diff --git a/src/arcade/patch/agent/process/PatchProcessMetabolismComplex.java b/src/arcade/patch/agent/process/PatchProcessMetabolismComplex.java index c4119bfc8..c5cfe0a3b 100644 --- a/src/arcade/patch/agent/process/PatchProcessMetabolismComplex.java +++ b/src/arcade/patch/agent/process/PatchProcessMetabolismComplex.java @@ -74,6 +74,7 @@ public class PatchProcessMetabolismComplex extends PatchProcessMetabolism { *
  • {@code LACTATE_RATE} = rate of lactate production *
  • {@code AUTOPHAGY_RATE} = rate of autophagy *
  • {@code GLUCOSE_UPTAKE_RATE} = rate of glucose uptake + *
  • {@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration * * * @param cell the {@link PatchCell} the process is associated with @@ -81,11 +82,6 @@ public class PatchProcessMetabolismComplex extends PatchProcessMetabolism { public PatchProcessMetabolismComplex(PatchCell cell) { super(cell); - // Initial internal concentrations. - intAmts = new double[2]; - intAmts[GLUCOSE] = extAmts[GLUCOSE]; - intAmts[PYRUVATE] = extAmts[GLUCOSE] * PYRU_PER_GLUC; - // Mapping for internal concentration access. String[] intNames = new String[2]; intNames[GLUCOSE] = "glucose"; @@ -101,6 +97,11 @@ public PatchProcessMetabolismComplex(PatchCell cell) { lactateRate = parameters.getDouble("metabolism/LACTATE_RATE"); autophagyRate = parameters.getDouble("metabolism/AUTOPHAGY_RATE"); glucoseUptakeRate = parameters.getDouble("metabolism/GLUCOSE_UPTAKE_RATE"); + + // Initial internal concentrations. + intAmts = new double[2]; + intAmts[GLUCOSE] = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION"); + intAmts[PYRUVATE] = extAmts[GLUCOSE] * PYRU_PER_GLUC; } @Override diff --git a/src/arcade/patch/agent/process/PatchProcessMetabolismMedium.java b/src/arcade/patch/agent/process/PatchProcessMetabolismMedium.java index 40c795b48..b96e46d5b 100644 --- a/src/arcade/patch/agent/process/PatchProcessMetabolismMedium.java +++ b/src/arcade/patch/agent/process/PatchProcessMetabolismMedium.java @@ -60,6 +60,7 @@ public class PatchProcessMetabolismMedium extends PatchProcessMetabolism { *
  • {@code MINIMUM_MASS_FRACTION} = minimum viable cell mass fraction *
  • {@code AUTOPHAGY_RATE} = rate of autophagy *
  • {@code ATP_PRODUCTION_RATE} = rate of ATP production + *
  • {@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration * * * @param cell the {@link PatchCell} the process is associated with @@ -67,10 +68,6 @@ public class PatchProcessMetabolismMedium extends PatchProcessMetabolism { public PatchProcessMetabolismMedium(PatchCell cell) { super(cell); - // Initial internal concentrations. - intAmts = new double[1]; - intAmts[GLUCOSE] = extAmts[GLUCOSE]; - // Mapping for internal concentration access. String[] intNames = new String[1]; intNames[GLUCOSE] = "glucose"; @@ -83,6 +80,10 @@ public PatchProcessMetabolismMedium(PatchCell cell) { minimumMassFraction = parameters.getDouble("metabolism/MINIMUM_MASS_FRACTION"); autophagyRate = parameters.getDouble("metabolism/AUTOPHAGY_RATE"); atpProductionRate = parameters.getDouble("metabolism/ATP_PRODUCTION_RATE"); + + // Initial internal concentrations. + intAmts = new double[1]; + intAmts[GLUCOSE] = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION"); } @Override diff --git a/src/arcade/patch/agent/process/PatchProcessMetabolismRandom.java b/src/arcade/patch/agent/process/PatchProcessMetabolismRandom.java index 6f56285da..8719a578f 100644 --- a/src/arcade/patch/agent/process/PatchProcessMetabolismRandom.java +++ b/src/arcade/patch/agent/process/PatchProcessMetabolismRandom.java @@ -57,6 +57,7 @@ public class PatchProcessMetabolismRandom extends PatchProcessMetabolism { * * * * @param cell the {@link PatchCell} the process is associated with @@ -64,10 +65,6 @@ public class PatchProcessMetabolismRandom extends PatchProcessMetabolism { public PatchProcessMetabolismRandom(PatchCell cell) { super(cell); - // Initial internal concentrations. - intAmts = new double[1]; - intAmts[GLUCOSE] = extAmts[GLUCOSE]; - // Mapping for internal concentration access. String[] intNames = new String[1]; intNames[GLUCOSE] = "glucose"; @@ -76,6 +73,10 @@ public PatchProcessMetabolismRandom(PatchCell cell) { // Set loaded parameters. Parameters parameters = cell.getParameters(); averageCellVolume = parameters.getDouble("CELL_VOLUME"); + + // Initial internal concentrations. + intAmts = new double[1]; + intAmts[GLUCOSE] = parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION"); } @Override diff --git a/src/arcade/patch/agent/process/PatchProcessMetabolismSimple.java b/src/arcade/patch/agent/process/PatchProcessMetabolismSimple.java index 5cc84646c..897ca07de 100644 --- a/src/arcade/patch/agent/process/PatchProcessMetabolismSimple.java +++ b/src/arcade/patch/agent/process/PatchProcessMetabolismSimple.java @@ -46,6 +46,7 @@ public class PatchProcessMetabolismSimple extends PatchProcessMetabolism { *
  • {@code CONSTANT_GLUCOSE_UPTAKE_RATE} = constant glucose uptake rate *
  • {@code CONSTANT_ATP_PRODUCTION_RATE} = constant ATP production rate *
  • {@code CONSTANT_VOLUME_GROWTH_RATE} = constant volume growth rate + *
  • {@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration * * * @param cell the {@link PatchCell} the process is associated with @@ -53,10 +54,6 @@ public class PatchProcessMetabolismSimple extends PatchProcessMetabolism { public PatchProcessMetabolismSimple(PatchCell cell) { super(cell); - // Initial internal concentrations. - intAmts = new double[1]; - intAmts[GLUCOSE] = extAmts[GLUCOSE]; - // Mapping for internal concentration access. String[] intNames = new String[1]; intNames[GLUCOSE] = "glucose"; @@ -69,6 +66,11 @@ public PatchProcessMetabolismSimple(PatchCell cell) { glucoseUptakeRate = parameters.getDouble("metabolism/CONSTANT_GLUCOSE_UPTAKE_RATE"); atpProductionRate = parameters.getDouble("metabolism/CONSTANT_ATP_PRODUCTION_RATE"); volumeGrowthRate = parameters.getDouble("metabolism/CONSTANT_VOLUME_GROWTH_RATE"); + + // Initial internal concentrations. + intAmts = new double[1]; + intAmts[GLUCOSE] = + parameters.getDouble("metabolism/INITIAL_GLUCOSE_CONCENTRATION") * volume; } @Override diff --git a/src/arcade/patch/parameter.patch.xml b/src/arcade/patch/parameter.patch.xml index 4c64a22bc..e73cdc9e3 100644 --- a/src/arcade/patch/parameter.patch.xml +++ b/src/arcade/patch/parameter.patch.xml @@ -48,6 +48,7 @@ +