A computationally-efficient method for evaluating friction in molecular rotary bearings is presented. This method estimates drag from fluctuations in molecular dynamics simulations via the fluctuation–dissipation theorem. This is effective even for simulation times short compared to a bearing's energy damping time and for rotation speeds comparable to or below typical thermal values. We apply this method to two molecular rotary bearings of similar size at 300 K: previously studied nested (9,9) (14,14) double-walled carbon nanotubes and a hypothetical rotary joint consisting of single acetylenic bonds in a rigid diamondoid housing. The acetylenic joint has a rotational frictional drag coefficient of 2 × 10−35 kg m2 s−1. The friction for the nested nanotubes is 120 times larger, comparable to values reported by previous studies. This fluctuation-based method could evaluate dissipation in a variety of molecular systems with similarly rigid and symmetric bearings.
@cite_36: With the hope of directing future bottom-up fabrication through bulk external stimuli (such as electric fields) on nanometer-sized transporters, we sought to study controlled molecular motion on surfaces through the rational design of surface-capable molecular structures called nanocars. Here we show that the observed movement of the nanocars is a new type of fullerene-based wheel-like rolling motion, not stick−slip or sliding translation, due to evidence including directional preference in both direct and indirect manipulation and studies of related molecular structures.
@cite_9: We developed molecular models describing the thermally initiated motion of nanocars, nanosized vehicles composed of two to four spherical fullerene wheels chemically coupled to a planar chassis, on a met al surface. The simulations were aimed at reproducing qualitative features of the experimentally observed migration of nanocars over gold crystals as determined by scanning tunneling microscopy. Coarse-grained-type molecular dynamics simulations were carried out for the species "Trimer" and "Nanotruck", the simplified versions of the experimentally studied nanomachines. Toward this goal, we developed a version of the rigid body molecular dynamics based on the symplectic quaternion scheme in conjunction with the Nose-Poincare thermostat approach. Interactions between rigid fragments were described by using the corrected CHARMM force field parameters, while several empirical models were introduced for interactions of nanocars with gold crystals. With the single adjusted potential parameter, the computed trajectories are consistent with the qualitative features of the thermally activated migration of the nanocars: the primary pivoting motion of Trimer and the two-dimensional combination of translations and pivoting of Nanotruck. This work presents a first attempt at a theoretical analysis of nanocars' dynamics on a surface by providing a computationally minimalist approach.
@cite_5: We use a molecular dynamics simulation to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. Brenner's reactive hydrocarbon potential is used to model interatomic forces within each molecular gear. A Lennard-Jones 6-12 potential or the Buckingham (exp +6) potential plus electrostatic interaction terms are used for intermolecular interactions between gears. A number of gear and gear shaft configurations are simulated on parallel computers. One gear is powered by forcing the atoms near the end of the nanotube to rotate, and a second gear is allowed to rotate by keeping the atoms near the end of its nanotube constrained to a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. Results suggest that these gears can operate at up to 50-100 GHz in a vacuum at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering the temperature and or rotation rate. M This article features multimedia enhancements available from the abstract page in the online journal; see http: www.iop.org.
@cite_47: An empirical many-body potential-energy expression is developed for hydrocarbons that can model intramolecular chemical bonding in a variety of small hydrocarbon molecules as well as graphite and diamond lattices. The potential function is based on Tersoff's covalent-bonding formalism with additional terms that correct for an inherent overbinding of radicals and that include nonlocal effects. Atomization energies for a wide range of hydrocarbon molecules predicted by the potential compare well to experimental values. The potential correctly predicts that the -bonded chain reconstruction is the most stable reconstruction on the diamond 111 surface, and that hydrogen adsorption on a bulk-terminated surface is more stable than the reconstruction. Predicted energetics for the dimer reconstructed diamond 100 surface as well as hydrogen abstraction and chemisorption of small molecules on the diamond 111 surface are also given. The potential function is short ranged and quickly evaluated so it should be very useful for large-scale molecular-dynamics simulations of reacting hydrocarbon molecules.
@cite_13: Over the past two years at the Materials and Process Simulation Center, we have been developing simulation approaches for studying the molecular nanomachine designs pioneered by Drexler and Merkle. These nanomachine designs, such as planetary gears and neon pump, are described with atomistic details and involve up to 10 000 atoms. With the Dreiding and universal force fields, we have optimized the structures of the two planetary gear designs and the neon pump. At the Fourth Foresight conference, we reported rotational impulse dynamics studies of the first and second generation designs of planetary gears undergoing very high-frequency rotational motions. We will explore stability of these designs in the lower frequency regimes which require long time simulations. We will report the molecular mechanics and molecular dynamics simulations performed on these model systems. We explore the following modes in these studies: (1) impulse mode; (2) constant angular velocity—perpetual rotation; (3) constant torque—acceleration from rest. M This article features multimedia enhancements available from the abstract page in the online journal; see http: www.iop.org.
In addition to the relatively simple cases of nested nanotubes and graphene-graphene sliding, MD studies have evaluated more complex nanomachines. One example is a study of meshing gears made from functionalized carbon nanotubes @cite_5 using the Brenner potential @cite_47 . In @cite_13 a complex molecular planetary gear mechanism is analyzed using the UFF forecefield and Gasteiger partial charges. In @cite_9 a custom integrator is used with a custom force field based on CHARMM and AMBER force fields, with partial charges determined by calculations, to model the behavior of the experimentally realized nanocars" @cite_36 rolling on a gold surface.