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Architecture Docs → ABIO execution

Step

Single time advancement applying reactions.

Overview

Step represents a single time advancement in the simulation, computing reaction rates and updating concentrations accordingly.

Properties Type Description
dt float Time delta for this step
Methods Description
apply Apply reactions to advance state by dt

Protocol Definition

from typing import Protocol

class Step(Protocol):
    """Single time advancement."""

    dt: float  # time delta

    def apply(self, state: State, container: BioContainer) -> State:
        """Apply reactions to advance state by dt."""
        ...

Methods

apply(state, container) -> State

Computes all reaction rates from current concentrations, applies stoichiometric updates, handles transport, and returns the new state.

Algorithm

  1. For each reaction, compute rate from current concentrations
  2. Compute concentration deltas: Δ[molecule] = rate × stoichiometry × dt
  3. Apply transport reactions between compartments
  4. Return new state with updated concentrations and timestamp

See Also