arXiv subjects

Daan Frenkel

Publications and source records attributed to Daan Frenkel.

At least 91 records · Page 5Linked to original sources

arXiv2011

Direct determination of the size of basins of attraction of jammed solids

We propose a free-energy based Monte-Carlo method to measure the volume of potential-energy basins in configuration space. Using this approach we can estimate the number of distinct potential-energy minima, even when this number is much too large to be sampled directly. We validate our approach by comparing our results with the direct enumeration of distinct jammed states in small packings of frictionless spheres. We find that the entropy of distinct packings is extensive and that the entropy of distinct hard-sphere packings must have a maximum as a function of packing fraction.

cond-mat.soft↗

arXiv2010

Real-time monitoring of complex moduli from micro-rheology

We describe an approach to online analysis of micro-rheology data using a multi-scale time-correlation method. The method is particularly suited to process high-volume data streams and compress the relevant information in real time. Using this, we can obtain complex moduli of visco-elastic media without suffering from the high-frequency artefacts that are associated with the truncation errors in the most widely used versions of micro-rheology. Moreover, the present approach obviates the need to choose the time interval for data acquisition beforehand. We test our approach first on an artificial data set and then on experimental data obtained both for an optically trapped colloidal probe in water and a similar probe in poly-ethylene glycol solutions at various concentrations. In all cases, we obtain good agreement with the bulk rheology data in the region of overlap. We compare our method with the conventional Kramers-Kronig transform approach and find that the two methods agree over most of the frequency regime. For the same data set, the present approach is superior to Kramers-Kronig at high frequencies and can be made to perform at least comparable at low frequencies.

cond-mat.soft↗

arXiv2010

Pair interactions between complex mesoscopic particles from Widom's particle-insertion method

We demonstrate that Widom's particle insertion technique provides a convenient and efficient method to determine the effective pair interaction between complex, composite soft-matter particles in the zero-density limit. By means of three different test systems, i.e. amphiphilic dendrimers, electrostatic polymers and colloids coated with electrostatic polymers, we demonstrate the validity and the power of the presented method.

cond-mat.soft↗

arXiv2009

Phase diagram of Hertzian spheres

We report the phase diagram of interpenetrating Hertzian spheres. The Hertz potential is purely repulsive, bounded at zero separation, and decreases monotonically as a power law with exponent 5/2, vanishing at the overlapping threshold. This simple functional describes the elastic interaction of weakly deformable bodies and, therefore, it is a reliable physical model of soft macromolecules, like star polymers and globular micelles. Using thermodynamic integration and extensive Monte Carlo simulations, we computed accurate free energies of the fluid phase and a large number of crystal structures. For this, we defined a general primitive unit cell that allows for the simulation of any lattice. We found multiple re-entrant melting and first-order transitions between crystals with cubic, trigonal, tetragonal, and hexagonal symmetries.

cond-mat.soft↗

arXiv2009

Homogeneous Bubble Nucleation driven by local hot spots: a Molecular Dynamics Study

We report a Molecular Dynamics study of homogenous bubble nucleation in a Lennard-Jones fluid. The rate of bubble nucleation is estimated using forward-flux sampling (FFS). We find that cavitation starts with compact bubbles rather than with ramified structures as had been suggested by Shen and Debenedetti (J. Chem. Phys. 111:3581, 1999). Our estimate of the bubble-nucleation rate is higher than predicted on the basis of Classical Nucleation Theory (CNT). Our simulations show that local temperature fluctuations correlate strongly with subsequent bubble formation - this mechanism is not taken into account in CNT.

physics.chem-ph↗

arXiv2009

Out-of-equilibrium processes in suspensions of oppositely charged colloids: liquid-to-crystal nucleation and gel formation

We study the kinetics of the liquid-to-crystal transformation and of gel formation in colloidal suspensions of oppositely charged particles. We analyse, by means of both computer simulations and experiments, the evolution of a fluid quenched to a state point of the phase diagram where the most stable state is either a homogeneous crystalline solid or a solid phase in contact with a dilute gas. On the one hand, at high temperatures and high packing fractions, close to an ordered-solid/disordered-solid coexistence line, we find that the fluid-to-crystal pathway does not follow the minimum free energy route. On the other hand, a quench to a state point far from the ordered-crystal/disordered-crystal coexistence border is followed by a fluid-to-solid transition through the minimum free energy pathway. At low temperatures and packing fractions we observe that the system undergoes a gas-liquid spinodal decomposition that, at some point, arrests giving rise to a gel-like structure. Both our simulations and experiments suggest that increasing the interaction range favors crystallization over vitrification in gel-like structures.

