Large-scale grid-enabled lattice-Boltzmann simulations of complex fluid flow in porous media and under shear

Well designed lattice-Boltzmann codes exploit the essentially embarrassingly parallel features of the algorithm and so can be run with considerable efficiency on modern supercomputers. Such scalable codes permit us to simulate the behaviour of increasingly large quantities of complex condensed matter systems. In the present paper, we present some preliminary results on the large scale three-dimensional lattice-Boltzmann simulation of binary immiscible fluid flows through a porous medium derived from digitised x-ray microtomographic data of Bentheimer sandstone, and from the study of the same fluids under shear. Simulations on such scales can benefit considerably from the use of computational steering and we describe our implementation of steering within the lattice-Boltzmann code, called LB3D, making use of the RealityGrid steering library. Our large scale simulations benefit from the new concept of capability computing, designed to prioritise the execution of big jobs on major supercomputing resources. The advent of persistent computational grids promises to provide an optimal environment in which to deploy these mesoscale simulation methods, which can exploit the distributed nature of compute, visualisation and storage resources to reach scientific results rapidly; we discuss our work on the grid-enablement of lattice-Boltzmann methods in this context.Comment: 17 pages, 6 figures, accepted for publication in Phil.Trans.R.Soc.Lond.

Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational grids

During the last two years the RealityGrid project has allowed us to be one of the few scientific groups involved in the development of computational grids. Since smoothly working production grids are not yet available, we have been able to substantially influence the direction of software development and grid deployment within the project. In this paper we review our results from large scale three-dimensional lattice Boltzmann simulations performed over the last two years. We describe how the proactive use of computational steering and advanced job migration and visualization techniques enabled us to do our scientific work more efficiently. The projects reported on in this paper are studies of complex fluid flows under shear or in porous media, as well as large-scale parameter searches, and studies of the self-organisation of liquid cubic mesophases. Movies are available at http://www.ica1.uni-stuttgart.de/~jens/pub/05/05-PhilTransReview.htmlComment: 18 pages, 9 figures, 4 movies available, accepted for publication in Phil. Trans. R. Soc. London Series

Minimal model of self-replicating nanocells: a physically embodied information-free scenario

The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell assumes that it includes information-carrying molecules as an essential ingredient, a dividing cell-like structure can be built from a metabolism-container coupled system, only. An example of such a system, modeled with dissipative particle dynamics, is presented here. This article demonstrates how a simple coupling between a precursor molecule and surfactant molecules forming micelles can experience a growth-division cycle in a predictable manner, and analyzes the influence of crucial parameters on this replication cycle. Implications of these results for origins of cellular life and living technology are outlined.Comment: 9 pages, 10 figure

Towards a mesoscopic model of water-like fluids with hydrodynamic interactions

We present a mesoscopic lattice model for non-ideal fluid flows with directional interactions, mimicking the effects of hydrogen-bonds in water. The model supports a rich and complex structural dynamics of the orientational order parameter, and exhibits the formation of disordered domains whose size and shape depend on the relative strength of directional order and thermal diffusivity. By letting the directional forces carry an inverse density dependence, the model is able to display a correlation between ordered domains and low density regions, reflecting the idea of water as a denser liquid in the disordered state than in the ordered one

Lattice-Boltzmann studies of fluid flow in porous media with realistic rock geometries

AbstractWe present results of lattice-Boltzmann simulations to calculate flow in realistic porous media. Two examples are given for lattice-Boltzmann simulations in two- and three-dimensional (2D and 3D) rock samples. First, we show lattice-Boltzmann simulation results of the flow in quasi-two-dimensional micromodels. The third dimension was taken into account using an effective viscous drag force. In this case, we consider a 2D micromodel of Berea sandstone. We calculate the flow field and permeability of the micromodel and find excellent agreement with Microparticle Image Velocimetry (μ-PIV) experiments. Then, we use a particle tracking algorithm to calculate the dispersion of tracer particles in the Berea geometry, using the lattice-Boltzmann flow field.Second, we use lattice-Boltzmann simulations to calculate the flow in Bentheimer sandstone. The data set used in this study was obtained using X-ray microtomography (XMT). First, we consider a single phase flow. We systematically study the effect of system size and validate Darcy’s law from the linear dependence of the flux on the body force exerted. We observe that the values of the permeability measurements as a function of porosity tend to concentrate in a narrower region of the porosity, as the system size of the computational sub-sample increases. Finally, we compute relative permeabilities for binary immiscible fluids in the XMT rock sample

Primary and secondary prevention of human papillomavirus-associated cancer: it's not all about women

To date, we have two important weapons in the prevention of uterine cervical cancer: vaccine program and organized screening. The most important task for the prevention of cervical cancer is to accelerate an integrated approach of vaccination and screenin

Cervical cancer screening based on human papilloma virus-DNA testing: a scientific heritage to microbiologists or to pathologists? An on-going dilemma

Among the 28 current Members of the European Union, approximately 34,000 new cases of cervical cancer occur annually, with 13,000 related deaths. In Italy, about 2900 cases of cervical cancer are diagnosed annually (crude incidence rate/100,000/year=9.4). As a direct consequence, about 1016 deaths related to cervical cancer are reported annually in Italy (crude mortality rate/100,000/year=3.3). Cervical cancer stands in the 15th rank among female cancers and is currently the 3rd most common cancer in women aged 15-44 years in Italy. [..

Ab initio analysis of the x-ray absorption spectrum of the myoglobin-carbon monoxide complex: Structure and vibrations

We present a comparison between Fe K-edge x-ray absorption spectra of carbonmonoxy-myoglobin and its simulation based on density-functional theory determination of the structure and vibrations and spectral simulation with multiple-scattering theory. An excellent comparison is obtained for the main part of the molecular structure without any structural fitting parameters. The geometry of the CO ligand is reliably determined using a synergic approach to data analysis. The methodology underlying this approach is expected to be especially useful in similar situations in which high-resolution data for structure and vibrations are available.Comment: 13 pages, 3 figure