Pore free energy, calculation

The other major limitation of membrane simulations is the time and length scale we are able to simulate. We are currently able to reach a microsecond, but tens to hundreds of nanosecond simulations are more common, especially in free energy calculations. The slow diffusion of lipids means we are not able to observe many biologically interesting phenomena using equilibrium simulations. For example, we would not observe pore formation in an unperturbed bilayer system during an equilibrium simulation, and even pore dissipation is at the limits of current computational accessibility. 

LJ in a planar slit V-L P-T, P-pore width Free-energy calculations 74... 

Wohlert, J., den Otter, W.K., Edholm, O., Briels, W.J. Free energy of a trans-membrane pore calculated from atomistic molecular dynamics simulations. J. Chem. Phys. 2006, 124, 154905. 

As a typical example of CEDFT calculations, we present in Fig. 1 the capillary condensation isotherm of N2 in a cylindrical pore mimicking the pore channel in MCM-41 mesoporous molecular sieves. The isotherm is presented in co-ordinates adsorption N versus chemical potential p Calculations were performed at 77 K for the internal diameter of 3.3 nm up to the saturation conditions, point H. We used Tarazona s representation of the Helmholtz free energy [6] with the parameters for fluid-fluid and solid-fluid interaction potentials, which were employed in our previous papers [7]. We distinguish three regions on the isotherm. The adsorption branch OC corresponds to consecutive formation of adsorption layers. Note that the sharp transitions between the consecutive layers are not observed in experiments. They are caused by a well-known shortcoming of the model employed, which ignores intrinsic to real... 

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