Arnaud Marmier

Electrostatic versus polarization effects in the adsorption of aromatic molecules of varied polarity on an insulating hydrophobic surface

Ab initio calculations have been used to investigate the electronic and energetic behaviour accompanying the adsorption of aromatic molecules of different polarities onto an insulating hydrophobic surface, as a convenient model for the study of characteristic weak adsorption processes in biochemistry (ligand–receptor interactions) and geochemistry (aromatic pollutants on soil minerals). Four poly-chlorinated dibenzo-p-dioxin molecules of different polarities were chosen as adsorbates; the surface was the (001) surface of pyrophyllite, a chemically inert, weakly polar, covalently bonded surface. The fairly weak interactions were observed to be dominated by local electrostatics rather than global multipoles or hybridization. The polarization induced on the adsorbate has been analysed. A small transfer of electron density was also observed from the molecule to the surface.

Modelling inorganic solids and their interfaces: A combined approach of atomistic and electronic structure simulation techniques

We are seeking to combine the reliability of the structures and energies obtained from quantum mechanical methods with the insights given by larger scale simulations, which are better able to search configurational space. We will discuss our recent work using quantum mechanical methods, based on DFT, which have been applied to the study of a number of solids. Al2O3, CeO2, MnO2 and CaCO3, and compare these with results using atomistic simulation where the forces between atoms are modelled using interatomic potentials. The results show that such quantum methods can be used successfully to screen the different potential models and where necessary, provide sufficient data to allow us to re-consider the potential models. In addition, we show examples where the quantum based methods can give further insights into the reactivity, particularly of surfaces. However, it still remains computationally expensive to search all possible configurations and by using the atomistic simulations to search through different configurations we can identify new structures which can be verified with the quantum based simulations.

Self diffusion of argon in flexible, single wall, carbon nanotubes

The high-throughput Condor environment now allows many simulations to be performed on related systems, whether the focus is on improving the statistics or on broadening the range of conditions under which these simulations run. We illustrate the scope of the approach by using equilibrium molecular dynamics (EMD) to calculate self-diffusivities of argon atoms diffusing through single wall carbon nanotubes (SWNT). The diameters of the tubes and their helicities were varied and different argon loadings were studied. We also considered the effect of the rigidity/flexibility of the tube on the diffusivity. We found that the helicity and flexibility of the tubes have almost no noticeable influences. The size of the pore had a small effect, but the diffusivity depended essentially on the fluid loading.

Atomistic simulation of charged iron oxyhydroxide surfaces in contact with aqueous solution.

Molecular dynamics simulations of aqueous solution/goethite interfaces show that the classical models of the electrical double layer do not accurately describe the distribution of ions near the surface (such a distribution is present even when the surface is neutral) and that the explicit treatment of solvent molecules is essential to capture the effects of the surface on the liquid phase.

Application of molecular dynamics DL_POLY codes to interfaces of inorganic materials

Three recent applications of the DL_POLY molecular dynamics code are described, which demonstrate the flexibility and viability of the code for extending our understanding of the structure, stability and reactivity of ceramics and minerals at the atomic level. The first is an investigation into differences in oxygen atom mobility in bulk and at the most stable {111} surface of ceria. The results show enhanced surface transport but that it is via subsurface oxygen. Secondly, we investigate how polychloro-dibenzo-pdioxins (PCDDs) molecules might adsorb on clay surfaces. The resulting adsorption energies show a clear relationship with chlorine content of the molecule. Finally, we apply DL_POLY to comparing the aggregation of magnesium oxide and calcium carbonate nanoparticles. We find that very small calcium carbonate nanoparticles are amorphous and their aggregation shows no preferred orientation in contrast to magnesium oxide, which remain highly crystalline and combine in a highly structural specific way.

From HADES to PARADISE-atomistic simulation of defects in minerals

The development of the HADES code by Michael Norgett in the 1970s enabled, for the first time, the routine simulation of point defects in inorganic solids at the atomic scale. Using examples from current research we illustrate how the scope and applications of atomistic simulations have widened with time and yet still follow an approach readily identifiable with this early work. Firstly we discuss the use of the Mott–Littleton methodology to study the segregation of various isovalent cations to the (00.1) and (01.2) surfaces of haematite (α-Fe2O3). The results show that the size of the impurities has a considerable effect on the magnitude of the segregation energy. We then extend these simulations to investigate the effect of the concentration of the impurities at the surface on the segregation process using a supercell approach. We consider next the effect of segregation to stepped surfaces illustrating this with recent work on segregation of La3+ to CaF2 surfaces, which show enhanced segregation to step edges. We discuss next the application of lattice dynamics to modelling point defects in complex oxide materials by applying this to the study of hydrogen incorporation into β-Mg2SiO4. Finally our attention is turned to a method for considering the surface energy of physically defective surfaces and we illustrate its approach by considering the low index surfaces of α-Al2O3.

eScience for molecular-scale simulations and the eMinerals project

We review the work carried out within the eMinerals project to develop eScience solutions that facilitate a new generation of molecular-scale simulation work. Technological developments include integration of compute and data systems, developing of collaborative frameworks and new researcher-friendly tools for grid job submission, XML data representation, information delivery, metadata harvesting and metadata management. A number of diverse science applications will illustrate how these tools are being used for large parameter-sweep studies, an emerging type of study for which the integration of computing, data and collaboration is essential.

Negative linear compressibility in common materials

Negative linear compressibility (NLC) is still considered an exotic property, only observed in a few obscure crystals. The vast majority of materials compress axially in all directions when loaded in hydrostatic compression. However, a few materials have been observed which expand in one or two directions under hydrostatic compression. At present, the list of materials demonstrating this unusual behaviour is confined to a small number of relatively rare crystal phases, biological materials, and designed structures, and the lack of widespread availability hinders promising technological applications. Using improved representations of elastic properties, this study revisits existing databases of elastic constants and identifies several crystals missed by previous reviews. More importantly, several common materials—drawn polymers, certain types of paper and wood, and carbon fibre laminates—are found to display NLC. We show that NLC in these materials originates from the misalignment of polymers/fibres. Using a beam model, we propose that maximum NLC is obtained for misalignment of 26°. The existence of such widely available materials increases significantly the prospects for applications of NLC.

The eMinerals collaboratory: tools and experience

Collaboratories provide an environment where researchers at distant locations work together at tackling important scientific and industrial problems. In this paper we outline the tools and principles used to form the eMinerals collaboratory, and discuss the experience, from within, of working towards establishing the eMinerals project team as a functioning virtual organisation. Much of the emphasis of this paper is on experience with the IT tools. We introduce a new application sharing tool.

Determination of the anisotropic elastic properties of Ge1Sb2Te4

The elastic properties of Ge–Sb–Te (GST) alloys are important for phase-change devices (such as CD-RW, DVD-RW, Blu-ray, or phase-change random access memory) because the transition between the crystalline and amorphous phases involves a volume change accommodated by a strain estimated to be between 150 MPa and 10 GPa. However, the elastic properties of GST alloys are poorly characterized and the experimental and theoretical values show large discrepancies. We carry out a careful analysis of the elastic properties of a model system, crystalline Ge1Sb2Te4, using density functional theory and elastic anisotropy considerations. We show that Ge1Sb2Te4 exhibits significant anisotropy in its elastic properties.