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25 // 25 //
26 #include "EmDNAChemistry.hh" 26 #include "EmDNAChemistry.hh"
27 <<
28 #include "G4DNAChemistryManager.hh" 27 #include "G4DNAChemistryManager.hh"
29 #include "G4DNAWaterDissociationDisplacer.hh" 28 #include "G4DNAWaterDissociationDisplacer.hh"
30 #include "G4ProcessManager.hh" 29 #include "G4ProcessManager.hh"
31 #include "G4SystemOfUnits.hh" 30 #include "G4SystemOfUnits.hh"
32 31
33 // *** Processes and models for Geant4-DNA 32 // *** Processes and models for Geant4-DNA
34 33
35 #include "BoundedBrownianAction.hh" 34 #include "BoundedBrownianAction.hh"
36 <<
37 #include "G4DNABrownianTransportation.hh" 35 #include "G4DNABrownianTransportation.hh"
38 #include "G4DNAElectronHoleRecombination.hh" 36 #include "G4DNAElectronHoleRecombination.hh"
39 #include "G4DNAElectronSolvation.hh" 37 #include "G4DNAElectronSolvation.hh"
40 #include "G4DNAMolecularDissociation.hh" 38 #include "G4DNAMolecularDissociation.hh"
41 #include "G4DNAMolecularReactionTable.hh" 39 #include "G4DNAMolecularReactionTable.hh"
42 #include "G4DNAMolecularStepByStepModel.hh" 40 #include "G4DNAMolecularStepByStepModel.hh"
43 #include "G4DNASancheExcitationModel.hh" <<
44 #include "G4DNASmoluchowskiReactionModel.hh" 41 #include "G4DNASmoluchowskiReactionModel.hh"
>> 42 #include "G4DNASancheExcitationModel.hh"
45 #include "G4DNAVibExcitation.hh" 43 #include "G4DNAVibExcitation.hh"
46 // particles 44 // particles
47 45
48 #include "G4Electron.hh" 46 #include "G4Electron.hh"
>> 47
49 #include "G4Electron_aq.hh" 48 #include "G4Electron_aq.hh"
50 #include "G4H2O.hh" 49 #include "G4H2O.hh"
51 #include "G4H2O2.hh" 50 #include "G4H2O2.hh"
52 #include "G4H3O.hh" 51 #include "G4H3O.hh"
53 #include "G4HO2.hh" 52 #include "G4HO2.hh"
54 #include "G4Hydrogen.hh" 53 #include "G4Hydrogen.hh"
55 #include "G4MoleculeTable.hh" 54 #include "G4MoleculeTable.hh"
56 #include "G4O2.hh" 55 #include "G4O2.hh"
57 #include "G4O3.hh" 56 #include "G4O3.hh"
58 #include "G4OH.hh" 57 #include "G4OH.hh"
59 #include "G4Oxygen.hh" 58 #include "G4Oxygen.hh"
60 #include "G4PhysicsListHelper.hh" 59 #include "G4PhysicsListHelper.hh"
61 /****/ 60 /****/
62 #include "G4DNAMoleculeEncounterStepper.hh" 61 #include "G4DNAMoleculeEncounterStepper.hh"
63 #include "G4DNAScavengerProcess.hh" 62 #include "G4DNAScavengerProcess.hh"
64 #include "G4MolecularConfiguration.hh" 63 #include "G4MolecularConfiguration.hh"
65 #include "G4ProcessTable.hh" 64 #include "G4ProcessTable.hh"
66 #include "G4VChemistryWorld.hh" 65 #include "G4VChemistryWorld.hh"
67 /****/ 66 /****/
68 #include "G4ChemicalMoleculeFinder.hh" 67 #include "G4ChemicalMoleculeFinder.hh"
69 // factory 68 // factory
70 #include "ChemOxygenWaterBuilder.hh" << 69 #include "G4PhysicsConstructorFactory.hh"
>> 70
71 #include "ChemPureWaterBuilder.hh" 71 #include "ChemPureWaterBuilder.hh"
72 72
73 #include "G4ChemDissociationChannels_option1.h 73 #include "G4ChemDissociationChannels_option1.hh"
74 #include "G4PhysicsConstructorFactory.hh" << 74 #include "ChemOxygenWaterBuilder.hh"
75 75
76 G4_DECLARE_PHYSCONSTR_FACTORY(EmDNAChemistry); 76 G4_DECLARE_PHYSCONSTR_FACTORY(EmDNAChemistry);
77 77
78 EmDNAChemistry::EmDNAChemistry() : G4VUserChem << 78 EmDNAChemistry::EmDNAChemistry()
79 { << 79 : G4VUserChemistryList(true) {
80 G4DNAChemistryManager::Instance()->SetChemis 80 G4DNAChemistryManager::Instance()->SetChemistryList(this);
81 } 81 }
82 82
83 //....oooOO0OOooo........oooOO0OOooo........oo 83 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
84 84
85 EmDNAChemistry::~EmDNAChemistry() = default; 85 EmDNAChemistry::~EmDNAChemistry() = default;
86 86
87 //....oooOO0OOooo........oooOO0OOooo........oo 87 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
88 88
89 void EmDNAChemistry::ConstructMolecule() << 89 void EmDNAChemistry::ConstructMolecule() {
90 { << 90
91 G4ChemDissociationChannels_option1::Construc 91 G4ChemDissociationChannels_option1::ConstructMolecule();
92 auto table = G4MoleculeTable::Instance(); 92 auto table = G4MoleculeTable::Instance();
