arXiv subjects

Daan Frenkel

Publications and source records attributed to Daan Frenkel.

At least 19 recordsLinked to original sources

arXiv2026

Monte-Carlo study of Compositional Heterogeneity in Multicomponent Cluster Crystals

Soft (sub)micron-sized particles with bounded interactions can form cluster crystals, periodic structures in which multiple particles occupy the same lattice site. While the thermodynamics of monodisperse cluster crystals is well understood, less is known about how compositional disorder affects their stability. Using Monte Carlo simulations and density functional theory we show that binary cluster crystals undergo a density driven transition from a homogeneous mixed state to a heterogeneous ``alloy" like solid in which lattice sites spontaneously differentiate into populations with distinct compositions and occupancies while preserving the underlying crystal symmetry. The transition is accompanied by a sharp increase in the equilibrium lattice site density and by increased compositional fluctuations, but we see no evidence for macroscopic phase separation. We demonstrate that this transition is governed by competition between clustering and demixing instabilities and derive a simple scaling law for the demixing density as a function of temperature, composition, and particle size mismatch, in quantitative agreement with simulation.

cond-mat.soft↗

arXiv2025

The Second Gibbs Paradox

In his Equilibrium of Heterogeneous Substances Gibbs seems to suggest that the chemical potential of a crystal nucleus need not be equal to that of the coexisting fluid. In the field, Gibbs's statement has been something of a hot potato. I argue that a consistent treatment of point defects in the critical nucleus is essential for clarifying the meaning of the chemical potential of the nucleus. In the end -- as always -- Gibbs was right.

cond-mat.soft↗

arXiv2022

Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers

Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding of the scaffold strand, is unclear. Here, using Monte Carlo simulations of a lattice model of DNA origami, we find that some, but not all, designs can have a nucleation barrier and that this barrier disappears at lower temperatures, rationalizing the success of isothermal assembly. We show that the height of the nucleation barrier depends primarily on the coaxial stacking of staples that are adjacent on the same helix, a parameter that can be modified with staple design. Creating a nucleation barrier to DNA-origami assembly could be useful in optimizing assembly times and yields, while eliminating the barrier may allow for fast molecular sensors that can assemble/disassemble without hysteresis in response to changes in the environment.

cond-mat.soft↗

arXiv2021

Temperature Protocols to Guide Selective Self-Assembly of Competing Structures

Multi-component self-assembly mixtures offer the possibility of encoding multiple target structures with the same set of interacting components. Selective retrieval of one of the stored structures has been attempted by preparing an initial state that favours the assembly of the required target, through seeding, concentration patterning or specific choices of interaction strengths. This may not be possible in an experiment where on-the-fly reconfiguration of the building blocks to switch functionality may be required. In this paper, we explore principles of inverse design of a multi-component self-assembly mixture capable of encoding two competing structures that can be selected through simple temperature protocols. We design the target structures to realise the generic situation in which one of targets has the lower nucleation barrier while the other is globally more stable. We observe that to avoid the formation of spurious or chimeric aggregates, the number of neighbouring component pairs that occur in both structures should be minimal. Our design also requires the inclusion of components that are part only of one of the target structures, but we observe that to maximize the selectivity of retrieval, the component library itself should be maximally shared by the two targets. We demonstrate that temperature protocols can be designed which lead to the formation of either one of the target structures with high selectivity. We discuss the important role played by secondary aggregation products, which we term vestigial aggregates.

cond-mat.soft↗

arXiv2021

Challenges in modelling diffusiophoretic transport

The methodology to simulate transport phenomena in bulk systems is well-established. In contrast, there is no clear consensus about the choice of techniques to model cross-transport phenomena and phoretic transport, mainly because some of the hydrodynamic descriptions are incomplete from a thermodynamic point of view. In the present paper, we use a unified framework to describe diffusio-osmosis(phoresis), and we report non-equilibrium Molecular Dynamics (NEMD) on such systems. We explore different simulation methods to highlight some of the technical problems that arise in the calculations. For diffusiophoresis, we use two NEMD methods: boundary-driven and field-driven. Although the two methods should be equivalent in the limit of very weak gradients, we find that finite Peclet-number effects are much stronger in boundary-driven flows than in the case where we apply fictitious color forces.

