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Graduate students work in the Simmerling lab from a
variety of different graduate programs at Stony Brook. Interested
students should look at the different programs and choose the one that
best fits their background as well as the course requirements of teach
program. The links below will take you to the home page for each
graduate program in which we participate. We also strongly encourage
you to contact us to discuss these programs if you are not sure which
is best.
Affiliated
Graduate Programs at Stony Brook
Computational
Structural Biology
The Simmerling lab at Stony Brook
University carries out research in the area of computational structural
biology. In particular, the lab focuses on understanding how dynamic
structural changes are involved in the behavior of biomoleculs such as
proteins and nucleic acids. Recent advances in computer hardware and
simulation algorithms have established computational methods as a
robust and important component of biomolecular research. These
simulations are highly complementary to experimental tools, and methods
such as molecular dynamics simulation are able to provide a detailed
description of the motions of individual atoms over short timescales
that are typically inaccessible to experiment. Simulations are not
limited to the averages over time and over large numbers of molecules
that prevent crystallographic or NMR experiments from characterizing
transiently populated conformations such as important intermediates in
multi-step conformational changes. In additional to direct dynamics,
treatment of simulation data using statistical mechanics can provide
valuable thermodynamic properties such as binding affinities or the
free energy profiles resulting from conformational changes.
In addition to projects related to specific biological problems, much
of the research in the Simmerling lab focuses on the development of new
methods for biomolecular simulation. The Simmerling lab develops the
Amber simulation package in collaboration with several other research
groups. Of particular interest are development of new methods for
efficient simulation of conformational changes and development and
validation of the molecular mechanics force fields that determine the
accuracy of the resulting simulation data.
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