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.

Management of diverticular fistulae to the female genital tract

OBJECTIVE

Fistulae to the female genital tract are an infrequent but severe complication of diverticular disease. The purpose of this study was to evaluate treatment and outcome in patients with diverticular colo-genital fistulae.

METHOD

Sixty women treated for diverticular fistulae (DF) to the female genital tract during 1992-2004 were identified. Clinic and operative charts were reviewed. Mean age was 70 years and mean follow-up time after surgery was 1 year.

RESULTS

Most common presenting symptoms were vaginal discharge of faeces or gas (95% of patients) and abdominal pain (43%). About 75% of patients had undergone a hysterectomy. Forty-six patients underwent at least one radiological contrast study and the fistula was demonstrated in 35 (76%) patients. Fifty-seven patients had surgery, and findings included colo-vaginal fistulae (n = 47), colo-uterine fistulae (n = 2) and multiple fistulae involving vagina and other organs (n = 8). A sigmoid resection and primary anastomosis was performed in 51 and a Hartmann procedure with colostomy in six patients. Sixteen (28%) patients experienced morbidity after surgery, including anastomotic dehiscence (n = 4) and ureteric injury (n = 3). There was no mortality.

CONCLUSION

Diverticular fistulae to the female genital tract usually occur in elderly patients with a prior hysterectomy. Radiological contrast studies demonstrate the fistulous tract in most cases. Sigmoid resection and primary anastomosis results in a satisfactory outcome in the majority of patients.

Atomistic modeling of multilayered ceria nanotubes

Ceria has become a very important material for catalytic applications. Many applications take advantage of its high oxygen storage capacity (OSC). We propose a new polycrystalline multilayered nanotube structure that could go some way to further unlocking the oxygen storage capabilities of the material. We illustrate how our simulation models are constructed and further investigate the potential reactivity of the new structure, by comparing predictions of vacancy cluster segregation behavior to that predicted for the most stable flat {111} surface.

Oxygen transport in unreduced, reduced and Rh(iii)-doped CeO2nanocrystals

Ceria, CeO2, based materials are a major (active) component of exhaust catalysts and promising candidates for solid oxide fuel cells. In this capacity, oxygen transport through the material is pivotal. Here, we explore whether oxygen transport is influenced (desirably increased) compared with transport within the bulk parent material by traversing to the nanoscale. In particular, atomistic models for ceria nanocrystals, including perfect: CeO2; reduced: CeO1.95 and doped: Rh0.1Ce0.9O1.95, have been generated. The nanocrystals were about 8 nm in diameter and each comprised about 16,000 atoms. Oxygen transport can also be influenced, sometimes profoundly, by microstructural features such as dislocations and grain-boundaries. However, these are difficult to generate within an atomistic model using, for example, symmetry operations. Accordingly, we crystallised the nanocrystals from an amorphous precursor, which facilitated the evolution of a variety of microstructures including: twin-boundaries and more general grain-boundaries and grain-junctions, dislocations and epitaxy, isolated and associated point defects. The shapes of the nanocrystals are in accord with HRTEM data and comprise octahedral morphologies with {111} surfaces, truncated by (dipolar) {100} surfaces together with a complex array of steps, edges and corners. Oxygen transport data was then calculated using these models and compared with data calculated previously for CeO1.97/ YSZ thin films and the (bulk) parent material, CeO197. Oxygen transport was calculated to increase in the order: CeO2 nanocrystal < (reduced) CeO1.95 nanocrystal approximately Rh0.1Ce0.9O1.95 nanocrystal < CeO1.97/YSZ thin film < (reduced) CeO1.97 (bulk) parent material; the mechanism was determined to be primarily vacancy driven. Our findings indicate that reducing one- (thin film) or especially three- (nanocrystal) dimensions to the nanoscale may prove deleterious to oxygen transport. Conversely, we observed dynamic evolution and annihilation of surface vacancies via surface oxygens migrating to the bulk of the nanocrystal; the vacancies left are then filled by other oxygens moving to the surface. Coupled with previous simulation studies, in which we calculated that oxygen extraction from the surface of a ceria nanocrystal was energetically easier compared with the bulk surface, our calculations predict that ceria nanocrystals would facilitate effective oxidative catalysis. This study describes framework simulation procedures, which can be used in partnership with experiment, to explore transport in nanocrystalline ionic systems, which include complex microstructures. Such data can provide predictions for experiment or help reduce the number of experiments required.

