College of Arts & Sciences

Joshua Weisberg

College of Arts & Sciences Physics

Faculty Mentor: Dr. Brigita Urbanc

Toward a Coarse-Grained Lipid Bilayer: Discrete Molecular Dynamics Study

Alzheimer’s disease (AD) is the prevalent form of dementia in elderly. AD pathology is associated with aberrant assembly of amyloid β-protein (Aβ) into oligomers, which are hypothesized to get embedded into a cellular membrane and form pores acting as ion channels, which cause influx of calcium ions, leading to cell death. The goal of our research project is to simulate a lipid bilayer using efficient discrete molecular dynamics in order to study interactions between Aβ oligomers and a membrane. In our simulations, we modeled each lipid molecule by three beads, one representing the hydrophilic head and two corresponding to hydrophobic tail beads. To simulate a bilayer, we placed 200 spatially separated lipid molecules into a cubic lattice and coded in attraction potentials between the tail beads, which facilitated their self-assembly into a bilayer. After simulations of lipid self-assembly at different temperatures, including room to physiological temperature range (0.13 < T <0.15), were completed, we calculated the specific heat to identify the temperatures, at which the gas-liquid and liquid-gel phase transitions occurred. Using Visual Molecular Dynamics to display the lipid self-assembly trajectories, we confirmed that a stable liquid phase of a lipid bilayer in the temperature range [0.12, 0.25]. We will further characterize the gel and the liquid phases of the lipid bilayer in terms of its orientational order, density profiles, and diffusion constants.