Molecular Simulation of Lipids and Water: Atomistic, Coarse-Grained, and Mixed Resolutions

Abstract

Lipids and water are fundamental ingredients of living matter. Lipids form membranes which are employed by living organisms to enclose cells and organelles, transmit information, control molecular transport, and store energy. Water is the universal biological solvent. This presentation will focus on the investigation of lipid and water systems using different molecular dynamics simulation approaches. We will show results from all-atom simulations of mixed bilayers composed of lamellar and nonlamellar lipids. In particular, a quantitative characterisation has been obtained of the internal distributions (profiles) of lateral pressure, electric field, and dipole potential. These properties, very difficult to measure experimentally, are thought to play key roles in many membrane phenomena, including nonspecific lipid-mediated mechanisms of protein regulation. We will also describe the development of coarse-grained models, that are simplified representations in which entire groups of several nearby atoms are reduced to single particles. In particular, we will present recent results on the ELBA water model, where a water molecule is reduced to a single sphere embedded with a point dipole [1,2]. The ELBA model is remarkably accurate, and can be combined directly with atomistic force fields in mixed resolution systems [3]; however, recent results also highlight a number of issues in relation to ionic screening and phase behavior. Finally, we will report on ongoing efforts to develop a new “ultra coarse-grained” model for lipids and water, aimed at further increasing computational efficiency while retaining only the essential underlying physics.[1] M. Orsi, Mol. Phys. (2014), 112, 1566-1576.[2] W. Ding, M. Palaiokostas, M. Orsi, Mol. Simulat. (2015), http://dx.doi.org/10.1080/08927022.2015.1047367.[3] M. Orsi, W. Ding, M. Palaiokostas, J. Chem. Theory Comput. (2014), 10, 4684-4693.