# Team:Michigan/Modeling

(Difference between revisions)
 Revision as of 22:49, 20 October 2009 (view source)â Older edit Revision as of 22:51, 20 October 2009 (view source)Newer edit â Line 7: Line 7: Cell Lysis happens when holin creates pores in membrane and lysozyme enters Cell Lysis happens when holin creates pores in membrane and lysozyme enters Assume rate of cell death â[holin](# cells), rate of cell growth in exponential phase Assume rate of cell death â[holin](# cells), rate of cell growth in exponential phase + [[Image:Equation1.jpg]] [[Image:Equation1.jpg]] == Transcription of Repressor: == == Transcription of Repressor: == + [[Image:Equation2.jpg]] [[Image:Equation2.jpg]] đ([đ]) is a function of toluene concentration đ([đ]) is a function of toluene concentration Use Hill Equation to describe binding affinity of toluene to Pu promoter. Use Hill Equation to describe binding affinity of toluene to Pu promoter. + [[Image:Equation3.jpg]] [[Image:Equation3.jpg]] Line 43: Line 46: ''Dimerization:'' ''Dimerization:'' Since holin and antiholin form a complex Since holin and antiholin form a complex + [[Image:Equation7.jpg]] [[Image:Equation7.jpg]] Using the translation rates and incorporating dimerization using the law of mass action, Using the translation rates and incorporating dimerization using the law of mass action, + [[Image:Equation8.jpg]] [[Image:Equation8.jpg]]

## Revision as of 22:51, 20 October 2009

HOME THE TEAM THE PROJECT MODELING REGISTRY PARTS NOTEBOOK SAFETY

## Cell Growth/Death

Cell Lysis happens when holin creates pores in membrane and lysozyme enters Assume rate of cell death â[holin](# cells), rate of cell growth in exponential phase

## Transcription of Repressor:

đ([đ]) is a function of toluene concentration

Use Hill Equation to describe binding affinity of toluene to Pu promoter.

## Transcription of Lysozyme and Holin:

Assume transcription rate is proportional to # of free operator sites (which should be the same for both lysozyme and holin, since they are downstream of the same promoter)

Assume transcription rates for H and L are the same

## Repression of Lysozyme and Holin Transcription

Repressor binds with free operator site, preventing transcription of lysozyme and holin. Use a model invoking law of mass action.

Assuming that fops and Rfops do not undergo spontaneous degradation.

## Production of Repressor

Using the translation rate for R and taking into consideration the binding of R with fops,

## Production of Proteins

Production of antiholin, under constitutive promoter, is at a constant rate ÎłA, which depends on the promoter that is used

Dimerization: Since holin and antiholin form a complex

Using the translation rates and incorporating dimerization using the law of mass action,

## Assumptions

Can set ÎłA equal to rate of production of holin in the case that all operating sites are free

• This is in order to balance antiholin and holin levels without repression
• This can be tuned so that timing of cell death works out
• Set antiholin production rate to that of holin in the absence of repression
• Put this through the transcription and translation equations to obtain production rate

Assume degradation rates of all mRNAs are the same

• Can directly search for these rates in literature
• Can use half life to calculate rate