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_8: Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of a...
@cite_0: We report the parameters for a new generic force field, DREIDING, that we find useful for predicting structures and dynamics of organic, biological, and main-group inorganic molecules. The philosophy in DREIDING is to use general force constants and geometry parameters based on simple hybridization considerations rather than individual force constants and geometric parameters that depend on the particular combination of atoms involved in the bond, angle, or torsion terms. Thus all bond distances are derived from atomic radii, and there is only one force constant each for bonds, angles, and inversions and only six different values for torsional barriers. Parameters are defined for all possible combinations of atoms and new atoms can be added to the force field rather simply. This paper reports the parameters for the "nonmet allic" main-group elements (B, C, N, 0, F columns for the C, Si, Ge, and Sn rows) plus H and a few met als (Na, Ca, Zn, Fe). The accuracy of the DREIDING force field is tested by comparing with (i) 76 accurately determined crystal structures of organic compounds involving H, C, N, 0, F, P, S, CI, and Br, (ii) rotational barriers of a number of molecules, and (iii) relative conformational energies and barriers of a number of molecules. We find excellent results for these systems.
@cite_43: Recent experiments on microscopic graphite mesas demonstrate reproducible high-speed microscale superlubricity, even under ambient conditions. Here, we explore the same phenomenon on the nanoscale, by studying a graphene flake sliding on a graphite substrate, using molecular dynamics. We show that superlubricity is punctuated by high-friction transients as the flake rotates through successive crystallographic alignments with the substrate. Further, we introduce two novel routes to suppress frictional scattering and achieve persistent superlubricity. We use graphitic nanoribbons to eliminate frictional scattering by constraining the flake rotation, an approach we call frictional waveguides. We can also effectively suppress frictional scattering by biaxial stretching of the graphitic substrate. These new routes to persistent superlubricity at the nanoscale may guide the design of ultra-low dissipation nanomechanical devices.
@cite_16: The self-retracting motion of a graphene flake on a stack of graphene flakes is studied using molecular dynamics simulations. It is shown that in the case when the extended flake is initially rotated to an incommensurate state, there is no barrier to the self-retracting motion of the flake and the flake retracts as fast as possible. If the extended flake is initially commensurate with the other flakes, the self-retracting motion is hindered by potential energy barriers. However, in this case, the rotation of the flake to incommensurate states is often observed. Such a rotation is found to be induced by the torque acting on the flake on hills of the potential relief of the interaction energy between the flakes. Contrary to carbon nanotubes, telescopic oscillations of the graphene flake are suppressed because of the high dynamic friction related to the excitation of flexural vibrations of the flake. This makes graphene promising for the use in fast-responding electromechanical memory cells.
@cite_17: The weak interlayer binding in two-dimensional layered materials such as graphite gives rise to poorly understood low-friction characteristics. Accurate measurements of the adhesion forces governing the overall mechanical stability have also remained elusive. We report on the direct mechanical measurement of line tension and friction forces acting in sheared mesoscale graphite structures. We show that the friction is fundamentally stochastic in nature and is attributable to the interaction between the incommensurate interface lattices. We also measured an adhesion energy of 0.227 ± 0.005 joules per square meter, in excellent agreement with theoretical models. In addition, bistable all-mechanical memory cell structures and rotational bearings have been realized by exploiting position locking, which is provided solely by the adhesion energy.
A MD model of experimentally realized graphene-on-graphene sliding is presented in @cite_17 . The self-retracting motion of sheared graphene sheets is studied with an in-house MD integrator in @cite_16 . Energy dissipation during high speed sliding of graphene sheets is investigated with GROMACS @cite_8 and the DREIDING force field @cite_0 in @cite_43 .