Our paradigm for the course is modeling interesting phenomena in molecular biology or chemistry using mathematical tools.  We will examine several topics in detail, beginning with stereochemical topology.  We will further explore topics, such as global radius of curvature and DNA supercoiling, at a level that depends on the interests and experience of the students enrolled.

Students should have some sophistication in both mathematics and the life sciences.

You might also find useful the following (in order of increasing sophistication), any of which you’re welcome to browse through during my office hours.

The Knot Book, by Colin Adams
DNA Topology, by A. D. Bates and A. Maxwell
Knot Theory and its Applications, by K. Murasugi
Topology:  A First Course, by J. R. Munkres
Knots and Links, by D. Rolfsen

Molecular Biology of the Cell, Fourth Edition, by Alberts et al
Sterochemistry of Organic Componds, by Eliel and Wilen
Basic Organic Sterochemistry, by Eliel, Wilenand, and Doyle

You may  browse any of these books in my office during office hours.

Each weekly class session will be divided into two segments.  One part will be a traditional lecture that highlights some of the current week’s reading.  The other part will be a combination of discussion and/or student presentation.  There will be a brief break in between for caffeine/glucose intake.

There will be weekly readings, which are a combination of texts and articles.  You will be graded on your participation (10% of your final grade) during our weekly discussions of this material.  You will have weekly homework, (25% of your final grade) that you may work on with others, but must turn in on your own.  Homework is due at the beginning of each class period, and will never be accepted late. To allow for sickness, emergencies, etc, your lowest homework score will be dropped from the average.   You will give at least two in-class presentations on material relevant to our class (15% of your final grade).  You will have a midterm, on topological stereochemistry (25% of your final grade). You will also have a final group project, (25% of your final grade), which will be an opportunity to study in greater depth, and subsequently model, a biological system of interest to your group. This could be an extension whose base was either a relevant seminar you attended, a discussion with a scientist on campus, or material from our class.  We will have a poster session of your projects during a class period and you (as a group) will turn in a written report (including references and non-technical introduction).

Some active researchers in the math/bio field include: Ned Seeman, Jon Simon, DeWitt Sumners, Lou Kauffman, Kurt Mislow, Dorothy Buck, and Corinne Cerf

• Knots, including Knot Tables, HOMFLY polynomials, and Knot Classification
• More Knot Theory, including a table of oriented links
• Practice your Ambient Isotopies