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You can start with deterministic model using ODEs for reaction rates. However, if you are considering diffusion then you would have to use Partial differential equations for Fick's diffusion law. You can, however, assume that there is no "diffusion" but just transport of the signal molecule from a well mixed system (medium) to another well mixed system ...


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This is a general answer for all three of your related questions: This one How does Temperature influences the rate of protein turnover? How is the rate of transcription influenced by temperature? Since you said: I want to simulate the evolution of genetic architecture when after a sudden change in temperature or in an environment that is ...



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