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.

Highly optimized simulations on single- and multi-GPU systems of the 3D Ising spin glass model

We present a highly optimized implementation of a Monte Carlo (MC) simulator for the three-dimensional Ising spin-glass model with bimodal disorder, i.e.; the 3D Edwards-Anderson model running on CUDA enabled GPUs. Multi-GPU systems exchange data by means of the Message Passing Interface (MPI). The chosen MC dynamics is the classic Metropolis one, which is purely dissipative, since the aim was the study of the critical off-equilibrium relaxation of the system.

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.

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.

The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells.

Background Cell organization is governed and maintained via specific interactions among its constituent macromolecules. Comparison of the experimentally determined protein interaction networks in different model organisms has revealed little conservation of the specific edges linking ortholog proteins. Nevertheless, some topological characteristics of the graphs representing the networks - namely non-random degree distribution and high clustering coefficient - are shared by networks of distantly related organisms.

Impact of the Peterlin approximation on polymer dynamics in turbulent flows

We study the impact of the Peterlin approximation on the statistics of the end-to-end separation of polymers in a turbulent flow. The finitely extensible nonlinear elastic (FENE) model and the FENE model with the Peterlin approximation (FENE-P) are numerically integrated along a large number of Lagrangian trajectories resulting from a direct numerical simulation of three-dimensional homogeneous isotropic turbulence. Although the FENE-P model yields results in qualitative agreement with those of the FENE model, quantitative differences emerge.

On the nonlinear stability of a continuous duopoly model with constant conjectural variation

The paper concerns a continuous model governed by a ODE system originated by a discrete duopoly model with bounded rationality, based on constant conjectural variation. The aim of the paper is to show (i) the existence of an absorbing set in the phase space; (ii) linear stability analysis of the critical points of the system; (iii) nonlinear, global asymptotic stability of equilibrium of constant conjectural variation.