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Typus
KomplettPlagiat
Bearbeiter
Klgn
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Untersuchte Arbeit:
Seite: 56, Zeilen: 1 ff. (entire page)
Quelle: Anézo 2003
Seite(n): 73, 74, 75, Zeilen: 73:7-9,13-20; 74:20-32; 75:1ff
[Within the cutoff sphere, solute and solvent are] simulated in atomic detail, whereas the solvent outside the sphere is treated as a dielectric continuum.

The selection of methodologies for the simulation of lipid bilayer membranes is particularly complex: many choices must be made concerning force fields, boundary conditions, treatment of long-range interactions, and other technical parameters. The fact that so many simulations carried out under different conditions lead to similar results is certainly a consequence of favorable combinations of parameters, one shortcoming compensating for another one. No choice is in any case perfect and every decision involves trade-offs. Compromises have to be made between accuracy and efficiency or more exactly, owing to the enormous computational intensiveness of membrane simulations, between accuracy and feasibility [62].

II.2.7 Limitations of the MD technique

Although a powerful technique in many aspects, molecular dynamics presents a number of important limitations which must be kept in mind when using this technique and analyzing the results.

One obvious limitation is the length of the simulated time scale. Most trajectories to date are confined to the 10 ns regime, which does not allow the investigation of many biologically relevant processes. Another limitation is the size of the simulated system: the largest system that can be currently handled contains about tens of thousands of atoms, which corresponds to system sizes of the order of 5–10 nm. Such systems are still very small and do not enable one to study phenomena only present over longer distances. To circumvent this size problem, periodic boundary conditions are used to extend the system in a periodical manner. This approximation can however introduce some artifacts into the molecular behavior of the lipids, especially when the simulation box is not large enough. Both limitations have their origins in the available computer power. With the continuous increase in computer speed and the improvement of the actual computational algorithms, time scales and system sizes will be enhanced by at least one order of magnitude in the [near future and one can expect that MD simulations of lipid bilayers will reach microsecond capabilities in the future.]


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

Within the cutoff sphere, solute and solvent are simulated in atomic detail, whereas the solvent outside the sphere is treated as a dielectric continuum. [...]

The selection of methodologies for the simulation of lipid bilayer membranes is particularly complex: many choices must be made concerning force fields, boundary conditions, treatment of long-range interactions, and other technical parameters. The fact that so many simulations carried out under different conditions lead to similar results is certainly a consequence of favorable combinations of parameters, one shortcoming compensating for another one. No choice is in any case perfect and every decision involves trade-offs. Compromises have to be made between accuracy and efficiency or more exactly, owing to the enormous computational intensiveness of membrane simulations, between accuracy and feasibility [96]. [...]

[page 74]

3.2.4 Limitations of the MD technique

Although a powerful technique in many aspects, molecular dynamics presents a number of important limitations which must be kept in mind when using this technique and analyzing the results.

One obvious limitation is the length of the simulated time scale. Most trajectories to date are confined to the 10 ns regime, which does not allow the investigation of many biologically relevant processes. Another limitation is the size of the simulated system: the largest system that can be currently handled contains about tens of thousands of atoms, which corresponds to system sizes of the order of 5–10 nm. Such systems are still very small and do not enable one to study phenomena only present over longer distances. To circumvent this size problem, periodic boundary conditions are used to extend the system in a periodical manner. This approximation can however introduce some artifacts into the molecular behavior of the lipids, especially when the simulation box is not large enough. Both limitations have their

[page 75]

origins in the available computer power. With the continuous increase in computer speed and the improvement of the actual computational algorithms, time scales and system sizes will be enhanced by at least one order of magnitude in the near future and one can expect that MD simulations of lipid bilayers will reach microsecond capabilities in the next five years.


[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.

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The source is not given. The references contain a text processing artefact: "Birhдuser"

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