Simulation of the channel

The preliminary results of our ion channel simulation are in! Basically current knowledge has it that when the channel is open, sodium ions will pass through freely because they are stripped of solvent water molecules. I theorized that the voltage sensing domain (VSD)or voltage sensing part of the protein would cooperate with this solvent stripping.The Gibbs free energy of solvation was calculated with the VSD in the upper (open) and down (closed) positions and the free energy values compared. The free energy was found to be lower for the open state corresponding to the solvent being more tightly held. This is contrary to what I had theorized - lower Gibbs free energy equates to higher stability of the solvated ion. In conclusion cooperatively might still be inferred if I suppose that contraction of the solvation shell would allow the ion to pass. As a follow up to the preliminary study, this possibility will be explored