physics.davidliao.com

Q: Why do we care about functions?

A: Physical concepts are relationships between experimentally measurable quantities. By introducing the concept of a "function" we can be more precise about what we mean by "relationship." Describing specific examples of relationships can often be involved and time-consuming. The concept of a function lets us assign short names by which we can efficiently refer to particular discussions of quantitative relationships, which include specification of the contexts in which these relationships are described.

If you are participating in the PIBS BP 219 course, please contact David Liao for a password for the online course materials. Go to course page (password required).

The following three definitions are all labeled "winner takes all." This erratum is relevant to some PSOC-related tutorials, animated population dynamics tutorial slides, and a tutorial appendix in the dissertation. Thanks to Qiucen Zhang for valuable conversations.

Non-Poissonian variance in the number of variants per plate can occur when mutants arise at a time before application of selection pressure. Spontaneous mutation can also generate variance, not only because the mutants arise early, but because they arise at a variety of early times, all preceding application of selection. Feedback and interaction effects limit the generalizability of these statements.

Useful slides from Matthias Heymann, Bioinformatics Learning and Study Session (NYU 2003 Oct 15) http://www.bioinformatics.nyu.edu/BLISS/HeymannSlides.ppt

Exam Committee: Robert H. Austin (advisor), Kirk McDonald, and Suzanne Staggs
Degree date: 2010 November

Traditional cancer research has hunted for "the" crucial mutations alleged to unleash "rogue" cells. The Princeton Physical Sciences-Oncology Center (PS-OC) is one of twelve National Cancer Institute centers looking for new perspectives to address the imprecision of prognosis and the evolution of drug resistance that remain concerns in current research. One emerging perspective is that cancer is not merely a "disease of the genes," but also a product of cell-cell interactions and cell-microenvironment interactions. A complementary perspective is that malignant behaviors are not constructed "from scratch," but rather are throwbacks to phenotypes that beneted early multi-cellular populations before being suppressed to allow the evolution of more recent multi-cellular organisms. Thus, simpler microorganisms might model multi-cellular behaviors relevant to cancer. One thrust distinguishing Princeton's PS-OC is the use of E. coli bacteria in microfabricated structures as a model for mammalian cell populations.

In this thesis, we model cell-environment and cell-cell interactions in E. coli in microfabricated devices.

Hamish Johnston, "Bacteria band together to beat the system," physicsworld.com, Institute of Physics, 2010 May 5. http://physicsworld.com/cws/article/news/42541

See the original article: http://prl.aps.org/abstract/PRL/v104/i16/e168102

This page contains links to computer demonstrations related to the four topics in the population dynamics tutorial. Source code for some of these demonstrations can be used to identify ways to write custom simulation scripts. The content is solely the responsibility of David Liao and does not necessarily represent the official views of the National Cancer Institute or the National Institutes of Health.

You can use these files to demonstrate the spatial games of Nowak and May using MatLab.

Nowak and May, "Evolutionary games and spatial chaos," Nature 359: 826--829 (1992).