Ry/Fragment 049 01

< Ry

31.177Seiten in
diesem Wiki

 Typus KomplettPlagiat Bearbeiter Klgn Gesichtet
Untersuchte Arbeit:
Seite: 49, Zeilen: 1 ff. (entire page)
Quelle: Anézo 2003
Seite(n): 65, 66, Zeilen: 65: 20-32; 66:1ff
[Furthermore, accurate experimental data about structural membrane parameters are often limited to a few single lipid component bilayers and, in the case of membranes made up of mixture of lipids, experiments provide only indirect guidance for assigning the appropriate] simulation cell dimensions, making membrane simulations using constant volume algorithms difficult.

NPT ensemble. The constant pressure and temperature or isobaric-isothermal ensemble NPT is most often applied to the simulation of membranes. After specification of the pressure tensor P, the size and shape of the simulation box adjust to maintain the pressure along each box dimension. Or, in other words, the computed pressure is fed back as a control on the size of the system. If the instantaneous pressure is higher (lower) than the set point, the system is expanded (contracted) slowly as the simulation proceeds. Thus, using this method, the initial dimensions of the system do not need to be approximated, since the system finds its size by itself, based on the force field employed. This ensemble opens up the possibility for validating simulations by checking their ability to reproduce important structural parameters like the area per lipid or the bilayer thickness when they are known and for predicting these parameters when they have not been determined experimentally. Generally, an isotropic pressure tensor (Pxx =Pyy =Pzz) is applied, with both lateral and perpendicular components usually equal to 1 bar (it should be noted that, within the numerical accuracy of pressure algorithms, a pressure of 1 bar is equivalent to a pressure of zero). An isotropic pressure implies that there is no surface tension in the bilayer. The greatest advantage of the NPT ensemble is that it provides a stringent test of the potential energy parameters implemented in the force field: the system adjusts its density according to the force field i.e., if the latter is appropriate, the right density will be naturally reached during the simulation.

NγT ensemble. The constant surface tension and temperature ensemble is a variant of the NPT ensemble and corresponds to a constant anisotropic pressure tensor. Anisotropic pressures along and perpendicular to the membrane plane give rise to a surface tension in the plane of the bilayer. The surface tension is defined by the relation δWdA, where δW represents the work required to change the surface area by dA. This also means that the surface tension is equal to the derivative of the free energy with respect to the area at [constant temperature and volume: $\gamma=\left ( \frac{\partial F}{\partial A} \right )_{T,V}$ .]

[page 65]

Furthermore, accurate experimental data about structural membrane parameters are often limited to a few single lipid component bilayers and, in the case of membranes made up of mixture of lipids, experiments provide only indirect guidance for assigning the appropriate simulation cell dimensions, making membrane simulations using constant volume algorithms difficult.

NPT ensemble The constant pressure and temperature or isobaric-isothermal ensemble NPT is most often applied to the simulation of membranes. After specification of the pressure tensor P, the size and shape of the simulation box adjust to maintain the pressure along each box dimension. Or, in other words, the computed pressure is fed back as a control on the size of the system. If the instantaneous pressure is higher (lower) than the set point, the system is expanded (contracted) slowly as the simulation proceeds. Thus, using this method, the initial dimensions of the system do not need to be approximated, since the system finds its size by itself, based on the force field employed. This ensemble opens up the possibility for

[page 66]

validating simulations by checking their ability to reproduce important structural parameters like the area per lipid or the bilayer thickness when they are known and for predicting these parameters when they have not been determined experimentally. Generally, an isotropic pressure tensor (Pxx = Pyy = Pzz) is applied, with both lateral and perpendicular components usually equal to 1 bar (it should be noted that, within the numerical accuracy of pressure algorithms, a pressure of 1 bar is equivalent to a pressure of zero). An isotropic pressure implies that there is no surface tension in the bilayer. The greatest advantage of the NPT ensemble is that it provides a stringent test of the potential energy parameters implemented in the force field: the system adjusts its density according to the force field i.e., if the latter is appropriate, the right density will be naturally reached during the simulation.

NγT ensemble The constant surface tension and temperature ensemble is a variant of the NPT ensemble and corresponds to a constant anisotropic pressure tensor. Anisotropic pressures along and perpendicular to the membrane plane give rise to a surface tension in the plane of the bilayer. The surface tension γ is defined by the relation δW = γ dA, where δW represents the work required to change the surface area by dA. This also means that the surface tension is equal to the derivative of the free energy with respect to the area at constant temperature and volume: $\gamma=\left ( \frac{\partial F}{\partial A} \right )_{T,V}$.

 Anmerkungen The source is not given. Sichter (Klgn), WiseWoman