Accurate ATP Accounting

[csmangum]

Accurate ATP Accounting

Description:

The simulation provides conflicting information about ATP production:

• After Glycolysis:

  ATP produced in this iteration: 8.0
  Total ATP produced so far: 8.0
  ATP produced in Glycolysis: 8.0

• Later in the Simulation:

  Total ATP Produced: 26.00
  Cytoplasm ATP: 26.00
  Mitochondrion ATP: 10.00

• At the End:

  Total ATP produced: 8.00

These inconsistencies suggest incorrect ATP accounting. For 4 glucose units undergoing glycolysis, the expected net ATP gain is 8 ATP (2 ATP per glucose molecule). Additionally, mitochondrial ATP production is reported without corresponding oxygen consumption or electron transport chain activity.

Recommendation:

• Recalculate ATP production to reflect the accurate net gain from glycolysis.
• Separate ATP contributions from glycolysis and cellular respiration.
• Ensure that mitochondrial ATP production is only included if aerobic respiration is properly simulated, accounting for oxygen consumption.

Acceptance Criteria:

• The simulation reports consistent and accurate ATP production figures throughout.
• ATP produced during glycolysis matches the expected net gain (e.g., 2 ATP per glucose molecule).
• Mitochondrial ATP production is only reported if cellular respiration is correctly simulated, including oxygen consumption.

Required Tests:

1. ATP Consistency Test:

   • Objective: Verify that ATP production numbers are consistent across all simulation outputs.
   • Procedure:
     • Run the simulation and collect all reported ATP production figures.
     • Compare the ATP totals at each reporting point to ensure consistency.
   • Expected Result: All ATP production figures match and accurately reflect the simulation's metabolic processes.

2. Glycolysis ATP Calculation Test:

   • Objective: Confirm that the net ATP gain from glycolysis is correct.
   • Procedure:
     • For the given number of glucose molecules, calculate the expected net ATP gain (2 ATP per glucose).
     • Compare this with the simulation's reported ATP production from glycolysis.
   • Expected Result: The simulation's ATP gain from glycolysis matches the expected value.

3. Mitochondrial ATP Verification Test:

   • Objective: Ensure mitochondrial ATP production is only included when appropriate.
   • Procedure:
     • Check whether the simulation includes oxygen consumption and the electron transport chain.
     • If not, mitochondrial ATP production should not be reported.
   • Expected Result: Mitochondrial ATP is only included if cellular respiration is fully simulated; otherwise, it's excluded.

4. Oxygen Consumption Correlation Test:

   • Objective: Correlate ATP production with oxygen consumption.
   • Procedure:
     • Monitor oxygen levels throughout the simulation.
     • Ensure that any reported mitochondrial ATP production corresponds with a decrease in oxygen levels.
   • Expected Result: Oxygen consumption aligns with mitochondrial ATP production, confirming aerobic respiration.