### 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.
- 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.

- Model results and their interpretation
- Critical presentation of the model outcomes.
- Consistency with available experimental data.
- Testable predictions.

- Biological background and model formulation
- 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% |