Science at the Edge Seminar Friday, September 22, 2006 Room 1400 Biomedical and Physical Sciences Bldg. 11:30 a.m. Speaker: Dr. Stephen Wells Center for Biological Physics Arizona State University Title: Geometric Simulation of Mobility in Macromolecules Abstract: Geometric simulation is an approach based on maintaining the constraints that relate large groups of atoms together, in contrast to conventional approaches based on two- and three-body potentials. Structure generation by geometric simulation allows us to ask and answer questions about structural variation that are hard to access by potential-based methods such as molecular dynamics. I will discuss two major applications of the method. A systematic study of zeolite structures over a range of volumes has allowed us to define a "flexibility window", a range of volumes within which the SiO4 structural units can be made perfectly tetrahedral; a distinctive feature is that experimentally determined zeolite structures lie consistently at the low-density end of the window, indicating that zeolites are maximally expanded given their constraints. In protein science, geometric simulation provides a method for rapid conformer generation, allowing us to explore the conformational variation of a protein structure while maintaining rigidity constraints. We are currently applying this method ("FRODA" algorithm) to areas including fitting to low-resolution electron density maps, and fragment folding for structural prediction.