Molecular Dynamics Simulations of Electrolyte Solutions at the (100) Goethite Surface

Molecular dynamics simulations of electrolyte solutions in contact with a neutral (100) goethite (alpha-FeOOH) surface were used to probe the structure of the mineral-water interface and gain insight into the adsorption properties of monovalent ions. Three electrolyte solutions were considered: NaCl, CsCl, and CsF. The electrolyte ions were chosen to cover a range of ionic sizes and affinities for the aqueous phase. The molecular dynamics simulations indicate the presence of a structured interfacial region resulting from the strong interaction of water with the mineral surface. The specific arrangement and preferred orientation of water that arise from this interaction create adsorption sites in the interfacial region, i.e., as far as 15 A away from the surface, and hence give rise to a strong correlation between the water and ion distributions. The structure of the hydrated ion, its effect on the water arrangement at the interface, and the strength of the ion-water bond are found to be key factors that determine the location and extent of ion adsorption at the interface. Additionally, in all simulations, we find a build up of positive charges near the surface due to cation adsorption, which is compensated by an accumulation of anions in the next few angströms. This creates an excess of negative charges, which is in turn compensated by an excess of positive charges, and so on. As we modeled a neutral surface, the structure of the electrolyte distribution arises from the complex interplay of the interactions between the surface, water, and the electrolyte ions rather than from the need to neutralize a surface charge. In addition, our simulations indicate that the electrolyte distribution does not resemble that of a classical electrical double layer. Indeed, our calculations predict the presence of several condensed layers and oscillations in the net charge away from the surface.

Surface Structure of (101̄0) and (112̄0) Surfaces of ZnO with Density Functional Theory and Atomistic Simulation

We have calculated the stability of two of the low-index surfaces known to dominate the morphology of ZnO as a function of stoichiometry. These two surfaces are (10(-)10) and (11(-)20). In each case, two terminations only are stable for a significant range of oxygen and hydrogen chemical potential: the pure stoichiometric surface and a surface covered in a monolayer of water. The mode by which the water adsorbs is however different for the two surfaces considered. On the (10(-)10) surface the close proximity of the water molecules means hydrogen bonding can occur between adjacent chemiabsorbed water molecules and hence there is little difference in the stability of the hydrated and hydroxylated surface, and in fact the most stable surface occurs with a combination of dissociated and undissociated water adsorption. In the case of the (11(-)20) surface, it is only when full dissociation has occurred that a hydrogen-bonding network can form. Our results also show good agreement between DFT and atomistic simulations, suggesting that potential based methods can usefully be applied to ZnO.

Atomistic simulation studies of magnetite surface structures and adsorption behavior in the presence of molecular and dissociated water and formic acid

Static energy minimization techniques have been used to elucidate the surface structures of magnetite crystals in pure and hydroxylated forms. Adsorption energy values in the presence of molecular water, dissociate water and simple carboxylic group molecule (formic acid) are calculated and we found that the carboxylic group do not adsorb strongly in most of the pure and hydroxylated surfaces in comparison to water. Since the associated calcium minerals are floated from magnetite using fatty acid collector, our calculations corroborate the flotation practice of removing these impurity minerals from magnetite.

Reduction of NO2 on Ceria Surfaces

Cerium dioxide, CeO2, plays an important role in catalysis, due to its ability to store and release oxygen depending on the conditions present in the catalyst environment. To understand the role of ceria in catalytic reactions, we need to study the details of the interaction of ceria surfaces with environmentally sensitive molecules. In this work, we examine the adsorption of the NO2 molecule onto defective (reduced) surfaces of ceria using density functional theory with a correction for on-site Coulomb interactions (DFT+U), which allows for a consistent description of pure and reduced ceria. The interaction of NO2 with defective (111), (110), and (100) surfaces gives an adsorbate-surface structure in which the bond lengths around one Ce(III) ion from the reduced surface shorten, while one N-O bond lengthens. Analysis of the electronic structure and spin density distributions demonstrates that one Ce(III) has been reoxidized to Ce(IV), with the formation of adsorbed NO2-. Finally, we discuss the energetics of the interaction of NO2 with ceria.

