As computational resources continue to increase in power, larger and larger simulation systems are becoming viable for atomistic simulation, and we anticipate soon being able to construct models of entire cells. However, as we move into this new space in cellular simulation, scalable methodologies need to be developed to handle the intricacies of constructing the membrane envelope. In particular, embedding proteins into non-planar geometries to avoid modeling artifacts such as ring penetrations or inadvertent water pore formation requires careful attention to the original molecular placement.<br/><br/>In our procedure, membrane, protein, and water are initially placed using ultra coarse-grained simulation and a masking process to avoids overlap between components, utilizing ideas from the computer graphics literature. In addition, our process correctly estimates the number of components needed for a complete cellular membrane model. This scalable procedure allows for membrane construction at arbitrary scale, and is demonstrated by constructing an approximate membrane envelope for a small bacterial cell, complete with diverse membrane-embedded proteins that would be essential to bacterial function. While our current membrane envelope may deform during simulation due to a lack of internal cellular structure, it nonetheless represents a substantial advance towards enabling cell-scale simulation.

Cell-scale computational modeling methodologies for living membranes

253rd National Meeting (2017)

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