A Practical Guide to Features

This section describes the following features and outlines step-by-step how to apply them in practice:

Using programmed temperature in a simulation

Kinetiscope's programmed temperature feature allows you to simulate systems where the reaction temperature is not constant but varies in a well-defined way under control of an external thermal source. Practical examples of this situation include a manufacturing process line where an oven or hotplate is programmed to provide a particular thermal profile, a thermogravimetric analyzer where a chemical sample is heated while measuring mass loss due to volatilization and decomposition.

Applying programmed temperature in practice

Programmed temperature may be used in single-reactor, compartmental and three-dimensional reaction schemes. To implement a simulation that uses programmed temperature, you need the following information:

  1. A description of the system that allows you to choose which type of reaction scheme is best suited
  2. A set of reaction steps that describe the chemistry of the system
  3. If your system includes materials transport, a set of transfer steps
  4. , for example as gradient-driven diffusion
  5. Temperature-dependent rate constants in the form of Arrhenius parameters for each reaction step and transfer step
  6. Data describing the time/temperature behavior of the system.

    This can be a table of experimental measurements, a linear rate, or an estimate or calculation of how the system is expected to vary with time

To carry out a programmed temperature simulation:
  1. Create a new reaction scheme.

    For a compartmental reaction scheme, add compartments and transfer paths as needed to construct your description of the system.

  2. Add reaction steps and transfer steps as needed, using temperature-dependent rate constants for each step.

    To do so, use the tool bar for single-reactor reaction schemes; edit compartments and transfer paths for compartmental and three-dimensional reaction schemes.

  3. Set the reaction conditions to Temperature follows a linear profile or Temperature follows a user-defined profile.
  4. Enter the temperature profile, either as a linear temperature ramp or a set of time/temperature data pairs.
  5. Run the simulation.

Examples using programmed temperature

Click the description to load the example reaction scheme into Kinetiscope.

Electrochemical reactions

Kinetiscope's allows you to simulate systems containing electrochemical reaction steps whose rates are controlled by an applied voltage. The applied voltage may be held constant or may be varied with time.

Applying electrochemical reactions in practice

Electrochemical reactions may be used only in three-dimensional reaction schemes. To implement a simulation that uses electrochemical reactions, you need the following information:

  1. A description of the geometry of the system, such as electrode area and dimensions of the liquid volume
  2. A set of reaction steps that describes the chemistry of the system and includes electrochemical oxidation and reduction steps
  3. A set of diffusion steps (transfer steps) for the mobile species in the system
  4. For each electrochemical step, voltage-dependent rate constant parameters in Butler-Volmer form
  5. Rate constants for all other reaction steps, in either temperature-dependent or temperature-independent form
  6. Rate constants for each diffusion (transfer) step, in either temperature-dependent or temperature-independent form
  7. Data describing the voltage/temperature behavior of the system

    This can be a single value, a table of experimental measurements, a linear rate, or an estimate or calculation of how the system is expected to vary with time

To carry out an electrochemical simulation:
  1. Create a new three-dimensional reaction scheme.

    At least one compartment will serve as an electrode (a source and sink for electrons), and the remaining compartments define the electrolyte. The area of the electrode interface in contact with the electrolyte is a factor in the electrochemical rate.

  2. Add reaction steps as needed, using voltage-dependent rate constants for each electrochemical step.

    To do so, edit the compartments. Note that in order to be active, electrochemical steps must be in a compartment that interfaces with an electrode compartment.

  3. Add an electron transfer step between each electrode and each electrolyte compartment it interfaces with.

    To do so, edit the transfer paths.

  4. Add diffusion steps for all chemical species between electrolyte compartments.

    To do so, edit the transfer paths.

  5. Set the reaction conditions to Voltage is constant or Voltage follows a linear profile or Voltage follows a user-defined profile.
  6. If needed, enter the voltage profile, either as a linear voltage ramp or a set of time/voltage data pairs.
  7. Run the simulation.
The Electrochemistry Tutorial provides a detailed step-by-step description of this procedure.

