Efficient configurational-bias Monte-Carlo simulations of chain molecules with `swarms' of trial configurations

Proposed here is a dynamic Monte-Carlo algorithm that is efficient in simulating dense systems of long flexible chain molecules. It expands on the configurational-bias Monte-Carlo method through the simultaneous generation of a large set of trial configurations. This process is directed by attempting to terminate unfinished chains with a low statistical weight, and replacing these chains with clones (enrichments) of stronger chains. The efficiency of the resulting method is explored by simulating dense polymer brushes. A gain in efficiency of at least three orders of magnitude is observed with respect to the configurational-bias approach, and almost one order of magnitude with respect to recoil-growth Monte-Carlo. Furthermore, the inclusion of `waste recycling' is observed to be a powerful method for extracting meaningful statistics from the discarded configurations

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

The role of long-range forces in the phase behavior of colloids and proteins

The phase behavior of colloid-polymer mixtures, and of solutions of globular proteins, is often interpreted in terms of a simple model of hard spheres with short-ranged attraction. While such a model yields a qualitative understanding of the generic phase diagrams of both colloids and proteins, it fails to capture one important difference: the model predicts fluid-fluid phase separation in the metastable regime below the freezing curve. Such demixing has been observed for globular proteins, but for colloids it appears to be pre-empted by the appearance of a gel. In this paper, we study the effect of additional long-range attractions on the phase behavior of spheres with short-ranged attraction. We find that such attractions can shift the (metastable) fluid-fluid critical point out of the gel region. As this metastable critical point may be important for crystal nucleation, our results suggest that long-ranged attractive forces may play an important role in the crystallization of globular proteins. However, in colloids, where refractive index matching is often used to switch off long-ranged dispersion forces, gelation is likely to inhibit phase separation.Comment: EURO-LATEX, 6 pages, 2 figure

Equation of state of metallic hydrogen from Coupled Electron-Ion Monte Carlo simulations

We present a study of hydrogen at pressures higher than molecular dissociation using the Coupled Electron-Ion Monte Carlo method. These calculations use the accurate Reptation Quantum Monte Carlo method to estimate the electronic energy and pressure while doing a Monte Carlo simulation of the protons. In addition to presenting simulation results for the equation of state over a large region of phase space, we report the free energy obtained by thermodynamic integration. We find very good agreement with DFT calculations for pressures beyond 600 GPa and densities above $\rho=1.4 g/cm^3$. Both thermodynamic as well as structural properties are accurately reproduced by DFT calculations. This agreement gives a strong support to the different approximations employed in DFT, specifically the approximate exchange-correlation potential and the use of pseudopotentials for the range of densities considered. We find disagreement with chemical models, which suggests a reinvestigation of planetary models, previously constructed using the Saumon-Chabrier-Van Horn equations of state.Comment: 9 pages, 7 figure

Vapor-liquid surface tension of strong short-range Yukawa fluid

The thermodynamic properties of strong short-range attractive Yukawa fluids, k=10, 9, 8, and 7, are determined by combining the slab technique with the standard and the replica exchange Monte Carlo (REMC) methods. A good agreement was found among the coexistence curves of these systems calculated by REMC and those previously reported in the literature. However, REMC allows exploring the coexistence at lower temperatures, where dynamics turns glassy. To obtain the surface tension we employed, for both methods, a procedure that yields the pressure tensor components for discontinuous potentials. The surface tension results obtained by the standard MC and REMC techniques are in good agreement.Comment: 6 pages, 4 figure

Anomalous Dynamic Arrest in a Mixture of Big and Small Particles

We present molecular dynamics simulations on the slow dynamics of a mixture of big and small soft-spheres with a large size disparity. Dynamics are investigated in a broad range of temperature and mixture composition. As a consequence of large size disparity, big and small particles exhibit very different relaxation times. As previously reported for simple models of short-ranged attractive colloids and polymer blends, several anomalous dynamic features are observed: i) sublinear behavior for mean squared displacements, ii) concave-to-convex crossover for density-density correlators, by varying temperature or wavevector, iii) logarithmic decay for specific wavevectors of density-density correlators. These anomalous features are observed over time intervals extending up to four decades, and strongly resemble predictions of the Mode Coupling Theory (MCT) for state points close to higher-order MCT transitions, which originate from the competition between different mechanisms for dynamic arrest. For the big particles we suggest competition between soft-sphere repulsion and depletion effects induced by neighboring small particles. For the small particles we suggest competition between bulk-like dynamics and confinement, respectively induced by neighboring small particles and by the slow matrix of big particles. By increasing the size disparity, a new relaxation scenario arises for the small particles. Self-correlators decay to zero at temperatures where density-density correlations are frozen. The behavior of the latters resembles features characteristic of type-A MCT transitions, defined by a zero value of the critical non-ergodicity parameter.Comment: Version 2. Added major new result

[N]pT ensemble and finite-size scaling study of the GEM-4 critical isostructural transition

First-order transitions of system where both lattice site occupancy and lattice spacing fluctuate, such as cluster crystals, cannot be efficiently studied by traditional simulation methods. These methods necessarily fix one of these two degrees of freedom, but this difficulty is surmounted by the generalized [N]pT ensemble [J. Chem. Phys. 136, 214106 (2012)]. Here it is shown that histogram reweighting and the [N]pT ensemble can be used to study an isostructural transition between cluster crystals of different occupancy in the generalized exponential model of index 4 (GEM-4). Extending this scheme to finite-size scaling studies also allows to accurately determine the critical point parameters and to verify that it belongs to the Ising universality class.Comment: 5 pages, 4 figure

Transport properties of room temperature ionic liquids from classical molecular dynamics

Room Temperature Ionic Liquids (RTILs) have attracted much of the attention of the scientific community in the past decade due the their novel and highly customizable properties. Nonetheless their high viscosities pose serious limitations to the use of RTILs in practical applications. To elucidate some of the physical aspects behind transport properties of RTILs, extensive classical molecular dynamics (MD) calculations are reported. Bulk viscosities and ionic conductivities of butyl-methyl-imidazole based RTILs are presented over a wide range of temperatures. The dependence of the properties of the liquids on simulation parameters, e.g. system size effects and choice of the interaction potential, is analyzed

Janssen effect and the stability of quasi 2-D sandpiles

We present the results of three dimensional molecular dynamics study of global normal stresses in quasi two dimensional sandpiles formed by pouring mono dispersed cohesionless spherical grains into a vertical granular Hele-Shaw cell. We observe Janssen effect which is the phenomenon of pressure saturation at the bottom of the container. Simulation of cells with different thicknesses shows that the Janssen coefficient $\kappa$ is a function of the cell thickness. Dependence of global normal stresses as well as $\kappa$ on the friction coefficients between the grains ($\mu_p$) and with walls ($\mu_w$) are also studied. The results show that in the range of our simulations $\kappa$ usually increases with wall-grain friction coefficient. Meanwhile by increasing $\mu_p$ while the other system parameters are fixed, we witness a gradual increase in $\kappa$ to a parameter dependent maximal value

Using bijective maps to improve free energy estimates

We derive a fluctuation theorem for generalized work distributions, related to bijective mappings of the phase spaces of two physical systems, and use it to derive a two-sided constraint maximum likelihood estimator of their free energy difference which uses samples from the equilibrium configurations of both systems. As an application, we evaluate the chemical potential of a dense Lennard-Jones fluid and study the construction and performance of suitable maps.Comment: 17 pages, 11 figure