  Classical topological concepts are applied to understand high performance
computing simulations of molecules writhing in three dimensional space. These
simulations produce peta-bytes of floating point data, to describe 3
dimensional changes in molecular structure. A zero-th order analysis is
achieved by viewing a computer animation synchronized with these changes. The
performance demands for animation of this voluminous data can become
problematic, but techniques from low-dimensional topology are helpful. The 3D
molecule is reduced to a lower dimensional model of a 1-manifold, which
undergoes a piecewise linear approximation for animation. An example is
presented here to show how a 1-manifold and its PL approximation could come to
have different embeddings as molecular writhing proceeds. This should serve as
a cautionary warning to animators to respect established sufficient conditions
for topological preservation so that the movies generated will faithfully
reflect the topology of the underlying model. To obtain this result, techniques
from low-dimensional topology were joined with experimental mathematics and
numerical analyses.