Examples using programmed temperature

Click the description to load the example reaction scheme into Kinetiscope.

Using programmed external stimulus

Kinetiscope's programmed stimulus feature allows you to simulate systems where an external factor modulates the kinetics. Practical examples of this situation include chemistry initiated by a pulsed source such as a valve, a pump or a light beam.

Applying programmed stimulus in practice

Programmed stimulus may be used in compartmental and three-dimensional reaction schemes. To implement a simulation that uses programmed stimulus, you need the following information:

  1. A description of the system that allows you to choose which type of reaction scheme is best suited
  2. A set of reaction steps that describe the chemistry of the system
  3. If your system includes materials transport, a set of transfer steps
  4. .
  5. For each reaction step or transfer step that is to be controlled by external stimulus, a stimulus-dependent rate parameter k' for use in the equation

    k  = k' Se (3)

    where Se is the value of the programmed external stimulus at a given instant in elapsed time, and k' is the proportionality coefficient relating the rate constant k to the external stimulus value.

  6. For all other reaction steps and transfer steps, rate constants in either temperature-dependent or temperature-independent form
  7. Data describing the time/stimulus behavior of the system.

    This can be a table of experimental measurements or an estimate or calculation of how the system is expected to vary with time

To carry out a programmed stimulus simulation:
  1. Create a new reaction scheme.

    For a compartmental reaction scheme, add compartments and transfer paths as needed to construct your description of the system.

  2. Add reaction steps and transfer steps as needed, using stimulus-dependent rate constants as needed.

    To do so, edit compartments and transfer paths.

  3. Set the reaction conditions to Temperature follows an external stimulus.
  4. Enter the stimulus profile as a set of time/external stimulus data pairs.
  5. Run the simulation.
The Compartmental Scheme Tutorial provides a detailed step-by-step description of this procedure.

Examples using programmed stimulus

Click the description to load the example reaction scheme into Kinetiscope.

Using copy-and-paste to build out a three-dimensional reaction scheme

Three-dimensional reaction schemes can be configured to contain thousands of compartments and an even larger number of transfer paths, far too many objects to individually edit and initialize.

The general approach to initially building out a three-dimensional reaction scheme with regions of different composition, chemistry and transport behavior is to perform a series of copy-and-paste operations that sequentially initialize different regions of the whole reaction volume.

Kinetiscope's copy-and-paste feature makes this straightforward. A common and general approach is to

  1. Edit a single compartment, using the Compartment Editor Dialog to add reaction steps common to a particular spatial region of your system, and setting concentrations of species in the compartment to the desired values.
  2. Copy the single compartment to Kinetiscope's clipboard.
  3. Select an array of compartments in the scheme diagram using the Select... submenu.
  4. Paste the clipboard compartment into the selection.

The Three-dimensional Scheme Tutorial provides a detailed step-by-step description of this procedure.

You may use the same approach to initialize a selection of transfer paths with a set of transfer steps. When pasting you may select which properties of the object on the clipboard are to be pasted into the selection.

Three different methods are available for selecting groups of compartments and transfer paths.

Single object level
You may select an individual compartment or individual transfer path by a single click of the left mouse button.
Selection context menu
Each compartment has a context menu available by clicking the right mouse button. A Select... submenu allows you to quickly select a column, row or plane of compartments for modification.
Selection based on characteristics
For complex schemes, Kinetiscope provides a tool for selecting compartments and transfer paths based on their locations in the reaction volume, their orientation, colors and names. You access this tool using the Advanced Selection Dialog.

Setting concentrations in a three-dimensional reaction scheme

Four different methods are available for setting initial species concentrations.

