Glycolysis: Converts glucose into pyruvate, generating ATP and NADH.

[csmangum]

Issue: Model Glycolysis Pathway

Description:
Implement the glycolysis pathway in the biological cell simulation. Glycolysis is a series of ten enzyme-catalyzed reactions that convert glucose into pyruvate, producing ATP and NADH in the process. This pathway is crucial for cellular energy production and serves as the foundation for both aerobic and anaerobic respiration.

Tasks:

• [ ] Define the key metabolites involved (e.g., glucose, pyruvate, ATP, NADH).
• [ ] Implement each of the ten reactions with appropriate enzyme-catalyzed steps:
  • [ ] Hexokinase (Glucose to Glucose-6-phosphate)
  • [ ] Phosphoglucose isomerase (G6P to Fructose-6-phosphate)
  • [ ] Phosphofructokinase-1 (F6P to Fructose-1,6-bisphosphate)
  • [ ] Aldolase (F1,6BP to Glyceraldehyde-3-phosphate and Dihydroxyacetone phosphate)
  • [ ] Triose phosphate isomerase (DHAP to Glyceraldehyde-3-phosphate)
  • [ ] Glyceraldehyde-3-phosphate dehydrogenase (G3P to 1,3-Bisphosphoglycerate)
  • [ ] Phosphoglycerate kinase (1,3BPG to 3-Phosphoglycerate)
  • [ ] Phosphoglycerate mutase (3PG to 2-Phosphoglycerate)
  • [ ] Enolase (2PG to Phosphoenolpyruvate)
  • [ ] Pyruvate kinase (PEP to Pyruvate)
• [ ] Set up reactions to consume 2 ATP and produce 4 ATP and 2 NADH.
• [ ] Ensure accurate mass balance and energy conservation.
• [ ] Validate the pathway by simulating glycolysis with different initial glucose concentrations.

Acceptance Criteria:

• The simulation should convert glucose to pyruvate, with accurate ATP and NADH yields.
• The pathway should correctly reflect the input of 2 ATP and output of 4 ATP and 2 NADH, resulting in a net gain of 2 ATP.
• [x] #46
• Proper logging for each reaction step to facilitate debugging and tracking.