 |
Center for Nonlinear Studies |
Hydrodynamic interactions in the low Reynolds number, "2D+3D" world of the cell membrane are long-ranged, with important consequences for the encounters of membrane proteins that underlie all signaling, and for interpreting experimental measurements on membrane protein mobility. For example, the well known Saffman-Delbruck theory (later extended by Hughes, Pailthorpe, and White)[1,2] is only correct for an infinite, homogeneous, free-standing membrane. These assumptions are not satisfied in cell membranes (crowded with proteins, coupled to the cytoskeleton) or in many experimental systems (supported bilayers), or in simulations (dramatically finite compared to the Saffman-Delbruck lengthscale).[3] We have therefore developed a modeling framework which captures molecular level interactions via a widely used coarse-grained model (Martini) while incorporating solvent hydrodynamics via the fast, particle-based mult-particle collision methods for hydrodynamics method.[4] The implementation (STRD Martini) is implemented in an in-house version of Gromacs, scales to thousands of processors, and agrees quantitatively with theoretical predictions for diffusion in finite membranes.[5]
1. PG Saffman and M Delbruck PNAS 72:3111(1975) 2. BD Hughes, BA Pailthorpe, LR White J. Fl. Mech. 110:349(1981) 3. E. Lyman, C-L Hsieh, C. Eggeling Biophys. J. 115:595(2018) 4. A. Zgorski and E. Lyman Biophys. J. 111:2689(2016) 5. BA Camley, MG Lerner, RW Pastor, FLH Brown J. Chem. Phys. 143:243113(2015)
Host: Angel Garcia