Setting concentrations at the single compartment level
You may set initial concentrations of all species in an individual compartment by double-clicking that compartment in the scheme diagram. This opens the Compartment Editor Dialog.
Setting concentrations in a selection
As noted above, there a several mechanisms for selecting a group of compartments. You may use this to initialize a initial concentrations in a group compartments in a targeted way. The general approach is to:

  1. Edit a single compartment, setting concentrations of all species to specific values.
  2. Copy the single compartment to Kinetiscope's clipboard.
  3. Select an group of compartments.
  4. Paste the clipboard compartment into the selection, using the Replace Compartment Dialog to set only the concentrations in the selected compartments to the new values.
Setting all compartments to a single concentration value
Use the Set Concentrations Page of the Advanced Functions Dialog to change the concentration of a specific species in all compartments to a single value.
Setting a different concentration in each compartment
The Advanced Functions Dialog provides a means to quickly initialize the concentration of a species to a different concentration in each compartment. The concentration values are read from a text file containing a table giving the ordinal location of a compartment along with the initial concentration value.

Using variable volume

If a reaction scheme is multi-phase, for example if a solid undergoes decomposition and releases a gaseous product, then the volume of the solid changes, and so do concentrations of all species in the solid. Kinetiscope's variable volume allows the volume change and its effect on the system's kinetics to be accurately accounted for. For many common systems, for example reactions in a dilute solution, volume change is negligible and can safely be ignored, but in concentrated liquid or solid solution the effects of volume change can be substantial.

Single reactor reaction schemes, because they are nominally a homogeneous volume, handle variable volume simulations differently than do compartmental and three-dimensional reaction schemes. For single reactor reaction schemes only, you must also specify the physical state of each species. Although a mixture of phases is allowed to be generated during a single reactor simulation, only one phase may be present initially. Only the volume of that initial phase is tracked.

With compartmental and three-dimensional reaction schemes, each compartment is a single phase. Evolution of a gaseous product (or absorption of a gaseous reactant) is readily handled by considering certain compartments to represent the gas phase, others to represent the condensed phase, and providing a transfer step between compartments of different phases to allow for volatilization.

Once a species is transferred from a condensed phase compartment to a gaseous phase compartment (i.e., it is volatilized), its density changes and this must be accounted for. A simple means to do this is to include in the gaseous compartment a reaction step that rapidly converts the condensed variant of a species into its gaseous variant.

Applying variable volume temperature in practice

To implement a variable volume simulation, you need the following information:

  1. A description of the system that allows you to choose which type of reaction scheme is best suited
  2. A set of reaction steps that describe the chemistry of the system
  3. If your system includes materials transport, a set of transfer steps
  4. rate constants for chemistry and transfer
  5. A value for the molar density of each species, the number of moles of the species contained in a unit volume. The molar density is the gravimetric density divided by the molecular weight of the species, equal to the inverse of the molar volume. Data describing the time/temperature behavior of the system.

To carry out a variable volume simulation:

  1. Create a new reaction scheme.

    For a compartmental reaction scheme, add compartments and transfer paths as needed to construct your description of the system.

  2. Add reaction steps and transfer steps as needed

    To do so, use the tool bar for single-reactor reaction schemes; edit compartments and transfer paths for compartmental and three-dimensional reaction schemes.

  3. Set the reaction conditions to Volume is variable.
  4. Enter the molar densities for each species on the Species Data Page
  5. Run the simulation.

Examples using variable volume

Click the description to load the example reaction scheme into Kinetiscope.

Creating an expanding spatial grid

For some reaction-diffusion systems, it is beneficial to adjust compartment dimensions so that fine-grained spatial detail can be captured and accurately portrayed in a region of high reactivity and large concentration gradients, even though the overall system may be dimensioned at a length scale larger by orders of magnitude. This situation commonly arises, for example, in electrochemical reactions at an electrode interface.

Kinetiscope provides a function for quickly dimensioning an array of compartments to create a nonuniform spatial grid of compartments. This function is accessed from the Advanced Dimensioning Page of the Advanced Functions Dialog.

This dimensioning function is applicable to all three-dimensional reaction schemes. You can apply the function to all three axes in sequence.

The Electrochemistry Tutorial provides a detailed step-by-step description of how to set up an exponentially expanding grid.

Examples using an expanding spatial grid

Click the description to load the example reaction scheme into Kinetiscope.