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Unformatted text preview: MIT 20.181 Module 3 Class 4 notes (DRAFT) 29 November 2006 Exact Methods for Computing Biological System Dynamics Drew Endy ( http://mit.edu/endy/ ) Goals Covered Last Time E. Review how the physics model leads to computational method F. What is the complete computational method? Goals for Today G. What is the difference between a reaction rate and a reaction propensity? H. How can we make this stuff compute faster? 55. What is the difference between a reaction rate and a reaction propensity? Most folks think about and use continuous, approximate methods. Thus, most descrip tions (models) of biological systems use continuous rate constants to describe reaction kinetics. Can we convert from continuous reaction rate constants to reaction propensi ties? Yes. The key is to look at the units of the constants. Consider the following system: A <> B+C A > B+C, with rate k off = 1/time B+C > A, with rate k on = 0.6E9/molar/time k off is a firstorder reaction, whose rate is equivalent to the chance that an individual re action event will take place, c . k on is a secondorder reaction. Here, the units don t match. We need to convert from 1/molar/second to 1/#/time. Molar has units of moles per volume. So, the units of k on are 1/(moles/volume)/time. We can convert this to 1/#/time by multiplying the denomi nator by the (numbers of molecules / mole) and the volume of the system....
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This note was uploaded on 11/11/2011 for the course BIO 20.010j taught by Professor Lindagriffith during the Spring '06 term at MIT.
 Spring '06
 LindaGriffith

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