We developed and optimized implicit solvent coarse-grained (CG) model for both qualitative (with top-down modeling method) and quantitative simulations (with bottom-up modeling method). The use of implicit solvent enables simulations on large length- and time-scales with a computational speedup more than three to four orders of magnitude compared to all-atom bilayer simulations. The top-down qualitative CG modeling is powerful for exploring macroscopic large-scale physical mechanism and generic properties. While the quantitative CG modeling is especially useful for studying the phenomena at mesoscopic spatial and temporal scales which nevertheless require a fair description of chemical specificity.
Top-Down CG Modeling
- Z.-J. Wang, D. Frenkel. Modeling flexible amphiphilic bilayers: a solvent-free off-lattice Monte Carlo study. Journal of Chemical Physics, 2005, 122: 234711. [Reprinted in: Virtual Journal of Biological Physics Research, 10(1), July 1, 2005] [DOI]
Bottom-Up CG Modeling
- Z.-J. Wang, M. Deserno. Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field. New Journal of Physics, 2010, 12(9): 095004. [DOI]
- Z.-J. Wang, M. Deserno. A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations.Journal of Physical Chemistry B, 2010, 114(34): 11207-11220. [DOI]
- T. Bereau, Z.-J. Wang, M. Deserno. More than the sum of its parts: Coarse-grained peptide-lipid interactions from a simple cross-parametrization. Journal of Chemical Physics, 2014, 140(11): 115101.[DOI]