Steered molecular dynamics as "computer viscosimeter"

Tourleigh, Y.V.; Shaitan, K.V.

Авторы: Tourleigh Yegor V., Shaitan Konstantin V.
Сборник: Biophysical Journal, 88 (1, part 2)
Тезисы
Год издания: 2005
Первая страница: 514A
Аннотация: Diffusion processes in bilayers 1-palmitoyl-2-oleyl-sn-glycero-3-phosphatidylcholine (POPC) were studied by MD and SMD methods. The system under investigation contains 44 molecules of water per molecule of POPC. Transmembrane transport of aminoacid residues, Van-der-Waals spheres and a carbon nanotube (13,5 A in diameter, 35 A in length, type of packing - armchair) were analyzed. Amber99 force field was used. The model of water selected for the calculation was TIP3P. Thermostat on the base of virtual collisional medium, periodic boundary condition, NPT ensemble at anisotropic pressure (Berendsen barostat) were used. The forcefield and MD protocol assured the correspondence between the most important experimental parameters. For the study of particularities of viscous heterogeneity steered molecular dynamics approach (SMD) was applied, i.e. external forces were imposed onto certain particles. The velocity of particle in membrane depends on the values of external force and microviscosity. The values of membrane microviscosity and molecules’ diffusion coefficients were estimated from Stokes-Einstein relation. The obtained results indicate the non-Newtonian nature of the medium and slight non-equilibrium of the system at velocities about 1-10 A/ps. The results are consistent with available averaged experimental dates. It’s worth noting that the viscosity in the central part of lipid bilayer is several times lower than the averaged one.
Добавил в систему: Турлей Егор Владимирович

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