Course Description
In this course you will learn to construct kinetic and equilibrium mathematical models of biomolecular interactions, and apply these quantitative analyses to biological problems across a wide range of levels of organization, from individual molecular interactions to populations of cells.
Textbook
Lauffenburger, Douglas A., and J. Jennifer Linderman. Receptors: Models for Binding, Trafficking, and Signaling. New York: Oxford University Press, 1996. ISBN: 0195106636.
Supplemental Texts
Hammes, Gordon G. Thermodynamics and Kinetics for the Biological Sciences. Hoboken, NJ: John Wiley and Sons, 2000. ISBN: 0471374911.
Creighton, Thomas E. Proteins: Structures and Molecular Properties. 2nd ed. New York, NY: W. H. Freeman and Company, 1993. ISBN: 0716723174.
Bailey, James, and David F. Ollis. Biochemical Engineering Fundamentals. 2nd ed. Burr Ridge, IL: McGraw Hill Higher Education, 1986. ISBN: 0070032122.
Steinfeld, Jeffrey I., J. S. Francisco, and W. L. Hase. Chemical Kinetics and Dynamics. 2nd ed. E. Rutherford, NJ: Prentice Hall PTR, 1998. ISBN: 0137371233.
Cantor, Charles R., and Paul R. Schimmel. Biophysical Chemistry. New York, NY: Worth Publishers, 1980. ISBN: 0716711885, 0716711907, 0716711923.
Blanch, Harvey W., and D. S. Clark, eds. Biochemical Engineering. New York, NY: Marcel Dekker, 1997. ISBN: 0824700996.
Shargel, Leon, et al. Applied Biopharmaceutics and Pharmacokinetics. New York, NY: McGraw-Hill Professional Publishing, 2004. ISBN: 0071375503.
Carberry, James J. Chemical and Catalytic Reaction Engineering. New York, NY: McGraw-Hill, 1976. ISBN: 0070097909.
Strogatz, Steven H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering. Cambridge, MA: Perseus Publishing, 2000. ISBN: 0738204536.
Assignments
There will be a total of twelve assignments. Initial homework assignments will focus on mathematical modeling and concepts covered in class, including some work in MATLAB®. Later assignments will consist of more involved work in MATLAB®, implementing models described in assigned papers from the literature.
Grading Scale for Model Implementations (PDF)
Literature Paper Presentations and Discussion
Format
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2 papers presented and discussed per class meeting (additional background papers may be provided).
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Each paper will be presented in 2 parts of roughly equivalent length.
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Biological background and model formulation
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Key terms and simplified basic concepts of the relevant biology (scanned figures from basic textbooks might help).
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Open questions in the field.
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Potential technological and/or biomedical applications.
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Present a schematic cartoon of the essential components of the model.
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Highlight and discuss the model equations, origin of each term, and reason for rejection of alternative forms.
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Experimental basis of parameter estimates or regression fits.
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Method of solution, analytical or numerical.
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Model results and their interpretation
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Two students will prepare to present each section above, and will make a joint presentation together.
Grading
Homework |
50% |
Final (Finals Week) |
30% |
Class Participation |
20% |