Reaction-Diffusion (RXD) Tutorials

NEURON’s rxd module lets you model intracellular and extracellular chemistry — calcium dynamics, IP₃ signaling, buffering, gene regulation, and more — alongside electrophysiology. Start with the main tutorial, then explore the examples below.

See also: Basic Reaction-Diffusion in the Programmer’s Reference.

Core Tutorials

• Reaction-diffusion introduction
  • Overview
  • Math
  • Reading the data
  • Examples
• Initialization Strategies
  • Option 1: NEURON and NMODL defaults
  • Option 2: Uniform initial concentration
  • Option 3: Initializing to a function of position
  • Option 4: to steady state
• Varying initial concentrations and parameters
• Radial diffusion
• Reaction-diffusion thresholds
• Extracellular reaction-diffusion tutorial
  • Download files
  • Getting started
• Restricting reactions to a part of a region
  • Overview
  • Setup NEURON library and imports
  • Setup the model
  • Morphology and discretization
  • The rxd.Region
  • The rxd.Species
  • The rxd.Reaction and its localization
  • Run and visualize the simulation

Application Examples

• Example: Degradable buffer
• Example: Circadian rhythm
• Example: Calcium waves
• Example: combining MOD file ion channels with rxd
• IP3 demo