Gay-Berne Ellipsoids Research Articles

Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation model

AbstractThe development of a coarse‐grained reduced‐representation model of the hydrocarbon region of a biological membrane is reported. The potential is based on the popular Gay–Berne model of liquid crystals, and involves the linking of individual Gay–Berne ellipsoids by harmonic springs to form each hydrocarbon chain. Diffusion coefficients and order parameters have been calculated by molecular dynamics computer simulations for a range of parameter sets. The results clearly demonstrate the presence of a phase transition from an ordered low‐temperature solid phase reminiscent of the Lβ′ phase of phospholipids, to a high‐temperature disordered phase reminiscent of the Lα phase. Order parameters calculated for each layer of the model are consistent with the experimental segmental order parameters reported for dipalmitoyl phosphatidylcholine. The application of this model to the study of small molecule diffusion within the membrane core is proposed. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1622–1633, 2001

Molecular shape and flexoelectricity

Monte Carlo simulations were performed of systems of wedge-shaped objects formed from Gay-Berne ellipsoids joined to Lennard-Jones spheres. We studied two different wedge shapes, one more asymmetric than the other. The bend and splay flexoelectric coefficients were measured in the isotropic and smectic phases using linear response theory, and found to be negligibly small in the isotropic phase. We found a close connection between the properties of the intermolecular potential and the flexoelectric coefficients measured in the smectic phase. In particular, negligible bend coefficients were found for both shapes and a larger magnitude of the splay coefficient for the more prominent wedge, in accord with Meyer's original mechanism for flexoelectricity. The less prominent wedge produced a splay flexoelectric coefficient with the opposite sign due to the attractive tail of the intermolecular potential and the relative narrowness of the molecular head.

Defect configurations and dynamical behavior in a gay-berne nematic emulsion

To model a nematic emulsion consisting of a surfactant-coated water droplet dispersed in a nematic host, we performed a molecular dynamics simulation of a droplet immersed in a system of 2048 Gay-Berne ellipsoids in a nematic phase. Strong radial anchoring at the surface of the droplet induced a Saturn ring defect configuration, consistent with theoretical predictions for very small droplets. A surface ring configuration was observed for lower radial anchoring strengths, and a pair of point defects was found near the poles of the droplet for tangential anchoring. We also simulated the falling ball experiment and measured the drag force anisotropy, in the presence of strong radial anchoring as well as zero anchoring strength.

Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres

Detailed molecular dynamics simulations of the rotational and the translational motions of Gay–Berne ellipsoids in a sea of Lennard-Jones spheres have been carried out. It is found that while the translational motion of an ellipsoid is isotropic at low density, it becomes increasingly anisotropic with density until the ratio of the parallel to the perpendicular diffusion coefficients becomes nearly equal to the value of the aspect ratio at high density. The latter is in agreement with the prediction of Navier–Stokes hydrodynamics with slip boundary condition. The product of the translational diffusion coefficient and the rotational correlation time also attains a hydrodynamic-like density independent behavior only at high density. The reorientational correlation function becomes nonexponential at high density and low temperature where it also develops a slow decay. The perpendicular component of the velocity time correlation function exhibits a clear double minimum, only at high density, which becomes more pronounced as the aspect ratio is increased.