93 93
94 auto H3OpB = table->GetConfiguration("H3Op(B 94 auto H3OpB = table->GetConfiguration("H3Op(B)");
95 H3OpB->SetDiffusionCoefficient(9.46e-9 * (m2 95 H3OpB->SetDiffusionCoefficient(9.46e-9 * (m2 / s));
96 96
97 auto OHm = table->GetConfiguration("OHm(B)") 97 auto OHm = table->GetConfiguration("OHm(B)");
98 OHm->SetDiffusionCoefficient(5.3e-9 * (m2 / 98 OHm->SetDiffusionCoefficient(5.3e-9 * (m2 / s));
99 table->CreateConfiguration("H2O", G4H2O::Def 99 table->CreateConfiguration("H2O", G4H2O::Definition());
100 100
101 auto G4NO2 = new G4MoleculeDefinition("NO_2" << 101 auto G4NO2 = new G4MoleculeDefinition("NO_2",/*mass*/ 30,
102 /*D*/ << 102 /*D*/ 0 * (m * m / s),
103 /*char << 103 /*charge*/0,
104 /*elec << 104 /*electronL*/0,
105 /*radi << 105 /*radius*/0.17 * nm);//should be corrected
106 << 106
107 auto G4NO3 = new G4MoleculeDefinition("NO_3" << 107 auto G4NO3 = new G4MoleculeDefinition("NO_3",/*mass*/ 38,
108 /*D*/ << 108 /*D*/ 0 * (m * m / s),
109 /*char << 109 /*charge*/0,
110 /*elec << 110 /*electronL*/0,
111 /*radi << 111 /*radius*/0.17 * nm);//should be corrected
112 112
113 table->CreateConfiguration("NO2", G4NO2); 113 table->CreateConfiguration("NO2", G4NO2);
114 table->CreateConfiguration("NO2m", G4NO2, << 114 table->CreateConfiguration("NO2m",
115 -1, // charge << 115 G4NO2,
>> 116 -1, // charge
116 0 * (m2 / s)); 117 0 * (m2 / s));
117 table->CreateConfiguration("NO2mm", G4NO2, << 118 table->CreateConfiguration("NO2mm",
118 -2, // charge << 119 G4NO2,
>> 120 -2, // charge
119 0 * (m2 / s)); 121 0 * (m2 / s));
120 122
121 table->CreateConfiguration("NO3m", G4NO3, << 123 table->CreateConfiguration("NO3m",
122 -1, // charge << 124 G4NO3,
>> 125 -1, // charge
123 0 * (m2 / s)); 126 0 * (m2 / s));
124 127
125 table->CreateConfiguration("NO3mm", G4NO3, << 128 table->CreateConfiguration("NO3mm",
126 -2, // charge << 129 G4NO3,
>> 130 -2, // charge
127 0 * (m2 / s)); 131 0 * (m2 / s));
128 132
129 // FrickeDosimeter << 133 //FrickeDosimeter
130 auto G4Fe = new G4MoleculeDefinition("Fe", 134 auto G4Fe = new G4MoleculeDefinition("Fe",
131 /*mass* << 135 /*mass*/ 55.84 * g / Avogadro * c_squared,
132 /*D*/ 0 << 136 /*D*/ 0 * (m * m / s),
133 /*charg << 137 /*charge*/ 0,
134 /*elect << 138 /*electronL*/ 0,
135 /*radiu << 139 /*radius*/ 0.35 * nm); // can be adjusted
136 140
137 table->CreateConfiguration("Fe0", G4Fe); 141 table->CreateConfiguration("Fe0", G4Fe);
138 142
139 table->CreateConfiguration("Feppp", G4Fe, << 143 table->CreateConfiguration("Feppp",
140 3, // charge << 144 G4Fe,
141 4.86e-10 * (m2 / << 145 3, // charge
142 << 146 4.86e-10 * (m2 / s));//Michael Spiro* and Andrew M. Creeth
143 table->CreateConfiguration("Fepp", G4Fe, << 147
144 2, // charge << 148 table->CreateConfiguration("Fepp",
>> 149 G4Fe,
>> 150 2, // charge
145 5.78e-10 * (m2 / 151 5.78e-10 * (m2 / s));
146 // HSO4- << 152 //HSO4-
147 auto G4HSO4 = new G4MoleculeDefinition("HSO4 153 auto G4HSO4 = new G4MoleculeDefinition("HSO4",
148 /*mas << 154 /*mass*/ 55.84 * g / Avogadro * c_squared,
149 /*D*/ << 155 /*D*/ 0 * (m * m / s),
150 /*cha << 156 /*charge*/ 0,
151 /*ele << 157 /*electronL*/ 0,
152 /*rad << 158 /*radius*/ 0.35 * nm); // can be adjusted
153 table->CreateConfiguration("HSO4m", G4HSO4, << 159 table->CreateConfiguration("HSO4m",
154 -1, // charge << 160 G4HSO4,
>> 161 -1, // charge
155 0 * (m2 / s)); 162 0 * (m2 / s));
156 163
157 // SO4- << 164 //SO4-
158 auto G4SO4 = new G4MoleculeDefinition("SO4", 165 auto G4SO4 = new G4MoleculeDefinition("SO4",
159 /*mass << 166 /*mass*/ 55.84 * g / Avogadro * c_squared,
160 /*D*/ << 167 /*D*/ 0 * (m * m / s),
161 /*char << 168 /*charge*/ 0,
162 /*elec << 169 /*electronL*/ 0,
163 /*radi << 170 /*radius*/ 0.35 * nm); // can be adjusted
164 table->CreateConfiguration("SO4m", G4SO4, << 171 table->CreateConfiguration("SO4m",
165 -1, // charge << 172 G4SO4,
>> 173 -1, // charge
166 0 * (m2 / s)); 174 0 * (m2 / s));
167 } 175 }
168 176
