Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
WntCellCycleOdeSystem.cpp
1/*
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34*/
35
36#include "WntCellCycleOdeSystem.hpp"
37#include "CellwiseOdeSystemInformation.hpp"
38
39// These #includes are needed for the constructor and EvaluateYDerivatives()
40#include "ApcOneHitCellMutationState.hpp"
41#include "ApcTwoHitCellMutationState.hpp"
42#include "BetaCateninOneHitCellMutationState.hpp"
43
45 boost::shared_ptr<AbstractCellMutationState> pMutationState,
46 std::vector<double> stateVariables)
48 mpMutationState(pMutationState),
49 mWntLevel(wntLevel)
50{
52
67 Init(); // set up parameter values
68
69 // Set up a Wnt signalling pathway in a steady state
70 double destruction_level = ma5d/(ma4d*wntLevel+ma5d);
71 double beta_cat_level_1 = -1.0;
72 double beta_cat_level_2 = -1.0;
73
74 if (!mpMutationState)
75 {
76 // No mutations specified
77 }
79 {
80 // APC +/- : only half are active
81 beta_cat_level_1 = 0.5*ma2d/(ma2d+0.5*ma3d*destruction_level);
82 beta_cat_level_2 = 0.5*ma2d/(ma2d+0.5*ma3d*destruction_level);
83 }
85 {
86 // APC -/-
87 destruction_level = 0.0; // no active destruction complex
88 beta_cat_level_1 = 0.5; // fully active beta-catenin
89 beta_cat_level_2 = 0.5; // fully active beta-catenin
90 }
92 {
93 // Beta-cat delta 45
94 beta_cat_level_1 = 0.5*ma2d/(ma2d+ma3d*destruction_level);
95 beta_cat_level_2 = 0.5;
96 }
97 else
98 {
99 // healthy cells
100 beta_cat_level_1 = 0.5*ma2d/(ma2d+ma3d*destruction_level);
101 beta_cat_level_2 = 0.5*ma2d/(ma2d+ma3d*destruction_level);
102 }
103
104 // Cell-specific initial conditions
105 SetDefaultInitialCondition(5, destruction_level);
106 SetDefaultInitialCondition(6, beta_cat_level_1);
107 SetDefaultInitialCondition(7, beta_cat_level_2);
108 SetDefaultInitialCondition(8, wntLevel);
109
110 if (stateVariables != std::vector<double>())
111 {
112 SetStateVariables(stateVariables);
113 }
114}
115
116void WntCellCycleOdeSystem::SetMutationState(boost::shared_ptr<AbstractCellMutationState> pMutationState)
117{
118 mpMutationState = pMutationState;
119}
120
125
127{
128 // Initialise model parameter values
129 // Swat (2004) Parameters
130 double k1 = 1.0;
131 double k2 = 1.6;
132 double k3 = 0.05;
133 double k16 = 0.4;
134 double k34 = 0.04;
135 double k43 = 0.01;
136 double k61 = 0.3;
137 double k23 = 0.3;
138 double a = 0.04;
139 double J11 = 0.5;
140 double J12 = 5.0;
141 double J61 = 5.0;
142 double J62 = 8.0;
143 double J13 = 0.002;
144 double J63 = 2.0;
145 double Km1 = 0.5;
146 double Km2 = 4.0;
147 double Km4 = 0.3;
148 double kp = 0.05;
149 double phi_pRb = 0.005;
150 double phi_E2F1 = 0.1;
151 double phi_CycDi = 0.023;
152 double phi_CycDa = 0.03;
153 double phi_pRbp = 0.06;
154
155 // Mirams et al. parameter values
156 double a1 = 0.423;
157 double a2 = 2.57e-4;
158 double a3 = 1.72;
159 double a4 = 10.0;
160 double a5 = 0.5;
161 double WntMax = 10.0;
162 double mitogenic_factorF = 6.0e-4;
163 double APC_Total = 0.02;
164
165 // Non-dimensionalise...