cond-mat.soft↗

arXiv2021

Thermodynamics and kinetics of crystallisation in deeply supercooled Stillinger-Weber silicon

We study the kinetics of crystallization in deeply supercooled liquid silicon employing computer simulations and the Stillinger-Weber three body potential. The free energy barriers to crystallisation are computed using umbrella sampling Monte Carlo simulations, and for selected low temperature and zero pressure state points, using unconstrained molecular dynamics simulations to reconstruct the free energy from a mean first passage time formulation. We focus on state points that have been described in earlier work [Sastry and Angell, Nature Mater., 2, 739, 2003] as straddling a first order liquid-liquid phase transition (LLPT) between two metastable liquid states. It was argued subsequently [Ricci et al., Mol. Phys., 117, 3254, 2019] that the apparent phase transition is in fact due the loss of metastability of the liquid state with respect to the globally stable crystalline state. The presence or absence of a barrier to crystallization for these state points is therefore of importance to ascertain, with due attention to ambiguities that may arise from the choice of order parameters. We discuss our choice of order parameters and also our choice of methods to calculate the free energy at deep supercooling. We find a well-defined free energy barrier to crystallisation and demonstrate that both umbrella sampling and mean first passage time methods yield results that agree quantitatively. Our results thus provide strong evidence against the possibility that the liquids at state points close to the reported LLPT exhibit slow, spontaneous crystallisation, but they do not address the existence of a LLPT (or lack thereof). We also compute the free energy barriers to crystallisation at other state points over a broad range of temperatures and pressures, and discuss the effect of changes in the microscopic structure of the metastable liquid on the free energy barrier heights.

cond-mat.soft↗

arXiv2021

Estimation of the equilibrium free energy for glasses using the Jarzynski equality

The free energy of glasses cannot be estimated using thermodynamic integration, as glasses are intrinsically not in equilibrium. We present numerical simulations showing that, in contrast, plausible free-energy estimates of a Kob-Andersen glass can be obtained using the Jarzynski relation. Using the Jarzynski relation, we also compute the chemical potential difference of the two components of this system, and find that, in the glassy regime, the Jarzynski estimate matches well with the extrapolated value of the supercooled liquid. Our findings are of broader interest as they show that the Jarzynski method can be used under conditions where the thermodynamic integration approach, which is normally more accurate, breaks down completely. Systems where such an approach might be useful are gels and jammed, glassy structures formed by compression.

cond-mat.stat-mech↗

arXiv2021

Heterogeneous versus homogeneous crystal nucleation in hard spheres

Hard-sphere model systems are well-suited in both experiment and simulations to investigate fundamental aspects of the crystallization of fluids. In experiments on colloidal models of hard-sphere fluids, the uid is unavoidably at contact with the walls of the sample cell, where heterogeneous crystallization may take place. In this work we use simulations to investigate the competition between homogeneous and heterogeneous crystallization. We report simulations of wall-induced nucleation for different confining walls. Combining the results of these simulations with earlier studies of homogeneous allows us to asses the competition between homogeneous and heterogeneous nucleation as a function of wall type, fluid density and the system size. On at walls, heterogeneous nucleation will typically overwhelm homogeneous nucleation. However, even for surfaces randomly coated with spheres with a diameter that was some three times larger than that of the fluid spheres - as has been used in some experiments - heterogeneous nucleation is likely to be dominant for volume fractions smaller than 0.535. Only for a disordered coating that has the same structure as the liquid holds promise did we find the nucleation was likely to occur in the bulk. Hence, such coatings might be used to suppress heterogeneous nucleation in experiments. Finally, we report the apparent homogeneous nucleation rate taking into account the formation of crystallites both in the bulk and at the walls. We find that the apparent overall nucleation rates coincides with those reported in "homogeneous nucleation" experiments. This suggests that heterogeneous nucleation at the walls could partly explain the large discrepancies found between experimental measurements and simulation estimates of the homogeneous nucleation rate.

cond-mat.soft↗

arXiv2021

Reduced variance analysis of molecular dynamics simulations by linear combination of estimators

