Flexible Spanners for Tracking Proximity in Folding Molecules

Robert Gdanitz, Senior Research Associate in the Department of Physics at North Carolina A&T State University, has been named a PI on the BioGeometry project effective June 2003. Robert is a theoretical physical chemist with expertise in developing electronic structures as well as force field methods. He interacts with group members at Chapel Hill, Duke, and Stanford to further develop his method to predict molecular crystal structures. Robert has local as well as national collaborations on projects of biochemical interest, which will further strengthen the bond of NCA&T to the remainder of the BioGeometry group. Since most molecular forces act between pairs of atoms but are shortrange, it is often important to know which atoms are near which in a molecule. For example, molecular dynamics (MD) computations often maintain so-called “neighbor lists” for each atom; these are lists of all the other atoms in the molecule that are within a certain short distance of the given atom (see Fig. 1). These lists might be used to cut-off Lennard-Jones interactions for pairs of atoms more than 10Å apart, to speed up the c o m p u t a t i o n . Knowledge of atom proximities is also important in Monte-Carlo (MC) simulations, in order to generate collision-free conformational moves that are likely to be of low enough energy to be accepted. Fundamental geometric packing arguments tell us that an atom can have only a few near neighbors (but possibly many far neighbors) --and thus near-neighbor information can be compactly encoded. What makes the proximity maintenance problem hard, however, is that a deforming molecule is a system with many degrees of freedom, all of which change across every MD or MC step.