The highly conserved zinc finger CCCTC-binding factor (CTCF) regulates genomic imprinting and gene expression by acting as a transcriptional activator or repressor of promoters and insulator of enhancers. The multiple functions of CTCF are accomplished by co-association with other protein partners and are dependent on genomic context and tissue specificity. Despite the critical role of CTCF in the organization of genome structure, to date, only a subset of CTCF interaction partners have been identified.

Network flows and specifically water flow in open canals can be modeled by systems of balance laws defined on graphs. The shallow water or Saint-Venant system of balance laws is one of the most used model and present two phases: fluvial or sub-critical and torrential or super-critical. Phase transitions may occur within the same canal but transitions related to networks are less investigated. In this paper we provide a complete characterization of possible phase transitions for a case study of a simple scenario with two canals and one junction.

In order to understand the flow profiles of complex fluids, a crucial issue concerns the emergence of spatial correlations among plastic rearrangements exhibiting cooperativity flow behaviour at the macroscopic level. In this paper, the rate of plastic events in a Poiseuille flow is experimentally measured on a confined foam in a Hele-Shaw geometry. The correlation with independently measured velocity profiles is quantified by looking at the relationship between the localisation length of the velocity profiles and the localisation length of the spatial distribution of plastic events.

A special feature of Rayleigh-Taylor systems with chemical reactions is the competition between turbulent mixing and the "burning processes", which leads to a highly non-trivial dynamics. We studied the problem performing high resolution numerical simulations of a 2d system, using a thermal lattice Boltzmann (LB) model.

We propose numerical simulations of viscoelastic fluids based on a hybrid algorithm combining Lattice-Boltzmann models (LBM) and Finite Differences (FD) schemes, the former used to model the macroscopic hydrodynamic equations, and the latter used to model the polymer dynamics. The kinetics of the polymers is introduced using constitutive equations for viscoelastic fluids with finitely extensible non-linear elastic dumbbells with Peterlin's closure (FENE-P).

We present the results of our numerical simulations of the Rayleigh-Taylor turbulence, performed using a recently proposed (Sbragaglia et al 2009 J. Fluid Mech. 628 299, Scagliarini et al 2010 Phys. Fluids 22 055101) lattice Boltzmann method that can describe consistently a thermal compressible flow subjected to an external forcing. The method allowed us to study the system in both the nearly Boussinesq regime and the strongly compressible regime. Moreover, we show that when the stratification is important, the presence of the adiabatic gradient causes the arrest of the mixing process.

A numerical study of turbulence seeded with light particles is presented. We analyze the statistical properties of coherent, small-scale structures by looking at the trapping events of light particles inside vortex filaments. We study the properties of particles attracting set, measuring its fractal dimension and the probability that the separation between two particles remains within the dissipative scale, even for time lapses as long as the large-scale correlation time, T(L).

In this paper we present an implementation for the QPACE supercomputer of a Lattice Boltzmann model of a fluid-dynamics flow in 2 dimensions. QPACE is a massively parallel application-driven system powered by the Cell processor. We review the structure of the model, describe in details its implementation on QPACE and finally present performance data and preliminary physics results. (C) 2010 Published by Elsevier Ltd.