It comes as no surprise that the number of algorithms needed to describe complex molecular structures and activities is large. Parallel computers have anywhere from tens to tens of thousands of processing units that work simultaneously. The following graph provides an example of performance analysis. Researchers must program each processor with algorithms that mimic any of a variety of qualities of the molecule to be modeled. The biological molecules of interest in this project have upwards of tens of thousands of atoms.
Researchers describe molecular systems on three strategic levels.
Algorithms for such models employ equations for statistical distributions, including the Poisson-Boltzmann equation. Algorithms for these models employ Newtonian or Hamiltonian mechanics. A third level, the quantum mechanical level, considers forces and particles inside the atom. Once algorithms are constructed, Scott and colleagues face the daunting task of incorporating them into computer software. The fields of mathematics and computer science truly merge at this point.