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Recent experiments and computer simulations observe various geometrical formations of nanobubbles in van der Waals heterostructures. Among the well studied dome and tent geometries, there is yet least understood pancake graphene nanobubbles (GNB). This more exotic form exhibits discrete values of vertical sizes around just a few diameters of the molecules trapped inside the GNBs. We develop a model based on the membrane theory and confined fluids thermodynamics. Our approach describes the equilibrium properties of such flat GNBs. We show that discrete pancake geometry is the result of disjoining pressure induced by the trapped fluid inside GNB. The calculated total energy defines a discrete series of the metastable states with the pancake heights, which are multiple to molecular diameter. We observe that the value and the distribution of the total energy minima crucially depend on the temperature. The energy barriers between metastable states decrease as the temperature becomes larger. Also, we demonstrate that the pancake forms are favorable in the cases of sufficiently low membrane-substrate adhesion energy and the small number of trapped molecules. These properties are in agreement with the published simulations and experiments. The numerical comparison of our result with molecular dynamics results additionally shows the adequacy of the proposed model.