Stability of simulation of a population of chemical polymers on the massively parallel processor

An investigation is described of the suitability of the massively parallel processor (MPP) for the extension of a program which simulates the degradation of the heparin polymer by the enzyme heparinase. The architecture of the MPP offers massive fine-grained parallelism, with the following limitations: there is a single instruction stream, i.e. each of the 16384 processing elements (PEs) executes the same instruction; each PE communicates directly with only four neighboring PEs, and the opposite edges of the grid of PEs are logically connected to each other; and each PE has 1024 bits of local random access memory as well as (slower) access to a large (20 Mbyte) staging memory. A report on the use of the MPP Pascal programming language to implement the simulation program is provided, including the representation of polymer chains, the cleaving of chains into smaller chains, and the search for (stable) chains which are impervious to the actions of heparinase