Molecular Dynamics Simulations of Axonal Membrane in Traumatic Brain Injury

University essay from KTH/Skolan för teknik och hälsa (STH)

Abstract: The following project presents in silico investigation of axonal damage in Diffuse Axonal Injury (DAI). When axons face a shear force, orientation of the lipids in the axonal membrane gets disrupted. Depending on the value of the force, a tensile strain causes the axons to get partially or fully deformed and in some cases a pore forms in the membrane. Using Molecular Dynamic (MD) simulation and a coarse grain model, a series of bilayers with various bilayer structure (single bilayer, parallel bilayer and cylindrical bilayer) and similar composition to biological axonal membrane were simulated. This was initially done to investigate the strain rate dependency of the bilayers, and their viscoelastic ability on returning to their original shape from their deformed forms. To achieve this, various deformation velocities were applied to the bilayers reaching 20% strain and relaxing the bilayer after. Additionally, the bilayers were deformed further until they reached a pore. It was found that the bilayers can almost recover from their deformed forms to their original length when they were deformed at 20% strain level. In conjunction, no correlation between the deformation velocity and lipid deformation was observed. Further, it was found that bilayers with different lipid percentage to axonal bilayer has different strain values for water penetration and for pore formation. The strain value for cylindrical bilayer was found very high compared to the strain values found in vitro. The strain for pore formation of parallel and single bilayer was found to be around 80% to 90% and for water penetration was found to be 70% for single bilayer and 50% for parallel bilayer. A slight difference in strain for pore formation between single and parallel bilayer was found which showed the bilayer structure can play a role in simulation results. The effect of the length in the simulations results was also observed where shorter bilayers showed lower strain for pore formation compared to longer bilayers. 

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