Georgia Institute of Technology College of Sciences

The expression dynamics of interacting genes depends on the topology of the regulatory network, the quantitative nature of feedbacks and interactions between DNA, RNA and proteins, and the biochemical state of the intracellular and surrounding environment. In this talk we show that dynamics of a gene regulatory network can also depend sensitively on the copy number of genes and promoters. Genetic regulatory networks include an overrepresentation of subgraphs commonly known as network motifs. We consider positive feedback, bistable feedback, and toggle switch motifs and show that variation in gene copy number can cause a sequence of saddle-node bifurcations in the corresponding differential equations models, which leads to multiple orders of magnitude change in gene expression. A similar analysis of a 3-gene motif with successive inhibition (the ``repressilator'') reveals that changes in gene copy number can also cause a Hopf bifurcation, thus leading to a qualitative switch in system behavior among oscillatory and equilibrium dynamics. Importantly, we show that these bifurcations exist over a wide range of parameter values, thus reinforcing our claim that copy number is a key control parameter in the expression dynamics of regulatory networks.

A plasma is a completed ionized gas. In many applications such as in nuclear fusion or astrophysical phenomena, the plasma has very high temperature and low density, thus collisions can be ignored. The standard kinetic models for a collisionless plasma are the Vlasov- Maxwell and Vlasov-Poisson systems. The Vlasov-Poisson system is also used to model galaxy dynamics, where a star plays the role of a particle. There exists infinitely many equilibria for Vlasov models and their stability is a very important issue in physics. I will describe some of my works on stability and instability of various Vlasov equilibria.

The tau-leaping algorithm is proposed by D.T. Gillespie in 2001 for accelerating the simulation for chemical reaction systems. It is faster than the traditional stochastic simulation algorithm (SSA), which is an exact simulation algorithm. In this lecture, I will overview some recent mathematical results on tau-leaping done by our group, which include the rigorous analysis, construction of the new algorithm, and the systematic analysis of the error.

Comparison geometry studies Riemannian manifolds with a given curvature bound. This minicourse is an introduction to volume comparison (as developed by Bishop and Gromov), which is fundamental in understanding manifolds with a lower bound on Ricci curvature. Prerequisites are very modest: we only need basics of Riemannian geometry, and fluency with fundamental groups and metric spaces. The second (2 hour) lecture is about Gromov-Hausdorff convergence, which provides a natural framework to studying degenerations of Riemannian metrics.