166 mk2d = k2/(Km2*phi_E2F1);
167 mk3d = k3*a1*mitogenic_factorF/(Km4*phi_E2F1*a2);
168 mk34d = k34/phi_E2F1;
169 mk43d = k43/phi_E2F1;
170 mk23d = k23*Km2/(Km4*phi_E2F1);
171 mad = a/Km2;
172 mJ11d = J11*phi_E2F1/k1;
173 mJ12d = J12*phi_E2F1/k1;
174 mJ13d = J13*phi_E2F1/k1;
175 mJ61d = J61*phi_E2F1/k1;
176 mJ62d = J62*phi_E2F1/k1;
177 mJ63d = J63*phi_E2F1/k1;
178 mKm1d = Km1/Km2;
179 mkpd = kp/(Km2*phi_E2F1);
180 mphi_r = phi_pRb/phi_E2F1;
181 mphi_i = phi_CycDi/phi_E2F1;
182 mphi_j = phi_CycDa/phi_E2F1;
183 mphi_p = phi_pRbp/phi_E2F1;
184 ma2d = a2/phi_E2F1;
185 ma3d = a3*APC_Total/phi_E2F1;
186 ma4d = a4*WntMax/phi_E2F1;
187 ma5d = a5/phi_E2F1;
188 mk16d = k16*Km4/phi_E2F1;
189 mk61d = k61/phi_E2F1;
190 mPhiE2F1 = phi_E2F1;
191}
192
193void WntCellCycleOdeSystem::EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY)
194{
195 double r = rY[0];
196 double e = rY[1];
197 double i = rY[2];
198 double j = rY[3];
199 double p = rY[4];
200 double c = rY[5];
201 double b1 = rY[6];
202 double b2 = rY[7];
203 double wnt_level = rY[8];
204
205 double dx1 = 0.0;
206 double dx2 = 0.0;
207 double dx3 = 0.0;
208 double dx4 = 0.0;
209 double dx5 = 0.0;
210 double dx6 = 0.0;
211 double dx7 = 0.0;
212 double dx8 = 0.0;
213
214 /*
215 * The variables are
216 * 1. r = pRb
217 * 2. e = E2F1
218 * 3. i = CycD (inactive)
219 * 4. j = CycD (active)
220 * 5. p = pRb-p
221 * 6. c = APC (Active)
222 * 7. b = Beta-Catenin
223 */
224
225 // Bit back-to-front, but work out the Wnt section first...
226
227 // Mutations take effect by altering the level of beta-catenin
228 if (!mpMutationState)
229 {
230 // No mutations specified
231 }
232 else if (mpMutationState->IsType<ApcOneHitCellMutationState>()) // APC +/-
233 {
234 dx6 = ma5d*(1.0-c) - ma4d*wnt_level*c;
235 dx7 = ma2d*(0.5-b1) - 0.5*ma3d*b1*c;
236 dx8 = ma2d*(0.5-b2) - 0.5*ma3d*b2*c;
237 }
238 else if (mpMutationState->IsType<ApcTwoHitCellMutationState>()) // APC -/-
239 {
240 dx6 = 0.0;
241 dx7 = ma2d*(0.5-b1);
242 dx8 = ma2d*(0.5-b2);
243 }
244 else if (mpMutationState->IsType<BetaCateninOneHitCellMutationState>()) // Beta-Cat D45
245 {
246 dx6 = ma5d*(1.0-c) - ma4d*wnt_level*c;
247 dx7 = ma2d*(0.5-b1) - ma3d*b1*c;
248 dx8 = ma2d*(0.5-b2);
249 }
250 else
251 {
252 // da
253 dx6 = ma5d*(1.0-c) - ma4d*wnt_level*c;
254 // db
255 dx7 = ma2d*(0.5-b1) - ma3d*b1*c;
256 dx8 = ma2d*(0.5-b2) - ma3d*b2*c;
257 }
258
259 // Now the cell cycle stuff...