169 //....oooOO0OOooo........oooOO0OOooo........oo 177 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
170 178
171 void EmDNAChemistry::ConstructDissociationChan << 179 void EmDNAChemistry::ConstructDissociationChannels() {
172 { <<
173 G4ChemDissociationChannels_option1::Construc 180 G4ChemDissociationChannels_option1::ConstructDissociationChannels();
174 } 181 }
175 182
176 //....oooOO0OOooo........oooOO0OOooo........oo 183 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
177 184
178 void EmDNAChemistry::ConstructReactionTable(G4 << 185 void EmDNAChemistry::ConstructReactionTable(
179 { << 186 G4DNAMolecularReactionTable *pReactionTable) {
180 ChemOxygenWaterBuilder::OxygenScavengerReact 187 ChemOxygenWaterBuilder::OxygenScavengerReaction(pReactionTable);
181 ChemOxygenWaterBuilder::SecondOrderReactionE 188 ChemOxygenWaterBuilder::SecondOrderReactionExtended(pReactionTable);
182 ChemPureWaterBuilder::WaterScavengerReaction 189 ChemPureWaterBuilder::WaterScavengerReaction(pReactionTable);
183 } 190 }
184 191
185 //....oooOO0OOooo........oooOO0OOooo........oo 192 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
186 193
187 void EmDNAChemistry::ConstructProcess() << 194 void EmDNAChemistry::ConstructProcess() {
188 { <<
189 auto table = G4MoleculeTable::Instance(); 195 auto table = G4MoleculeTable::Instance();
190 auto O2 = table->GetConfiguration("O2"); 196 auto O2 = table->GetConfiguration("O2");
191 auto O2m = table->GetConfiguration("O2m"); 197 auto O2m = table->GetConfiguration("O2m");
192 auto HO2 = table->GetConfiguration("HO2°"); << 198 auto HO2 = table->GetConfiguration("HO2");
193 199
194 auto e_aq = table->GetConfiguration("e_aq"); 200 auto e_aq = table->GetConfiguration("e_aq");
195 auto OH = table->GetConfiguration("°OH"); << 201 auto OH = table->GetConfiguration("OH");
196 auto OHm = table->GetConfiguration("OHm"); 202 auto OHm = table->GetConfiguration("OHm");
197 203
198 auto NO2 = table->GetConfiguration("NO2"); 204 auto NO2 = table->GetConfiguration("NO2");
199 auto NO2m = table->GetConfiguration("NO2m"); 205 auto NO2m = table->GetConfiguration("NO2m");
200 auto NO2mm = table->GetConfiguration("NO2mm" 206 auto NO2mm = table->GetConfiguration("NO2mm");
201 auto NO3m = table->GetConfiguration("NO3m"); 207 auto NO3m = table->GetConfiguration("NO3m");
202 auto NO3mm = table->GetConfiguration("NO3mm" 208 auto NO3mm = table->GetConfiguration("NO3mm");
203 209
204 auto H2O2 = table->GetConfiguration("H2O2"); 210 auto H2O2 = table->GetConfiguration("H2O2");
205 auto H = table->GetConfiguration("H"); 211 auto H = table->GetConfiguration("H");
206 212
207 auto* H3OpB = table->GetConfiguration("H3Op( << 213 auto *H3OpB = table->GetConfiguration("H3Op(B)");
208 auto* OHmB = table->GetConfiguration("OHm(B) << 214 auto *OHmB = table->GetConfiguration("OHm(B)");
209 auto* HO2m = table->GetConfiguration("HO2m") << 215 auto *HO2m = table->GetConfiguration("HO2m");
210 auto* Om = table->GetConfiguration("Om"); << 216 auto *Om = table->GetConfiguration("Om");
211 auto* O3m = table->GetConfiguration("O3m"); << 217 auto *O3m = table->GetConfiguration("O3m");
212 auto* H3Op = table->GetConfiguration("H3Op") << 218 auto *H3Op = table->GetConfiguration("H3Op");
213 219
214 fpChemistryWorld->ConstructChemistryComponen 220 fpChemistryWorld->ConstructChemistryComponents();
215 auto confinedBox = fpChemistryWorld->GetChem 221 auto confinedBox = fpChemistryWorld->GetChemistryBoundary();
216 222
217 auto* ph = G4PhysicsListHelper::GetPhysicsLi << 223 auto *ph = G4PhysicsListHelper::GetPhysicsListHelper();
218 224
219 //========================================== 225 //===============================================================
220 // Extend vibrational to low energy 226 // Extend vibrational to low energy
221 // Anyway, solvation of electrons is taken i 227 // Anyway, solvation of electrons is taken into account from 7.4 eV
222 // So below this threshold, for now, no accu 228 // So below this threshold, for now, no accurate modeling is done
223 // 229 //
