Paper title:

Collective Diffusion Model for Water Permeation through Microscopic Channels

 

Journal:

J. Phys. Chem. B 2012, 116, 13459?13466

 

Author/s:

Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten

Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews, Urbana, Illinois 61801, USA

 

Summary:

This paper proposes a collective diffusion model which can be used to determine the osmotic permeability of a water channel from molecular dynamics (MD) simulations.

Equilibrium MD simulations were performed in 2 setups, one with (6,6) CNT and another with (15,15) CNT. After a simulation time of 40 and 20 ns, respectively, diffusion coefficients were obtained from MSD values.

Nonequilibrium simulations were performed by adding a chemical potential difference. Chemical potential difference was added by inducing a hydrostatic pressure difference. This was done by applying a constant force on all the water molecules of a water layer with defined thickness.

The study was able to show how water transport behaves according to the collective diffusion model. In the collective diffusion model, water movement at equilibrium is described as an unbiased diffusion along a single collective coordinate. On the other hand, water movement in the presence of a chemical potential difference is described as a one-dimensional diffusion in a linear potential.

Contribution and application:

This paper gives a good explanation about the difference between equilibrium and nonequilibrium MD simulations in the context of water transport in channels. It also discusses the limitations of the small timescale of MD simulations in relation to osmotic studies. The paper also gives a detailed method of calculating diffusion coefficients (molecules/ns) across a CNT.

By: Hannah Ebro

hannah@gist.ac.kr