Sander Pronk

Finite-size corrections to the free energies of crystalline solids

We analyze the finite-size corrections to the free energy of crystals with a fixed center of mass. When we explicitly correct for the leading (ln N/N) corrections, the remaining free energy is found to depend linearly on 1/N. Extrapolating to the thermodynamic limit (N → ∞), we estimate the free energy of a defect-free crystal of particles interacting through an r–12 potential. We also estimate the free energy of perfect hard-sphere crystal near coexistence: at ρσ3 = 1.0409, the excess free energy of a defect-free hard-sphere crystal is 5.918 89(4)kT per particle. This, however, is not the free energy of an equilibrium hard-sphere crystal. The presence of a finite concentration of vacancies results in a reduction of the free energy that is some two orders of magnitude larger than the present error estimate.

Can stacking faults in hard-sphere crystals anneal out spontaneously?

We estimate the rate at which randomly stacked hard-sphere crystals transform into the thermodynamically stable face-centered cubic phase. As an input for this estimate we need both the free-energy difference between bulk face-centered cubic (fcc) and hexagonal close packed (hcp) phases, and the hcp–fcc interfacial free energy. The latter quantity was computed using a lattice-switch Monte Carlo (MC) simulation method. We find the interfacial free energy to be nonzero but extremely small: 26 ± 6 · 10–5kT/σ2, where σ is the particle diameter. The free energy difference between the bulk phases was calculated using two different techniques. On the basis of our simulation results we estimate that in hard-sphere colloidal suspensions millimeter-sized randomly stacked crystal will anneal to form essentially pure fcc crystal on a time scale of months to years.

There and (Slowly) Back Again: Entropy-Driven Hysteresis in a Model of DNA Overstretching

When pulled along its axis, double-stranded DNA elongates abruptly at a force of approximately 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to a molten state consisting of unhybridized single strands. The second picture introduces an elongated hybridized phase called S-DNA. Little thermodynamic evidence exists to discriminate directly between these competing pictures. Here we show that within a microscopic model of DNA we can distinguish between the dynamics associated with each. In experiment, considerable hysteresis in a cycle of stretching and shortening develops as temperature is increased. Since there are few possible causes of hysteresis in a system whose extent is appreciable in only one dimension, such behavior offers a discriminating test of the two pictures of overstretching. Most experiments are performed upon nicked DNA, permitting the detachment (unpeeling) of strands. We show that the long-wavelength progression of the unpeeled front generates hysteresis, the character of which agrees with experiment only if we assume the existence of S-DNA. We also show that internal melting can generate hysteresis, the degree of which depends upon the nonextensive loop entropy of single-stranded DNA.

Limits of filopodium stability.

Filopodia are long, fingerlike membrane tubes supported by cytoskeletal filaments. Their shape is determined by the stiffness of the actin filament bundles found inside them and by the interplay between the surface tension and bending rigidity of the membrane. Although one might expect the Euler buckling instability to limit the length of filopodia, we show through simple energetic considerations that this is in general not the case. By further analyzing the statics of filaments inside membrane tubes, and through computer simulations that capture membrane and filament fluctuations, we show under which conditions filopodia of arbitrary lengths are stable. We discuss several in vitro experiments where this kind of stability has already been observed. Furthermore, we predict that the filaments in long, stable filopodia adopt a helical shape.

Large difference in the elastic properties of fcc and hcp hard-sphere crystals

We report a numerical calculation of the elastic constants of the fcc and hcp crystal phases of monodisperse hard-sphere colloids. Surprisingly, some of these elastic constants are very different (up to 20%), even though the free-energy, pressure, and bulk compressibility of the two crystal structures are very nearly equal. As a consequence, a moderate deformation of a hard-sphere crystal may make the hcp phase more stable than the fcc phase. This finding has implications for the design of patterned templates to grow colloidal hcp crystals. We also find that, below close-packing, there is a small, but significant, difference between the distances between hexagonal layers (c/a ratios) of fcc and hcp crystals.

Melting of polydisperse hard disks

The melting of a polydisperse hard-disk system is investigated by Monte Carlo simulations in the semigrand canonical ensemble. This is done in the context of possible continuous melting by a dislocation-unbinding mechanism, as an extension of the two-dimensional hard-disk melting problem. We find that while there is pronounced fractionation in polydispersity, the apparent density-polydispersity gap does not increase in width, contrary to 3D polydisperse hard spheres. The point where the Youngs modulus is low enough for the dislocation unbinding to occur moves with the apparent melting point, but stays within the density gap, just like for the monodisperse hard-disk system. Additionally, we find that throughout the accessible polydispersity range, the bound dislocation-pair concentration is high enough to affect the dislocation-unbinding melting as predicted by Kosterlitz, Thouless, Halperin, Nelson, and Young.

Large effect of polydispersity on defect concentrations in colloidal crystals

We compute the equilibrium concentration of stacking faults and point defects in polydisperse hard-sphere crystals. We find that, while the concentration of stacking faults remains similar to that of monodisperse hard-sphere crystals, the concentration of vacancies decreases by about a factor of 2. Most strikingly, the concentration of interstitials in the maximally polydisperse crystal may be some six orders of magnitude larger than in a monodisperse crystal. We show that this dramatic increase in interstitial concentration is due to the increased probability of finding small particles and that the small-particle tail of the particle size distribution is crucial for the interstitial concentration in a colloidal crystal.

Microscopic implications of S-DNA

Recent experiments [J. van Mameren, Proc. Natl. Acad. Sci. U.S.A. 106, 18231 (2009)] provide a detailed spatial picture of overstretched DNA, showing that under certain conditions the two strands of the double helix separate at about 65 pN. It was proposed that this observation rules out the existence of an elongated, hybridized form of DNA (S-DNA). Here, we argue that the S-DNA picture is consistent with the observation of unpeeling during overstretching. We demonstrate that assuming the existence of S-DNA does not imply DNA overstretching to consist of the complete or near-complete conversion of the molecule from B to S form. Instead, this assumption implies in general a more complex dynamic coexistence of hybridized and unhybridized forms of DNA. We argue that such coexistence can rationalize several recent experimental observations.