Glossary


annotation
This is a section of text placed on a scheme diagram to provide explanatory information.
check box
One or more check boxes are provided for some program options to allow possible settings to be selected. None or all may be chosen in any combination.
clipboard
This is a location where reaction steps, transfer steps, compartments or transfer paths cut or copied from the reaction scheme are placed. Kinetiscope uses an internal clipboard to store these. The computer operating system has an independent clipboard that can hold text and bitmap-type images copied from Kinetiscope.
color map
a color map represents the values of a scalar parameter as a varying series of screen colors.
compartment
A compartment is a spatial element that has a finite volume. The volume may be explicitly defined by the user through the Compartment's geometry or may be inferred or assumed from the user-defined reaction conditions. A compartment is a container for reaction steps.
context menu
This provides a list of actions for a particular object. A context menu is accessed using a single click of the right mouse button while the mouse cursor is over the object.
data entry field
Dialog windows for data input have one or more spaces where numbers or text can be typed. These data entry fields become active when the cursor is placed on them.
deterministic
A deterministic simulation is one in which a system of equations is solved to predict the time history of a reacting system.
dial
This control indicates the current value of a parameter by the position of an index mark and allows that value to be changed by moving the index mark by rotation.
dialog
Also known as a dialog box or dialog window, a dialog is a small window that displays information that may be modified, or prompts for a response. Usually a dialog blocks other interaction with the program while it is displayed.
event
A simulation is carried out by selecting reaction steps from the reaction scheme, and updating the system. Each selection cycle is an event.
Fickian diffusion
a mass diffusion process where the rate of diffusion is proportional to a constant multiplied by the concentration gradient of the diffusing species.
list box
A set of names or lines of data are displayed in a list box so that one or more can be selected for actions such as data entry. There are three types of list boxes: single selection, where only one item can be selected at a time, multiple selection, where more than one item can be selected, and drop down, which shows only the currently selected item but is displayed in full when its button is pushed.
inductive
This is a method of reasoning which is commonly used to develop complex models. Experimental data are analyzed to extract a simple mechanism, which is then used to make specific predictions about the behavior of the system under different conditions. These predictions are compared to new experiments,which are used in turn to refine the model in an iterative way.
main window
The main window contains a collection of scheme windows and results windows created through actions on a main menu and a main tool bar.
message box
a small dialog window that queries the user or provides notification of an important event that requires attention. .
particle
A simulation system contains a number of particles used to represent molecules, atoms and pseudo-species which participate in the reaction scheme. Each particle is proportional to a concentration or an amount, depending on the reaction conditions selected.
periodic boundary conditions
This method allows a single unit cell of a large repeating structure to be accurately represented in a simulation.
profile
This is a list of time-value points which establishes an instantaneous value in a simulation. three types of profiles are used: temperature profiles, voltage profiles and external stimulus profiles.
pseudo-species
Simulations can be structured so that parts of molecules, or particular groups of molecules are followed in the mechanism, rather than actual molecules. These pseudo-species are useful devices for simplifying reaction schemes, or highlighting important features of a reaction.
push button
Push buttons located on dialog windows allow various actions to be chosen.
radio button
A set of radio buttons is used to represent several possible settings available for a particular program option. They are used when one, but only one, of the settings must be selected.
random number seed
This is a number between 1 and 32767 which is used to initiate a sequence of random numbers for selection of events in the simulation.
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 file.
reaction step
A reaction step defines a single chemical reaction in a mechanism, including the reactant and product species, their stoichiometries, the rate law and rate parameters.
results window
A results window displays a graphical representation of the results of a simulation.
scheme diagram
A scheme diagram displays in a symbolic graphical format all the compartments and transfer paths comprising a reaction scheme, and illustrates their interactions.
scheme window
A scheme window presents all the elements of a reaction scheme for viewing and editing. It contains multiple pages that group together related parameters.
scroll bar
A screen control element that allows you to scroll text or graphics for viewing even if it is larger than the window. The view is changed by dragging the slider bar.
slider
This control indicates the current value of a parameter by the position of a handle and allows that value to be changed by moving the handle.
species
This is a unique molecular entity identified with a single name or mnemonic throughout a reaction scheme.
spin box
A spin box displays one value from a set. Click the up and down arrows with the left mouse button to change the value displayed.
stochastic
The stochastic simulation is a probabilistic method for predicting the time evolution of a reacting system.
sub-menu
Selection of one of the menu names listed in the main window causes a list of options to appear beneath it. This list is a sub-menu.
temperature convergence standard
This is a parameter used in variable temperature calculations. When the temperature is updated, it is calculated iteratively from the enthalpy and temperature-dependent heat capacity of the system. The convergence standard is used to compare temperatures from two successive iterations. If their difference is less than the standard, the calculation has converged.
time step
This is the calculated time which elapses between two events in a simulation.
timebase
The timebase in a simulation is the time history of the events which are selected.
tool bar
A horizontal row of pushbuttons decorated with icon images that initiate actions on the window or dialog that contains the tool bar.
tool tip
a text box containing brief explanatory text. Tool tips are shown by hovering the mouse cursor over an object or control.
transfer path
This defines a connection between two compartments through which materials transport can occur. A transfer path is a container for transfer steps.
transfer step
A transfer step describes the transfer of a single chemical species between two compartments, including the species identity, the rate law and rate parameters.