cond-mat.soft↗

arXiv2009

Computing stationary distributions in equilibrium and non-equilibrium systems with Forward Flux Sampling

We present a method for computing stationary distributions for activated processes in equilibrium and non-equilibrium systems using Forward Flux Sampling (FFS). In this method, the stationary distributions are obtained directly from the rate constant calculations for the forward and backward reactions; there is no need to perform separate calculations for the stationary distribution and the rate constant. We apply the method to the non-equilibrium rare event problem proposed by Maier and Stein, to nucleation in a 2-dimensional Ising system, and to the flipping of a genetic switch.

cond-mat.soft↗

arXiv2008

Waterlike thermodynamic anomalies in a repulsive-step potential system

We report a computer-simulation study of the equilibrium phase diagram of a three-dimensional system of particles with a repulsive step potential. The phase diagram is obtained using free-energy calculations. At low temperatures, we observe a number of distinct crystal phases. We show that at certain values of the potential parameters the system exhibits the water-like thermodynamic anomalies: density anomaly and diffusion anomaly. The anomalies disappear with increasing the repulsive step width: their locations move to the region inside the crystalline phase.

cond-mat.soft↗

arXiv2008

Homogeneous nucleation under shear in a two-dimensional Ising model: cluster growth, coalescence and breakup

We compute rates and pathways for nucleation in a sheared two dimensional Ising model with Metropolis spin flip dynamics, using Forward Flux Sampling (FFS). We find a peak in the nucleation rate at intermediate shear rate. We analyse the origin of this peak using modified shear algorithms and committor analysis. We find that the peak arises from an interplay between three shear-mediated effects: shear-enhanced cluster growth, cluster coalescence and cluster breakup. Our results show that complex nucleation behaviour can be found even in a simple driven model system. This work also demonstrates the use of FFS for simulating rare events, including nucleation, in nonequilibrium systems.

cond-mat.soft↗

arXiv2008

Dynamical heterogeneity in a glass forming ideal gas

We conduct a numerical study of the dynamical behavior of a system of three-dimensional crosses, particles that consist of three mutually perpendicular line segments rigidly joined at their midpoints. In an earlier study [W. van Ketel et al., Phys. Rev. Lett. 94, 135703 (2005)] we showed that this model has the structural properties of an ideal gas, yet the dynamical properties of a strong glass former. In the present paper we report an extensive study of the dynamical heterogeneities that appear in this system in the regime where glassy behavior sets in. On the one hand, we find that the propensity of a particle to diffuse is determined by the structure of its local environment. The local density around mobile particles is significantly less than the average density, but there is little clustering of mobile particles, and the clusters observed tend to be small. On the other hand, dynamical susceptibility results indicate that a large dynamical length scale develops even at moderate densities. This suggests that propensity and other mobility measures are an incomplete measure of dynamical length scales in this system.

cond-mat.dis-nn↗

arXiv2007

Quasi-binary amorphous phase in a 3D system of particles with repulsive-shoulder interactions

We report a computer-simulation study of the equilibrium phase diagram of a three-dimensional system of particles with a repulsive step potential. Using free-energy calculations, we have determined the equilibrium phase diagram of this system. At low temperatures, we observe a number of distinct crystal phases. However, under certain conditions the system undergoes a glass transition in a regime where the liquid appears thermodynamically stable. We argue that the appearance of this amorphous low-temperature phase can be understood by viewing this one-component system as a pseudo-binary mixture.

cond-mat.soft↗

arXiv2007

Phase coexistence of cluster crystals: beyond the Gibbs phase rule

We report a study of the phase behavior of multiple-occupancy crystals through simulation. We argue that in order to reproduce the equilibrium behavior of such crystals it is essential to treat the number of lattice sites as a constraining thermodynamic variable. The resulting free-energy calculations thus differ considerably from schemes used for single-occupancy lattices. Using our approach, we obtain the phase diagram and the bulk modulus for a generalized exponential model that forms cluster crystals at high densities. We compare the simulation results with existing theoretical predictions. We also identify two types of density fluctuations that can lead to two sound modes and evaluate the corresponding elastic constants.

