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      Computer simulations of plasma–biomolecule and plasma–tissue interactions for a better insight in plasma medicine

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          ReaxFF:  A Reactive Force Field for Hydrocarbons

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            A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons

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              Effect of lipid peroxidation on the properties of lipid bilayers: a molecular dynamics study.

              Lipid peroxidation plays an important role in cell membrane damage. We investigated the effect of lipid peroxidation on the properties of 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) lipid bilayers using molecular dynamics simulations. We focused on four main oxidation products of linoleic acid with either a hydroperoxide or an aldehyde group: 9-trans, cis-hydroperoxide linoleic acid, 13-trans, cis-hydroperoxide linoleic acid, 9-oxo-nonanoic acid, and 12-oxo-9-dodecenoic acid. These oxidized chains replaced the sn-2 linoleate chain. The properties of PLPC lipid bilayers were characterized as a function of the concentration of oxidized lipids, with concentrations from 2.8% to 50% for each oxidation product. The introduction of oxidized functional groups in the lipid tail leads to an important conformational change in the lipids: the oxidized tails bend toward the water phase and the oxygen atoms form hydrogen bonds with water and the polar lipid headgroup. This conformational change leads to an increase in the average area per lipid and, correspondingly, to a decrease of the bilayer thickness and the deuterium order parameters for the lipid tails, especially evident at high concentrations of oxidized lipid. Water defects are observed in the bilayers more frequently as the concentration of the oxidized lipids is increased. The changes in the structural properties of the bilayer and the water permeability are associated with the tendency of the oxidized lipid tails to bend toward the water interface. Our results suggest that one mechanism of cell membrane damage is the increase in membrane permeability due to the presence of oxidized lipids.
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                Author and article information

                Journal
                Journal of Physics D: Applied Physics
                J. Phys. D: Appl. Phys.
                IOP Publishing
                0022-3727
                1361-6463
                July 23 2014
                July 23 2014
                June 26 2014
                : 47
                : 29
                : 293001
                Article
                10.1088/0022-3727/47/29/293001
                349fb623-0033-47df-a565-8a36c3c4863e
                © 2014

                http://iopscience.iop.org/info/page/text-and-data-mining

                http://iopscience.iop.org/page/copyright

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