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Permeation of Organometallic Compounds through Phospholipid Membranes

von Dr. Raycho Yonchev

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[1.] Ry/Fragment 047 01 - Diskussion
Zuletzt bearbeitet: 2016-03-04 17:31:43 WiseWoman
Anézo 2003, Fragment, Gesichtet, KomplettPlagiat, Ry, SMWFragment, Schutzlevel sysop

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Seite: 47, Zeilen: 1 ff. (entire page)
Quelle: Anézo 2003
Seite(n): 63, 64, Zeilen: 63, 64
[PBC have been widely used in membrane] simulations, as they naturally emulate the effectively infinite extent of the membrane. PBC present nonetheless a few disadvantages. The use of PBC inhibits the occurrence of long wavelength fluctuations in the simulated membrane: for a box side L, the periodicity will suppress any fluctuations with a wavelength greater than L. The membrane simulated with PBC is indeed precluded from exhibiting bending or splay modes, because such modes would prevent the matching of the membrane with its image at the lateral boundaries of the central unit cell. It was also shown that PBC can induce some artifacts, such as the occurrence of spurious collective motions or orientations, e.g. an excessive collective tilt of the hydrocarbon chains [51] or the introduction of anisotropies into the membrane structure. Such effects can be alleviated by enlarging the simulation box: if the box is large enough, the boundaries have little effect on the interior of the box. This is of course at the cost of computational speed. It should be mentioned that, after the equilibration phase of the simulation has been reached, doing a sampling run on a large membrane patch is almost as economical as on a small one. A larger system gives indeed more information per picosecond of simulation time than a smaller one, since it provides data sampling not only temporally but also spatially. After equilibration of the system, a membrane consisting of 100 lipid molecules will provide as much data in a 100 ps simulation as a membrane of 50 lipids in 200 ps. The data collected with the larger membrane will be furthermore less affected by boundary artifacts.

The competing method to face edge effects is to enclose the system in a sphere, with restraints and often stochastic forces acting at the boundary to mimic an extended system. One possibility consists in surrounding the system with repulsive walls. Another possibility consists in constraining the outermost atoms to their initial position by a harmonic force. Stochastic boundary conditions fail, however, into generating an effectively infinite bilayer system and the restraints applied to the molecules located at the boundaries may influence the behavior of the rest of the system.

Although computationally more expensive, PBC are generally preferred to stochastic boundary conditions for the simulation of bilayer systems.


51. Chiu, S. W.; Clark, M. M.; Balaji, V.; Subramaniam, S.; Scott, H. L.; Jakobsson, E. Biophys. J. 1995, 69, 1230.

[page 63]

PBC have been widely used in membrane simulations, as they naturally emulate the effectively infinite extent of the membrane. PBC present nonetheless a few disadvantages. The use of PBC inhibits the occurrence of long wavelength fluctuations in the simulated membrane: for a box side L, the periodicity will suppress any fluctuations with

[page 64]

a wavelength greater than L [95]. The membrane simulated with PBC is indeed precluded from exhibiting bending or splay modes, because such modes would prevent the matching of the membrane with its image at the lateral boundaries of the central unit cell [96]. It was also shown that PBC can induce some artifacts, such as the occurrence of spurious collective motions or orientations, e.g. an excessive collective tilt of the hydrocarbon chains [97] or the introduction of anisotropies into the membrane structure. Such effects can be alleviated by enlarging the simulation box: if the box is large enough, the boundaries have little effect on the interior of the box. This is of course at the cost of computational speed. It should be mentioned that, after the equilibration phase of the simulation has been reached, doing a sampling run on a large membrane patch is almost as economical as on a small one. A larger system gives indeed more information per picosecond of simulation time than a smaller one, since it provides data sampling not only temporally but also spatially. After equilibration of the system, a membrane consisting of 100 lipid molecules will provide as much data in a 100 ps simulation as a membrane of 50 lipids in 200 ps; the data collected with the larger membrane will be furthermore less affected by boundary artifacts.

The competing method to face edge effects is to enclose the system in a sphere, with restraints and often stochastic forces acting at the boundary to mimic an extended system. One possibility consists in surrounding the system with repulsive walls. Another possibility consists in constraining the outermost atoms to their initial position by a harmonic force [44]. Stochastic boundary conditions fail, however, into generating an effectively infinite bilayer system and the restraints applied to the molecules located at the boundaries may influence the behavior of the rest of the system.

Although computationally more expensive, PBC are generally preferred to stochastic boundary conditions for the simulation of bilayer systems.


[44] 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.

[95] M. P. Allen and D. J. Tildesley. Computer Simulation of Liquids. Clarendon Press, Oxford, 1996.

[96] E. Jakobsson, S. Subramaniam, and H. L. Scott. Strategic Issues in Molecular Dynamics Simulations of Membranes. In: Biological Membranes: A Molecular Perspective from Computation and Experiment. K. M. Merz Jr. and B. Roux (Eds.), Birhäuser, Boston, 1996.

[97] S.-W. Chiu, M. M. Clark, V. Balaji, S. Subramaniam, H. L. Scott, and E. Jakobsson. Biophys. J., 69:1230–1245, 1995.

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