Time and place:
MWF 3rd Period (9:35-10:25), LIT 305.
Instructor:
Patrick De Leenheer
Office: 411 Little Hall
Office Hours: MWF 5th Period (11:45-12:35) or by appointment.
Email: deleenhe@ufl.edu
URL: www.math.ufl.edu/~deleenhe
Prerequisites:
Differential Equations and some analysis.
Text:
There is no required textbook. Copies will be distributed.
Course Objectives:
The purpose of this course is to make students competent at and confident about reading
research papers in the area of mathematical biology. Upon completion of this course, students should
be ready to start doing research in this discipline.
We will study several
examples from the recent biomolecular literature, both from a biological and a
mathematical perspective, with emphasis on the latter. Students will be reading these
papers in preparation for class, and we will discuss them during the class period, and they
Occasionally, students will be asked to present some of the material to the rest of the class.
Topics:
We will start with proving the zero deficiency theorem, a classical result concerning
chemical reaction kinetics. After that we will turn to the repressilator, a gene
network with usually 3 (but more generally an arbitrary number) of genes that repress each other
in a cyclic way. For now, I don't know yet what will come next.
(possible topics are circadian rhythms, pattern formation, stochastic biomolecular networks)
Some of the models -certainly those in the beginning- will be nonlinear ordinary differential
equation models, and we will focus in particular on the analysis of their asymptotic behavior. This requires some tools from
the area of dynamical systems, but also frequently from linear algebra, basic graph theory, analysis etc.
Later on in the course we might turn to stochastic models and/or PDE models. No particular prerequisites
will be assumed for this material, although you should expect to be flexible as you will use several
-reasonably basic- techniques from several branches of applied mathematics.
Grading:
Course grades will be completely determined by your class participation.
Grading Scale (maximum of 100%):
A: [>=85%] B+: [76-84%] B: [70-75%] C+: [65-69%] C: [60-64%] D+: [55-59%] D: [50-54%] E: [<50%]
University policy on accommodations for students with
disabilities:
"Students requesting classroom accommodation must first register with
the Dean of Students Office. The Dean of Students Office will provide
documentation to the student who must then provide this documentation
to the Instructor when requesting accommodation."