Constructing a New Reaction Scheme

This section introduces you to the types of reaction schemes that you may create using Kinetiscope, and outlines the steps you take to construct a new reaction scheme.

A reaction scheme consists of a series of reaction steps, materials transfer steps, the reaction species and their data, the reaction conditions, notebook texts and simulation options. These data are saved, along with any simulation results, in a structured manner as a single reaction scheme file. Kinetiscope can simultaneously load multiple reaction schemes, limited only by the available memory.

Compartments and Transfer Paths

A reaction scheme in Kinetiscope is constructed using the following two objects:

Compartments
A compartment is a spatial element that has a finite volume within which chemical reactions may occur.
Transfer Paths
A transfer path defines a connection between two compartments through which materials transport may occur.

Types of Reaction Schemes

A reaction scheme combines compartments, transfer paths and reaction conditions that in aggregate define all relevant properties of the system and dictate how it evolves with time during the simulation. Kinetiscope can handle three distinct types of reaction schemes, which configure compartments and transfer paths in different ways:

Single Reactor Model
In this model, the reacting system is considered to be well-mixed at all points in time so that concentration and temperature are uniform throughout the reaction volume. This can be considered a reaction scheme containing a single compartment and no transfer paths (and in fact Kinetiscope treats it so internally).
Compartmental Model
In this model, the reacting system is composed of a number of compartments connected by user-defined transfer paths through which materials may migrate. This type of model does not contain explicit spatial information about the reacting system, and the ensemble of compartments need not be contiguous in space. The chemical species move from one compartment to another with either a constant rate or with a rate proportional to its concentration in the source compartment. The network of transfer paths is entirely user-defined. A compartment may be connected to any number of transfer paths.
Three-Dimensional Model
In this model, the reacting system is considered a three-dimensional volume composed of contiguous hexahedral compartments with defined initial dimensions. The chemical species move from one compartment to a neighboring compartment through their mutual interface under Fickian (gradient-driven) diffusion. The number of transfer paths connected to a compartment is fully determined by the user-specified geometry and may not exceed six.

Constructing a Reaction Scheme

To build and edit a complete single-reactor reaction scheme you:

  1. Create a new single reactor scheme window.
  2. Use the tools provided by the scheme window to add reaction steps to the scheme.
  3. Enter equations, rate constants and rate laws.
  4. Select the reaction conditions.
  5. Set species data such as concentrations and physical data as. needed

To build and edit a complete compartmental reaction scheme you:

  1. Create a new compartmental scheme window.
  2. Use the tools provided by the scheme window to add compartments and transfer paths to the scheme.
  3. Add reaction steps to the compartments.
  4. Enter equations, rate constants and rate laws for the reactions.
  5. Set species concentrations in each compartment.
  6. Add transfer steps to the transfer paths.
  7. Enter rate constants for the transfer steps.
  8. Select the reaction conditions.
  9. Set species physical data as needed.

To build and edit a complete three-dimensional reaction scheme you:

  1. Create a new three-dimensional scheme window.
  2. Add reaction steps to the compartments.
  3. Enter equations, rate constants and rate laws for the reactions.
  4. Set species concentrations in each compartment.
  5. Add transfer steps to the transfer paths.
  6. Enter rate constants for the transfer steps.
  7. Use the tools provided by the scheme window to copy and paste compartments and transfer paths as needed to complete the scheme
  8. Select the reaction conditions.
  9. Set species physical data as needed.

You should work through one or more tutorials to gain some initial experience setting up reaction schemes, running simulations and examining simulation results.

Next Step

After you have constructed a reaction scheme following this checklist, you are ready to run a simulation.