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HW Assignment for Math 636 This page will give a complete listing of the reading and homework assignments that you are required to do. Some problems will be worked in WeBWorK. Instructions for logging into WeBWorK can be found at Logging into WeBWorK. Week 89: Read the material in the
lecture notes for Diabetes Modeling (4Panel). Other references include the articles of Gatewood, Ackerman, Rosevear, and Molnar and Mahaffy and Keshet. Week 1011: Lecture notes for Markov Chain Monte Carlo (4Panel) are being developed. Old notes are available for Monte Carlo simulations, Stochastic simulations, and Stochastic birth only process. There are a few MatLab programs that were used in lecture for Monte Carlo simulations (and one additional one mentioned). 1. Population decay (pop.m and Mpop.m). 2. Integration (mcint.m and g.m). 3. Computing Pi. 4. Game of craps. (craps.m and dice.m). The link to the video for the Disney film Our Friend the Atom for a chain reaction with mousetraps and the mousetrap MatLab code simulating the stochastic model for this movie. The original article by Schmitz and Kwak on the Deaconess Hospital simulation is available. Week 12: Lectures continue on stochastic processes. There are lecture notes for Stochastic Modeling (4Panel) (very incomplete). Additional references for the Stochastic simulations notes are found in the work by Gillespie in 1977. The Gillespie algorithm is valuable for studying biological systems with smaller numbers of molecules. A good example is a bifurcation study by Arkin, Ross, and McAdams (1998) on the lysogeniclytic switch in Phage Lambda infections of E. coli. There are lecture notes for Leslie Models. There are additional references on this topic about Loggerhead turtles and Semalparous organisms (and other articles by Cushing). Old Homework Assignments Week 1: You should familiarize yourself with this webpage and how to navigate the different sections. This will be a key page where I post Reading and Homework assignments. The dates for when those assignments are due will also be listed here. We will use a variety of computer programs, but primarily MatLab and Maple. MatLab can be downloaded from SDSU. Maple is available for purchase through the Maple Adoption program. All these programs are available in our computer labs. Read the lecture notes for Introduction (4Panel) and Linear and Polynomial Modeling (4Panel).
Week 2: Read the lecture notes on Allometric
and Dimensional Analysis (4Panel). There
is additional information in article for Atomic
Bomb Energy Part 1 and Part
2. Also, there is information on food energy and weight (Kleiber's Law) and the relation to pulse and weight (von Bertalanffy). You should begin finding an article in the Proceedings of the National Academy of Sciences (PNAS) from the last 5 years. You need to submit to me the title of the article, list of authors, volume number, and year by Tues. Sept. 12. A list of PNAS articles selected by the class will be regularly updated, and each student must choose a different article. You will write a 25 page review that summarizes the work done and discusses some mathematical modeling aspect in the article. I am primarily looking for good scientific writing and an understanding of the role of modeling in your article. Your review will be due Thurs. Sept. 28. Week 3: Reading the material
in the lecture notes under U. S. Population (4Panel) and Discrete Dynamical Models (4Panel). The link to the Lectures has a collection of MatLab files used to solve problems in these notes. You may use any software for your homework, but document what you use. Week 4: Read the material in the
lecture notes for the SIR Model for Influenza (4Panel).
Also, begin reading the material for population modeling with
differential equations. The lecture notes include Continuous models: Yeast data
and Malthusian growth (4Panel). Week 5: Read the material for population modeling with
differential equations. The lecture notes include Continuous models: Yeast data
and Malthusian growth (4Panel)
and Continuous models: Competition Model (4Panel). Week 6: Read the material in the
lecture notes for Continuous models: Competition Model (4Panel). Week 7: Read the material in the
lecture notes for Lotka Volterra models (4Panel) and Bifurcation Studies (4Panel). Highly recommended is the PBS American Experience on Rachel Carson, which helps explain the use of pesticides on the environment and her huge impact on both the environmental movement and the awareness of women in science. (Peanuts and link.)
For questions concerning the webpage contact Joseph Mahaffy.


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