Building upon recent developments of force-based estimators with a reduced variance for the computation of densities, radial distribution functions or local transport properties from molecular simulations, we show that the variance can be further reduced by considering optimal linear combinations of such estimators. This control variates approach, well known in Statistics and already used in other branches of computational Physics, has been comparatively much less exploited in molecular simulations. We illustrate this idea on the radial distribution function and the one-dimensional density of a bulk and confined Lennard-Jones fluid, where the optimal combination of estimators is determined for each distance or position, respectively. In addition to reducing the variance everywhere at virtually no additional cost, this approach cures an artefact of the initial force-based estimators, namely small but non-zero values of the quantities in regions where they should vanish. Beyond the examples considered here, the present work highlights more generally the underexplored potential of control variates to estimate observables from molecular simulations.

physics.chem-ph↗

arXiv2021

Computation of the chemical potential and solubility of amorphous solids

Using a recently developed technique to estimate the equilibrium free energy of glassy materials, we explore if equilibrium simulation methods can be used to estimate the solubility of amorphous solids. As an illustration, we compute the chemical potentials of the constituent particles of a two-component Kob-Andersen model glass former. To compute the chemical potential for different components, we combine the calculation of the overall free energy of the glass with a calculation of the chemical potential difference of the two components. We find that the standard method to compute chemical potential differences by thermodynamic integration yields not only a wide scatter in the chemical potential values but, more seriously, the average of the thermodynamic integration results is well above the extrapolated value for the supercooled liquid. However, we find that if we compute the difference of the chemical potential of the components with the the non-equilibrium free energy expression proposed by Jarzynski, we obtain a good match with the extrapolated value of the supercooled liquid. The extension of the Jarzynski method that we propose opens a potentially powerful route to compute free-energy related equilibrium properties of glasses. We find that the solubility estimate of amorphous materials obtained from direct coexistence simulations is only in fair agreement with the solubility prediction based on the chemical potential calculations of a hypothetical "well-equilibrated glass". In direct coexistence simulations, we find that, in qualitative agreement with experiments, the amorphous solubility decreases with time and attains a low solubility value.

cond-mat.stat-mech↗

arXiv2020

Nano-Pump base on Exothermic Surface Reactions

We present simulations indicating that it should be possible to construct a switchable nano-scale fluid pump, driven by exothermic surface reactions. Such a pump could, for instance, be controlled electro-chemically. In our simulations we explore a simple illustration of such a pump. We argue that the simplicity of the pump design could make it attractive for micro/nano-fluidics applications.

cond-mat.soft↗

arXiv2020

Numerical method for computing the free energy of glasses

We propose a numerical technique to compute the equilibrium free energy of glasses that cannot be prepared quasi-reversibly. For such systems, standard techniques for estimating the free energy by extrapolation, cannot be used. Instead, we use a procedure that samples the equilibrium partition function of the basins of attraction of the different inherent structures (local potential energy minima) of the system. If all relevant inherent structures could be adequately sampled in the (supercooled) liquid phase, our approach would be rigorous. In any finite simulation, we will miss the lower-energy inherent structures that become dominant at very low temperatures. We find that our free energy estimates for a Kob-Andersen glass are lower than those obtained by very slow cooling, even at temperatures down to one third of the glass transition temperature. The current approach could be applied to compute the chemical potential of ultra-stable glassy materials, and should enable the estimation of their solubility.

cond-mat.stat-mech↗

arXiv2020

Using Molecular Simulation to Compute Transport Coefficients of Molecular Gases

The existing kinetic theory of gases is based on an analytical approach that becomes intractable for all but the simplest molecules. Here we propose a simple numerical scheme to compute the transport properties of molecular gases in the limit of infinite dilution. The approach that we propose is approximate, but our results for the diffusivity $D$, the viscosity $η$ and the thermal conductivity $λ$ of hard spheres, Lennard-Jones particles and rough hard spheres, agree well with the standard (lowest order) Chapman-Enskog results. We also present results for a Lennard-Jones-dimer model for nitrogen, for which no analytical results are available. In the case of poly-atomic molecules (we consider n-octane), our method remains simple and gives good predictions for the diffusivity and the viscosity. Computing the thermal conductivity of poly-atomic molecules requires an approximate treatment of their quantized internal modes. We show that a well-known approximation that relates $λ$ to $D$ and $η$, yields good results. We note that our approach should yield a lower limit to the exact value of $D$, $η$ and $λ$. Interestingly, the most sophisticated (higher-order) Chapman-Enskog results for rough hard spheres seem to violate this bound.