224 G4VProcess* process = << 230 G4VProcess *process = G4ProcessTable::GetProcessTable()->FindProcess(
225 G4ProcessTable::GetProcessTable()->FindPro << 231 "e-_G4DNAVibExcitation", "e-");
226 232
227 if (process) { 233 if (process) {
228 auto vibExcitation = (G4DNAVibExcitation*) << 234 auto vibExcitation = (G4DNAVibExcitation *) process;
229 G4VEmModel* model = vibExcitation->EmModel << 235 G4VEmModel *model = vibExcitation->EmModel();
230 auto sancheExcitationMod = dynamic_cast<G4 << 236 auto sancheExcitationMod =
>> 237 dynamic_cast<G4DNASancheExcitationModel *>(model);
231 if (sancheExcitationMod) { 238 if (sancheExcitationMod) {
232 sancheExcitationMod->ExtendLowEnergyLimi 239 sancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
233 } 240 }
234 } 241 }
235 242
236 //========================================== 243 //===============================================================
237 // *** Electron Solvatation *** 244 // *** Electron Solvatation ***
238 // 245 //
239 process = G4ProcessTable::GetProcessTable()- << 246 process = G4ProcessTable::GetProcessTable()->FindProcess(
>> 247 "e-_G4DNAElectronSolvation", "e-");
240 248
241 if (process == nullptr) { 249 if (process == nullptr) {
242 ph->RegisterProcess(new G4DNAElectronSolva 250 ph->RegisterProcess(new G4DNAElectronSolvation("e-_G4DNAElectronSolvation"),
243 G4Electron::Definition 251 G4Electron::Definition());
244 } 252 }
245 253
246 //========================================== 254 //===============================================================
247 // Define processes for molecules 255 // Define processes for molecules
248 // 256 //
249 auto* theMoleculeTable = G4MoleculeTable::In << 257 auto *theMoleculeTable = G4MoleculeTable::Instance();
250 auto iterator = theMoleculeTable->GetDefinti << 258 auto iterator =
>> 259 theMoleculeTable->GetDefintionIterator();
251 iterator.reset(); 260 iterator.reset();
252 261
253 while (iterator()) { 262 while (iterator()) {
254 auto* moleculeDef = iterator.value(); << 263 auto *moleculeDef = iterator.value();
255 264
256 if (moleculeDef != G4H2O::Definition()) { 265 if (moleculeDef != G4H2O::Definition()) {
257 auto brown = new G4DNABrownianTransporta 266 auto brown = new G4DNABrownianTransportation("BrowianTransportation");
258 // hoang exp 267 // hoang exp
259 auto brownTransport = new BoundedBrownia 268 auto brownTransport = new BoundedBrownianAction();
260 brownTransport->SetBoundary(*confinedBox 269 brownTransport->SetBoundary(*confinedBox);
261 brown->SetUserBrownianAction(brownTransp 270 brown->SetUserBrownianAction(brownTransport);
262 // hoang exp 271 // hoang exp
263 272
264 ph->RegisterProcess(brown, moleculeDef); 273 ph->RegisterProcess(brown, moleculeDef);
265 } << 274 } else {
266 else { << 275 moleculeDef->GetProcessManager()->AddRestProcess(
267 moleculeDef->GetProcessManager()->AddRes << 276 new G4DNAElectronHoleRecombination(), 2);
268 auto brownTransport = new BoundedBrownia 277 auto brownTransport = new BoundedBrownianAction();
269 brownTransport->SetBoundary(*confinedBox 278 brownTransport->SetBoundary(*confinedBox);
270 auto dissociationProcess = new G4DNAMole << 279 auto dissociationProcess =
>> 280 new G4DNAMolecularDissociation("H2O_DNAMolecularDecay", fDecay);
271 dissociationProcess->SetUserBrownianActi 281 dissociationProcess->SetUserBrownianAction(brownTransport);
272 dissociationProcess->SetDisplacer(molecu << 282 dissociationProcess->SetDisplacer(moleculeDef,
>> 283 new G4DNAWaterDissociationDisplacer);
273 moleculeDef->GetProcessManager()->AddRes 284 moleculeDef->GetProcessManager()->AddRestProcess(dissociationProcess, 1);
274 } 285 }
275 286
276 if (moleculeDef == G4Hydrogen::Definition( 287 if (moleculeDef == G4Hydrogen::Definition()) {
277 // O2 288 // O2
278 auto scanvergerProcess = new G4DNAScaven << 289 auto scanvergerProcess =
>> 290 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
279 //-------------------------------------- 291 //------------------------------------------------------------------
280 // H + O2(B) -> HO2 292 // H + O2(B) -> HO2
