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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 first-order reaction, whose rate is equivalent to the chance that an individual re- action event will take place, c . k on is a second-order 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