cond-mat.soft↗

arXiv2007

Evidence for out-of-equilibrium crystal nucleation in suspensions of oppositely charged colloids

We report a numerical study of the rate of crystal nucleation in a binary suspension of oppositely charged colloids. Two different crystal structures compete in the thermodynamic conditions under study. We find that the crystal phase that nucleates is metastable and, more surprisingly, its nucleation free energy barrier is not the lowest one. This implies that, during nucleation, there is insufficient time for sub-critical nuclei to relax to their lowest free-energy structure. Such behavior is in direct contradiction with the common assumption that the phase that crystallizes most readily is the one with the lowest free-energy barrier for nucleation. The phenomenon that we describe should be relevant for crystallization experiments where competing solid structures are not connected by an easy transformation.

cond-mat.soft↗

arXiv2006

Complex Phase Behavior of Repulsive Step Potential Systems in Three Dimensions

The comprehensive computer simulation study of the phase diagram of the repulsive step potential system in three dimensions is represented. We show that the system with a simple purely repulsive isotropic potential demonstrates a number of unusual features. The maxima and minima on the melting curve are found for some regions of potential parameters. It is shown that the phase diagram in $ρ-T$ plane includes two isostructural crystalline parts separated by the disordered phase which is amorphous at low enough temperatures. Phase diagram in the (P-T) plane shows that the transition to the amorphous state occurs approximately along the extrapolated spinodals. Structural FCC-BCC phase transition is found at high densities.

cond-mat.soft↗

arXiv2006

Application of the Optimized Baxter Model to the hard-core attractive Yukawa system

We perform Monte Carlo simulations on the hard-core attractive Yukawa system to test the Optimized Baxter Model that was introduced in [P.Prinsen and T. Odijk, J. Chem. Phys. 121, p.6525 (2004)] to study a fluid phase of spherical particles interacting through a short-range pair potential. We compare the chemical potentials and pressures from the simulations with analytical predictions from the Optimized Baxter Model. We show that the model is accurate to within 10 percent over a range of volume fractions from 0.1 to 0.4, interaction strengths up to three times the thermal energy and interaction ranges from 6 to 20 % of the particle diameter, and performs even better in most cases. We furthermore establish the consistency of the model by showing that the thermodynamic properties of the Yukawa fluid computed via simulations may be understood on the basis of one similarity variable, the stickiness parameter defined within the Optimized Baxter Model. Finally we show that the Optimized Baxter Model works significantly better than an often used, naive method determining the stickiness parameter by equating the respective second virial coefficients based on the attractive Yukawa and Baxter potentials.

cond-mat.soft↗

arXiv2006

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.

cond-mat.other↗

arXiv2005

Simulating rare events in equilibrium or non-equilibrium stochastic systems

We present three algorithms for calculating rate constants and sampling transition paths for rare events in simulations with stochastic dynamics. The methods do not require a priori knowledge of the phase space density and are suitable for equilibrium or non-equilibrium systems in stationary state. All the methods use a series of interfaces in phase space, between the initial and final states, to generate transition paths as chains of connected partial paths, in a ratchet-like manner. No assumptions are made about the distribution of paths at the interfaces. The three methods differ in the way that the transition path ensemble is generated. We apply the algorithms to kinetic Monte Carlo simulations of a genetic switch and to Langevin Dynamics simulations of intermittently driven polymer translocation through a pore. We find that the three methods are all of comparable efficiency, and that all the methods are much more efficient than brute force simulation.

cond-mat.soft↗

arXiv2005

Lattice-Boltzmmann simulations of the sedimentation of charged disks

We report a series of Lattice-Boltzmann simulations of the sedimentation velocity of charged disks. In these simulations, we explicitly account for the hydrodynamic and electrostatic forces on disks and on their electrical double layer. By comparing our results with those for spheres with equal surface and charge, we can clarify the effect of the particle shape on the sedimentation process. We find that disks and spheres exhibit a different dependence of the sedimentation velocity on the Debye screening length. An analysis of the behavior of highly charged disks (beyond the scope of the linearized Poisson-Boltzmann equation) shows that, in that regime, the charge dependence of the sedimentation velocity of disks and spheres is similar. This suggests that, at high charge, the effective hydrodynamic shape of the disks becomes more spherical.

cond-mat.soft↗