Steve Andrews

Research Interests in theoretical and experimental systems biology:

My research is in the interdisciplinary field of systems biology.  Here, physics, chemistry, and biology methods are combined to interpret complex biological systems which typically range in size from several proteins to several cells.  In terms of fundamental science, a research goal is to understand the connections between the microscopic physical world of individual molecules and the macroscopic biological world of living organisms.  On the applied side, medical research is relying increasingly on systems level understandings of biochemistry in cancer cells, native and invasive bacteria, neural cells, and many other systems; an improved understanding of these systems will greatly assist drug discovery and other medical advances.  My research projects include:

Algorithm development for cell modeling
Computer simulations are are used in systems biology as a way to build intuition about the system dynamics, to test hypotheses, and to identify essential components of the system.  I am developing modeling tools that can simulate biochemical systems with a relatively high level of detail, in which individual molecules and spatial resolution are addressed, but that are also fast enough to allow the simulation of thousands of molecules over several seconds of real time.  In my initial work, I developed algorithms for simulating reactions between freely diffusing molecules in solution, and between molecules and surfaces, with high spatial resolution.  This work led to the Smoldyn computer program, which can be downloaded from the Software page.  My current algorithm development is for simulations that also account for polymers and membranes.  I am also working on incorporating these detailed methods into the multi-scale Moose simulation program.

Mechanics and dynamics of the bacterial cytoskeleton
The bacterial cytoskeleton is highly dynamic.  For example, the MinC, MinD, and MinE proteins of E. coli exhibit a remarkable oscillation between the cell poles: the MinD protein polymerizes in a helical coil that extends from one pole towards the cell center, is depolymerized by MinE, forms a new polymer from the opposite pole, and so on.  In another example, the FtsZ protein forms a central ring around the cell center that constricts during cell division to yield two daughter cells.  Using both simulation and experimental methods, I am investigating the shapes and dynamics of these cytoskeletal polymers.