Reactions

Reactions »
The Reactions Node displays the reactions in the project. Here, you may also add, delete and rename the reactions in the project. Grid Views Tabbed Views Actions Grid Views Reactions Stoichiometry Tabbed Views Reaction Types Reactions This grid displays the list of reactions with their overall properties which are organized in columns as explained below: The Include column is useful to include/uninclude a reaction in the model. Unincluded reactions are not shown in other nodes, and are ignored for modeling purposes. By default, any new reaction is included. The Reaction column denotes the name of the reaction. The reaction can be renamed by editing this field. The Equation column(read-only) displays the reaction equation, which is generated automatically based on the entries in the Stoichiometry Reaction: Reaction Name grid. The equations cannot be written directly. The Type column (Optional) is used to specify the reactions type. The type is chosen from a drop-list of available types within the project. The available types in the project are shown in the Types grid. Types have to be first added into this grid, before they are available in the drop list in the Reactions grid. The Quasi Equilibrium column is used to define the reactions that are assumed to be at equilibrium. This option is useful when modeling reaction systems in which there are some reversible reactions, whose forward and reverse rates are much greater than the overall rate of the reactions of interest. When this occurs, these reversible reactions can be considered to be equilibriated. This is called the quasi-equilibrium approximation. In reality, the estimation of the forward and reverse rate constants of these quasi-equilibrium reactions is nearly impossible from experimental data. We may only estimate the equilibrium constant for these reactions. Therefore, in Estimation mode, when a reaction is specified as quasi-equilibriated, REX automatically fixes the reverse reaction parameters for the reaction at its provided value. So, the equilibrium constant is estimated by only varying the forward rate parameters. You may explore the example to learn more about the application of the quasi-equilibrium approximation. The Notes column (Optional) is a text field (maximum 50 characters) used to store comments about the reactions. The Mark column is used to mark a series of reactions for actions such as Delete Marked and Copy Marked Adding a Reaction You may add a Reaction by any of these procedures: Directly: You may add a new reaction by going to the last row and entering the name of the desired reaction. The row will change to edit mode, and you can save this reaction with the <ENTER> key or by clicking on the pencil icon in the row header. This only enters the reaction name. The stoichiometry for this reaction then has to be added in the Stoichiometry Reaction grid, where you may select the compounds and add the stoichiometric coefficients. By executing the Add Reaction action. Example: Adding a Reaction Directly Deleting a Reaction A reaction may be deleted by selecting the reaction row and using the <DELETE> key. Note that deleting a reaction only removes the reaction from the project without affecting the compounds. Stoichiometry The Stoichiometry grid depends on the Reactions grid and is used to enter the stoichiometric coefficients for each reaction. You may add the reaction stoichiometry by going to the compound column and selecting the compounds that participate in the reaction and entering their coefficients in the coefficient column. The row will change to edit mode, and you can save this reaction with the <ENTER> key or by clicking on the pencil icon in the row header. Reactants should be entered with negative coefficients and products should be entered with positive coefficients. Consistency of the reaction stoichiometry can be checked in the Check Atom Balance node, provided that the formula for the compounds is loaded in the Formula node. This Check Atom Balance feature is not available when mass units (Mass Density) are used for Concentrations in the Units Configurations node. Note: When Mass Density is used as units of concentrations, the stoichiometric coefficients are related to mass and not moles. For example, methane combustion in molar terms is: CH₄ + 2O₂ → CO₂ + 2H₂O. However when dealing with mass, that reaction must be modified taking into account the molecular weights so it should be written as: 16CH₄ + 64O₂ → 44CO₂ + 36H₂O. When working with Mass Density, mass balance would require that the sum of the stoichiometric coefficients for the reactants is the same as the sum of coefficients of products. However, REX does not require the mass balance to hold - this is very useful for cellular systems, where byproducts are not often considered in the reactions. Reaction Types This view is not shown by default. You can visualise it by clicking on the Reaction Types tab. This is a documentation-only view, similar to the Compound Types. Here, you may add the type of reactions that are used in the project. If this reaction set becomes part of the Library, this allows the chemist to search for reactions based on reaction types. The Reactions Types grid is organized in two columns: The Type column is the name of the reaction type, new types may be added here. The types added here then become available for selection in the Reactions Grid. The Notes column is a text field (maximum 50 characters) used to store comments about the reactions types. Top of Topic Actions Add Reaction Delete Marked Copy Marked Quick Run Open Solver Add Reaction This action is used to add multiple reactions to the project. In the parameters dialog, enter the number of reactions (N) you wish to add, and the optional reaction type. REX then generates reactions with names r1 through rN of the specified type. Delete Marked This action is used to delete more than one reaction at the same time. Select the reactions you wish to delete by checking the Mark column for these reactions. Execute the Delete Marked action. Copy Marked This action is used to copy more than one reaction at the same time. Select the reactions you wish to copy by checking the Mark column for these reactions. Execute the Copy Marked action. Top of Topic See Also: Project Explorer Chemistry Reactions - Properties

