Assembly of Biomolecular Gigastructures and Visualization with the Vulkan Graphics API

Building and displaying
all-atom models of biomolecular structures
with millions or billions of atoms, like virus particles or cells,
remain a challenge due to the sheer size of the data, the required
levels of automated building, and the visualization limits of today’s
graphics hardware. Based on concepts introduced with the CellPack
program, we report new algorithms to create such large-scale models
using an intermediate coarse-grained “pet representation”
of biomolecules with 1/10th the normal size. Pet atoms are placed
such that they optimally trace the surface of the original molecule
with just ∼1/50th the original atom number and are joined with
covalent bonds. Molecular dynamics simulations of pet molecules allow
for efficient packing optimization, as well as the generation of realistic
DNA/RNA conformations. This pet world can be expanded back to the
all-atom representation to be explored and visualized with full details.
Essential for the efficient interactive visualization of gigastructures
is the use of multiple levels of detail (LODs), where distant molecules
are drawn with a heavily reduced polygon count. We present a grid-based
algorithm to create such LODs for all common molecular graphics styles
(including ball-and-sticks, ribbons, and cartoons) that do not require
monochrome molecules to hide LOD transitions. As a practical application,
we built all-atom models of SARS-CoV-2, HIV, and an entire presynaptic
bouton with 1 μm diameter and 3.6 billion atoms, using modular
building blocks to significantly reduce GPU memory requirements through
instancing. We employ the Vulkan graphics API to maximize performance
on consumer grade hardware and describe how to use the mmCIF format
to efficiently store such giant models. An implementation is available
as part of the YASARA molecular modeling and simulation program from www.YASARA.org. The free YASARA
View program can be used to explore the presented models, which can
be downloaded from www.YASARA.org/petworld, a Creative Commons platform for sharing giant biomolecular structures.