281 auto reactionData = new G4DNAMolecularRe << 293 auto reactionData = new G4DNAMolecularReactionData(
>> 294 1.3e10 * (1e-3 * m3 / (mole * s)), H, O2);
282 reactionData->AddProduct(HO2); 295 reactionData->AddProduct(HO2);
283 scanvergerProcess->SetReaction(H, reacti 296 scanvergerProcess->SetReaction(H, reactionData);
284 //-------------------------------------- 297 //------------------------------------------------------------------
285 // H + OH-(B) -> H2O + eaq- 2.49e3 / s 298 // H + OH-(B) -> H2O + eaq- 2.49e3 / s
286 reactionData = new G4DNAMolecularReactio << 299 reactionData = new G4DNAMolecularReactionData(
287 << 300 2.49e7 * (1e-3 * m3 / (mole * s)), H,
>> 301 OHmB); // 2.51e7 (H + OH-)* 1e-7 (pH) = 2.48e0
288 reactionData->AddProduct(e_aq); 302 reactionData->AddProduct(e_aq);
289 scanvergerProcess->SetReaction(H, reacti 303 scanvergerProcess->SetReaction(H, reactionData);
290 304
291 // H2O2 305 // H2O2
292 //-------------------------------------- 306 //------------------------------------------------------------------
293 // H + H202 -> OH + H20 307 // H + H202 -> OH + H20
294 // reactionData = new G4DNAMo 308 // reactionData = new G4DNAMolecularReactionData(
295 // 9.0e7 * (1e-3 * m3 309 // 9.0e7 * (1e-3 * m3 / (mole * s)), H,H2O2);
296 // reactionData->AddProduct(O 310 // reactionData->AddProduct(OH);
297 // scanvergerProcess->SetReac 311 // scanvergerProcess->SetReaction(H,reactionData);
298 ph->RegisterProcess(scanvergerProcess, m 312 ph->RegisterProcess(scanvergerProcess, moleculeDef);
299 } 313 }
300 if (moleculeDef == G4Electron_aq::Definiti 314 if (moleculeDef == G4Electron_aq::Definition()) {
301 auto scanvergerProcess = new G4DNAScaven << 315 auto scanvergerProcess =
302 G4DNAMolecularReactionData* reactionData << 316 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
>> 317 G4DNAMolecularReactionData *reactionData = nullptr;
303 //-------------------------------------- 318 //------------------------------------------------------------------
304 // e_aq + O2(B) -> O2- 319 // e_aq + O2(B) -> O2-
305 reactionData = new G4DNAMolecularReactio << 320 reactionData = new G4DNAMolecularReactionData(
>> 321 2.3e10 * (1e-3 * m3 / (mole * s)), e_aq, O2);
306 reactionData->AddProduct(O2m); 322 reactionData->AddProduct(O2m);
307 scanvergerProcess->SetReaction(e_aq, rea 323 scanvergerProcess->SetReaction(e_aq, reactionData);
308 //-------------------------------------- 324 //------------------------------------------------------------------
309 // eaq- + H3O+(B) -> H + H2O 2.09e3 / s 325 // eaq- + H3O+(B) -> H + H2O 2.09e3 / s
310 reactionData = << 326 reactionData = new G4DNAMolecularReactionData(
311 new G4DNAMolecularReactionData(2.25e10 << 327 2.25e10 * (1e-3 * m3 / (mole * s)), e_aq,
312 H3OpB); << 328 H3OpB); // 2.11e10 (e_aq + H3O+) * 1.0e-7 (Ph=7) = 2.09e3
313 reactionData->AddProduct(H); 329 reactionData->AddProduct(H);
314 scanvergerProcess->SetReaction(e_aq, rea 330 scanvergerProcess->SetReaction(e_aq, reactionData);
315 //-------------------------------------- 331 //------------------------------------------------------------------
316 // e_aq + NO2- -> NO2-- 332 // e_aq + NO2- -> NO2--
317 reactionData = new G4DNAMolecularReactio << 333 reactionData = new G4DNAMolecularReactionData(
>> 334 3.5e9 * (1e-3 * m3 / (mole * s)), e_aq, NO2m);
318 reactionData->AddProduct(NO2mm); 335 reactionData->AddProduct(NO2mm);
319 scanvergerProcess->SetReaction(e_aq, rea 336 scanvergerProcess->SetReaction(e_aq, reactionData);
320 //-------------------------------------- 337 //------------------------------------------------------------------
321 // e_aq + NO3- -> NO3-- 338 // e_aq + NO3- -> NO3--
322 reactionData = new G4DNAMolecularReactio << 339 reactionData = new G4DNAMolecularReactionData(
>> 340 9.7e9 * (1e-3 * m3 / (mole * s)), e_aq, NO3m);
323 reactionData->AddProduct(NO3mm); 341 reactionData->AddProduct(NO3mm);
324 scanvergerProcess->SetReaction(e_aq, rea 342 scanvergerProcess->SetReaction(e_aq, reactionData);
