Lately we've been working on our new computer simulation model of USS evolution.
I asked my favourite mathematical colleague about how to model mutation so that (1) transitions occurred at a different frequency than transversions, and (2) a desired base composition was maintained. She whipped out Wen-Hsiung Li's Molecular Evolution book and opened it to a page of equations describing various mathematical models of mutation that can be used to infer the evolutionary history of DNA sequences. These models include up to five different parameters (5 different Greek letters!), depending on how many independent factors are included in the model.
The equations accomplish the reverse of what we want, but she confidently offered to solve the most appropriate equations for us in a way that would let us use the desired final base composition of our sequence to calculate the values of the mutation parameters our program, and within 30 minutes she'd emailed the solutions to me. I think she used a program called Mathematica rather than mysterious mathematical superpowers to get the solutions. I still have to work through what she's sent, to see how our program will best use it.
p.s. The cells are once again growing normally in new batches of our usual medium. Unfortunately we still don't know the cause(s) of our recent problems.
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