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.

Exact rate calculations by trajectory parallelization and tilting.

A sampling procedure to compute exactly the rate of activated processes arising in systems at equilibrium or nonequilibrium steady state is presented. The procedure is a generalization of the method proposed in [A. Warmflash et al.

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies.

An improved and simplified version of the finite temperature string (FTS) method [W. E, W. Ren, and E.

Markovian milestoning with Voronoi tessellations.

A new milestoning procedure using Voronoi tessellations is proposed. In the new procedure, the edges of Voronoi cells are used as milestones, and the necessary kinetic information about the transitions between the milestones is calculated by running molecular dynamics (MD) simulations restricted to these cells. Like the traditional milestoning technique, the new procedure offers a reduced description of the original dynamics and permits to efficiently compute the various quantities necessary in this description.

On the assumptions underlying milestoning.

Milestoning is a procedure to compute the time evolution of complicated processes such as barrier crossing events or long diffusive transitions between predefined states. Milestoning reduces the dynamics to transition events between intermediates (the milestones) and computes the local kinetic information to describe these transitions via short molecular dynamics (MD) runs between the milestones. The procedure relies on the ability to reinitialize MD trajectories on the milestones to get the right kinetic information about the transitions.

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.

Molecular simulations of mesoscopic bilayer phases.

Dissipative particle dynamics simulations are used to study the self-assembly of lipids into bilayers. With a simple mesoscopic lipid-water model, we observe the formation of the liquid crystalline phase L(alpha) and gel phases in which the tails are interdigitated L(betaI) or noninterdigitated L(beta). For double-tail lipids experiments show all three phases, while for single-tail lipids only L(beta) and L(alpha) are observed.

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.

Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins.

Biological membranes are complex and highly cooperative structures. To relate biomembrane structure to their biological function it is often necessary to consider simpler systems. Lipid bilayers composed of one or two lipid species, and with embedded proteins, provide a model system for biological membranes.

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.