Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
TysonNovak2001OdeSystem.cpp
1/*
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34*/
35
36#include "TysonNovak2001OdeSystem.hpp"
37#include "OdeSystemInformation.hpp"
39
40TysonNovak2001OdeSystem::TysonNovak2001OdeSystem(std::vector<double> stateVariables)
42{
44
45 Init();
46
47 if (stateVariables != std::vector<double>())
48 {
49 SetStateVariables(stateVariables);
50 }
51}
52
57
59{
60 // Initialise model parameter values
61 mK1 = 0.04;
62 mK2d = 0.04;
63 mK2dd = 1.0;
64 mK2ddd = 1.0;
65 mCycB_threshold = 0.1;
66 mK3d = 1.0;
67 mK3dd = 10.0;
68 mK4d = 2.0;
69 mK4 = 35;
70 mJ3 = 0.04;
71 mJ4 = 0.04;
72 mK5d = 0.005;
73 mK5dd = 0.2;
74 mK6 = 0.1;
75 mJ5 = 0.3;
76 mN = 4u;
77 mK7 = 1.0;
78 mK8 = 0.5;
79 mJ7 = 1e-3;
80 mJ8 = 1e-3;
81 mMad = 1.0;
82 mK9 = 0.1;
83 mK10 = 0.02;
84 mK11 = 1.0;
85 mK12d = 0.2;
86 mK12dd = 50.0;
87 mK12ddd = 100.0;
88 mKeq = 1e3;
89 mK13 = 1.0;
90 mK14 = 1.0;
91 mK15d = 1.5;
92 mK15dd = 0.05;
93 mK16d = 1.0;
94 mK16dd = 3.0;
95 mJ15 = 0.01;
96 mJ16 = 0.01;
97 mMu = 0.01;
98 mMstar = 10.0;
99}
100
101void TysonNovak2001OdeSystem::EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY)
102{
103 double x1 = rY[0];
104 double x2 = rY[1];
105 double x3 = rY[2];
106 double x4 = rY[3];
107 double x5 = rY[4];
108 double x6 = rY[5];
109
110 double dx1 = 0.0;
111 double dx2 = 0.0;
112 double dx3 = 0.0;
113 double dx4 = 0.0;
114 double dx5 = 0.0;
115 double dx6 = 0.0;
116
117 double temp1 = 0.0;
118 double temp2 = 0.0;
119 double temp3 = 0.0;
120
130 dx1 = mK1-(mK2d+mK2dd*x2)*x1;
131
132 // The commented line below models the start transition, no cycling, without Cdc20A
133// temp1 = ((mK3d)*(1.0-x2))/(mJ3+1.0-x2);
134
135 temp1 = ((mK3d+mK3dd*x4)*(1.0-x2))/(mJ3+1.0-x2);
136 temp2 = (mK4*x6*x1*x2)/(mJ4+x2);
137 dx2 = temp1-temp2;
138
139 temp1 = mK5dd*(SmallPow(x1*x6/mJ5,mN)/(1+SmallPow(x1*x6/mJ5,mN)));
140 temp2 = mK6*x3;
141 dx3 = mK5d + temp1 - temp2;
142
143 temp1 = (mK7*x5*(x3-x4))/(mJ7+x3-x4);
144 temp2 = (mK8*mMad*x4)/(mJ8+x4);
145 temp3 = mK6*x4;
146 dx4 = temp1 - temp2 - temp3;
147
148 dx5 = mK9*x6*x1*(1.0-x5) - mK10*x5;
149
150 dx6 = mMu*x6*(1.0-x6/mMstar);
151
152 // Multiply by 60 beacuase the Tyson and Novak 2001 paper has time in minutes, not hours
153 rDY[0] = dx1*60.0;
154 rDY[1] = dx2*60.0;
155 rDY[2] = dx3*60.0;
156 rDY[3] = dx4*60.0;
157 rDY[4] = dx5*60.0;
158 rDY[5] = dx6*60.0;
159}
160
161void TysonNovak2001OdeSystem::AnalyticJacobian(const std::vector<double>& rSolutionGuess, double** jacobian, double time, double timeStep)
162{
163 timeStep *= 60.0; // to scale Jacobian so in hours not minutes
164 double x1 = rSolutionGuess[0];
165 double x2 = rSolutionGuess[1];
166 double x3 = rSolutionGuess[2];
167 double x4 = rSolutionGuess[3];
168 double x5 = rSolutionGuess[4];
169 double x6 = rSolutionGuess[5];
170
171 // f1
172 double df1_dx1 = -mK2d - mK2dd*x2;
173 double df1_dx2 = -mK2dd*x1;
174
175 jacobian[0][0] = 1-timeStep*df1_dx1;
176 jacobian[0][1] = -timeStep*df1_dx2;
177
178 // f2
179 double df2_dx1 = -mK4*x6*x2/(mJ4+x2);
180 double df2_dx2 = -mJ3*(mK3d + mK3dd*x4)/(SmallPow((mJ3 + 1 - x2),2))
181 -mJ4*mK4*x6*x1/(SmallPow((mJ4+x2),2));
182 double df2_dx4 = mK3dd*(1-x2)/(mJ3+1-x2);
183 double df2_dx6 = -mK4*x1*x2/(mJ4+x2);
184
185 jacobian[1][0] = -timeStep*df2_dx1;
186 jacobian[1][1] = 1-timeStep*df2_dx2;
187 jacobian[1][3] = -timeStep*df2_dx4;
188 jacobian[1][5] = -timeStep*df2_dx6;
189
190 //f3
191 double z = x1*x6/mJ5;
192 double df3_dx1 = (mK5dd*x6/mJ5)*mN*SmallPow(z,mN-1)/(SmallPow((1-SmallPow(z,mN)),2));
193 double df3_dx3 = -mK6;
194 double df3_dx6 = (mK5dd*x1/mJ5)*mN*SmallPow(z,mN-1)/(SmallPow((1-SmallPow(z,mN)),2));
195
196 jacobian[2][0] = -timeStep*df3_dx1;
197 jacobian[2][2] = 1-timeStep*df3_dx3;
198 jacobian[2][5] = -timeStep*df3_dx6;
