Knot Visualization Experiments for Verifiable Molecular Movies

TL;DR

This paper explores the use of low-dimensional topology to improve the visualization of complex molecular simulations, emphasizing the importance of topological fidelity in animated molecular movies.

Contribution

It introduces a topological approach to molecular visualization that reduces 3D data to 1-manifolds and highlights potential topological discrepancies in animations.

Findings

Different embeddings can occur during molecular writhing.

Topological preservation is crucial for accurate molecular animations.

Techniques from topology and experimental mathematics aid in analysis.

Abstract

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.