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
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.