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.
In coarse grained molecular dynamics (CGMD) simulations, small groups of atoms are treated as single particles (beads) and the forces between these particles are derived from the interatomic forces. The effect of this is to severely reduce the number of particles in a simulation, thereby allowing for the consideration of a larger number of atoms. It has also proven to be a valuable tool in probing time and length scales of systems beyond that used in all-atom molecular dynamics (AAMD) simulations. The down side of this is that the inter-particle interactions are less accurate. However, if these coarse grained particles are chosen carefully, such simulations can provide much useful information. There are different levels of how the coarse grains are constructed. For example, CG systems have been developed using tens or hundreds of atoms per CG bead in some studies of amino acids in biological science. By contrast, for other systems, a single CG bead is used to replace just two or three atoms.In this paper, the interaction of a carbon nanotube (CNT) with a lipid bilayer membrane is studied using both coarse grained and atomistic MD in an effort to understand the usefulness of the CGMD method for such simulations. Our preliminary studies of the interaction of a CNT with a lipid bilayer points indicates that such nano-tubes inserted into a membrane could be stable. This means that it could be used as an agent in the delivery of drugs. It would be good if these simulations could be repeated using AAMD simulations to confirm the validity of these results.
The attractive interactions between Boron, B, and Nitrogen, N, codoped atoms in graphene nanosheets are calculated based on Density Functional Theory, DFT, using Quantum Espresso software, QE. We realized that the electron density distribution is strongly localized along B-N bonds when there is a strong attractive force between the dopant's atoms; however, when there is a lesser attractive force, the electrons are delocalized over the B-N bond of the hexagonal graphene ring. The molecular dynamic simulation is done to determine the thermal stability of the nanosheets. Additionally, since graphene is made up of a hexagonal structure, the locations of B or N atoms in para-, meta-, and ortho-positions are more sensitive. Furthermore, the symmetry of spin up and spin down of the band structure show that these monolayers are nonmagnetic materials. Moreover, we employed Phonopy software to demonstrate the specific heat capacity of the monolayers from 0 K to 1000 K, which is in the high-temperature limit. Based on our estimations, the BN-codoped graphene monolayers are beneficial in thermoelectric and optoelectronic devices.
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