -> modification(or "damage")
616 
617  reactionData = new G4DNAMolecularReactionData(
618  0.0*(1e-3*m3/(mole*s)), histone, OH);
619  reactionData->AddProduct(histone);
620  reactionData->SetEffectiveReactionRadius(
621  2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
622  theReactionTable->SetReaction(reactionData);
623 
624  reactionData = new G4DNAMolecularReactionData(
625  0.0*(1e-3*m3/(mole*s)), histone, OHm);
626  reactionData->AddProduct(histone);
627  reactionData->SetEffectiveReactionRadius(
628  2.4*nm + G4OH::Definition()->GetVanDerVaalsRadius());
629  theReactionTable->SetReaction(reactionData);
630 
631  reactionData = new G4DNAMolecularReactionData(
632  0.0*(1e-3*m3/(mole*s)), histone, e_aq);
633  reactionData->AddProduct(histone);
634  reactionData->SetEffectiveReactionRadius(
635  2.4*nm + G4Electron_aq::Definition()->GetVanDerVaalsRadius());
636  theReactionTable->SetReaction(reactionData);
637 
638  reactionData = new G4DNAMolecularReactionData(
639  0.0*(1e-3*m3/(mole*s)), histone, H2);
640  reactionData->AddProduct(histone);
641  reactionData->SetEffectiveReactionRadius(
642  2.4*nm + G4H2::Definition()->GetVanDerVaalsRadius());
643  theReactionTable->SetReaction(reactionData);
644 
645  reactionData = new G4DNAMolecularReactionData(
646  0.0*(1e-3*m3/(mole*s)), histone, H3Op);
647  reactionData->AddProduct(histone);
648  reactionData->SetEffectiveReactionRadius(
649  2.4*nm + G4H3O::Definition()->GetVanDerVaalsRadius());
650  theReactionTable->SetReaction(reactionData);
651 
652  reactionData = new G4DNAMolecularReactionData(
653  0.0*(1e-3*m3/(mole*s)), histone, H);
654  reactionData->AddProduct(histone);
655  reactionData->SetEffectiveReactionRadius(
656  2.4*nm + G4Hydrogen::Definition()->GetVanDerVaalsRadius());
657  theReactionTable->SetReaction(reactionData);
658 
659  reactionData = new G4DNAMolecularReactionData(
660  0.0*(1e-3*m3/(mole*s)), histone, H2O2);
661  reactionData->AddProduct(histone);
662  reactionData->SetEffectiveReactionRadius(
663  2.4*nm + G4H2O2::Definition()->GetVanDerVaalsRadius());
664  theReactionTable->SetReaction(reactionData);
665 }
666 
667 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
668 
669 void G4EmDNAChemistry_option2::ConstructProcess()
670 {
671  auto pPhysicsListHelper =
672  G4PhysicsListHelper::GetPhysicsListHelper();
673  G4VProcess* pProcess =
674  G4ProcessTable::GetProcessTable()->
675  FindProcess("e-_G4DNAVibExcitation", "e-");
676 
677  if (pProcess != nullptr)
678  {
679  G4DNAVibExcitation* pVibExcitation =
680  (G4DNAVibExcitation*) pProcess;
681  G4VEmModel* pModel = pVibExcitation->EmModel();
682  G4DNASancheExcitationModel* pSancheExcitationMod =
683  dynamic_cast<G4DNASancheExcitationModel*>(pModel);
684  if(pSancheExcitationMod != nullptr)
685  {
686  pSancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
687  }
688  }
689 
690 //===============================================================
691 // Electron Solvatation
692 //
693  pProcess = G4ProcessTable::GetProcessTable()->
694  FindProcess("e-_G4DNAElectronSolvation", "e-");
695 
696  if (pProcess == nullptr)
697  {
698  pPhysicsListHelper->
699  RegisterProcess(new G4DNAElectronSolvation(
700  "e-_G4DNAElectronSolvation"), G4Electron::Definition());
701  }
702 
703 //===============================================================
704 // Define processes for molecules
705 //
706  G4MoleculeTable* pMoleculeTable =
707  G4MoleculeTable::Instance();
708  G4MoleculeDefinitionIterator iterator =
709  pMoleculeTable->GetDefintionIterator();
710  iterator.reset();
711  while (iterator())
712  {
713  G4MoleculeDefinition* pMoleculeDef = iterator.value();
714 
715  if(pMoleculeDef != G4H2O::Definition())
716  {
717  G4DNABrownianTransportation* pBrownianTransport =
718  new G4DNABrownianTransportation();
719  pPhysicsListHelper->
720  RegisterProcess(pBrownianTransport, pMoleculeDef);
721  }
722  else
723  {
724  pMoleculeDef->GetProcessManager()->
725  AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
726  G4DNAMolecularDissociation* pDissociationProcess =
727  new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
728  pDissociationProcess->SetDisplacer(pMoleculeDef,
729  new G4DNAWaterDissociationDisplacer);
730  pDissociationProcess->SetVerboseLevel(1);
731 
732  pMoleculeDef->GetProcessManager()->
733  AddRestProcess(pDissociationProcess, 1);
734  }
735  }
736  G4DNAChemistryManager::Instance()->Initialize();
737 }
738 
739 
740 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
741 
742 void G4EmDNAChemistry_option2::ConstructTimeStepModel(
743 G4DNAMolecularReactionTable* reactionTable)
744 {
745  G4VDNAReactionModel* reactionRadiusComputer =
746  new G4DNASmoluchowskiReactionModel();
747  reactionTable->PrintTable(reactionRadiusComputer);
748 
749  G4DNAMolecularStepByStepModel* stepByStep =
750  new G4DNAMolecularStepByStepModel();
751  stepByStep->SetReactionModel(reactionRadiusComputer);
752 
753  RegisterTimeStepModel(stepByStep, 0);
754 }