Dynamic maintenance and visualization of molecular surfaces

Molecular surface computations are often necessary in order to perform synthetic drug design A critical step in this process is the computation and update of an exact boundary representation for the molecular surface e g the Lee Richards sur face In this paper we introduce e cient techniques for computing a molecular sur face boundary representation as a set of NURBS non uniform rational B splines patches This representation introduces for molecules the same geometric data struc ture used in the solid modeling community and enables immediate access to a wide range of modeling operations and techniques Furthermore this allows the use of any general solid modeling or visualization system as a molecular modeling inter face However using such a representation in a molecular modeling environment raises several e ciency and update constraints especially in a dynamic setting For example changes in the probe radius result in both geometric and topological changes to the set of patches Our techniques provide the option of trading accuracy of the representation for the e ciency of the computation while still tracking the changes in the set of patches In particular we discuss two main classes of dynamic updates one that keeps the topology of the molecular con guration xed and a more complicated case where the topology may be updated continuously In general the generated output surface is represented in a format that can be loaded into standard solid modeling systems It can also be directly triangulated or rendered possibly at di erent levels of resolution by a standard graphics library such as OpenGL without any additional e ort Research supported in part by grants from NSF CCR DMS ACI and NASA NCC Preprint submitted to Elsevier Science March