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SimCell Help

1. Introduction
2. Create
    2.1 Objects
  2.1.1 Membrane
  2.1.2 DNA
  2.1.3 Gene
  2.1.4 Protein
  2.1.5 Membrane Protein
  2.1.6 Small Molecule
    2.2 Interactions
  2.2.1 Transport
  2.2.2 Bind and Stick
  2.2.3 Touch and Go
    2.3 Others
3. Menu
  2.1.1 File
  2.1.2 Edit
  2.1.3 Run
  2.1.4 Help
4. Simulator
    4.1 Screenshot
    4.2 Graph
    4.3 Region Graphing

 

Interactions

Molecular interactions within cells can also be described in a relatively simple, straight forward manner.  Specifically, there are 3 major types of pair wise interactions.  Any two molecules or molecular entities may bind and stick, touch and go, or be directionally transported.  Molecules that bind and stick have association and dissociation constants or on/off probabilities and rates.  Many protein receptors, DNA binding proteins, catabolic repressors and gene activators will bind and stick to a target molecule.  Under the SimCell rules, molecules that bind and stick with each other must necessarily transform themselves into a new entity (a third molecule) or, in the case of DNA binding, lead to changes in the creation or transcription rate of a third molecule.  In contrast to bind and stick interactions, non-interacting molecules will typically touch and go (bump), always leaving each other.  However, some touch and go operations do lead to a molecular transformation, particularly when we consider enzymes such as metabolic enzymes, nucleases or proteases.  While enzymatic catalysis technically involves some binding, given the time step used in our mesoscale simulations (1 ms), catalysis is, for all intents and purposes, instantaneous.  In these enzymatic touch and go operations, two objects will meet leaving one object in tact and one transformed.  Finally, in transport operations an object (usually a small molecule) is taken and almost instantaneously (< 1 microsecond) moved across a barrier (usually a membrane).  This is specialized case of touch and go, but with the requirement that the movement of the substrate is directional – not random.  

These three interaction scenarios and their corresponding interaction consequences can be summarized as follows.  Bind and stick interactions lead to either the generation of a new molecule type, with new properties, the enhanced transcription of one or more protein/RNA molecules, or the repressed transcription of one or more protein/RNA molecules.  Touch and go interactions lead to either no change, elimination of a target molecule or transformation of a target molecule to one having new properties. Transport leads to unidirectional movement across a barrier, bidirectional movement across a barrier or unidirectional movement across a barrier with a concomitant transformation of the target. 


To create a Interaction, select the Interaction Button.



On the Drawing Panel, with the Mouse - click, drag and release to form a line with double ended arrows between 2 Objects. An Interaction Information Window should appear if you were successful.

With the allowable rules stated in the Overview, certain objects are restricted from certain interactions so not all options will be available among 2 objects.

Transport


To form a Transport Interaction, Select the Transport Radio Button. This will spawn an additional panel with more radio buttons to the Right. On the panel to the Right, you have the choice of choosing: One Way (IN), One Way (OUT), Both Ways.
 

Interaction Types Description
One Way (Into the Membrane) Allows Movement of the Object into the Membrane via the Membrane Protein
One Way (Out of the Membrane) Allows Movement of the Object out of the Membrane via the Membrane Protein
Both Ways (In and Out of the Membrane) Allows the Object to move bidirectionally inside and outside of the the Membrane via the Membrane Protein




 

Bind and Stick


To form a Bind and Stick Interaction, Select the Bind and Stick Radio Button. This will spawn 2 additional panels, to the Right and to the South. On the panel to the Right, you can change the probability that a collision between the 2 objects will form an interaction and the affinity value at which the binding molecule will remain binded. To the South of the panel, you can have this Interaction result in an increase transcription by a factor (which can be entered on the panel to the right) or result in a decrease the transcription by a factor (which can be entered on the panel to the right) or result in a creation of a new molecule of a protein (which can be selected from the pull down menu to the right).

The Consequence Panels all the way at the bottom allow the user to determine what happens to each of the colliding molecules. Whether they will disappear or nothing happens for the Bind and Stick interaction.


 

Touch and Go


To form a Touch and Go Interaction, Select the Touch and Go Radio Button. On the panel to the Right, you can change the probability that a collision between the 2 objects will result in a specified consequence for an interaction.

The Consequence Panels all the way at the bottom allows the user to determine what will happen to each of the colliding molecules. Whether they will disappear, nothing or they will be converted into another molecule for the Touch and Go interaction. NOTE: The Disappears consequence takes precedence over any Converts option. So if one of the reacting molecules is set to disappear, then even if the other is set to convert to another molecule, the conversion will not happen.