Blue Waters Symposium 2019

The membranes that surround cells and organelles play a vital role in biological function, acting as semipermeable barriers that separate and protect cells and organelles from their surroundings. Molecular dynamics (MD) simulations provide the means to investigate the fundamental molecular mechanisms that give rise to membranes' biological functions, but it is exceedingly difficult to build MD models that capture cellular membranes' immense scales and complex geometries. To address this challenge, we previously introduced software called xMAS (Experimentally-Derived Membranes of Arbitrary Shape) Builder, and we used it to generate a ~4.5 billion atom (~1.9) model of a piece of the endoplasmic reticulum with a helicoidal shape called a Terasaki ramp. We also ran a long-term equilibrium MD simulation on a smaller test system to demonstrate that xMAS Builder produces stable, high quality models. Used to develop and test the base capabilities of xMAS Builder, these previous models were somewhat limited in that they were composed entirely of lipids. We now introduce an updated xMAS Builder capable of incorporating proteins into its membrane models.