LoD PLI: Level of Detail for Visualizing Time-Dependent, Protein-Lipid Interaction

Abstract:
In Molecular Dynamics (MD) Visualization, representative surfaces of varying resolution are commonly used to depict protein molecules while a variety of geometric shapes, ribbons, and spheres are used to represent residues and atoms at different levels of detail (LoD). The focus of the visualization is usually on individual atoms or molecules themselves and less often on the interaction space between them. Here we focus on LoD interaction between lipids and proteins and the space in which this occurs in the context of a membrane simulation. With naive approaches, particles may overlap and significant interaction details can be obscured due to clutter. Furthermore, the spatial complexity of the protein-lipid interaction (PLI) increases over time. Co-developed with an MD domain expert, we address the challenge of visualizing complex, time-dependent interactions between lipids and proteins by introducing two abstract LoD representations with six levels of detail for lipid molecules and protein interaction. We also propose a fast GPU-based projection that maps lipid-constituents involved in the interaction onto the abstract LoD protein interaction space. The tool provides fast LoD, the imagery of PLI for 336,260 particles over almost 2,000 time-steps. The result is a great simplification in both perception and cognition of this complex interaction that reveals new patterns and insight for computational biologists. We also report feedback from the domain expert to our visualization.