Biomolecular Kinetics and Cellular Dynamics (BE.420J)

Syllabus

Course Meeting Times

Lectures: 2 sessions / week, 1.5 hours / session

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, NY: Oxford University Press, 1995. ISBN: 9780195106633.

Supplemental Texts

Hammes, Gordon G. Thermodynamics and Kinetics for the Biological Sciences. Hoboken, NJ: John Wiley and Sons, 2000. ISBN: 9780471374916.

Creighton, Thomas E. Proteins: Structures and Molecular Properties. 2nd ed. New York, NY: W.H. Freeman and Company, 1993. ISBN: 9780716723172.

Bailey, James, and David F. Ollis. Biochemical Engineering Fundamentals. 2nd ed. New York, NY: McGraw Hill Higher Education, 1986. ISBN: 9780070032125.

Steinfeld, Jeffrey I., J. S. Francisco, and W. L. Hase. Chemical Kinetics and Dynamics. 2nd ed. E. Upper Saddle River, NJ: Prentice Hall PTR, 1998. ISBN: 9780137371235.

Cantor, Charles R., and Paul R. Schimmel. Biophysical Chemistry. New York, NY: W.H. Freeman, 1980. ISBN: 9780716711889, ISBN: 9780716711902, and ISBN: 9780716711926.

Blanch, Harvey W., and D. S. Clark, eds. Biochemical Engineering. Boca Raton, FL: CRC, 1997. ISBN: 9780824700997.

Shargel, Leon, et al. Applied Biopharmaceutics and Pharmacokinetics. New York, NY: McGraw-Hill Professional Publishing, 2004. ISBN: 9780071375504.

Carberry, James J. Chemical and Catalytic Reaction Engineering. New York, NY: McGraw-Hill, 1976. ISBN: 9780070097902.

Strogatz, Steven H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering. Cambridge, MA: Perseus Publishing, 2001. ISBN: 9780738204536.

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

• 2 papers presented and discussed per class meeting (additional background papers may be provided).
• Each paper will be presented in 2 parts of roughly equivalent length.
  1. Biological background and model formulation
     • Key terms and simplified basic concepts of the relevant biology (scanned figures from basic textbooks might help).
     • Open questions in the field.
     • Potential technological and/or biomedical applications.
     • Present a schematic cartoon of the essential components of the model.
     • Highlight and discuss the model equations, origin of each term, and reason for rejection of alternative forms.
     • Experimental basis of parameter estimates or regression fits.
     • Method of solution, analytical or numerical.
  2. Model results and their interpretation
     • Critical presentation of the model outcomes.
     • Consistency with available experimental data.
     • Testable predictions.
• Two students will prepare to present each section above, and will make a joint presentation together.

Grading

activities	percentages
Homework	50%
Final (Finals Week)	30%
Class Participation	20%