Efficient solvent-free dissipative particle dynamics for lipid bilayers
Sevink, G. J. A.; Fraaije, J. G. E. M.

We rigorously derived effective potentials for solvent-free DPD simulation of lipid bilayers. The derivation relies on an earlier developed hybrid particle/field method and is based on the idea that the solvent is always in local equilibrium on a coarse-grained time scale, given the instantaneous templates set by the self-assembly structure. By relating the parameters in the effective implicit-solvent potentials directly to the lipid-solvent interactions and membrane properties for the explicit solvent DPD model, we constitute an efficient and general procedure for reformulating any DPD membrane model in an implicit-solvent form. Here, we determined these membrane properties for two existing DPD models, via an analysis of membrane fluctuation spectra. Equivalent single-processor implicit- and explicit-solvent calculations show the trade-mark of implicit solvent simulation: a 20-fold reduction of the total simulation time for a system containing 92% solvent. This increased efficiency enabled us to realistically simulate the spontaneous formation of a similar to 20 nm diameter vesicle on a single processor overnight. We believe that this work will contribute to an enhanced computational study of large vesicles and thus a better understanding of experimental liposome dynamics.

A Multiscale Modeling Protocol To Generate Realistic Polymer Surfaces
Handgraaf, J. W.; Gracia, R. S.; Nath, S. K.; Chen, Z.; Chou, S. H.; Ross, R. B.; Schultz, N. E.; Fraaije, Jgem

We present a multiscale modeling protocol to generate realistic amorphous polymer surfaces. Our computational approach consists of several steps having different levels of molecular detail. Initially, we generate a course-grained polymer surface that is completely relaxed using mesoscopic simulation methods. In the second step we transform the equilibrated coarse-grained polymer surface to atomistic detail with a special "mapper" that takes as input the mesoscopic morphology and uses Monte Carlo techniques to generate the atomistic structure. In the final step the atomistically detailed surface is equilibrated by performing a short molecular dynamics simulation. The great advantage of this multiscale approach is that it. allows the study of compounds that have intrinsically (very) slow equilibration dynamics such as polymers, which would be difficult to study with conventional simulation methods only. In addition, the multiscale approach makes it straightforward to "move" between different levels of molecular detail and even zoom in on a relevant part of the mesoscopic structure and map only that part. As test cases we applied the multiscale modeling protocol to polyethylene, polypropylene, and polyacrylonitrile.