DynamO: A free O(N) general event-driven molecular-dynamics simulator

Molecular-dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N log(N)) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10^6 particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo

Simulations of dense granular flow: Dynamic Arches and Spin Organization

We present a numerical model for a two dimensional (2D) granular assembly, falling in a rectangular container when the bottom is removed. We observe the occurrence of cracks splitting the initial pile into pieces, like in experiments. We study in detail various mechanisms connected to the `discontinuous decompaction' of this granular material. In particular, we focus on the history of one single long range crack, from its origin at one side wall, until it breaks the assembly into two pieces. This event is correlated to an increase in the number of collisions, i.e. strong pressure, and to a momentum wave originated by one particle. Eventually, strong friction reduces the falling velocity such that the crack may open below the slow, high pressure `dynamic arch'. Furthermore, we report the presence of large, organized structures of the particles' angular velocities in the dense parts of the granulate when the number of collisions is large.Comment: Submitted to J. Phys.

Ligand-Receptor Interactions

The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the interest of biologists to the kinetic and mechanical properties of cell membrane receptors. The aim of this review is to give a description of these advances that benefitted from a largely multidisciplinar approach

Effects of the finite particle size in turbulent wall-bounded flows of dense suspensions

We use interface-resolved simulations to study finite-size effects in turbulent channel flow of neutrally-buoyant spheres. Two cases with particle sizes differing by a factor of 2, at the same solid volume fraction of 20% and bulk Reynolds number are considered. These are complemented with two reference single-phase flows: the unladen case, and the flow of a Newtonian fluid with the effective suspension viscosity of the same mixture in the laminar regime. As recently highlighted in Costa et al. (PRL 117, 134501), a particle-wall layer is responsible for deviations of the statistics from what is observed in the continuum limit where the suspension is modeled as a Newtonian fluid with an effective viscosity. Here we investigate the fluid and particle dynamics in this layer and in the bulk. In the particle-wall layer, the near wall inhomogeneity has an influence on the suspension micro-structure over a distance proportional to the particle size. In this layer, particles have a significant (apparent) slip velocity that is reflected in the distribution of wall shear stresses. This is characterized by extreme events (both much higher and much lower than the mean). Based on these observations we provide a scaling for the particle-to-fluid apparent slip velocity as a function of the flow parameters. We also extend the flow scaling laws in to second-order Eulerian statistics in the homogeneous suspension region away from the wall. Finite-size effects in the bulk of the channel become important for larger particles, while negligible for lower-order statistics and smaller particles. Finally, we study the particle dynamics along the wall-normal direction. Our results suggest that 1-point dispersion is dominated by particle-turbulence (and not particle-particle) interactions, while differences in 2-point dispersion and collisional dynamics are consistent with a picture of shear-driven interactions

Density profiles of a colloidal liquid at a wall under shear flow

Using a dynamical density functional theory we analyze the density profile of a colloidal liquid near a wall under shear flow. Due to the symmetries of the system considered, the naive application of dynamical density functional theory does not lead to a shear induced modification of the equilibrium density profile, which would be expected on physical grounds. By introducing a physically motivated dynamic mean field correction we incorporate the missing shear induced interparticle forces into the theory. We find that the shear flow tends to enhance the oscillations in the density profile of hard-spheres at a hard-wall and, at sufficiently high shear rates, induces a nonequilibrium transition to a steady state characterized by planes of particles parallel to the wall. Under gravity, we find that the center-of-mass of the density distribution increases with shear rate, i.e., shear increases the potential energy of the particles