Biological and non-biological interfaces were studied using all-atom molecular dynamics simulations to understand the interaction between different molecules at the atomic level. Simulation were run to analyze the dynamics and structure of cell membrane models and their interaction with a specific protein. Additionally, the effect of a small alcohol at the water-oil interface was examined as a model for amphiphilic molecules, which are relevant in chemistry and biology.

Previously developed organelle-specific membrane models for yeast S. cerevisiae (Biochem. 54:6852-6861) were improved to reflect leaflet asymmetry of the trans-Golgi network (TGN) and plasma membranes. Each model was built based on experimental trends to study interleaflet coupling and lipid clustering. The (previous) symmetric endoplasmic reticulum (ER) and TGN models were further used to study the effect of sterol type in the structural properties of the membrane, and lipid-protein interactions with a lipid transport protein in yeast, Osh4. The protein’s phenylalanine loop was determined to have the strongest interaction with the bilayer among the protein’s six binding regions (BBA-Biomemb. 1858:1584-1593). The protein’s lid, the ALPS-like motif (Amphipathic Lipid Packing Sensor), was also simulated with simple (2-lipid) bilayers and with the symmetric ER and TGN models. Key residues for peptide-membrane interaction were identified based on their interaction energy, and a time scale of ~1µs determined for stable peptide binding.

The interfacial dynamics between water and cyclohexane were examined in the presence of a hydrotrope - an amphiphilic molecule that reduces the interfacial tension between two liquids. Simulations were run for water-cyclohexane systems and all butanol isomers separately to understand the effect of this hydrotrope’s chemical structure on the interface. The results reproduced experimental data trends, showing that a hydrotrope concentration of as little as 0.6mol% in the aqueous phase reduces the interfacial tension to nearly half the value of a binary water-cyclohexane mixture. Tert-butanol was further compared with experimental studies showing that at low concentrations (< 10mol%) the simulations accurately reproduce experimental data. In addition, theoretical correlations from simulation data show the system follows van der Waals theory of smooth interfaces, and describe the crossover behavior of this hydrotrope from surfactant-like to co-solvent based on its concentration in solution, and describe the crossover behavior of this hydrotrope from surfactant-like to co-solvent based on its concentration in solution.