Abstract
We perform molecular dynamic simulations to understand the behavior and mechanism of AFM indentation through a lipid bilayer which is suspended by hydrophobic substrate on a nano pore. This work starts from the study of basic properties of lipid bilayer. By simulating lipid bilayer in bulk with solvent environment, we calculate membrane thickness, area per lipid, and order parameter. Three states are found from low temperature to high temperature: tilted gel state, interdigitated gel state, and liquid state. Besides main transition which is from gel state to liquid state, we also observe transition from tilted gel state to interdigitated gel state. The work in phase transition consists with many previous works, which demonstrate the reality of our model and setup. The second part of the work is AFM indentation of suspended lipid bilayer. We build the system with suspended lipid bilayer on a nano pore. After a long period of equilibrium, bilayer is indented by AFM probe. The shape of the side wall of substrate is a straight cliff with 90 degree at its corners. The probe is a half sphere located at the center of the pore. From the contact between the lipid bilayer and the probe, we conclude 5 stages: 1. the pressed lipid bilayer bends to arched curve, while the edges of lipid bilayer slide on the side wall of substrate. 2. The edges of lipid bilayer reach the end of pore on the side wall and stop sliding, while bending continuously proceeds. 3. The breaking at bottom monolayer happens in the center region, which cause chaotic distribution in the region. 4. Lipids at the region of monolayer breaking reform into interdigitated gel structure. 5. The fracture happens at the conjunction between transformed region and non-transformed region due to incongruence between the two regions. The sliding mechanism is mentioned first time and really surprises us. This mechanism eliminates the stress concentration between side wall of substrate and edge of lipid bilayer, and avoids the early breaking at the contact surface. At the end, we calculate the spring constant, maximum force on probe, and maximum depth of indentation. We find the data are in good agreement with experimental result. This further verifies the validity of our study. In the research, we employ some new methods such as Quasi-2D and phantom solvent which can be used in other researches in this field.