Mesoscale simulation of lipid bilayers: quasi-2D hydrodynamics and shear viscosity
| Author(s) | Zgorski, Andrew | |
| Date Accessioned | 2018-12-20T13:42:45Z | |
| Date Available | 2018-12-20T13:42:45Z | |
| Publication Date | 2018 | |
| SWORD Update | 2018-10-17T16:05:30Z | |
| Abstract | The computational capabilities of molecular dynamics (MD) simulations have greatly advanced in recent years, allowing for the modeling of ever more complex systems. In the field of membrane simulation, this has facilitated studies of both large, heterogeneous systems and dynamics on millisecond time scales. Concurrently, innovations in experimental technique have allowed for probing dynamics on length and time scales approaching those in simulation. As these efforts continue to progress, future extensions will allow for direct comparison between experiment and simulation, enabling further refinement to both. ☐ Membranes are quasi-2D viscous fluids which require accurate modeling of hydrodynamic transport to fully capture their dynamics. Relevant hydrodynamic theory predicts long-range coupling among proteins diffusing laterally in the membrane. In MD simulation, these long-distance interactions lead to self-interaction through the periodic image lattice and other finite size effects which may only be reduced by increasing the system size. Consequently, accurate modeling of bulk hydrodynamic transport using traditional MD (i.e. with explicit solvent particles) is not feasible. Calculating pairwise forces between the solvent particles demands an overwhelming majority of the available computational resources at the requisite system sizes. This predicament constitutes an unmet scientific need as novel algorithms and software implementations are required for accurate and efficient modeling of hydrodynamic interactions at scale. ☐ We have met that need by supplementing an implicit-solvent lipid model called Dry Martini with an efficient mesoscopic hydrodynamics model called multi-particle collision (MPC) dynamics. Our hybrid model, called STRD Martini, is implemented in the popular open-source MD software package GROMACS v5.0.1, opening the way to further studies of membrane dynamics with proper accounting for hydrodynamic interactions. The selection of MPC dynamics for the mesoscopic solvent model was motivated by its particle-based nature, which cleanly interfaces with existing GROMACS code. As such, GROMACS may treat MPC particles just as any other particle for the purposes of integration, parallelization, trajectory writing, analysis, and force calculation (when desired). When combined with domain decomposition, STRD Martini scales to thousands of processors, providing accurate hydrodynamics while running at least an order of magnitude faster than equivalent explicit-solvent simulations. ☐ The theory for membrane hydrodynamics in periodic geometries, called periodic Saffman-Delbrück theory, requires three parameters, two of which may be measured independently and a third which is a true fit parameter of the model. The independent parameters characterize the membrane surface viscosity and coefficient of friction between membrane leaflets. These parameters are not commonly calculated from simulation and remain uncharacterized for most popular membrane force fields. Following the blueprint of an earlier work, we further develop a protocol for conducting nonequilibrium shearing simulations to measure these parameters and apply the protocol to both coarse-grain and all-atom membranes. | en_US |
| Advisor | Lyman, Edward | |
| Degree | Ph.D. | |
| Department | University of Delaware, Department of Physics and Astronomy | |
| DOI | https://doi.org/10.58088/byb4-yy92 | |
| Unique Identifier | 1079758759 | |
| URL | http://udspace.udel.edu/handle/19716/24020 | |
| Language | en | |
| Publisher | University of Delaware | en_US |
| URI | https://search.proquest.com/docview/2131004084?accountid=10457 | |
| Keywords | Biological sciences | en_US |
| Keywords | Physical sciences | en_US |
| Keywords | Earth sciences | en_US |
| Keywords | Hydrodynamics | en_US |
| Keywords | Interleaflet friction | en_US |
| Keywords | Intermonolayer friction | en_US |
| Keywords | Lipid bilayer | en_US |
| Keywords | STRD martini | en_US |
| Keywords | Surface viscosity | en_US |
| Title | Mesoscale simulation of lipid bilayers: quasi-2D hydrodynamics and shear viscosity | en_US |
| Type | Thesis | en_US |