| Atomistic computational models of molecular systems hold great promise in that (1) they are capable of giving high-resolution insight, (2) they are comparatively inexpensive, (3) they are highly adjustable, (4) they are basically waste-free, and (5) validation thereof with experimental reference points is trivial. In the last few decades, computational approaches to aggregate systems such as lipid bilayers have come of age. The increase in processor speeds coupled with the power of parallelization and the development of elegant methods has brought into range simulations of systems as large as hundreds of thousands of atoms and timescales into the microsecond regime. With these capabilities, it is increasingly important to develop and qualify good models. This dissertation is divided into three parts, all of which serve to evaluate and refine an atomistic model of phosphatidylcholine lipid bilayers in the gel and/or liquid crystalline (LC) phase.;In the first part, di-stearoyl-phosphatidylcholine (DSPC, di-C18-PC) and di-myristoyl-phosphatidylcholine (DMPC, di-C14-PC) in the gel and LC phases were simulated in the semi-grand canonical ensemble (DeltamuPT ) at a temperature between their experimental main phase transition temperatures Tm,exp. Matched pairs (x DSPC,gel : xDSPC,LC) were identified that were in good agreement with experimental systems, and demixing was observed in the gel phase, where strong deviations from ideality were manifested by a tendency for the short-tail lipid to laterally associate. In the second part of this thesis, a two-phase (gel and LC) system was simulated with a pre-existing interface to probe the phase character over a range of temperatures. DSPC and di-palmitoyl-phosphatidylcholine (DPPC, di-C16-PC) were simulated in the isothermal-isobaric ensemble (NPT) at temperatures far below and above the supposed Tm. Both melting and congealing was observed, and fitting the rates of transition to an Arrhenius-like equation gave estimates of Tm,virtual within about 5 K, or a 2% error in terms of absolute temperature. Investigation of congealing interfaces revealed that, while tails of lipids deposited onto an existing gel adopt the same tilt angle and direction as the host gel, the glycerol backbones are arranged in a disordered pattern, even if the backbones of the host gel are aligned. This glycerol-backbone orientational disorder has been observed experimentally and is the focus of the next section. Finally, two gel models were described and compared. Except the gel model introduced in the first part of this thesis, all gel models described in the literature have been based on the crystal structure. Here, two gels are described and compared, one with disorder in the glycerol-backbone super-lattice, and the other aligned and oriented, like the crystal structure. The backbone-disordered gel is shown to be more like experimental gels structurally and thermodynamically. The structures of gels are shown to be highly influenced by the initial configuration, and the significant effect of backbone arrangement on the overall structure suggests that models of the gel phase should not be based on the crystal structure without regard to defects in the backbone super-lattice. |