325 //-------------------------------------- 343 //------------------------------------------------------------------
326 344
327 // H2O2 + e aq → OHm + OH 345 // H2O2 + e aq → OHm + OH
328 // reactionData = new G4DNAMo 346 // reactionData = new G4DNAMolecularReactionData(
329 // 1.1e10 * (1e-3 * m 347 // 1.1e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);//or
330 // reactionData->AddProduct(O 348 // reactionData->AddProduct(OHm);
331 // reactionData->AddProduct(O 349 // reactionData->AddProduct(OH);
332 // scanvergerProcess->SetReac 350 // scanvergerProcess->SetReaction(e_aq,reactionData);
333 351
334 ph->RegisterProcess(scanvergerProcess, m 352 ph->RegisterProcess(scanvergerProcess, moleculeDef);
335 } 353 }
336 if (moleculeDef == G4O2::Definition()) { 354 if (moleculeDef == G4O2::Definition()) {
337 auto scanvergerProcess = new G4DNAScaven << 355 auto scanvergerProcess =
338 G4DNAMolecularReactionData* reactionData << 356 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
>> 357 G4DNAMolecularReactionData *reactionData = nullptr;
339 //-------------------------------------- 358 //------------------------------------------------------------------
340 // O2- + H3O+(B) -> HO2 + H2O 4.73e3 / s 359 // O2- + H3O+(B) -> HO2 + H2O 4.73e3 / s
341 reactionData = << 360 reactionData = new G4DNAMolecularReactionData(
342 new G4DNAMolecularReactionData(4.78e10 << 361 4.78e10 * (1e-3 * m3 / (mole * s)), O2m,
343 H3OpB); << 362 H3OpB); // 4.78e10(O2- + H3O+) * 1e-7(pH7) = 4.73e3
344 reactionData->AddProduct(HO2); 363 reactionData->AddProduct(HO2);
345 scanvergerProcess->SetReaction(O2m, reac 364 scanvergerProcess->SetReaction(O2m, reactionData);
346 ph->RegisterProcess(scanvergerProcess, m 365 ph->RegisterProcess(scanvergerProcess, moleculeDef);
347 } 366 }
348 if (moleculeDef == G4ParticleTable::GetPar << 367 if (moleculeDef ==
349 auto scanvergerProcess = new G4DNAScaven << 368 G4ParticleTable::GetParticleTable()->FindParticle("OHm")) {
350 G4DNAMolecularReactionData* reactionData << 369 auto scanvergerProcess =
>> 370 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
>> 371 G4DNAMolecularReactionData *reactionData = nullptr;
351 //-------------------------------------- 372 //------------------------------------------------------------------
352 // OH- + H3O+(B) -> 2H2O 1.11e4 / s 373 // OH- + H3O+(B) -> 2H2O 1.11e4 / s
353 reactionData = << 374 reactionData = new G4DNAMolecularReactionData(
354 new G4DNAMolecularReactionData(1.13e11 << 375 1.13e11 * (1e-3 * m3 / (mole * s)), OHm,
355 H3OpB); << 376 H3OpB); // 1.13e11 (H3O+ + OH-) * 1e-7 (pH=7) =1.12e4
356 scanvergerProcess->SetReaction(OHm, reac 377 scanvergerProcess->SetReaction(OHm, reactionData);
357 ph->RegisterProcess(scanvergerProcess, m 378 ph->RegisterProcess(scanvergerProcess, moleculeDef);
358 } 379 }
359 if (moleculeDef == G4OH::Definition()) { 380 if (moleculeDef == G4OH::Definition()) {
360 auto scanvergerProcess = new G4DNAScaven << 381 auto scanvergerProcess =
361 G4DNAMolecularReactionData* reactionData << 382 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
>> 383 G4DNAMolecularReactionData *reactionData = nullptr;
362 384
363 //-------------------------------------- 385 //------------------------------------------------------------------
364 // OH + OH-(B) -> O- + H2O 6.24e2 / s 386 // OH + OH-(B) -> O- + H2O 6.24e2 / s
365 reactionData = << 387 reactionData = new G4DNAMolecularReactionData(
366 new G4DNAMolecularReactionData(1.27e10 << 388 1.27e10 * (1e-3 * m3 / (mole * s)), OH,
367 OHmB); << 389 OHmB); // 6.30e9 (OH + OH-) * 1e-7 (pH) = 6.24e2
368 reactionData->AddProduct(Om); 390 reactionData->AddProduct(Om);
369 scanvergerProcess->SetReaction(OH, react 391 scanvergerProcess->SetReaction(OH, reactionData);
370 392
371 //-------------------------------------- 393 //------------------------------------------------------------------
372 // OH + NO2- -> NO2 + OH- 394 // OH + NO2- -> NO2 + OH-
373 reactionData = new G4DNAMolecularReactio << 395 reactionData = new G4DNAMolecularReactionData(
