Magnetic hysteresis in a molecular Ising ferrimagnet: Glauber dynamics approach

We use agent-based modeling to investigate the effect of conservatism and partisanship on the efficiency with which large populations solve the density classification task – a paradigmatic problem for information aggregation and consensus building. We find that conservative agents enhance the populations’ ability to efficiently solve the density classification task despite large levels of noise in the system. In contrast, we find that the presence of even a small fraction of partisans holding the minority position will result in deadlock or a consensus on an incorrect answer. Our results provide a possible explanation for the emergence of conservatism and suggest that even low levels of partisanship can lead to significant social costs. Electronic supplementary material  Supplementary Online Material     

A multiscale molecular dynamics approach to contact mechanics

The friction and adhesion between elastic bodies are strongly influenced by the roughness of the surfaces in contact. Here we develop a multiscale molecular dynamics approach to contact mechanics, which can be used also when the surfaces have roughness on many different length-scales, e.g., for self affine fractal surfaces. As an illustration we consider the contact between randomly rough surfaces, and show that the contact area varies linearly with the load for small load. We also analyze the contact morphology and the pressure distribution at different magnification, both with and without adhesion. The calculations are compared with analytical contact mechanics models based on continuum mechanics.     

Electroless formation of silver nanoaggregates: an experimental and molecular dynamics approach

The ability to manipulate matter to create non-conventional structures is one of the key issues of material science. The understanding of assembling mechanism at the nanoscale allows us to engineer new nanomaterials, with physical properties intimately depending on their structure.

This paper describes new strategies to obtain and characterise metal nanostructures via the combination of a top-down method, such as electron beam lithography, and a bottom-up technique, such as the chemical electroless deposition. We realised silver nanoparticle aggregates within well-defined patterned holes created by electron beam lithography on silicon substrates. The quality characteristics of the nanoaggregates were verified by using scanning electron microscopy and atomic force microscopy imaging. Moreover, we compared the experimental findings to molecular dynamics simulations of nanoparticles growth. We observed a very high dependence of the structure characteristics on the pattern nanowell aspect ratio. We found that high-quality metal nanostructures may be obtained in patterns with well aspect ratio close to one, corresponding to a maximum diameter of 50 nm, a limit above which the fabricated structures become less regular and discontinuous. When regular shapes and sizes are necessary, as in nanophotonics, these results suggest the pattern characteristics to obtain isolated, uniform and reproducible metal nanospheres.     

Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics

We present a new method which combines Car-Parrinello and Born-Oppenheimer molecular dynamics in order to accelerate density functional theory based ab initio simulations. Depending on the system a gain in efficiency of 1 to 2 orders of magnitude has been observed, which allows ab initio molecular dynamics of much larger time and length scales than previously thought feasible. It will be demonstrated that the dynamics is correctly reproduced and that high accuracy can be maintained throughout for systems ranging from insulators to semiconductors and even to metals in condensed phases. This development considerably extends the scope of ab initio simulations.     

Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach

A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.     

Formation of surface nanobubbles and the universality of their contact angles: a molecular dynamics approach

We study surface nanobubbles using molecular dynamics simulation of ternary (gas, liquid, solid) systems of Lennard-Jones fluids. They form for a sufficiently low gas solubility in the liquid, i.e., for a large relative gas concentration. For a strong enough gas-solid attraction, the surface nanobubble is sitting on a gas layer, which forms in between the liquid and the solid. This gas layer is the reason for the universality of the contact angle, which we calculate from the microscopic parameters. Under the present equilibrium conditions the nanobubbles dissolve within less of a microsecond, consistent with the view that the experimentally found nanobubbles are stabilized by a nonequilibrium mechanism.     

Concentration dependence of the collective dynamics of swimming bacteria

At concentrations near the maximum allowed by steric repulsion, swimming bacteria form a dynamical state exhibiting extended spatiotemporal coherence. The viscous fluid into which locomotive energy of individual microorganisms is transferred also carries interactions that drive the coherence. The concentration dependence of correlations in the collective state is probed here with a novel technique that herds bacteria into condensed populations of adjustable concentration. For the particular thin-film geometry employed, the correlation lengths vary smoothly and monotonically through the transition from individual to collective behavior.     

Langevin dynamics deciphers the motility pattern of swimming parasites

The parasite African trypanosome swims in the bloodstream of mammals and causes the highly dangerous human sleeping sickness. Cell motility is essential for the parasite's survival within the mammalian host. We present an analysis of the random-walk pattern of a swimming trypanosome. From experimental time-autocorrelation functions for the direction of motion we identify two relaxation times that differ by an order of magnitude. They originate from the rapid deformations of the cell body and a slower rotational diffusion of the average swimming direction. Velocity fluctuations are athermal and increase for faster cells whose trajectories are also straighter. We demonstrate that such a complex dynamics is captured by two decoupled Langevin equations that decipher the complex trajectory pattern by referring it to the microscopic details of cell behavior.     

