# Ry/051

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Permeation of Organometallic Compounds through Phospholipid Membranes

von Dr. Raycho Yonchev

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 Zuletzt bearbeitet: 2016-01-31 20:13:09 WiseWoman Anézo 2003, Fragment, Gesichtet, KomplettPlagiat, Ry, SMWFragment, Schutzlevel sysop

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Quelle: Anézo 2003
Seite(n): 67, 68, Zeilen: 67:10ff; 68:1ff
[Marrink and Mark however showed in an extensive series of glycerolmonoolein (GMO) bilayer simulations that, at stress free conditions, the equilibrium area per lipid does not strongly] depend on the system size and concluded that the application of an external surface tension to compensate for suppressed fluctuations is not necessary [54].

In MD simulations of lipid bilayers is very important to choose the appropriate ensemble. While the NVT ensemble is the standard condition to simulate a protein in a crystal lattice, simulating a lipid bilayer at constant volume is rather not recommended, because the dimensions of the simulation unit cell are then determined by the area per lipid and the bilayer repeat spacing which are experimentally often not well known. Furthermore, even if the system density is correct, the NVT ensemble may dissimulate shortcomings in the force field. Performing simulations with the NPT ensemble has the advantage to let the implemented interaction potential determine the optimal system dimensions and then to assess the quality of the simulation by comparing the properties that one is interested in with available experimental data. Employing an isotropic pressure tensor is equivalent to imposing a condition of zero surface tension on the lipid interface. In the case of an unstressed bilayer, the surface tension is equal to zero at the free energy minimum. In the bilayer patches simulated, it has been argued that it is necessary to apply a finite surface tension to compensate the fact that longwave undulations are suppressed in smaller systems, especially under PBC. There is unfortunately little guide from experiment on the precise value to adopt for the surface tension. Lindahl and Edholm attempted to split up the surface stresses in a DPPC bilayer into several components and to determine each of them using local virial calculations [55]. They showed that the tension in the bilayer is the sum of two large opposing tensions: an attractive energy in the headgroup region and a repulsive one in the hydrocarbon region. For the overall surface tension to vanish, these two contributions must exactly balance. This is effectively what they found despite a large uncertainty. Such calculations are indeed very sensitive to the force field employed, the treatment of long-range electrostatics, and other technical parameters of the simulation protocol. Consequently, it is still not clear whether a surface tension has to be applied or not in lipid membrane simulations. But, insofar as it is very difficult to assign a concrete value to the surface tension and it is quite possible that the required tension is equal to zero, the [majority of lipid simulations are performed using the NPT ensemble, which seems to provide reliable macroscopic conditions.]

54. Marrink, S. J.; Mark, A. E. J. Phys. Chem. B 2001, 105, 6122.

55. Lindahl, E.; Edholm, O. J. Chem. Phys. 2000, 113, 3882.

[page 67]

Marrink and Mark however showed in an extensive series of glycerolmonoolein (GMO) bilayer simulations that, at stress free conditions, the equilibrium area per lipid does not strongly depend on the system size and concluded that the application of an external surface tension to compensate for suppressed fluctuations is not necessary [103].

Discussions are still ongoing to answer the question: “what are the appropriate ensembles for simulating hydrated lipid membranes?”. While the NVT ensemble is the standard condition to simulate a protein in a crystal lattice, simulating a lipid bilayer at constant volume is rather not recommended, because the dimensions of the simulation unit cell are then determined by the area per lipid and the bilayer repeat spacing which are experimentally often not well known. Furthermore, even if the system density is correct, the NVT ensemble may dissimulate shortcomings in the force field. Performing simulations with the NPT ensemble has the advantage to let the implemented interaction potential determine the optimal system dimensions and then to assess the quality of the simulation by comparing the properties that one is interested in with available experimental data. Employing an isotropic pressure tensor is equivalent to imposing a condition of zero surface tension on the lipid interface. In the case of an unstressed bilayer, the surface tension is equal to zero at the free energy minimum. In the bilayer patches simulated, it has been argued that it is necessary to apply a finite surface tension to compensate the fact that longwave undulations are suppressed in smaller systems, especially under PBC. There is unfortunately little guide from experiment on the precise value to adopt for the surface tension. Lindahl and Edholm attempted to split up the surface stresses in a DPPC bilayer into several components and to determine each of them using local virial calculations [104]. They showed that the tension in the bilayer is the sum of two large opposing tensions: an attractive energy in the headgroup region and

[page 68]

a repulsive one in the hydrocarbon region. For the overall surface tension to vanish, these two contributions must exactly balance. This is effectively what they found despite a large uncertainty. Such calculations are indeed very sensitive to the force field employed, the treatment of long-range electrostatics, and other technical parameters of the simulation protocol. Consequently, it is still not clear whether a surface tension has to be applied or not in lipid membrane simulations. But, insofar as it is very difficult to assign a concrete value to the surface tension and it is quite possible that the required tension is equal to zero, the majority of lipid simulations are performed using the NPT ensemble which seems to provide reliable macroscopic conditions.

[103] S. J. Marrink and A. E. Mark. J. Phys. Chem. B, 105:6122–6127, 2001.

[104] E. Lindahl and O. Edholm. J. Chem. Phys., 113:3882–3893, 2000.

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