In Fall 2010 I taught a new course on modeling methods in systems and synthetic biology: CBE 480A1: Kinetics of Biomolecular and Cellular Systems. This a course I am really excited by!! Here is the course description. Contact me if you want more details. I hope to be teaching this in Spring 2013, so consider taking it!

Course Description: This course is meant for senior undergraduate students and graduate students who are interested in the intersection of the biological sciences with the physical sciences. The philosophy of this course is that what makes biology different from the rest of the inanimate world is what’s increasingly referred to as ‘complexity’. Complexity means many things, but in the specific context which we will be studying in the cell, it means that biological systems are characterized by self-assembled networks of biochemical reactions that are organized in space and time, that are responsible for the cellular functions and behavior. The cell has a lot of interesting stuff going on that can be studied by physical scientists, such as for example the transport properties of proteins, the way proteins or molecular motors work, to give just two examples. Here we are asking a different set of questions. We are asking how these different parts come together to create the biological organism. We are very far from being able to answer this question in any generality. So in this course we will see that we are asking an even simpler question: how do these parts come together to give us an understanding of a specific response of an organism to a change in the system. In particular we ask how the cell is able to carry out some of their functional responses. For example, bacterial and mammalian cells undergo chemotaxis. But chemotaxis involves some rudimentary information processing. How do biological networks process information and how does that information processing lead to a cellular decision is the kind of question that we ask.

In the first part of the course we will look at really small systems and try to understand the consequences of nonlinearity. If we are looking for key terms that make up what I’ve called complexity, non-linearity is among the top on the list. What we’ll find is that nonlinear biochemical networks display fascinating and non-trivial behavior that has important biological consequences. We’ll then go on to look at noise in biochemical networks and how biological systems work in the presence of noise and even make use of noise. We’ll then analyze biochemical network in another way, in terms of overall structure and in terms of small functional units. In the process we’ll also encounter fascinating discussions on whether biological systems are robust, what robustness means, whether evolution is an optimizer etc etc. We’ll then look at some ways of dealing with much larger networks. This is a practical proposition for the biochemical networks that are involved in metabolism. Finally we’ll briefly discuss the buzz about the whole field of ‘omics’ and what it means.
Thus this course will provide an in-depth analysis of the systems approach to biology at the molecular and the cellular scales. Biological case studies include examination of the lac operon, lysis-lysogeny in phage infected bacteria, competence in B. subtillis, chemotaxis, differentiation of stem cells, the MAP kinase cascade in mammalian cells, circadian oscillations in biology etc.

In Fall 2011 I taught CBE331 which is a fluids mechanics course for CBE juniors!

In Spring 2012 I am teaching CBE 503 which is an advanced transport phenomena course for CBE graduate students.