Agent ID | Agent representation | Movement and/or transformation | Variable names within the code | Variable descriptions |
---|---|---|---|---|
Nuc | Cell nucleus | static | nuc_radius | Radius size around nucleus |
Mem | Cell membrane | static | radius lipid-density | Cell radius and position # of lipid agents |
Dl | Dl as initially transcribed | Dl moves towards Mem and converts to Dlm | delta-transcription-initial-rate | Chance that a single Dl will be produced |
Dlm | Dl associated with membrane | Dlm moves laterally from Mem to Mem Dlm converts Dlm’ | delta-transform-time | Time period before Dlm is converted to Dlm’ |
Dlm’ | Dl form that interacts with N from another cell | moves laterally from Mem to Mem Ages out | deltaAge | Time period a Dl will exist |
N | N as initially transcribed | N moves towards Mem and converts to Nm | notch-transcription-initial-rate | Chance that a single N will be produced |
Nm | N associated with membrane, interacts with Dl from another cell, cleaved | Nm moves laterally from Mem to Mem Nm converts to Nc when across from Dlm’ on another cell |  |  |
Nc | Cleaved N moves from cell membrane to nucleus | Nc converts to Nn when it reaches the nucleus | notch-cleave-transport | Sets randomness, direction and time frame of movement |
Nn | Nuclear form of N, transcription factor | Ages out Alters N transcription Alters Dl transcription | notchAge cleaved-nuc-notchcount | Time period a N will exist Alters N and Dl initial transcription rates |