Coarse-grained (CG) dissipative particle dynamics (DPD) equation can be derived from the generalized Langevin equation under Markovian approximations. The mean force and the friction coefficients in the radial and transverse directions needed for DPD equation are obtained directly from the all atomistic molecular dynamics (AAMD) simulations. However, the dissipative and friction forces are overestimated in the Markovian approximation, which results in wrong dynamic properties for the condensed system, such as CG water in the DPD simulations. To account for the non-Markovian dynamics, we introduced a rescaling factor to the friction coefficients. The value of the factor is estimated by matching the diffusivity of water.<br/>    The efficiency of the bottom-up coarse-graining based on AAMD is still limited because only one water molecule is mapped to a CG bead in order to avoid the effects of diffusion. To connect atomic-scale information to the meso-scale interaction for DPD beads composed of a few molecules or molecular fragments, ab initio calculation were utilized for the calculation of the DPD pair-wise interacting parameters. Electrostatic interactions between charged beads can be implicitly treated in this method.<br/>    We also constructed CG models of phospholipids and polypeptides based on a top-down CG mapping scheme. We derived the relationship between the DPD repulsive force and Flory-Huggins c-parameters and optimized the DPD force parameters. The feasibility of this model is demonstrated by simulating the structural and thermodynamic properties of lipid bilayer membranes.<br/>    Computational time spent on explicit solvent interations is the dominant contribution for CG symulations. More effective solvent-free DPD simulations are then expected. It was shown that the solvent degrees of freedom can be averaged out via particle/continuum method based on the idea that on a CG time scale, the solvent is always in local equilibrium. We derived the implicit-solvent DPD poentials for the lipid bilayer based on the above four-to-one CG model. The bilayers and vesicles obtained by this method have identical strcutures to the explicit-solvent bilayers.

Parametrization of dissipative particle dynamics: From bottom-up coarse graining to implicit-solvent modelling

254th National Meeting (2017)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.