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|There are two types of representations of lipid bilayers – mean field representation and atomistic one. From the choice of the representation depends the accuracy of the modeled lipid bilayer.
In mean field simulations, lipid bilayer is represented by simple hydrophobic slab, oriented in x, y-plane, which separates two hydrophilic phases. In this model lipid and water molecules are not explicitly included. The empirical potential energy function describes the partitioning of hydrophilic and hydrophobic parts of a given molecule into the lipid bilayer. This function contains bonded and non-bonded terms to which a hydrophobic interaction term is added . This representation is further refined by introducing of dipole potential which decreases dielectricity across the water/lipid interfacial region from the water phase to the hydrocarbon interior .
In atomistic representation each lipid and water molecules are clear defined, which provides detail information for lipid bilayer at atomic level. The detail level can vary depending on the used representation – all-atom or united-atom. In all-atom representation, all hydrogen atoms are included, while in united-atom representation non-polar hydrogen atoms are merged into the central carbon atoms and only polar hydrogen atoms are treated separately. All-atom representations give better results but are not appropriate for large systems, because of time consumption, while reduced number of non-bond interactions in united-atom models speeds up calculations.
22. Wiese, M. Computer Simulations [sic] of Phospholipids and Drug-Phospholipid Interactions. In Drug - Membrane Interactions; Seydel, J. K., Wiese, M., Eds.; Wiley - VCH Verlag: Weinheim, 2002.
23. Rocca, P. L.; Shai, Y.; Sansom, M. S. P. Biophys. Chem. 1999, 76, 145.
|A system can be simulated using two types of representation: a mean field representation or an atomistic one. The choice of the one or the other approach defines the degree of accuracy with which the lipid bilayer is modeled.
In mean field simulations, the lipid bilayer is generally represented by a simple hydrophobic slab, oriented in the x,y-plane and separating two hydrophilic phases. In this bilayer model, lipid and water molecules are not explicitly included. An empirical potential energy function describes the partitioning of hydrophilic and hydrophobic parts of a given molecule into the lipid bilayer. This function consists of bonded and non-bonded terms to which a hydrophobic interaction term is added . This mean field representation has been further refined by introducing a dipole potential that accounts for the decrease in dielectricity across the water/lipid interfacial region from the water phase to the hydrocarbon interior .
Atomistic simulations treat lipid and water molecules explicitly, providing a more detailed insight into the lipid bilayer at the atomic level. The level of detail may vary depending on the type of the atomic representation used. In an all-atom representation, all hydrogens are included explicitly; in a united-atom representation, non-polar hydrogens (e.g. hydrogens of methylene and methyl groups) are merged into the central carbon atoms, polar hydrogens only are treated explicitly. All-atom representations give in principle better results for stud-
ies on diffusion and relaxation phenomena, but are computationally expensive and become unsuitable for large systems. The reduced number of non-bonded interactions in a united-atom model makes this representation very attractive, since the calculations are considerably speeded up.
 M. Wiese. Computer Simulation of Phospholipids and Drug-Phospholipid Interactions. In: Drug-Membrane Interactions. J. K. Seydel and M. Wiese (Eds.), Wiley-VCH Verlag GmbH, Weinheim, 2002.
 P. La Rocca, Y. Shai, and M. S. P. Sansom. Biophys. Chem., 76:145–159, 1999.
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