A new approach to molecular dynamics modeling developed by Moldyn Inc., Cambridge, Mass., with co-funding from NIST's Advanced Technology Program, produces simulations of molecular movements and properties 100 times faster than conventional methods.

The new technique relies on substructuring, which organizes groups of similarly behaving atoms into interacting flexible bodies, to cut dramatically the number of calculations needed to estimate the behavior of large molecules such as proteins. The method was adapted from aerospace modeling techniques used to account for forces on hundreds of thousands of parts in spacecraft and satellites. The graphic above compares the results from Moldyn's analysis of a DNA molecule (right), versus a more conventional all-atom-based program.