199
200 // f4
201 double df4_dx3 = mJ7*mK7*x5/(SmallPow(mJ7+x3-x4,2));
202 double df4_dx4 = -mJ7*mK7*x5/(SmallPow(mJ7+x3-x4,2)) - mK6 - mJ8*mK8*mMad/(SmallPow(mJ8+x4,2));
203 double df4_dx5 = mK7*(x3-x4)/(mJ7+x3-x4);
204
205 jacobian[3][2] = -timeStep*df4_dx3;
206 jacobian[3][3] = 1-timeStep*df4_dx4;
207 jacobian[3][4] = -timeStep*df4_dx5;
208
209 // f5
210 double df5_dx1 = mK9*x6*(1-x5);
211 double df5_dx5 = -mK10 - mK9*x6*x1;
212 double df5_dx6 = mK9*x1*(1-x5);
213
214 jacobian[4][0] = -timeStep*df5_dx1;
215 jacobian[4][4] = 1-timeStep*df5_dx5;
216 jacobian[4][5] = -timeStep*df5_dx6;
217
218 // f6
219 double df6_dx6 = mMu - 2*mMu*x6/mMstar;
220
221 jacobian[5][5] = 1-timeStep*df6_dx6;
222}
223
224bool TysonNovak2001OdeSystem::CalculateStoppingEvent(double time, const std::vector<double>& rY)
225{
226 std::vector<double> dy(rY.size());
227 EvaluateYDerivatives(time, rY, dy);
228
229 // Only call this a stopping condition if the mass of the cell is over 0.6
230 // (normally cycles from 0.5-1.0 ish!)
231 return ( (rY[5] > 0.6 ) && (rY[0] < mCycB_threshold) && dy[0] < 0.0 );
232}
233
234double TysonNovak2001OdeSystem::CalculateRootFunction(double time, const std::vector<double>& rY)
235{
236 std::vector<double> dy(rY.size());
237 EvaluateYDerivatives(time, rY, dy);
238
239 // Only call this a stopping condition if the mass of the cell is over 0.6
240 // (normally cycles from 0.5-1.0 ish!)
241 if (rY[5]<0.6)
242 {
243 return 1.0;
244 }
245
246 if (dy[0] >= 0.0)
247 {
248 return 1.0;
249 }
250 return rY[0]-mCycB_threshold;
251}
252
253template<>
255{
256 /*
257 * Initialise state variables.
258 *
259 * These initial conditions are the approximate steady state
260 * solution values while the commented out conditions are taken
261 * from the Tyson and Novak 2001 paper.
262 */
263 this->mVariableNames.push_back("CycB");
264 this->mVariableUnits.push_back("nM");
265// this->mInitialConditions.push_back(0.1);
266 this->mInitialConditions.push_back(0.099999999999977);
267
268 this->mVariableNames.push_back("Cdh1");
269 this->mVariableUnits.push_back("nM");
270// this->mInitialConditions.push_back(9.8770e-01);
271 this->mInitialConditions.push_back(0.989026454281841);
272
273 this->mVariableNames.push_back("Cdc20T");
274 this->mVariableUnits.push_back("nM");
275// this->mInitialConditions.push_back(1.5011e+00);
276 this->mInitialConditions.push_back(1.547942029285891);
277
278 this->mVariableNames.push_back("Cdc20A");
279 this->mVariableUnits.push_back("nM");
280// this->mInitialConditions.push_back(1.2924e+00);
281 this->mInitialConditions.push_back(1.421110920155839);
282
283 this->mVariableNames.push_back("IEP");
284 this->mVariableUnits.push_back("nM");
285// this->mInitialConditions.push_back(6.5405e-01);
286 this->mInitialConditions.push_back(0.672838844290094);
287
288 this->mVariableNames.push_back("mass");
289 this->mVariableUnits.push_back("");
290// this->mInitialConditions.push_back(4.7039e-01);
291 this->mInitialConditions.push_back(0.970831277863956 / 2);
292
293 this->mInitialised = true;
294}
295
296// Serialization for Boost >= 1.36
#define CHASTE_CLASS_EXPORT(T)
void SetStateVariables(const std::vector< double > &rStateVariables)
boost::shared_ptr< AbstractOdeSystemInformation > mpSystemInfo
static boost::shared_ptr< OdeSystemInformation< ODE_SYSTEM > > Instance()
void EvaluateYDerivatives(double time, const std::vector< double > &rY, std::vector< double > &rDY)
TysonNovak2001OdeSystem(std::vector< double > stateVariables=std::vector< double >())
bool CalculateStoppingEvent(double time, const std::vector< double > &rY)
virtual void AnalyticJacobian(const std::vector< double > &rSolutionGuess, double **jacobian, double time, double timeStep)
double CalculateRootFunction(double time, const std::vector< double > &rY)