Nanocomputation of Mechanical Properties in Nanobio Membrane

Abstract

It is very essential to know mechanical properties in different regions of nanobio membrane as one of the most important parts of living systems. Here the coarse-grained (CG) simulations method have been used to study the pressure profile in a system including nanobio membrane and water. CG simulations have become an important tool to study many biomolecular processes, exploring scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization has been ignored in the initial CG water molecules model. Given the important role of water as a solvent in biological systems, its treatment is very important to the properties derived from simulation studies. Till now two models have been parameterized to simulate water: i) standard MARTINI water and ii) polarizable coarse-grained water model. Both of mentioned water models are proper to be used in combination with the CG MARTINI force field. In this work both of these models have been used for simulation. One micro second CG molecular dynamics simulation has been done for two separate systems. Each system includes water and hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) lipid nanobio membrane. The difference between two systems is in simulated water models that one system has standard MARTINI water and the other one has polarizable water. In each case pressure profile calculation has been done via Virial pressure theorem. Results indicate that using polarizable water model leads to higher picks in pressure profile in water region near surface of nanobio membrane. This can be related to density of polarizable water and also may play role as a small barrier.