# IGEM:IMPERIAL/2006/project/Oscillator/project browser/Test Sensing Predator Construct/Modelling

### From OpenWetWare

Super Parts | Predator Construct | |||
---|---|---|---|---|

Actual Part | ||||

Sub Parts | <bbpart>R0062</bbpart> | <bbpart>B0034</bbpart> | <bbpart>C0062</bbpart> | <bbpart>I13504</bbpart> |

- Specifications
- Design
**Modelling**- Implementation
- Testing/Validation

## Model assumptions and relevance

- General assumptions on gene expression modelling:
- Quasi-steady state hypothesis on mRNA expression.
- Gene activation can be approximated by Hill equations.

- Assumptions linked to the quorum sensing:
- As a first approximation, we assume that luxR and AHL molecules form a heterodimer (even if it has been found that the complex formed is more complicated).
- The degradation rate of luxR and aiiA is mainly due to the growth dilution.

## Model description of the oscillator

**Full derivation of the above equations.**

## Model description of the growth of the predator

- mathematical description of the predator growth and death:

- insert a graphical representation if possible (e.g. CellDesigner display)
- link to SBML file or matlab.

## Model variables and parameters for the growth of the predator

(list all the variables and parameters of the model in a table, specifying if their values are known, unknown, to be measured.)

Variables
| ||||

Name | Description | Initial Value | Confidence | Reference |
---|---|---|---|---|

AHL | homoserine lactone acting as the prey-molecule | 0 | depends how good is the control of the prey positive feedback | links |

luxR | molecule acting as the sensing module for the predator | 0 | to be measured as we might have to deal with some leakage of the promoter | links |

aiiA | molecule acting as the killing module of the prey for the predator | 0 | to be measured as we might have to deal with some leakage of the promoter | links |

Parameters
| ||||

Name | Description | Value | Confidence | Reference |
---|---|---|---|---|

c | maximum synthesis rate of the pLux promoter | to be characterized | to be measured | links |

c0 | dissociation constant according to Hill eq | to be characterized | to be measured | links |

gd | growth dilution | to be characterized | to be measured | links |

## Characterization

- Parameters c & c0 for characterization have to be extracted.
- gd[luxR] and gd[aiiA] can be controlled by the chemostat.