Hybrid Particle-Field Coarse-Grained Models for Biological Phospholipids

Abstract

In the framework of a recently developed scheme for a hybrid particle-field simulation technique where self-consistent field theory (SCF) and molecular dynamics (MD) are combined [ J. Chem. Phys. 2009 , 130 , 214106 ], specific coarse-grained models for phospholipids and water have been developed. We optimized the model parameters, which are necessary in evaluating the interactions between the particles and the density fields, so that the coarse-grained model can reproduce the structural properties of the reference particle-particle simulations. The development of these specific coarse-grained models suitable for hybrid particle-field simulations opens the way toward simulations of large-scale systems employing models with chemical specificity, especially for biological systems.

Spontaneous insertion of carbon nanotube bundles inside biomembranes: A hybrid particle-field coarse-grained molecular dynamics study

“…The coarse-grained models adopted in this study for lipids have been extensively described and validated in two previous papers [39,40] and recently reviewed in the framework of efficient strategies for biomembranes modelling [33]. The main advantage of hybrid MD-SCF scheme is that the most computationally expensive part of the MD simulations, i.e.…”

“…The calculations of the fields have been performed using a grid with a resolution of 0.705 nm and an update frequency of 300 steps. This choice of the grid size guarantees good reproduction of lipid properties [39,40]. Furthermore the value 0.705 nm is almost half of the CNTs diameters, in this way excluded volume interactions between CNTs is properly described by the incompressibility condition (second addend of eq.…”

Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics

“…in which the projection algorithm is called every tenth time step, was considered in the original MD-SCF model, and even larger values were found suited in specific cases. 29 This value is determined by the optimum between efficiency and both the effective particle dynamics and field resolution, in particular how fast the density fields at the chosen resolution changes given the underlying particle dynamics. The value f up = 10 was considered a conservative choice, 29 and we will use it as the initial value.…”

“…29 This value is determined by the optimum between efficiency and both the effective particle dynamics and field resolution, in particular how fast the density fields at the chosen resolution changes given the underlying particle dynamics. The value f up = 10 was considered a conservative choice, 29 and we will use it as the initial value. Nevertheless, later on, we discuss the need for using smaller values.…”

“…27 The transferability between CGMD and MD-SCF was validated for a number of cases, including for phospholipid membranes. 29 By selecting a global Andersen thermostat for the particle evolution, 26 however, the advantage of retaining solvent degrees of freedom has not been fully exploited. Improving the kinetic description, such that it realistically addresses phenomena that play a key role both in the early stage of phase separation and in membrane dynamics and remodelling, would make the method stand out among competitors, and introduce the option to simulate lipid structures of truly relevant dimensions with proper resolution and dynamics.…”