Sampling along reaction coordinates with the Wang-Landau method

The multiple range random walk algorithm recently proposed by Wang and Landau [Phys. Rev. Lett. 86, 2050 (2001)] is adapted to the computation of free energy profiles for molecular systems along reaction coordinates. More generally, we show how to extract partial averages in various statistical ensembles without invoking simulations with constraints, biasing potentials or unknown parameters. The method is illustrated on a model 10-dimensional potential energy surface, for which analytical results are obtained. It is then applied to the potential of mean force associated with the dihedral angle of the butane molecule in gas phase and in carbon tetrachloride solvent. Finally, isomerization in a small rocksalt cluster, Na4F4, is investigated in the microcanonical ensemble, and the results are compared to those of parallel tempering Monte Carlo.Comment: 6 pages, 5 figure

Non-equilibrium dynamics of an active colloidal "chucker"

We report Monte Carlo simulations of the dynamics of a "chucker": a colloidal particle which emits smaller solute particles from its surface, isotropically and at a constant rate k_c. We find that the diffusion constant of the chucker increases for small k_c, as recently predicted theoretically. At large k_c the chucker diffuses more slowly due to crowding effects. We compare our simulation results to those of a "point particle" Langevin dynamics scheme in which the solute concentration field is calculated analytically, and in which hydrodynamic effects can be included albeit in an approximate way. By simulating the dragging of a chucker, we obtain an estimate of its apparent mobility coefficient which violates the fluctuation-dissipation theorem. We also characterise the probability density profile for a chucker which sediments onto a surface which either repels or absorbs the solute particles, and find that the steady state distributions are very different in the two cases. Our simulations are inspired by the biological example of exopolysaccharide-producing bacteria, as well as by recent experimental, simulation and theoretical work on phoretic colloidal "swimmers".Comment: re-submission after referee's comment

SEAHT: A computer program for the use of intersecting arcs of altimeter data for sea surface height refinement

The SEAHT program is designed to process multiple passes of altimeter data with intersecting ground tracks, with the estimation of corrections for orbital errors to each pass such that the data has the best overall agreement at the crossover points. Orbit error for each pass is modeled as a polynomial in time, with optional orders of 0, 1, or 2. One or more passes may be constrained in the adjustment process, thus allowing passes with the best orbits to provide the overall level and orientation of the estimated sea surface heights. Intersections which disagree by more than an input edit level are not used in the error parameter estimation. In the program implementation, passes are grouped into South-North passes and North-South passes, with the North-South passes partitioned out for the estimation of orbit error parameters. Computer core utilization is thus dependent on the number of parameters estimated for the set of South-North arcs, but is independent on the number of North-South passes. Estimated corrections for each pass are applied to the data at its input data rate and an output tape is written which contains the corrected data

Absolute FKBP binding affinities obtained via non-equilibrium unbinding simulations

We compute absolute binding affinities for two ligands bound to the FKBP protein using non-equilibrium unbinding simulations. The methodology is straight-forward, requiring little or no modification to many modern molecular simulation packages. The approach makes use of a physical pathway, eliminating the need for complicated alchemical decoupling schemes. Results of this study are promising. For the ligands studied here the binding affinities are typically estimated within less than 4.0 kJ/mol of the target values; and the target values are within less than 1.0 kJ/mol of experiment. These results suggest that non-equilibrium simulation could provide a simple and robust means to estimate protein-ligand binding affinities.Comment: 9 pages, 3 figures (no necessary color). Changes made to methodology and results between revision

Molecular simulations of entangled defect structures around nanoparticles in nematic liquid crystals

We investigate the defect structures forming around two nanoparticles in a Gay-Berne nematic liquid crystal using molecular simulations. For small separations, disclinations entangle both particles forming the figure of eight, the figure of omega and the figure of theta. These defect structures are similar in shape and occur with a comparable frequency to micron-sized particles studied in experiments. The simulations reveal fast transitions from one defect structure to another suggesting that particles of nanometre size cannot be bound together effectively. We identify the 'three-ring' structure observed in previous molecular simulations as a superposition of the different entangled and non-entangled states over time and conclude that it is not itself a stable defect structure.Comment: keywords: molecular-simulation, defects, nematic, disclination, algorithmic classification ; 8 pages, 7 figures, 1 tabl

Effect of vertical active vibration isolation on tracking performance and on ride qualities

An investigation to determine the effect on pilot performance and comfort of an active vibration isolation system for a commercial transport pilot seat is reported. The test setup consisted of: a hydraulic shaker which produced random vertical vibration inputs; the active vibration isolation system; the pilot seat; the pilot control wheel and column; the side-arm controller; and a two-axis compensatory tracking task. The effects of various degrees of pilot isolation on short-term (two-minute) tracking performance and comfort were determined

Understanding fragility in supercooled Lennard-Jones mixtures. I. Locally preferred structures

We reveal the existence of systematic variations of isobaric fragility in different supercooled Lennard-Jones binary mixtures by performing molecular dynamics simulations. The connection between fragility and local structures in the bulk is analyzed by means of a Voronoi construction. We find that clusters of particles belonging to locally preferred structures form slow, long-lived domains, whose spatial extension increases by decreasing temperature. As a general rule, a more rapid growth, upon supercooling, of such domains is associated to a more pronounced super-Arrhenius behavior, hence to a larger fragility.Comment: 14 pages, 14 figures, minor revisions, one figure adde