A look at how they are using their codes in the virus simulation provides insight into how they attack problems via the hierarchical approach to modeling. What they are optimizing The codes used in simulating the rhino virus 14 are two of many codes Goddard is now optimizing with NCSA s resources. Although applicable to molecular biology, the program and its two underlying codes are being adapted for other uses, such as in industrial polymers and electronic materials. The MPsim program, or Massively Parallel Simulator, was developed specifically by Goddard's group to simulate systems with greater than a million atoms. CMM overcomes a bottleneck in large systems that arises from having to sum long-range Coulomb interactions.
Coulomb forces are the electric charges between particles.
The electrostatic interaction between every particle must be calculated for all pairs of atoms. For a million-atom system, the number of calculations for Coulomb forces reaches into the trillions. Scientists know that the virus transmits its RNA to healthy cells by binding to receptors on the surface of the target cell. Once bound it releases its RNA through microscopic holes at the receptor sites. Scientists have speculated that drugs lessen or prevent colds by stiffening the walls of the receptor sites so that they cannot expand to accommodate the much larger viral RNA as it attempts to slither into the cell.