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Unformatted text preview: MIT 20.181 Module 3 Class 1 notes (DRAFT) 20 November 2006 Exact Methods for Computing Biological System Dynamics Drew Endy ( http://mit.edu/endy/ ) Goals for Today A. When to use computational methods? B. When to use exact methods? C. What is the underlying physics models used by exact methods? Introduction 1. Biological systems exist through time. So far in 20. 181 you ’ ve developed an under standing of computational methods for representing the behavior of biological systems on long time scales (e.g., evolution) and very short or instantaneous time scales (e.g., protein structure). 2. Here, we ’ re going to think about the behavior of biological systems on the timescale of an individual, and the computational methods that can be used to represent their be havior. 3. Such computational methods are useful for both analysis and design of systems. For example, given a model of an existing biological system, and a description of its current state, you can compute the expected future behavior (i.e., transitions from state to state) of the system. Similarly, given a speci¡cation of the desired behavior for some notional biological system, you can compute the behavior of possible biological systems, helping to select a design that encodes the desired solution. 4. Now, before we get too caught up in “biological systems” this and that, let me state directly that there ’ s nothing magical about the methods that we ’ ll develop. In fact, you ’ ll see that they are based on computational methods that were developed for simple chemical and physical systems. Whether or not such methods accurately depict the in ner workings of biological systems is a topic that you should think about! 5. Let ’ s consider an extraordinarily simple system, one involving ¡rstorder decay. A system containing molecule A decays into oblivion (below). MIT 20.181 Module 3 Class 1 notes (DRAFT) 20 November 2006 6. How will this system behave over time? Develop model for exponential decay based on classical chemical kinetics....
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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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