We use molecular dynamics simulations combined with iterative screening to test if one can design mechanically controllable and selective molecular pores. The first model pore is formed by two stacked carbon nanocones connected by aliphatic chains at their open tips, in analogy to aquaporins. It turns out that when one nanocone is gradually rotated with respect to the other, the molecular chains alter the size of the nanopore formed at the cone tips and control the flow rates of liquid pentane through it. The second model pore is formed by two carbon nanotubes joined by a cylindrical structure of antiparallel peptides. By application of a torque to one of the nanotubes, while holding the other, we can reversibly fold the peptides into forward or backward-twisted barrels. We have modified the internal residues in these barrels to make these pores selective and controllable. Eventually, we found a nanopore that in the two folded configurations has very different transmission rates for hydrated NH(3) molecules.

We demonstrate by molecular dynamics simulations that water nanodroplets can activate and guide the folding of planar graphene nanostructures. Once the nanodroplets are deposited at selected spots on the planar nanostructure, they can act as catalytic elements that initiate conformational changes and help to overcome deformation barriers associated with them. Nanodroplets can induce rapid bending, folding, sliding, rolling, and zipping of the planar nanostructures, which can lead to the assembly of nanoscale sandwiches, capsules, knots, and rings.

We present an ab initio study of carbon fullerenes, such as C(20), C(36), C(56), C(60), and C(68), that are substitutionally doped with transition metals coordinated to several nitrogen atoms. These capsules with porphyrinlike metal sites have remarkable electronic and spin polarizations. Additional doping by boron increases their highest occupied molecular orbital-lowest unoccupied molecular orbital gap, stabilizes their electronic structure, and causes their ground states to have higher spin multiplicity, where the spin density is spread over the capsule. These capsules could be applied in molecular electronics, catalysis, light harvesting, and nanomechanics.

We model the self-assembly of superlattices of colloidal semiconducting nanorods horizontally and vertically oriented on material substrates. The models include van der Waals and Coulombic coupling between nanorods with intrinsic electric dipoles and their coupling to the substrates. We also investigate the effect of external electric fields on the self-assembly processes. Our theoretical predictions for stable self-assembled superlattices agree well with the available experimental data.