>> 396 8e9 * (1e-3 * m3 / (mole * s)), OH, NO2m);
374 reactionData->AddProduct(NO2); 397 reactionData->AddProduct(NO2);
375 reactionData->AddProduct(OHm); 398 reactionData->AddProduct(OHm);
376 scanvergerProcess->SetReaction(OH, react 399 scanvergerProcess->SetReaction(OH, reactionData);
377 ph->RegisterProcess(scanvergerProcess, m 400 ph->RegisterProcess(scanvergerProcess, moleculeDef);
378 } 401 }
379 if (moleculeDef == G4ParticleTable::GetPar << 402 if (moleculeDef ==
380 auto scanvergerProcess = new G4DNAScaven << 403 G4ParticleTable::GetParticleTable()->FindParticle("HO_2m")) {
381 G4DNAMolecularReactionData* reactionData << 404 auto scanvergerProcess =
>> 405 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
>> 406 G4DNAMolecularReactionData *reactionData = nullptr;
382 //-------------------------------------- 407 //------------------------------------------------------------------
383 // HO2- + H3O+(B) -> H2O2 + H2O 4.98e3 / 408 // HO2- + H3O+(B) -> H2O2 + H2O 4.98e3 / s
384 reactionData = << 409 reactionData = new G4DNAMolecularReactionData(
385 new G4DNAMolecularReactionData(4.78e10 << 410 4.78e10 * (1e-3 * m3 / (mole * s)), HO2m,
386 H3OpB); << 411 H3OpB); // 5.00e10 (H3O+ + HO2-) * 1e-7(pH) = 4.95e3
387 reactionData->AddProduct(H2O2); 412 reactionData->AddProduct(H2O2);
388 scanvergerProcess->SetReaction(HO2m, rea 413 scanvergerProcess->SetReaction(HO2m, reactionData);
389 ph->RegisterProcess(scanvergerProcess, m 414 ph->RegisterProcess(scanvergerProcess, moleculeDef);
390 } 415 }
391 416
392 if (moleculeDef == G4HO2::Definition()) { 417 if (moleculeDef == G4HO2::Definition()) {
393 auto scanvergerProcess = new G4DNAScaven << 418 auto scanvergerProcess =
394 G4DNAMolecularReactionData* reactionData << 419 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
>> 420 G4DNAMolecularReactionData *reactionData = nullptr;
395 //-------------------------------------- 421 //------------------------------------------------------------------
396 // HO2 + OH-(B) -> O2- + H2O 6.24e2 / s 422 // HO2 + OH-(B) -> O2- + H2O 6.24e2 / s
397 reactionData = new G4DNAMolecularReactio << 423 reactionData = new G4DNAMolecularReactionData(
398 << 424 1.27e10 * (1e-3 * m3 / (mole * s)), HO2,
>> 425 OHmB); // 6.30e9(HO2 + OH-)*1e-7 (pH) = 6.24e2
399 reactionData->AddProduct(O2m); 426 reactionData->AddProduct(O2m);
400 scanvergerProcess->SetReaction(HO2, reac 427 scanvergerProcess->SetReaction(HO2, reactionData);
401 //-------------------------------------- 428 //------------------------------------------------------------------
402 ph->RegisterProcess(scanvergerProcess, m 429 ph->RegisterProcess(scanvergerProcess, moleculeDef);
403 } 430 }
404 if (moleculeDef == G4Oxygen::Definition()) 431 if (moleculeDef == G4Oxygen::Definition()) {
405 auto scanvergerProcess = new G4DNAScaven << 432 auto scanvergerProcess =
406 G4DNAMolecularReactionData* reactionData << 433 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
>> 434 G4DNAMolecularReactionData *reactionData = nullptr;
407 //-------------------------------------- 435 //------------------------------------------------------------------
408 // O- + H3O+(B) -> OH + H2O 4.73e3 / s 436 // O- + H3O+(B) -> OH + H2O 4.73e3 / s
409 reactionData = << 437 reactionData = new G4DNAMolecularReactionData(
410 new G4DNAMolecularReactionData(4.78e10 << 438 4.78e10 * (1e-3 * m3 / (mole * s)), Om,
411 H3OpB); << 439 H3OpB); // 4.78e10 (H3O+ + O2-) * 1e-7(pH) = 4.73e3
412 reactionData->AddProduct(OH); 440 reactionData->AddProduct(OH);
413 scanvergerProcess->SetReaction(Om, react 441 scanvergerProcess->SetReaction(Om, reactionData);
414 ph->RegisterProcess(scanvergerProcess, m 442 ph->RegisterProcess(scanvergerProcess, moleculeDef);
415 } 443 }
416 if (moleculeDef == G4O3::Definition()) { 444 if (moleculeDef == G4O3::Definition()) {
417 auto scanvergerProcess = new G4DNAScaven << 445 auto scanvergerProcess =
418 G4DNAMolecularReactionData* reactionData << 446 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
