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The following prototypes of nano-mechanical systems were done in the MulPhys framework using the Hedra solver with dynamical bonding model.

Molecular self-assembly around a Y-shaped frame

An animation (animated gif, 13MB).


Green balls represent freely moving atoms and red ones represent the atoms whose positions are fixed in space. The interaction potential between the atoms is of Lennart-Jones type. Each green atom can form of up to 6 bonds with other green atoms (blue segments) and one bond with a red atom (not shown). Green atoms are generated randomly in space around the red Y-frame and move following the interaction forces. The kinematics of the motion is not momentum conservative in this hypothetical case, considering possible radiative losses and probabilistic character of motion on nano-scales.

Formation of a diamond lattice


The lattice is generated in multiple steps. Each step involvs adding new atoms to the free-bonds of boundary attoms (yellow), which then become lattice-bound (green).

5-atom lattice: two generations

Green atoms are those inside the lattice, yellow - at the boundary.

17-atom lattice: three generations

Multi-atom lattice: 8 generations.

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