drenm_lec5

drenm_lec5 - MIT 20.181 Module 3 Class 5 notes (DRAFT) 6...

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Unformatted text preview: MIT 20.181 Module 3 Class 5 notes (DRAFT) 6 December 2006 Exact Methods for Computing Biological System Dynamics Drew Endy ( http://mit.edu/endy/ ) Goals Covered Last Time G. What is the difference between a reaction rate and a reaction propensity? H. How can we make this stuff compute faster? Goals for Today I. How is reaction time updated w/o resampling? J. Back to the biology! What is this stuff good for? [Genetic Memory] 68. Summary of Next Reaction method s algorithm. 1a. Set initial numbers of molecules for all species, set time at zero, generate re- action dependancy graph. 1b. Compute a i for all reactions 1c. Compute reaction event times for all reactions via = (1/ a )*ln(1/ r ) 1d. Store a and values. 2. Find the reaction which will occur next. Carry out reaction and update time. 3a. Update a for any reaction whose substrate numbers have changed. 3b. Update times for any reaction whose a was updated (see 69 below)....
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drenm_lec5 - MIT 20.181 Module 3 Class 5 notes (DRAFT) 6...

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