Mathematical beading can be viewed as a process of analog computation. Combining the physical properties of beads, the figure-eight stitch and suitable algorithms, an approximate three-dimensional molecular structure for a molecule can be created through beading. The hard-sphere repulsion among beads and fishing strings that hold the whole structure together effectively mimic repulsion and attraction in the microscopic molecules. We demonstrate these ideas by creating a bead model of two-layer Sierpin ́ski buckyball fused by 60 buckyballs.