All MD simulations were performed using the large-scale atomic/molecular massively parallel simulator (LAMMPS) (31) simulation package and visualized using open visualization tool (OVITO) (32). Parameters corresponding to MoS2 for the Stillinger-Weber potential were obtained from (33). Use of this potential also required making appropriate changes to one of the LAMMPS source files as described in the paper of Jiang et al. (34). The substrate in these simulations is modeled as a planar triangular lattice of particles that are displaced in the z direction that conform to a donut geometry. The interaction between the flake and the substrate particles is Lennard-Jones with parameters σ = 5.0 Å and ε = 0.1 eV. Initially, a rectangular flake consisting of two zigzag rows of MoS2 having a width (in the x direction) of 400 Å was relaxed on the substrate. The bottom-most, the left-most, and the right-most atoms in the x direction were constrained to move in the y/z direction only. Subsequently, another zigzag row was added, and the total energy was minimized, while maintaining the same constraints. The relaxation of atoms was performed by energy minimization by first using the quickmin algorithm in LAMMPS (which essentially performs low-temperature MD) and then followed by conjugate-gradient minimization.

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