Structure of Dipalmitoylphosphatidylcholine/Cholesterol Bilayer at Low and High Cholesterol Concentrations: Molecular Dynamics Simulation

By using molecular dynamics simulation technique we studied the changes occurring in membranes constructed of dipalmitoylphosphatidylcholine (DPPC) and cholesterol at 8:1 and 1:1 ratios. We tested two different initial arrangements of cholesterol molecules for a 1:1 ratio. The main difference between two initial structures is the average number of nearest-neighbor DPPC molecules around the cholesterol molecule. Our simulations were performed at constant temperature (T = 50 degrees C) and pressure (P = 0 atm). Durations of the runs were 2 ns. The structure of the DPPC/cholesterol membrane was characterized by calculating the order parameter profiles for the hydrocarbon chains, atom distributions, average number of gauche defects, and membrane dipole potentials. We found that adding cholesterol to membranes results in a condensing effect: the average area of membrane becomes smaller, hydrocarbon chains of DPPC have higher order, and the probability of gauche defects in DPPC tails is lower. Our results are in agreement with the data available from experiments

Phase-ordering dynamics of the Gay-Berne nematic liquid crystal

Phase-ordering dynamics in nematic liquid crystals has been the subject of much active investigation in recent years in theory, experiments and simulations. With a rapid quench from the isotropic to nematic phase a large number of topological defects are formed and dominate the subsequent equilibration process. We present here the results of a molecular dynamics simulation of the Gay-Berne model of liquid crystals after such a quench in a system with 65536 molecules. Twist disclination lines as well as type-1 lines and monopoles were observed. Evidence of dynamical scaling was found in the behavior of the spatial correlation function and the density of disclination lines. However, the behavior of the structure factor provides a more sensitive measure of scaling, and we observed a crossover from a defect dominated regime at small values of the wavevector to a thermal fluctuation dominated regime at large wavevector.Comment: 18 pages, 16 figures, animations available at http://www.physics.brown.edu/Users/faculty/pelcovits/lc/coarsening.htm

Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane.

The structural and dynamical properties of a hydrated proton near the surface of DMPC membrane were studied using a molecular dynamics simulation. The proton transport between water molecules was modeled using the second generation multistate empirical valence bond model. The proton diffusion was found to be inhibited at the membrane surface. The potential of mean force for the proton adsorption to the membrane surface and its release back into the bulk water was also determined, yielding a small barrier in each direction. An efficient algorithm for Ewald summation calculations for the multistate empirical valence bond model is also introduced

Calculating the bulk modulus for a lipid bilayer with nonequilibrium molecular dynamics simulation.

Nonequilibrium molecular dynamics (NEMD) computer simulations are used to calculated the bulk modulus for a dimyristoylphosphatidylcholine bilayer. A methodology is developed whereby NEMD can be effectively used to calculate material properties for complex systems that undergo long time-scale conformational changes. It is found that the bulk modulus upon expansion from a zero stress state agrees well with experimental estimates. However, it is also found that the modulus upon contraction from a zero stress state is larger. From a molecular perspective, it is possible to explain this phenomena by examining the molecular origins of the pressure response. The finding that the two moduli are not equal upon compression and expansion is in apparent contradiction to osmotic stress experiments where the area modulus was found to be the same upon expansion and contraction. This issue is addressed

Interfacing molecular dynamics and macro-scale simulations for lipid bilayer vesicles.

A continuum-level model for a giant unilamellar vesicle (GUV) is bridged to a corresponding atomistic model of a dimyristoylphosphatidylcholine (DMPC) bilayer at various cholesterol concentrations via computation of the bulk modulus. The bulk modulus and other microscopically determined parameters are passed to a continuum-level model operating in time- and length-scales orders of magnitude beyond that which is accessible by atomistic-level simulation. The continuum-level simulation method used is the material point method (MPM), and the particular variation used here takes advantage of the spherical nature of many GUVs. An osmotic pressure gradient due to a solvent concentration change is incorporated into the continuum-level simulation, resulting in osmotic swelling of the vesicle. The model is then extended to treat mixtures of DMPC and cholesterol, where small domains of different composition are considered