>> 447 G4DNAMolecularReactionData *reactionData = nullptr;
419 //-------------------------------------- 448 //------------------------------------------------------------------
420 // O3- + H3O+(B) -> OH + O2 + H2O 8.91e3 449 // O3- + H3O+(B) -> OH + O2 + H2O 8.91e3 / s
421 reactionData = << 450 reactionData = new G4DNAMolecularReactionData(
422 new G4DNAMolecularReactionData(9.0e10 << 451 9.0e10 * (1e-3 * m3 / (mole * s)), O3m,
423 H3OpB); << 452 H3OpB); // 9.0e10 (O3- + H3O+) * 1e-7(pH) = 8.91e3
424 reactionData->AddProduct(OH); 453 reactionData->AddProduct(OH);
425 reactionData->AddProduct(O2); 454 reactionData->AddProduct(O2);
426 //-------------------------------------- 455 //------------------------------------------------------------------
427 scanvergerProcess->SetReaction(O3m, reac 456 scanvergerProcess->SetReaction(O3m, reactionData);
428 ph->RegisterProcess(scanvergerProcess, m 457 ph->RegisterProcess(scanvergerProcess, moleculeDef);
429 } 458 }
430 if (moleculeDef == G4H3O::Definition()) { 459 if (moleculeDef == G4H3O::Definition()) {
431 auto scanvergerProcess = new G4DNAScaven << 460 auto scanvergerProcess =
432 G4DNAMolecularReactionData* reactionData << 461 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
>> 462 G4DNAMolecularReactionData *reactionData = nullptr;
433 //-------------------------------------- 463 //------------------------------------------------------------------
434 // H3O+ + OH-(B) -> 2H2O 1.11e4 / s 464 // H3O+ + OH-(B) -> 2H2O 1.11e4 / s
435 reactionData = << 465 reactionData = new G4DNAMolecularReactionData(
436 new G4DNAMolecularReactionData(1.13e11 << 466 1.13e11 * (1e-3 * m3 / (mole * s)), H3Op,
437 OHmB); << 467 OHmB); // 1.13e11 (H3O+ + OH-) * 1e-7 (pH=7) = 1.12e4
438 scanvergerProcess->SetReaction(H3Op, rea 468 scanvergerProcess->SetReaction(H3Op, reactionData);
439 ph->RegisterProcess(scanvergerProcess, m 469 ph->RegisterProcess(scanvergerProcess, moleculeDef);
440 } 470 }
441 if (moleculeDef == G4H2O2::Definition()) { 471 if (moleculeDef == G4H2O2::Definition()) {
442 auto scanvergerProcess = new G4DNAScaven << 472 auto scanvergerProcess =
443 G4DNAMolecularReactionData* reactionData << 473 new G4DNAScavengerProcess("G4DNAScavengerProcess", *confinedBox);
>> 474 G4DNAMolecularReactionData *reactionData = nullptr;
444 //-------------------------------------- 475 //------------------------------------------------------------------
445 // H2O2 + OH-(B) -> HO2- + H2O 4.66e2 / 476 // H2O2 + OH-(B) -> HO2- + H2O 4.66e2 / s
446 reactionData = << 477 reactionData = new G4DNAMolecularReactionData(
447 new G4DNAMolecularReactionData(1.27e10 << 478 1.27e10 * (1e-3 * m3 / (mole * s)), H2O2,
448 OHmB); << 479 OHmB); // 4.71e8 (H2O2 + OH-) * 1e-7 (pH) = 4.66e1
449 reactionData->AddProduct(HO2m); 480 reactionData->AddProduct(HO2m);
450 scanvergerProcess->SetReaction(H2O2, rea 481 scanvergerProcess->SetReaction(H2O2, reactionData);
451 ph->RegisterProcess(scanvergerProcess, m 482 ph->RegisterProcess(scanvergerProcess, moleculeDef);
452 } 483 }
453 } 484 }
454 G4DNAChemistryManager::Instance()->Initializ 485 G4DNAChemistryManager::Instance()->Initialize();
455 } 486 }
456 487
457 //....oooOO0OOooo........oooOO0OOooo........oo 488 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
458 489
459 void EmDNAChemistry::ConstructTimeStepModel(G4 << 490 void EmDNAChemistry::ConstructTimeStepModel(
460 { << 491 G4DNAMolecularReactionTable *reactionTable) {
461 auto reactionRadiusComputer = new G4DNASmolu 492 auto reactionRadiusComputer = new G4DNASmoluchowskiReactionModel();
462 reactionTable->PrintTable(reactionRadiusComp 493 reactionTable->PrintTable(reactionRadiusComputer);
463 auto stepByStep = new G4DNAMolecularStepBySt 494 auto stepByStep = new G4DNAMolecularStepByStepModel();
464 stepByStep->SetReactionModel(reactionRadiusC 495 stepByStep->SetReactionModel(reactionRadiusComputer);
465 RegisterTimeStepModel(stepByStep, 0); 496 RegisterTimeStepModel(stepByStep, 0);
466 } 497 }
467 498
468 //....oooOO0OOooo........oooOO0OOooo........oo <<
469 499