Reactions

This grid displays the list of reactions with their overall properties which are organized in columns as explained below:

The Include column is useful to include/uninclude a reaction in the model. Unincluded reactions are not shown in other nodes, and are ignored for modeling purposes. By default, any new reaction is included.
The Reaction column denotes the name of the reaction. The reaction can be renamed by editing this field.
The Equation column(read-only) displays the reaction equation, which is generated automatically based on the entries in the Stoichiometry Reaction: Reaction Name grid. The equations cannot be written directly.
The Type column (Optional) is used to specify the reactions type. The type is chosen from a drop-list of available types within the project. The available types in the project are shown in the Types grid. Types have to be first added into this grid, before they are available in the drop list in the Reactions grid.
The Quasi Equilibrium column is used to define the reactions that are assumed to be at equilibrium.
This option is useful when modeling reaction systems in which there are some reversible reactions, whose forward and reverse rates are much greater than the overall rate of the reactions of interest. When this occurs, these reversible reactions can be considered to be equilibriated. This is called the quasi-equilibrium approximation. In reality, the estimation of the forward and reverse rate constants of these quasi-equilibrium reactions is nearly impossible from experimental data. We may only estimate the equilibrium constant for these reactions. Therefore, in Estimation mode, when a reaction is specified as quasi-equilibriated, REX automatically fixes the reverse reaction parameters for the reaction at its provided value. So, the equilibrium constant is estimated by only varying the forward rate parameters.
You may explore the example to learn more about the application of the quasi-equilibrium approximation.
The Notes column (Optional) is a text field (maximum 50 characters) used to store comments about the reactions.
The Mark column is used to mark a series of reactions for actions such as Delete Marked and Copy Marked

Adding a Reaction

You may add a Reaction by any of these procedures:

Directly: You may add a new reaction by going to the last row and entering the name of the desired reaction. The row will change to edit mode, and you can save this reaction with the <ENTER> key or by clicking on the pencil icon in the row header. This only enters the reaction name. The stoichiometry for this reaction then has to be added in the Stoichiometry Reaction grid, where you may select the compounds and add the stoichiometric coefficients.
By executing the Add Reaction action.

Example: Adding a Reaction Directly

Deleting a Reaction

A reaction may be deleted by selecting the reaction row and using the <DELETE> key. Note that deleting a reaction only removes the reaction from the project without affecting the compounds.

Stoichiometry

The Stoichiometry grid depends on the Reactions grid and is used to enter the stoichiometric coefficients for each reaction. You may add the reaction stoichiometry by going to the compound column and selecting the compounds that participate in the reaction and entering their coefficients in the coefficient column. The row will change to edit mode, and you can save this reaction with the <ENTER> key or by clicking on the pencil icon in the row header. Reactants should be entered with negative coefficients and products should be entered with positive coefficients. Consistency of the reaction stoichiometry can be checked in the Check Atom Balance node, provided that the formula for the compounds is loaded in the Formula node. This Check Atom Balance feature is not available when mass units (Mass Density) are used for Concentrations in the Units Configurations node.

Note:
When Mass Density is used as units of concentrations, the stoichiometric coefficients are related to mass and not moles.
For example, methane combustion in molar terms is: CH₄ + 2O₂ → CO₂ + 2H₂O. However when dealing with mass, that reaction must be modified taking into account the molecular weights so it should be written as: 16CH₄ + 64O₂ → 44CO₂ + 36H₂O. When working with Mass Density, mass balance would require that the sum of the stoichiometric coefficients for the reactants is the same as the sum of coefficients of products. However, REX does not require the mass balance to hold - this is very useful for cellular systems, where byproducts are not often considered in the reactions.

Reaction Types

This view is not shown by default. You can visualise it by clicking on the Reaction Types tab. This is a documentation-only view, similar to the Compound Types. Here, you may add the type of reactions that are used in the project. If this reaction set becomes part of the Library, this allows the chemist to search for reactions based on reaction types. The Reactions Types grid is organized in two columns:

The Type column is the name of the reaction type, new types may be added here. The types added here then become available for selection in the Reactions Grid.
The Notes column is a text field (maximum 50 characters) used to store comments about the reactions types.

Reactions »