What is it about?
This scientific visualization depicts a bacterial molecular landscape and explores the speed of diffusion and biochemical reactions that power life at the molecular scale.
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Why is it important?
For this visualization of a Lactobacillus bacterium cross-section, proteomic atlases were consulted to identify the most abundant molecular species and their relative amounts in both the cytoplasm (~100 different proteins) and the membrane (~50 proteins). In all, instances of ~100,000 different proteins, and ~500,000 DNA base-pairs were included in the model to account for the correct amount of DNA in the cross section. Simulating diffusion and compartmentalization of the different molecular actors (proxies for DNA strands, globular or transmembrane proteins, glycans, etc) at such different timescales required us to adapt existing algorithms to reduce computational costs, while providing flexibility for pre-viz and art-direction. Custom workflows were created for the automated import of hundreds of different molecules and their subsequent procedural clustering into regions of the cellular model according to their function.
Perspectives
The goal of these kinds of visualization is both to engage various audiences about the nature of the molecular world and also to drive new questions. For scientists, it is also about recognizing what is the missing data? For educators, how does this visualization help to remedy common misconceptions about cells in today's classrooms? This particular visualization was made possible using Autodesk Maya’s Bifrost Graph Editor in combination with our custom software, Molecular Maya (a plug-in for Autodesk Maya), that facilitates not only the import of molecular structure coordinates (i.e. proteins, nucleic acids, carbohydrates, lipids and other structural coordinates from the Protein Data Bank and other sources) but also to rig and simulate individual coarse-grained molecular models.
Gael McGill
Digizyme Inc.
Read the Original
This page is a summary of: Bacterial Molecular Landscape: Visualizing Earth's Simplest Life Form, August 2025, ACM (Association for Computing Machinery),
DOI: 10.1145/3698896.3725524.
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