Pattern Formation in the Inhomogeneous Cooling State of Granular Fluids

We present results from comprehensive event-driven (ED) simulations of nonlinear pattern formation in freely-evolving granular gases. In particular, we focus on the the morphologies of density and velocity fields in the inhomogeneous cooling state (ICS). We emphasize the strong analogy between the ICS morphologies and pattern formation in phase ordering systems with a globally conserved order parameter.Comment: 11 pages, 4 figures. to appear in Europhys. Let

Dry and wet interfaces: Influence of solvent particles on molecular recognition

We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our basic model showing that the selectivity of the recognition process can be enhanced by considering the explicit influence of single solvent particles. When the number of cavities at the interface of a protein-protein complex is fixed as an intrinsic geometric constraint, there typically exists a characteristic fraction that should be filled with water molecules such that the selectivity exhibits a maximum. In addition the optimum fraction depends on the hydrophobicity of the interface so that one has to distinguish between dry and wet interfaces.Comment: 11 pages, 7 figure

Influence of correlations on molecular recognition

The influence of the patchiness and correlations in the distribution of hydrophobic and polar residues at the interface between two rigid biomolecules on their recognition ability is investigated in idealised coarse-grained lattice models. A general two-stage approach is utilised where an ensemble of probe molecules is designed first and the recognition ability of the probe ensemble is related to the free energy of association with both the target molecule and a different rival molecule in a second step. The influence of correlation effects are investigated using numerical Monte Carlo techniques and mean field methods. Correlations lead to different optimum characteristic lengths of the hydrophobic and polar patches for the mutual design of the two biomolecules on the one hand and their recognition ability in the presence of other molecules on the other hand.Comment: 15 pages, 5 figure

Packings of 3D stars: stability and structure

© 2016, Springer-Verlag Berlin Heidelberg.We describe a series of experiments involving the creation of cylindrical packings of star-shaped particles, and an exploration of the stability of these packings. The stars cover a broad range of arm sizes and frictional properties. We carried out three different kinds of experiments, all of which involve columns that are prepared by raining star particles one-by-one into hollow cylinders. As an additional part of the protocol, we sometimes vibrated the column before removing the confining cylinder. We rate stability in terms of r, the ratio of the mass of particles that fall off a pile when it collapsed, to the total particle mass. The first experiment involved the intrinsic stability of the column when the confining cylinder was removed. The second kind of experiment involved adding a uniform load to the top of the column, and then determining the collapse properties. A third experiment involved testing stability to tipping of the piles. We find a stability diagram relating the pile height, h, versus pile diameter, (Formula presented.) , where the stable and unstable regimes are separated by a boundary that is roughly a power-law in h versus (Formula presented.) with an exponent that is less than unity. Increasing vibration and friction, particularly the latter, both tend to stabilize piles, while increasing particle size can destabilize the system under certain conditions

The Granular Phase Diagram

The kinetic energy distribution function satisfying the Boltzmann equation is studied analytically and numerically for a system of inelastic hard spheres in the case of binary collisions. Analytically, this function is shown to have a similarity form in the simple cases of uniform or steady-state flows. This determines the region of validity of hydrodynamic description. The latter is used to construct the phase diagram of granular systems, and discriminate between clustering instability and inelastic collapse. The molecular dynamics results support analytical results, but also exhibit a novel fluctuational breakdown of mean-field descriptions.Comment: 15 pages, 4 figure

Evolution of displacements and strains in sheared amorphous solids

The local deformation of two-dimensional Lennard-Jones glasses under imposed shear strain is studied via computer simulations. Both the mean squared displacement and mean squared strain rise linearly with the length of the strain interval $\Delta \gamma$ over which they are measured. However, the increase in displacement does not represent single-particle diffusion. There are long-range spatial correlations in displacement associated with slip lines with an amplitude of order the particle size. Strong dependence on system size is also observed. The probability distributions of displacement and strain are very different. For small $\Delta \gamma$ the distribution of displacement has a plateau followed by an exponential tail. The distribution becomes Gaussian as $\Delta \gamma$ increases to about .03. The strain distributions consist of sharp central peaks associated with elastic regions, and long exponential tails associated with plastic regions. The latter persist to the largest $\Delta \gamma$ studied.Comment: Submitted to J. Phys. Cond. Mat. special volume for PITP Conference on Mechanical Behavior of Glassy Materials. 16 Pages, 8 figure