Studying the adsorption of polymers and biomolecules on surfaces using enhanced sampling methods

We discuss how to use Wang-Landau simulations in an efficient manner to investigate the statistical mechanics of individual lattice polymers and peptides adsorbed at a planar surface. For nearest neighbor interactions, we show that a single Wang-Landau simulation, recording the density of states as a function of numbers of internal contacts and of surface beads, is sufficient to give a full description of the phase behavior of both adsorbed and desorbed states of single molecules. It is not necessary to introduce a second confining wall. Moreover, moves are never rejected due to overlap with the surface. The proposed “wall-free” method has already been applied to homo-polymers and hetero-polymers (lattice peptides using the HP model) on a uniform surface, and on regularly patterned surfaces. We give here a specific example to indicate how the relative adsorption strengths of a given peptide on different surfaces may be calculated

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

Effect of the Berendsen thermostat on dynamical properties of water

The effect of the Berendsen thermostat on the dynamical properties of bulk SPC/E water is tested by generating power spectra associated with fluctuations in various observables. The Berendsen thermostat is found to be very effective in preserving temporal correlations in fluctuations of tagged particle quantities over a very wide range of frequencies. Even correlations in fluctuations of global properties, such as the total potential energy, are well-preserved for time periods shorter than the thermostat time constant. Deviations in dynamical behaviour from the microcanonical limit do not, however, always decrease smoothly with increasing values of the thermostat time constant but may be somewhat larger for some intermediate values of $\tau_B$, specially in the supercooled regime, which are similar to time scales for slow relaxation processes in bulk water.Comment: 21 pages, 5 figures, To be published in Mol. Phy

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

Forward Flux Sampling-type schemes for simulating rare events: Efficiency analysis

We analyse the efficiency of several simulation methods which we have recently proposed for calculating rate constants for rare events in stochastic dynamical systems, in or out of equilibrium. We derive analytical expressions for the computational cost of using these methods, and for the statistical error in the final estimate of the rate constant, for a given computational cost. These expressions can be used to determine which method to use for a given problem, to optimize the choice of parameters, and to evaluate the significance of the results obtained. We apply the expressions to the two-dimensional non-equilibrium rare event problem proposed by Maier and Stein. For this problem, our analysis gives accurate quantitative predictions for the computational efficiency of the three methods.Comment: 19 pages, 13 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

Heat Conduction in two-dimensional harmonic crystal with disorder

We study the problem of heat conduction in a mass-disordered two-dimensional harmonic crystal. Using two different stochastic heat baths, we perform simulations to determine the system size (L) dependence of the heat current (J). For white noise heat baths we find that J ~ 1/L^a with $a \approx 0.59$ while correlated noise heat baths gives $a \approx 0.51$. A special case with correlated disorder is studied analytically and gives a=3/2 which agrees also with results from exact numerics.Comment: Revised version. 4 pages, 3 figure

Anomalies in a waterlike model confined between plates

Using molecular dynamic simulations we study a waterlike model confined between two fixed hydrophobic plates. The system is tested for density, diffusion and structural anomalous behavior and compared with the bulk results. Within the range of confining distances we had explored we observe that in the pressure-temperature phase diagram the temperature of maximum density (TMD line), the temperature of maximum and minimum diffusion occur at lower temperatures when compared with the bulk values. For distances between the two layers below a certain threshold ,$d\le d_c$, only two layers of particles are formed, for $d\ge d_c$ three or more layers are formed. In the case of three layers the central layer stays liquid while the contact layers crystallize. This result is in agreement with simulations for atomistic models

Softness dependence of the Anomalies for the Continuous Shouldered Well potential

By molecular dynamic simulations we study a system of particles interacting through a continuous isotropic pairwise core-softened potential consisting of a repulsive shoulder and an attractive well. The model displays a phase diagram with three fluid phases, a gas-liquid critical point, a liquid-liquid critical point, and anomalies in density, diffusion and structure. The hierarchy of the anomalies is the same as for water. We study the effect on the anomalies of varying the softness of the potential. We find that, making the soft-core steeper, the regions of density and diffusion anomalies contract in the T - {\rho} plane, while the region of structural anomaly is weakly affected. Therefore, a liquid can have anomalous structural behavior without density or diffusion anomalies. We show that, by considering as effective distances those corresponding to the maxima of the first two peaks of the radial distribution function g(r) in the high-density liquid, we can generalize to continuous two-scales potentials a criterion for the occurrence of the anomalies of density and diffusion, originally proposed for discontinuous potentials. We observe that the knowledge of the structural behavior within the first two coordination shells of the liquid is not enough to establish the occurrence of the anomalies. By introducing the density derivative of the the cumulative order integral of the excess entropy we show that the anomalous behavior is regulated by the structural order at distances as large as the fourth coordination shell. By comparing the results for different softness of the potential, we conclude that the disappearing of the density and diffusion anomalies for the steeper potentials is due to a more structured short-range order. All these results increase our understanding on how, knowing the interaction potential, we can evaluate the possible presence of anomalies for a liquid

Crystallization and gelation in colloidal systems with short-ranged attractive interactions

We systematically study the relationship between equilibrium and non-equilibrium phase diagrams of a system of short-ranged attractive colloids. Using Monte Carlo and Brownian dynamics simulations we find a window of enhanced crystallization that is limited at high interaction strength by a slowing down of the dynamics and at low interaction strength by the high nucleation barrier. We find that the crystallization is enhanced by the metastable gas-liquid binodal by means of a two-stage crystallization process. First, the formation of a dense liquid is observed and second the crystal nucleates within the dense fluid. In addition, we find at low colloid packing fractions a fluid of clusters, and at higher colloid packing fractions a percolating network due to an arrested gas-liquid phase separation that we identify with gelation. We find that this arrest is due to crystallization at low interaction energy and it is caused by a slowing down of the dynamics at high interaction strength. Likewise, we observe that the clusters which are formed at low colloid packing fractions are crystalline at low interaction energy, but glassy at high interaction energy. The clusters coalesce upon encounter.Comment: 8 pages, 8 figure