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Along with several other investigators
at Stanford, we have established a National Center for Physics-Based
Simulation of Biological Structures (SimBioS).
This Center is developing, and supporting a simulation tool kit
(SimTK) that enables
biomedical scientists to develop and share accurate models and simulations
of biological structures - from atoms to organisms. NMBL scientists
and engineers are focused on building the SimTK software and using
it to study the dynamics of molecular motors and whole-body motions.
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SimTK
enables physics-based modeling and simulation of biological structures,
including (A) RNA folding, (B) myosin dynamics, (C) neuromuscular
dynamics, and (D) cardiovascular dynamics. Data describing atomic
structures, anatomical geometry, and other parameters are used to
build models. A model describes the geometry, biology, and physics
of the system through governing equations. A simulation is produced
by integration of the governing equations. Simulations are compared
to data describing the performance of the system to test the accuracy
of the functional predictions. This modeling and simulation framework
provides a powerful paradigm for approaching biological problems
with a structural perspective across a broad range of scales, from
atoms to organisms. |