A non-equilibrium molecular dynamics approach to fluid transfer through microporous membranes

The colour field non-equilibrium molecular dynamics method is applied to model fluid transfer between two fluid phases separated by microporous membranes (i.e. pore width ≤ 2 nm). The model is simple. All particles show short range spherical interactions, but reproduce the main features of the experimental phenomenology of molecular sieve membranes. An external force is applied to the fluid particles and, due to the presence of the membrane, a stationary flux across the system results. A range of mass transfer coefficients was investigated and the fluxes were found to be linear with force intensities. The density was found to have a small effect on molecular mobility, while temperature had a more significant effect, showing the features of an activated process. In addition, the changes in these fluxes with the membrane size, and the cross interaction parameters between the fluid and the membrane particles were examined.     

Hugoniot curve calculation of nitromethane decomposition mixtures:A reactive force field molecular dynamics approach

We investigate the Hugoniot curve, shock–particle velocity relations, and Chapman–Jouguet conditions of the hot dense system through molecular dynamics(MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C–O bond and the formation of C–C bond start at 10.0–11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C–N bond breaking is the main event of the shock-induced nitromethane decomposition.     

The unified approach to density functional and molecular dynamics in real space

The lagrangean introduced in ref.[1] is modified with the introduction of an auxiliary field that represents the Hartree potential. While leading to the same results, the present version of the theory offers considerable practical and theoretical advantages. In particular, it provides the possibility of working entirely in real space, reducing the number of operations required. An interesting and potentially useful isomorphism of local density theory to a continuous spin lattice model is pointed out.     

Two-body collision induced light scattering: Comparison between a memory function approach and molecular dynamics experiments

Two-body collision induced light scattering in gases is investigated by a gaussian memory function approach based on the Mori theory. Molecular dynamics “experiments” have also been performed to check the method in the DID approximation. The results are compared with two-body experimental spectral shape in argon.     

Molecular mobility of sorbitol and maltitol: A ^13C NMR and molecular dynamics approach

Molecular mobility in two similar organic glass formers, namely sorbitol and maltitol, is studied in order to understand their difference in the cross-over between and relaxations, far above their respective glass transition temperatures. In this goal, the individual mobility of each carbon atom of the 6 carbon chain present both in sorbitol and maltitol is studied by means of ^13C nuclear magnetic resonance and molecular dynamics simulations. Both techniques imply that the mobility of carbons located at the end of the 6 carbon chain is greater than that of any other carbon of this chain and that the difference in carbon mobility is greater within the sorbitol moiety of maltitol than in sorbitol. The relaxation time obtained by magnetic resonance for carbons at the end of the 6 carbon chain is related to the relaxation time and the one of carbons in the middle of the chain is in relation with the value of the relaxation time. This result may suggest that the merging between the and relaxation processes in both sugars would be related to the decrease of the differences in mobility between the atoms of 6 carbon chain. Received 4 October 1999 and Received in final form 27 December 1999     

Finite-temperature quasicontinuum: molecular dynamics without all the atoms

Using a combination of statistical mechanics and finite-element interpolation, we develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasicontinuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nano-indentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.     

Cluster-solid interactions: A molecular dynamics investigation

Abstract

The interaction of small energetic clusters of metal atoms with surfaces has been investigated by molecular dynamics computer simulations. A wide variety of cluster-solid combinations have been studied so that the effects of the energy, size, and angle of incidence of the cluster, and the relative elastic properties of the cluster and substrate could be elucidated. ‘Soft landings’ were also investigated. From these studies, a mechanism map for cluster-solid interactions is developed. The results have particular importance for cluster beam deposition of thin films. The simulations are fully dynamical and 3-dimensional; they employ embedded-atom method potentials, which have been modified for interactions at close separations. A scheme for reducing the CPU time that is required for these and other simulations of radiation effects is described.     

Solvation dynamics in methanol: Experimental and molecular dynamics simulation studies

We have investigated the ultrafast dynamics of methanol by time dependent fluorescent shift experiments and molecular dynamic simulations. The experiments were performed with two different probe molecules, 1-aminonaphthalene and coumarin 153. The molecular dynamic simulations employed these probes as well as small atomic and diatomic solutes. We find a previously unobserved fast decay component in the solvation response of methanol. The molecular dynamics results are in good agreement with this experimental result. The origin of this fast response and the linearity of the solvent response are discussed.