Brownian ratchet for directional nanoparticle transport by repetitive stretch-relaxation of DNA

Brownian motion subject to a periodic and asymmetric potential can be biased by external, nonequilibrium fluctuations, leading to directional movement of Brownian particles. Sequence-dependent flexibility variation along double-stranded DNA has been proposed as a tool to develop periodic and asymmetric potentials for DNA binding of cationic nanoparticles with sizes below tens of nanometers. Here, we propose that repetitive stretching and relaxation of a long, double-stranded DNA molecule with periodic flexibility gradient can induce nonequilibrium fluctuations that tune the amplitude of asymmetric potentials for DNA-nanoparticle binding to result in directional transport of nanometer-sized particles along DNA. Realization of the proposed Brownian ratchet was proven by Brownian dynamics simulations of coarse-grained models of a single, long DNA molecule with flexibility variation and a cationic nanoparticle.

Liquid-like properties of cyclopentadienyl complexes of barium: molecular dynamics simulations of nanoscale droplets

Cyclopentadienyl complexes of barium have great utility in materials science and engineering, in particular, as precursors in the atomic layer deposition processes, which are required to be fluidic as well as thermally stable and volatile. Here, we investigated the liquid-like properties of cyclopentadienyl barium complexes including (Me₅C₅)₂Ba, (^tBu₃C₅H₂)₂Ba, (ⁱPr₄C₅H)₂Ba, (ⁱPr₅C₅)₂Ba, and [(SiMe₃)₃C₅H₂]₂Ba, using molecular dynamics simulations of nanoscale droplets. The compounds were modeled using a recently developed generic force field, GFN-FF. Nanoscale droplets with about 5.0 nm diameters were formed by aggregating 96 molecules of each compound. Simulation results reveal that substituting methyl groups of (Me₅C₅)₂Ba with other alkyl and silyl moieties has a non-negligible effect on the intra- and intermolecular structure and dynamics. In particular, in contrast to more flexible (Me₅C₅)₂Ba, the substitution with five iso-propyl groups to form (ⁱPr₅C₅)₂Ba adds rigidity to the complex with restricted orientational fluctuations for two cyclopentadienyl ligands and arranges molecules parallel to each other with greater probability. In addition, comparison between (^tBu₃C₅H₂)₂Ba, with three tert-butyl groups, and its silyl analogue, [(SiMe₃)₃C₅H₂]₂Ba, reveals that intermolecular interactions between the molecules with silyl groups are softer than those with tert-butyl groups and result in broader radial distribution functions, whereas the dynamic properties are similar for both compounds. This work suggests that molecular dynamics simulations contribute to molecular-level understanding of the effect of chemical substitution in organometallic compounds on the intra- and intermolecular properties of molecular liquids.