Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
Alarcon2004OxygenBasedCellCycleOdeSystem.cpp
1/*
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34*/
35
36#include "Alarcon2004OxygenBasedCellCycleOdeSystem.hpp"
37#include "CellwiseOdeSystemInformation.hpp"
38
40 bool isLabelled,
41 std::vector<double> stateVariables)
43 mOxygenConcentration(oxygenConcentration),
44 mIsLabelled(isLabelled)
45{
47
58 Init(); // set up parameters
59
60 // Parameter values are taken from the Alarcon et al. (2004) paper
61 if (mIsLabelled) // labelled "cancer" cells
62 {
63 ma1 = 0.04;
64 mc1 = 0.007;
65 mxThreshold = 0.004;
66 myThreshold = 0.05;
67 }
68 else // normal cells
69 {
70 ma1 = 0.05;
71 mc1 = 0.1;
72 mxThreshold = 0.004;
73 myThreshold = 0.2;
74 }
75
76 // Cell-specific initial conditions
78 SetDefaultInitialCondition(5, oxygenConcentration);
79
80 if (stateVariables != std::vector<double>())
81 {
82 SetStateVariables(stateVariables);
83 }
84}
85
90
92{
93 // Parameter values are taken from the Alarcon et al. (2004) paper
94 ma2 = 1.0;
95 ma3 = 0.25;
96 ma4 = 0.04;
97 mb3 = 10.0;
98 mb4 = 5.5;
99 mc2 = 0.01;
100 md1 = 0.01;
101 md2 = 0.1;
102 mJ3 = 0.04;
103 mJ4 = 0.04;
104 mEta = 0.01;
105 mMstar = 10.0;
106 mB = 0.01;
107}
108
109void Alarcon2004OxygenBasedCellCycleOdeSystem::EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY)
110{
111 double x = rY[0];
112 double y = rY[1];
113 double z = rY[2];
114 double mass = rY[3];
115 double u = rY[4];
116 double oxygen_concentration = rY[5];
117
118 double dx = 0.0;
119 double dy = 0.0;
120 double dz = 0.0;
121 double dmass = 0.0;
122 double du = 0.0;
123
124 /*
125 % The variables are
126 % 1. x = Cdh1-APC complexes
127 % 2. y = cyclin-CDK
128 % 3. z = p27
129 % 4. m = mass
130 % 5. u = RBNP
131 */
132
133 dx = ((1 + mb3*u)*(1-x))/(mJ3 + 1 - x) - (mb4*mass*x*y)/(mJ4 + x);
134 dy = ma4 -(ma1 + ma2*x + ma3*z)*y;
135
136 // Parameter values are taken from the Alarcon et al. (2004) paper
137 if (mIsLabelled) // labelled "cancer" cells
138 {
139 dz = mc1 - mc2*oxygen_concentration*z/(mB + oxygen_concentration);
140 }
141 else // normal cells
142 {
143 dz = mc1*(1 - mass/mMstar) - mc2*oxygen_concentration*z/(mB + oxygen_concentration);
144 }
145
146 dmass = mEta*mass*(1 - mass/mMstar);
147 du = md1 - (md2 + md1*y)*u;
148
149 // Rescale time to be in hours
150 rDY[0] = 60.0*dx;
151 rDY[1] = 60.0*dy;
152 rDY[2] = 60.0*dz;
153 rDY[3] = 60.0*dmass;
154 rDY[4] = 60.0*du;
155 rDY[5] = 0.0; // do not change the oxygen concentration
156}
157
158bool Alarcon2004OxygenBasedCellCycleOdeSystem::CalculateStoppingEvent(double time, const std::vector<double>& rY)
159{
160 return (rY[0] < mxThreshold && rY[1] > myThreshold);
161}
162
163template<>
165{
166 this->mVariableNames.push_back("Cdh1_APC_complexes");
167 this->mVariableUnits.push_back("non_dim");
168 this->mInitialConditions.push_back(0.9);
169
170 this->mVariableNames.push_back("cyclin_CDK");
171 this->mVariableUnits.push_back("non_dim");
172 this->mInitialConditions.push_back(0.01);
173
174 this->mVariableNames.push_back("p27");
175 this->mVariableUnits.push_back("non_dim");
176 this->mInitialConditions.push_back(0.0);
177
178 this->mVariableNames.push_back("mass");
179 this->mVariableUnits.push_back("non_dim");
180 this->mInitialConditions.push_back(NAN); // will be filled in later
181
182 this->mVariableNames.push_back("RBNP");
183 this->mVariableUnits.push_back("non_dim");
184 this->mInitialConditions.push_back(1.0);
185
186 this->mVariableNames.push_back("O2");
187 this->mVariableUnits.push_back("non_dim");
188 this->mInitialConditions.push_back(NAN); // will be filled in later
189
190 this->mInitialised = true;
191}
192
194{
195 mIsLabelled = isLabelled;
196}
197
202
207
208// 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
Alarcon2004OxygenBasedCellCycleOdeSystem(double oxygenConcentration, bool isLabelled, std::vector< double > stateVariables=std::vector< double >())
void EvaluateYDerivatives(double time, const std::vector< double > &rY, std::vector< double > &rDY)
bool CalculateStoppingEvent(double time, const std::vector< double > &rY)