Maddalena Venturoli

Molecular simulations of lipid-mediated protein-protein interactions

Recent experimental results revealed that lipid-mediated interactions due to hydrophobic forces may be important in determining the protein topology after insertion in the membrane, in regulating the protein activity, in protein aggregation and in signal transduction. To gain insight into the lipid-mediated interactions between two intrinsic membrane proteins, we developed a mesoscopic model of a lipid bilayer with embedded proteins, which we studied with dissipative particle dynamics. Our calculations of the potential of mean force between transmembrane proteins show that hydrophobic forces drive long-range protein-protein interactions and that the nature of these interactions depends on the length of the protein hydrophobic segment, on the three-dimensional structure of the protein and on the properties of the lipid bilayer. To understand the nature of the computed potentials of mean force, the concept of hydrophilic shielding is introduced. The observed protein interactions are interpreted as resulting from the dynamic reorganization of the system to maintain an optimal hydrophilic shielding of the protein and lipid hydrophobic parts, within the constraint of the flexibility of the components. Our results could lead to a better understanding of several membrane processes in which protein interactions are involved.

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

We 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 (@m-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 Darcys 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.

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

During the last 2.5 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 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 2.5 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-organization of liquid cubic mesophases.

Simulating the self-assembly of model membranes

Dissipative particle dynamics simulations are presented of the self assembly of surfactant bilayers. The effect of changes in the chain length and stiffness of the surfactants on the properties of the model membranes are studied. We observe that changes of the stiffness have significant effects if these changes are made close to the head group of the surfactant. If, on the other hand, changes are made at the end of the tail of the surfactant, the properties of the bilayer are similar to the properties of a bilayer consisting of flexible chains.

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 digitized X–ray micro–tomographic 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 prioritize 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 computer, visualization and storage resources to reach scientific results rapidly; we discuss our work on the grid–enablement of lattice Boltzmann methods in this context.