Course Schedule for APC/MOL 360

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Schedule by Date
Unit 1: Population Dynamics
Unit 2: Chemical Reactions/Kinetics
Unit 3: Diffusion

Unit 4: Elective

 

 

Important Dates: 

 

Tentative Schedule

 

 

 

 

Week

Sections

 

(3/16)

MID-TERM

 

1

1.1-1.7

 

(3/28)

DECLARE ELECTIVE TOPIC

 

2

1.8, 4.1-4.2, PDE's

 

(~5/9)

PRESENTATIONS

 

3

PDE's, 4.3-4.4

 

??

FINAL EXAM

 

4

4.5-4.8, 5.1-5.2

 

 

 

 

5

5.3-5.6

 

 

 

 

6

chemical kinetics

 

 

 

 

7

5.8-5.10

 

 

 

 

8

probability, diffusion

 

 

 

 

9

6.1-6.4

 

 

 

 

10

6.5-6.8

 

 

 

 

11

model testing & likelihood

 

12

 PCA

 

Unit 1: Population Dynamics

Papers:

R.M. May.  Simple Mathematical Models with very Complicated Dynamics, Nature, Vol. 261, p. 459, 10 June 1976

(Note: Figures 2 & 3 should be reversed.)

H. Kierstead and L.B. Slobodkin. The Size of Water Masses Containing Plankton Blooms, Journal of Marine Research Vol. 12, 1953. pp 141-147

MATLAB files

difference1.m, logistic.m

Additional material:

Fourier Series tutorial (Mathematica file)

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Unit 2: Chemical Reactions/Kinetics

Paper:

A. Turing. The Chemical Basis of Morphogenesis, Philosophical Transactions of the Royal Society of London, (Series B, No.641, Vol. 237, 14 August 1952).

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Unit 3: Diffusion

Paper:

A. Einstein. On the Motion of Small Particles Suspended in Liquids at Rest Required by the Molecular-Kinetic Theory of Heat. Ann. Phys. Vol. 17, No. 549, 1905.

Matlab File:

random_walk1.m

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Unit 4: Elective

Papers on PCA/SVD:

M.E. Wall, A. Rechsteiner and L.M. Rocha. Singular value decomposition and principal component analysis In A Practical Approach to Microarray Data Analysis. D.P. Berrar, W. Dubitzky, M. Granzow, eds. pp. 91-109, Kluwer: Norwell, MA (2003). LANL LA-UR-02-4001.

E.G. Emberly, R. Mukhopadhyay, N.S. Wingreen and C. Tang. Flexibility of alpha-Helices: Results of a Statistical Analysis of Database Protein Structures . J. Mol. Biol. , Vol. 327, No. 1, pp 229-237. 2003.

O. Alter, P.O. Brown and D. Botstein.  Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling. Proc. Natl. Acad. Sci. USA, Vol. 97, pp 10101-10106, 2000.

Possible topics:

Choose a topic from the text not covered in class.

Neuroscience: How does a nerve work?

Neural networks: How do we make decisions?

Knots & DNA: Does nature really cut-and-paste?

Evolution: How long does it take for a mouse to evolve into an elephant?

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