cond-mat.soft↗

arXiv2020

Computing the heat conductivity of fluids from density fluctuations

Equilibrium molecular dynamics simulations, in combination with the Green-Kubo (GK) method, have been extensively used to compute the thermal conductivity of liquids. However, the GK method relies on an ambiguous definition of the microscopic heat flux, which depends on how one chooses to distribute energies over atoms. This ambiguity makes it problematic to employ the GK method for systems with non-pairwise interactions. In this work, we show that the hydrodynamic description of thermally driven density fluctuations can be used to obtain the thermal conductivity of a bulk fluid unambiguously, thereby bypassing the need to define the heat flux. We verify that, for a model fluid with only pairwise interactions, our method yields estimates of thermal conductivity consistent with the GK approach. We apply our approach to compute the thermal conductivity of a non-pairwise additive water model at supercritical conditions, and then of a liquid hydrogen system described by a machine-learning interatomic potential, at 33 GPa and 2000 K.

physics.comp-ph↗

arXiv2020

Studying polymer diffusiophoresis with Non-Equilibrium Molecular Dynamics

We report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute which has a concentration gradient, and examine the variation of the induced diffusiophoretic velocity of the polymer chains as the interaction between the monomer and the solute is varied. We find that there is a non-monotonic relation between the diffusiophoretic mobility and the strength of the monomer-solute interaction. In addition we find a weak dependence of the mobility on the length of the polymer chain, which shows clear difference from the diffusiophoresis of a solid particle. Interestingly, the hydrodynamic flow through the polymer is much less screened than for pressure driven flows.

cond-mat.soft↗

arXiv2020

Effect of the interaction strength and anisotropy on the diffusio-phoresis of spherical colloids

Gradients in temperature, concentration or electrostatic potential cannot exert forces on a bulk fluid; they can, however, exert forces on a fluid in a microscopic boundary layer surrounding a (nano)colloidal solute, resulting in so-called phoretic flow. Here we present a simulation study of phoretic flow around a spherical colloid held fixed in a concentration gradient. We show that the resulting flow velocity depends non-monotonically on the strength of the colloid-fluid interaction. The reason for this non-monotonic dependence is that solute particles are effectively trapped in a shell around the colloid and cannot contribute to diffusio-phoresis. We also observe that the flow depends sensitively on the anisotropy of solute-colloid interaction.

cond-mat.soft↗

arXiv2020

'Rocket propulsion' of Janus micro-swimmers

We report simulations of a spherical Janus particle undergoing exothermic surface reactions around one pole only. Our model excludes self-phoretic transport by design. Nevertheless, net motion occurs from direct momentum transfer between solvent and colloid, with speed scaling as the square root of the energy released during the reaction. We find that such propulsion is dominated by the system's short-time response, when neither the time dependence of the flow around the colloid nor the solvent compressibility can be ignored. Our simulations agree reasonably well with previous experiments.

cond-mat.soft↗

arXiv2019

Information density, structure and entropy in equilibrium and non-equilibrium systems

During a spontaneous change, a macroscopic physical system will evolve towards a macro-state with more realizations. This observation is at the basis of the Statistical Mechanical version of the Second Law of Thermodynamics, and it provides an interpretation of entropy in terms of probabilities. However, we cannot rely on the statistical-mechanical expressions for entropy in systems that are far from equilibrium. In this paper, we compare various extensions of the definition of entropy, which have been proposed for non-equilibrium systems. It has recently been proposed that measures of information density may serve to quantify entropy in both equilibrium and nonequilibrium systems. We propose a new "bit-wise" method to measure the information density for off lattice systems. This method does not rely on coarse-graining of the particle coordinates. We then compare different estimates of the system entropy, based on information density and on the structural properties of the system, and check if the various entropies are mutually consistent and, importantly, whether they can detect non-trivial ordering phenomena. We find that, except for simple (one-dimensional) cases, the different methods yield answers that are at best qualitatively similar, and often not even that, although in several cases, different entropy estimates do detect ordering phenomena qualitatively. Our entropy estimates based on bit-wise data compression contain no adjustable scaling factor, and show large quantitative differences with the thermodynamic entropy obtained from equilibrium simulations. Hence, our results suggest that, at present, there is not yet a single, structure-based entropy definition that has general validity for equilibrium and non equilibrium systems.

cond-mat.stat-mech↗