Graduation Year


Document Type




Degree Name

Master of Science (M.S.)

Degree Granting Department

Biology (Cell Biology, Microbiology, Molecular Biology)

Major Professor

Sameer Varma, Ph.D.

Co-Major Professor

Sagar Pandit, Ph.D.

Committee Member

H. Lee Woodcock, Ph.D.

Committee Member

Jianjun Pan, Ph.D.


Gouy-Chapman Theory, Molecular Dynamics


Phospholipids are present in all parts of cells and are used in many signalling and struc- tural roles. As structural molecules they act as the main component of cellular membranes. Bilayer properties are heavily influenced by the structure of their component polar lipids, and different lipids are found in different organisms. A distinguishing feature of Archaeal plasma membranes is that their phospholipids contain ether-links, as opposed to bacterial and eukaryotic plasma membranes where phospholipids primarily contain ester-links. In our work we examine the effects of salt on bilayer structure in the case of both ester- and ether-linked lipid bilayers. We use molecular dynamics simulations and compare equilibrium properties of two model lipid bilayers in NaCl salt solution — POPC and its ether-linked analog that we refer to as HOPC. We make the following key observations. The headgroup region of HOPC “adsorbs” fewer ions compared to the headgroup region of POPC. Consistent with this, we note that the Debye screening length in the HOPC system is ∼10% shorter than that in the POPC system. Herein, we introduce a protocol to identify the lipid-water inter- facial boundary that reproduces the bulk salt distribution consistent with Gouy-Chapman theory. We also note that the HOPC bilayer has excess solvent in the headgroup region when compared to POPC, coinciding with a trough in the electrostatic potential. Waters in this region have longer autocorrelation times and smaller lateral diffusion rates compared to the corresponding region in the POPC bilayer, suggesting that the waters in HOPC are more strongly coordinated to the lipid headgroups. Furthermore, we note that it is this region of tightly coordinated waters in the HOPC system that has a lower density of Na+ ions. Based on these observations we conclude that an ether-linked lipid bilayer has a lower vbinding affinity for Na+ compared to an ester-linked lipid bilayer.