A40.00003. Multibillion Atom Molecular Dynamics Simulations of Cellular Membranes

Presented by: Noah Trebesch


Membranes are the basic organizational and defensive unit of the cell, and they thus play a vital role in biological function. Electron microscopy (EM) can provide 3D structures of these membranes, and, with the advent of exascale computing, there is a new opportunity to use molecular dynamics (MD) simulations to elucidate the intricate biophysical connection between the complex structure and function of these membranes. To take advantage of this opportunity, we have developed xMAS (Experimentally-Derived Membranes of Arbitrary Shape) Builder, software designed to turn low resolution EM-based structures of cellular membranes into atomistic models that are suitable for MD. Using xMAS Builder, we have built the first cell-scale (~4.5 billion atom) model of a representative cellular membrane (a helicoidal system from the endoplasmic reticulum), and we have also built several models of a smaller synthetic system with equivalent complexity. Preliminary simulations of these models have demonstrated their potential to reveal fundamental insights into the general behavior of cellular membranes, supporting the expectation that xMAS Builder will soon enable MD simulations that leverage exascale computing to provide detailed biophysical characterization of these key biological systems.


  • Noah Trebesch
  • Emad Tajkhorshid


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