The application of condensed matter methods to the study of the conformation and elastic properties of biopolymers and the transport of DNA through cell membranes

Matthai, Clarence Cherian; March, N. H.

doi:10.1007/s00214-011-1022-9

Cited by 1 publication

(1 citation statement)

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“…While none of these can hope to describe all the chemical processes accurately, the goal has been to construct force fields that are accurate enough but which can also be used for large scale simulations, both from the point of system sizes and simulation time. 3,4 In modelling the diffusion of atoms, ions, or molecules across the biological membranes it is therefore important to utilise force fields that reproduce amongst other things, the experimentally determined diffusion coefficients.…”

Section: Introductionmentioning

confidence: 99%

Computer simulations of the diffusion of Na+ and Cl− ions across POPC lipid bilayer membranes

Salih

Matthai

2017

The Journal of Chemical Physics

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We have carried out molecular dynamics simulations using NAMD to study the diffusivity of Na and Cl ions across a POPC lipid bilayer membrane. We show that an imbalance of positively and negatively charged ions on either side of the membrane leads to the diffusion of ions and water molecules. We considered the cases of both weak and very strong charge imbalance across the membrane. The diffusion coefficients of the ions have been determined from the mean square displacements of the particles as a function of time. We find that for strong electrochemical gradients, both the Na and Cl ions diffuse rapidly through pores in the membrane with diffusion coefficients up to ten times larger than in water. Rather surprisingly, we found that although the Na ions are the first to begin the permeation process due to the lower potential barrier that they experience compared to the Cl ions, the latter complete the permeation across the barrier more quickly due to their faster diffusion rates.

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Section: Introductionmentioning

confidence: 99%