Studying the mechanical properties of cells in a model system is useful for exploration of cell-targeted methods for Alzheimer’s disease and cancer patients. Cell structure between these cells have many mechanical differences that have yet to be analyzed. Studying the mechanical properties of a cell can aid in determining if they can be manipulated to enhance cell structure. This collaborative study focuses on the elastic and viscoelastic properties of the Xenopus Laevis Oocyte cell membrane. The three main components of the Oocyte bilayer (Cholesterol, Phosphatidylcholine, and Sphingo lipids) were simulated in both an all-atom (AA) and coarse-grained (CG) periodic environment. The differences between AA and CG simulations were determined to see which method would give reliable membrane structure coordinates. There are advantages to using CG simulations opposed to AA simulations because the surface area of the membrane is needed opposed to individual atoms. An example of a simple membrane simulation is to build an environment containing DDPC in water, run this simulation to get trajectories, and transform the membrane surface to get height undulation values. The environment of simple membranes was generated using CHARMM (online graphical user interface tool) with the single lipid types: DDPC, DPPC, POPC, PYPC, PSM, NSM and CHOL. The trajectories and structure files were found using the Molecular Dynamic (MD) simulation software’s: GROMACS, LAMMPS, and OPENMM. The structure was monitored using VMD (visualization software) and analyzed using R-Studio (statistical computing programming language). A fluctuation spectrum of the membrane was obtained by graphing average height versus the wave numbers. This resulted in identifying the bending rigidity values and elastic constants.

Mechanical properties of molecular dynamic simulated membranes

ACS Spring 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.