Pass initial glucose concentration as parameter for metabolism modules

src/arcade/patch/agent/process/PatchProcessMetabolismComplex.java

@@ -74,18 +74,14 @@ public class PatchProcessMetabolismComplex extends PatchProcessMetabolism {
      *   <li>{@code LACTATE_RATE} = rate of lactate production
      *   <li>{@code AUTOPHAGY_RATE} = rate of autophagy
      *   <li>{@code GLUCOSE_UPTAKE_RATE} = rate of glucose uptake
+     *   <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
      * </ul>
      *
      * @param cell the {@link PatchCell} the process is associated with
      */
     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

src/arcade/patch/agent/process/PatchProcessMetabolismMedium.java

@@ -60,17 +60,14 @@ public class PatchProcessMetabolismMedium extends PatchProcessMetabolism {
      *   <li>{@code MINIMUM_MASS_FRACTION} = minimum viable cell mass fraction
      *   <li>{@code AUTOPHAGY_RATE} = rate of autophagy
      *   <li>{@code ATP_PRODUCTION_RATE} = rate of ATP production
+     *   <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
      * </ul>
      *
      * @param cell the {@link PatchCell} the process is associated with
      */
     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

src/arcade/patch/agent/process/PatchProcessMetabolismRandom.java

@@ -57,17 +57,14 @@ public class PatchProcessMetabolismRandom extends PatchProcessMetabolism {
      *
      * <ul>
      *   <li>{@code CELL_VOLUME} = cell volume
+     *   <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
      * </ul>
      *
      * @param cell the {@link PatchCell} the process is associated with
      */
     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

src/arcade/patch/agent/process/PatchProcessMetabolismSimple.java

@@ -46,17 +46,14 @@ public class PatchProcessMetabolismSimple extends PatchProcessMetabolism {
      *   <li>{@code CONSTANT_GLUCOSE_UPTAKE_RATE} = constant glucose uptake rate
      *   <li>{@code CONSTANT_ATP_PRODUCTION_RATE} = constant ATP production rate
      *   <li>{@code CONSTANT_VOLUME_GROWTH_RATE} = constant volume growth rate
+     *   <li>{@code INITIAL_GLUCOSE_CONCENTRATION} = initial cell internal glucose concentration
      * </ul>
      *
      * @param cell the {@link PatchCell} the process is associated with
      */
     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

src/arcade/patch/parameter.patch.xml

@@ -48,6 +48,7 @@
     <population.process process="metabolism" id="CONSTANT_GLUCOSE_UPTAKE_RATE" value="929.88" unit="fmol glucose/min/M glucose" description="constant glucose uptake rate" />
     <population.process process="metabolism" id="CONSTANT_ATP_PRODUCTION_RATE" value="4.9817" unit="fmol ATP/cell/min" description="constant ATP production rate" />
     <population.process process="metabolism" id="CONSTANT_VOLUME_GROWTH_RATE" value="2.819" unit="um^3/min" description="constant volume growth rate"/>
+    <population.process process="metabolism" id="INITIAL_GLUCOSE_CONCENTRATION" value="0.17" unit="fmol/um^3" description="initial cell internal glucose concentration"/>
 
     <!-- signaling process parameters -->
     <population.process process="signaling" id="MIGRATORY_THRESHOLD" value="10" description="threshold fold change in PLCg for migration" />