| Mailing address: Molecular Sciences Institute 2168 Shattuck Avenue Berkeley, CA 94704 Cell phone: 510-710-9989 E-mail: steven.s.andrews@gmail.com Web page: http://www.smoldyn.org/andrews/index.html Research: Computational systems biologist Current research group: Molecular Sciences Institute Recent research groups: Bhalla Laboratory Arkin Laboratory Groves Laboratory |
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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.