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We use molecular dynamics simulations to investigate various scenarios where the ordering and dynamics of particles in motion across a surface is affected by the presence of quenched disorder on that surface, and can affect it in turn. Firstly, we consider a "conformal crystal" structure for superconducting vortex pinning. This 2D structure is generated mathematically by a conformal transformation of a regular hexagonal lattice, and possesses local hexagonal ordering, but globally features a density gradient in one dimension and an arching structure in the other dimension. We show that a vortex pinning array based on this structure has superior magnetization and transport properties compared to other previously considered pinning arrays, and can be used to construct a highly efficient vortex ratchet. We explain the effectiveness of the conformal array in terms of a local commensuration effect. Experimental results confirm our simulation results.
Secondly, we simulate an nanoassembly experiment where the particles affect the substrate itself. The energy of run-and-tumble active matter particles (such as {\it E. coli} bacteria undergoing chemotactic motion) is harnessed to push together two movable walls arranged in a Casimir geometry. The magnitude of the attractive force between the walls exhibits an unusual exponential dependence on the wall separation. The attraction is due to a depleted concentration of bacteria in the region between the walls, which arises from the wall-hugging motion of the bacteria as well as a geometrical shadowing effect.
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