260
261 // dr
262 dx1 = e/(mKm1d+e)*mJ11d/(mJ11d+r)*mJ61d/(mJ61d+p) - mk16d*r*j+mk61d*p-mphi_r*r;
263 // de
264 dx2 = mkpd+mk2d*(mad*mad+e*e)/(1+e*e)*mJ12d/(mJ12d+r)*mJ62d/(mJ62d+p) - e;
265 // di
266 dx3 = mk3d*(b1+b2) + mk23d*e*mJ13d/(mJ13d+r)*mJ63d/(mJ63d+p) + mk43d*j - mk34d*i*j/(1+j) - mphi_i*i;
267 // dj
268 dx4 = mk34d*i*j/(1+j) - (mk43d+mphi_j)*j;
269 // dp
270 dx5 = mk16d*r*j - mk61d*p - mphi_p*p;
271
272 double factor = mPhiE2F1*60.0; // convert non-dimensional d/dt s to d/dt in hours
273
274 rDY[0] = dx1*factor;
275 rDY[1] = dx2*factor;
276 rDY[2] = dx3*factor;
277 rDY[3] = dx4*factor;
278 rDY[4] = dx5*factor;
279 rDY[5] = dx6*factor;
280 rDY[6] = dx7*factor; // beta-cat allele 1
281 rDY[7] = dx8*factor; // beta-cat allele 2
282 rDY[8] = 0.0; // do not change the Wnt level
283}
284
285const boost::shared_ptr<AbstractCellMutationState> WntCellCycleOdeSystem::GetMutationState() const
286{
287 return mpMutationState;
288}
289
290bool WntCellCycleOdeSystem::CalculateStoppingEvent(double time, const std::vector<double>& rY)
291{
292 double r = rY[0];
293 double e = rY[1];
294 double p = rY[4];
295 double dY1 = mkpd+mk2d*(mad*mad+e*e)/(1+e*e)*mJ12d/(mJ12d+r)*mJ62d/(mJ62d+p) - e;
296 double factor = mPhiE2F1*60.0; // Convert non-dimensional d/dt s to d/dt in hours.
297 dY1 = dY1*factor;
298
299 assert(!std::isnan(rY[1]));
300 assert(!std::isnan(dY1));
301 return (rY[1] > 1.0 && dY1 > 0.0);
302}
303
304double WntCellCycleOdeSystem::CalculateRootFunction(double time, const std::vector<double>& rY)
305{
306 return rY[1] - 1.0;
307}
308
309template<>
311{
312 this->mVariableNames.push_back("pRb");
313 this->mVariableUnits.push_back("non_dim");
314 this->mInitialConditions.push_back(7.357000000000000e-01);
315
316 this->mVariableNames.push_back("E2F1");
317 this->mVariableUnits.push_back("non_dim");
318 this->mInitialConditions.push_back(1.713000000000000e-01);
319
320 this->mVariableNames.push_back("CycD_i");
321 this->mVariableUnits.push_back("non_dim");
322 this->mInitialConditions.push_back(6.900000000000001e-02);
323
324 this->mVariableNames.push_back("CycD_a");
325 this->mVariableUnits.push_back("non_dim");
326 this->mInitialConditions.push_back(3.333333333333334e-03);
327
328 this->mVariableNames.push_back("pRb_p");
329 this->mVariableUnits.push_back("non_dim");
330 this->mInitialConditions.push_back(1.000000000000000e-04);
331
332 this->mVariableNames.push_back("APC");
333 this->mVariableUnits.push_back("non_dim");
334 this->mInitialConditions.push_back(NAN); // will be filled in later
335
336 this->mVariableNames.push_back("Beta_Cat1");
337 this->mVariableUnits.push_back("non_dim");
338 this->mInitialConditions.push_back(NAN); // will be filled in later
339
340 this->mVariableNames.push_back("Beta_Cat2");
341 this->mVariableUnits.push_back("non_dim");
342 this->mInitialConditions.push_back(NAN); // will be filled in later
343
344 this->mVariableNames.push_back("Wnt");
345 this->mVariableUnits.push_back("non_dim");
346 this->mInitialConditions.push_back(NAN); // will be filled in later
347
348 this->mInitialised = true;
349}
350
352{
353 return mWntLevel;
354}
355
356// Serialization for Boost >= 1.36
#define CHASTE_CLASS_EXPORT(T)
void SetStateVariables(const std::vector< double > &rStateVariables)
void SetDefaultInitialCondition(unsigned index, double initialCondition)
boost::shared_ptr< AbstractOdeSystemInformation > mpSystemInfo
boost::shared_ptr< AbstractCellMutationState > mpMutationState
void SetMutationState(boost::shared_ptr< AbstractCellMutationState > pMutationState)
const boost::shared_ptr< AbstractCellMutationState > GetMutationState() const
WntCellCycleOdeSystem(double wntLevel=0.0, boost::shared_ptr< AbstractCellMutationState > pMutationState=boost::shared_ptr< AbstractCellMutationState >(), std::vector< double > stateVariables=std::vector< double >())
void EvaluateYDerivatives(double time, const std::vector< double > &rY, std::vector< double > &rDY)
double CalculateRootFunction(double time, const std::vector< double > &rY)
bool CalculateStoppingEvent(double time, const std::vector< double > &rY)