Mathematical modeling of mammalian iron metabolism (collaboration with VBI REU program) - Reinhard Laubenbacher
Iron is a key ingredient for any aerobic organism, and is required for oxygen transport, cellular respiration, and many other metabolic processes. At the same time, iron poses a serious problem for the body in the presence of reactive oxygen species, which arise as natural byproducts of cell metabolism. Poorly bound iron can interact with hydrogen peroxide, for example, to produce dangerous species such as the hydroxyl radical, which is highly reactive and damaging to many cellular components. So organisms have developed an elaborate control system to ensure that iron is available when and where needed, but that no excess unbound iron is present to cause problems. This control system can only be properly understood through mathematical models that can be analyzed and simulated on a computer. Some of the projects will focus on the modeling of this control system, as well as applications to cancer and the innate immune response to fungal infections.
Mathematical algorithms and software for modeling and simulation in systems biology - Reinhard Laubenbacher
Molecular systems biology takes a network approach to the understanding of biological systems. Rather than studying individual genes or proteins and their relationships, the object of study is networks of these molecular species. A key tool for this approach is the construction of mathematical models that incorporate biological information and experimental data. There are several different modeling paradigms, including, in particular, systems of ordinary differential equations and discrete models such as Boolean network models and so-called agent-based models. Some of the projects this coming summer will focus on the development of mathematical algorithms for the construction, analysis, and simulation of both continuous and discrete models and their implementation in software packages. The algorithms and software will in part be motivated by the models constructed for iron metabolism, and the groups working on this topic will collaborate with the groups working on topics in Theme 1.