Chapter 14
Metabolism as Directed Flow Algebra

Glycolysis is one of the most fundamental metabolic pathways, converting glucose into smaller molecules while releasing usable energy.
This process occurs in nearly all living cells and forms the starting point for many other metabolic reactions.

This chapter examines glycolysis as a sequence of controlled chemical transitions that initiate the cellular extraction of energy from nutrients.

The Krebs cycle continues the energy extraction process by further oxidising metabolic intermediates derived from glycolysis.
Through a circular series of reactions, it generates molecules that carry high-energy electrons for later use.

This chapter explores the Krebs cycle as a repeating metabolic loop that supports sustained energy production within the cell.

The electron transport chain converts the stored energy of electrons into a proton gradient across the mitochondrial membrane.
This gradient ultimately drives the production of ATP, the primary energy currency of the cell.

This chapter examines the electron transport chain as a structured energy conversion system that links electron flow to cellular energy generation.

Cells continuously transform energy from one form into another to sustain biological processes. Chemical energy from nutrients is converted into gradients, molecular motion, and cellular work.

This chapter explores how biological systems maintain coherent energy transformations that support stable and sustained cellular activity.

Metabolic pathways consist of interconnected chemical states linked by enzyme-driven reactions.
Each reaction moves molecules from one state to another within a broader metabolic network.

This chapter examines metabolism as a state transition system in which biological reactions form a structured network of chemical transformations.

Biological reactions must occur within strict physical and chemical constraints to maintain cellular viability.
Enzymes, compartmentalisation, and regulatory mechanisms ensure that metabolic flows remain controlled and efficient.

This chapter explores how metabolic systems preserve essential constraints while directing chemical flow through complex biological networks.