Nanomatrix: Scalable Construction of Crowded Biological Environments

We present a novel method for the interactive construction and rendering of extremely large molecular scenes, capable of representing multiple biological cells in atomistic detail. Our method is designed for scenes that are procedurally constructed based on a given set of building rules. Rendering large scenes typically requires the entire scene to be available in-core, or alternatively, it requires out-of-core management to load data into the memory hierarchy as a part of the rendering loop. Instead of out-of-core memory management, we propose procedurally generating the scene on-demand on the fly. The key concept is a positional- and view-dependent procedural scene-construction strategy, where only a fraction of the atomistic scene around the camera is available in the GPU memory at any given time. The atomistic detail is populated into a uniform-space partitioning using a grid covering the entire scene. Most grid cells are not filled with geometry, only those that are potentially seen by the camera are populated. The atomistic detail is populated in a compute shader and its representation is connected with acceleration data structures for hardware ray-tracing of modern GPUs. Distant objects, where atomistic detail is not perceivable from a given viewpoint, are represented by a triangle mesh mapped with a seamless texture generated from the rendering of geometry with atomistic detail. The algorithm consists of two pipelines, the construction-compute pipeline and rendering pipeline, which work together to render molecular scenes at an atomistic resolution beyond the limit of the GPU memory containing trillions of atoms. The proposed technique is demonstrated on multiple models of SARS-CoV-2 and the red blood cell.