Colloquium: Large scale simulations on GPU clusters

Graphics processing units (GPU) are currently used as a cost-effective platform forcomputer simulations and big-data processing. Large scale applications require thatmultiple GPUs work together but the efficiency obtained with cluster of GPUs is, at times,sub-optimal because the GPU features are not exploited at their best. We describe how itis possible to achieve an excellent efficiency for applications in statistical mechanics,particle dynamics and networks analysis by using suitable memory access patterns andmechanisms like CUDA streams, profiling tools, etc.

Clustering of vertically constrained passive particles in homogeneous isotropic turbulence

We analyze the dynamics of small particles vertically confined, by means of a linear restoring force, to move within a horizontal fluid slab in a three-dimensional (3D) homogeneous isotropic turbulent velocity field. The model that we introduce and study is possibly the simplest description for the dynamics of small aquatic organisms that, due to swimming, active regulation of their buoyancy, or any other mechanism, maintain themselves in a shallow horizontal layer below the free surface of oceans or lakes.

Travelling wave solutions of a parabolic-hyperbolic system for contact inhibition of cell-growth

We consider a cell growth model involving a nonlinear system of partial differential equations which describes the growth of two types of cell populations with contact inhibition. Numerical experiments show that there is a parameter regime where, for a large class of initial data, the large time behaviour of the solutions is described by a segregated travelling wave solution with positive wave speed c.

A MATHEMATICAL MODEL FOR THE ENHANCED CYTOPLASMIC TRANSPORT How to Get (Faster) to the Nucleus

We consider a simple model for signal transport in the cytoplasm. Following some recent experimental evidences, the standard diffusion model is supplemented by advection operated through an attachement/detachement mechanism along microtubules. This model is given by a system of partial differential equations which are cast in different dimensions and connected by suitable exchange rules. A numerical scheme is introduced and some simulations are presented and discussed to show the performances of our model.

On a pseudoparabolic regularization of a forward-backward-forward equation

We consider an initial-boundary value problem for a degenerate pseudoparabolic regularization of a nonlinear forward-backward-forward parabolic equation, with a bounded nonlinearity which is increasing at infinity. We prove existence of suitably defined nonnegative solutions of the problem in a space of Radon measures. Solutions satisfy several monotonicity and regularization properties; in particular, their singular part is nonincreasing and may disappear in finite time.

Law of the wall in an unstably stratified turbulent channel flow

We perform direct numerical simulations of an unstably stratified turbulent channel flow to address the effects of buoyancy on the boundary layer dynamics and mean field quantities. We systematically span a range of parameters in the space of friction Reynolds number (Re<inf>?</inf>)and Rayleigh number (Ra). Our focus is on deviations from the logarithmic law of the wall due to buoyant motion. The effects of convection in the relevant ranges are discussed, providing measurements of mean profiles of velocity, temperature and Reynolds stresses as well as of the friction coefficient.

Slicing black hole spacetimes

A general framework is developed to investigate the properties of useful choices of stationary spacelike slicings of stationary spacetimes whose congruences of timelike orthogonal trajectories are interpreted as the world lines of an associated family of observers, the kinematical properties of which in turn may be used to geometrically characterize the original slicings.