Continuum limit of amorphous elastic bodies (III): Three dimensional systems

Extending recent numerical studies on two dimensional amorphous bodies, we characterize the approach of elastic continuum limit in three dimensional (weakly polydisperse) Lennard-Jones systems. While performing a systematic finite-size analysis (for two different quench protocols) we investigate the non-affine displacement field under external strain, the linear response to an external delta force and the low-frequency harmonic eigenmodes and their density distribution. Qualitatively similar behavior is found as in two dimensions. We demonstrate that the classical elasticity description breaks down below an intermediate length scale $\xi$, which in our system is approximately 23 molecular sizes. This length characterizes the correlations of the non-affine displacement field, the self-averaging of external noise with distance from the source and gives the lower wave length bound for the applicability of the classical eigenfrequency calculations. We trace back the "Boson-peak" of the density of eigenfrequencies (obtained from the velocity auto-correlation function) to the inhomogeneities on wave lengths smaller than $\xi$.Comment: 27 pages, 11 figures, submitted to Phys. Rev.

Dynamical Monte Carlo Study of Equilibrium Polymers (II): The Role of Rings

We investigate by means of a number of different dynamical Monte Carlo simulation methods the self-assembly of equilibrium polymers in dilute, semidilute and concentrated solutions under good-solvent conditions. In our simulations, both linear chains and closed loops compete for the monomers, expanding on earlier work in which loop formation was disallowed. Our findings show that the conformational properties of the linear chains, as well as the shape of their size distribution function, are not altered by the formation of rings. Rings only seem to deplete material from the solution available to the linear chains. In agreement with scaling theory, the rings obey an algebraic size distribution, whereas the linear chains conform to a Schultz--Zimm type of distribution in dilute solution, and to an exponentional distribution in semidilute and concentrated solution. A diagram presenting different states of aggregation, including monomer-, ring- and chain-dominated regimes, is given

Melting and Pressure-Induced Amorphization of Quartz

It has recently been shown that amorphization and melting of ice were intimately linked. In this letter, we infer from molecular dynamics simulations on the SiO2 system that the extension of the quartz melting line in the metastable pressure-temperature domain is the pressure-induced amorphization line. It seems therefore likely that melting is the physical phenomenon responsible for pressure induced amorphization. Moreover, we show that the structure of a "pressure glass" is similar to that of a very rapidly (1e+13 to 1e+14 kelvins per second) quenched thermal glass.Comment: 9 pages, 4 figures, LaTeX2

Compaction dynamics of a granular media under vertical tapping

We report new experimental results on granular compaction under consecutive vertical taps. The evolution of the mean volume fraction and of the mean potential energy of a granular packing presents a slow densification until a final steady-state, and is reminiscent to usual relaxation in glasses via a stretched exponential law. The intensity of the taps seems to rule the characteristic time of the relaxation according to an Arrhenius's type relation >. Finally, the analysis of the vertical volume fraction profile reveals an almost homogeneous densification in the packing.Comment: 7 pages, 4 figures, to appear in Europhysics Letter

Driven activation versus thermal activation

Activated dynamics in a glassy system undergoing steady shear deformation is studied by numerical simulations. Our results show that the external driving force has a strong influence on the barrier crossing rate, even though the reaction coordinate is only weakly coupled to the nonequilibrium system. This "driven activation" can be quantified by introducing in the Arrhenius expression an effective temperature, which is close to the one determined from the fluctuation-dissipation relation. This conclusion is supported by analytical results for a simplified model system.Comment: 5 pages, 3 figure

First-order transition in small-world networks

The small-world transition is a first-order transition at zero density $p$ of shortcuts, whereby the normalized shortest-path distance undergoes a discontinuity in the thermodynamic limit. On finite systems the apparent transition is shifted by $\Delta p \sim L^{-d}$. Equivalently a ``persistence size'' $L^* \sim p^{-1/d}$ can be defined in connection with finite-size effects. Assuming $L^* \sim p^{-\tau}$, simple rescaling arguments imply that $\tau=1/d$. We confirm this result by extensive numerical simulation in one to four dimensions, and argue that $\tau=1/d$ implies that this transition is first-order.Comment: 4 pages, 3 figures, To appear in Europhysics Letter

Discrete aqueous solvent effects and possible attractive forces

We study discrete solvent effects on the interaction of two parallel charged surfaces in ionic aqueous solution. These effects are taken into account by adding a bilinear non-local term to the free energy of Poisson-Boltzmann theory. We study numerically the density profile of ions between the two plates, and the resulting inter-plate pressure. At large plate separations the two plates are decoupled and the ion distribution can be characterized by an effective Poisson-Boltzmann charge that is smaller than the nominal charge. The pressure is thus reduced relative to Poisson-Boltzmann predictions. At plate separations below ~2 nm the pressure is modified considerably, due to the solvent mediated short-range attraction between ions in the the system. For high surface charges this contribution can overcome the mean-field repulsion giving rise to a net attraction between the plates.Comment: 12 figures in 16 files. 19 pages. Submitted to J. Chem. Phys., July 200

A repulsive reference potential reproducing the dynamics of a liquid with attractions

A well-known result of liquid state theory is that the structure of dense fluids is mainly determined by repulsive forces. The WCA potential, which cuts intermolecular potentials at their minima, is therefore often used as a reference. However, this reference gives quite wrong results for the viscous dynamics of the Kob-Andersen binary Lennard-Jones liquid [Berthier and Tarjus, Phys. Rev. Lett. 103, 170601 (2009)]. We show that repulsive inverse-power law potentials provide a useful reference for this liquid by reproducing its structure, dynamics, and isochoric heat capacity

Universal velocity distributions in an experimental granular fluid

We present experimental results on the velocity statistics of a uniformly heated granular fluid, in a quasi-2D configuration. We find the base state, as measured by the single particle velocity distribution $f(c)$, to be universal over a wide range of filling fractions and only weakly dependent on all other system parameters. There is a consistent overpopulation in the distribution's tails, which scale as $f\propto\exp(\mathrm{const.}\times c^{-3/2})$. More importantly, the high probability central region of $f(c)$, at low velocities, deviates from a Maxwell-Boltzmann by a second order Sonine polynomial with a single adjustable parameter, in agreement with recent theoretical analysis of inelastic hard spheres driven by a stochastic thermostat. To our knowledge, this is the first time that Sonine deviations have been measured in an experimental system.Comment: 13 pages, 15 figures, with minor corrections, submitted to Phys. Rev.

Electrostatic attraction between cationic-anionic assemblies with surface compositional heterogeneities

Electrostatics plays a key role in biomolecular assembly. Oppositely charged biomolecules, for instance, can co-assembled into functional units, such as DNA and histone proteins into nucleosomes and actin-binding protein complexes into cytoskeleton components, at appropriate ionic conditions. These cationic-anionic co-assemblies often have surface charge heterogeneities that result from the delicate balance between electrostatics and packing constraints. Despite their importance, the precise role of surface charge heterogeneities in the organization of cationic-anionic co-assemblies is not well understood. We show here that co-assemblies with charge heterogeneities strongly interact through polarization of the domains. We find that this leads to symmetry breaking, which is important for functional capabilities, and structural changes, which is crucial in the organization of co-assemblies. We determine the range and strength of the attraction as a function of the competition between the steric and hydrophobic constraints and electrostatic interactions.Comment: JCP June/200