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43-million-atom mitochondrion in VMD 2.0.

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Visualizing mitochondrion in VMD 2.0.

Computer simulations of biological systems have approached the scale of whole cells and organelles, pushing VMD to its limits. VMD 2 can now load particular structures about ten times faster. Two of its analysis routines have moved to GPUs for the first time: solvent-accessible surface area (76x faster) and contact analysis (up to 420x faster), making molecular analysis on billion-atom cellular systems practical. Additionally, VMD 2 now draws molecules using a new (ANARI) standard on latest NVIDIA machines and a rewritten internal ray tracer, producing atomistic views of mitochondrion and viruses. Multi-node rendering is coming next, bringing interactive, cell-scale models within reach.

Editorials

The Future of Biomolecular Modeling

A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee. Read more

The Annals of MDFF

MDFF is a computational method that yields structures of massive biomolecular assemblies at atomic detail, using hybrid experimental data. Now Illinois scientists are applying MDFF to fascinating systems like the ribosome and HIV. By Lisa Pollack. Read more

Announcements

  • Workshop on Computational Biophysics 2026
  • Cade Duckworth awarded prestigious 2026-27 MCB/Biophysics Graduate Fellowship
  • Yupeng Li-Beckman Institute Graduate Fellow
  • Restricted Surface Diffusion of Cytochromes on Bioenergetic Membranes with Anionic Lipids


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