Molecular dynamics simulations of unsaturated lipid bilayers

Alexander L. Rabinovich; Nikolay K. Balabaev

doi:10.1117/12.417651

1 February 2001 Molecular dynamics simulations of unsaturated lipid bilayers

Alexander L. Rabinovich, Nikolay K. Balabaev

Proceedings Volume 4348, Fourth International Workshop on Nondestructive Testing and Computer Simulations in Science and Engineering; (2001) https://doi.org/10.1117/12.417651
Event: Fourth International Workshop on Nondestructive Testing and Computer Simulations in Science and Engineering, 2000, St. Petersburg, Russian Federation

Abstract

Molecular dynamics simulations were carried out for bilayers of lipid molecules having stearic acid (C_18:0) chain in position '3-D' (using the nomenclature of M. Sundaralingam, 1972) and fatty acid chain C_18:0, C_18:1(omega 9), C_18:2(omega 6), C_18:3(omega 3), C_20:4(omega 6) or C_22:6(omega 3) in position '2-D'. To investigate the properties of the bilayers two models were considered. In the first model, the simulation cells of the bilayers consisted of 96 phosphatidylcholine (PC) molecules and 2304 water molecules: 48 lipid molecules per layer and 24 H₂O molecules per lipid. The water was modeled by explicit TIP3P water molecules. In the second model, the head group of the lipid molecules was treated as an effective sphere -- diacylglycerolipids (DGs) were considered, the interface of each monolayer was modeled by a flat surface; no water molecules were present explicitly. The bilayers consisted of 48 X 2 equals 96 glycerolipids arranged in a rectangular simulation cell. Various properties of the bilayers -- the C-H bond order parameter -S_CH profiles of the hydrocarbon tails, the root-mean-square values of the positional fluctuations of the lipid chain carbons, mass density distributions of lipid molecules and water along the normals were investigated.

Citation Download Citation

Alexander L. Rabinovich and Nikolay K. Balabaev "Molecular dynamics simulations of unsaturated lipid bilayers", Proc. SPIE 4348, Fourth International Workshop on Nondestructive Testing and Computer Simulations in Science and Engineering, (1 February 2001); https://doi.org/10.1117/12.417651

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