CeO2catalysed conversion of CO, NO2and NO from first principles energetics

First principles calculations using density functional theory with corrections for on-site Coulomb interactions (DFT + U) are presented in which we compute the energy for the conversion of CO to CO(2), NO(2) to NO and NO to N(2) over ceria surfaces. The surface sensitivity is discussed on the basis of the vacancy formation energies.

Ab Initio Surface Phase Diagram of the {101̄4} Calcite Surface

Electronic structure calculations, performed at the density functional theory level, were employed to study the surface termination of the {104} calcite surface in contact with a gaseous phase containing water and carbon dioxide. A surface phase diagram was generated to investigate the change in surface termination as a function of temperature, pressure, and gas-phase composition. This diagram revealed that a nonstoichiometric termination could occur in atmospheric conditions at high relative humidity, hence suggesting that nonstoichiometric surfaces can play a major role in the chemistry of calcite surfaces.

Competitive Adsorption on Wollastonite: An Atomistic Simulation Approach

Atomistic simulation techniques are used to simulate surface structure and adsorption behavior of scarcely floatable wollastonite mineral in the presence of molecular and dissociated water, methanoic acid, and methylamine. The latter two additives represent the two widely used collector head-group molecules. The static energy minimization code METADISE was used to perform the simulation to obtain pure surface energy and adsorption energy in the presence of added molecule. The hydroxylation was performed on those surfaces where low-coordinated silicon was made to saturate by bonding with hydroxyl group, and the subsequent charge neutralization was maintained by adding proton on single-coordinated surface oxygen. A comparison of surface energies revealed that all the surfaces become stabilized in the presence of added molecules; however, the presence of methylamine decreased the surface energy to lower values. Adsorption of dissociated water is preferred by the {100} and {102} surfaces, whereas the {001} surface preferred methylamine adsorption, because these show highly negative adsorption energies. In terms of molecular adsorption, the preferred adsorption sequence for all the surfaces is methylamine > methanoic acid > water without considering coadsorption. For the {100} and {102} surfaces, the adsorption energy values of carboxylic acid and amine are more negative than that of water and therefore we conclude that both carboxyl and amine head-group molecules adsorb preferably on wollastonite. Our simulation verify usability of carboxylic acid head group as widely used collectors for wollastonite flotation and, at the same time, it predicts the use of amine head-group collectors as possible modifiers, which corresponds well with our experimental findings.

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.

Oxidising CO to CO2 using ceria nanoparticles

We calculate, using simulated amorphisation and recrystallisation (A&R), that ceria (CeO2) nanoparticles, about 8 nm in diameter, comprise a high concentration of labile surface oxygen species, which we suggest will help promote the oxidation of CO to CO2. In particular, the ceria nanoparticle contains a high proportion of reactive {100} surfaces, surface steps and corner sites. When reduced to CeO1.95, the associated Ce3+ species and oxygen vacancies decorate step, corner and {100} sites in addition to plateau positions on {111}. The energetics of CO oxidation to CO2, catalysed by a ceria nanoparticle, is calculated to be lower compared with CO oxidation associated with the lowest energy surface (i.e. CeO2(111)) of the corresponding 'bulk' material. Our calculated morphologies for the ceria nanoparticles are in accord with experiment.

Shape of CeO2 nanoparticles using simulated amorphisation and recrystallisation

Evolutionary simulation has been used to generate full atomistic models for CeO2 nanoparticles, which comprise [100]-truncated [111] octahedra in accord with experiments.

Free Energy of Adsorption of Water and Metal Ions on the {101̄4} Calcite Surface

We calculated the free energy profiles of water and three metal ions (magnesium, calcium, and strontium) adsorbing on the [1014] calcite surface in aqueous solution. The approach uses molecular dynamics with parametrized equations to describe the interatomic forces. The potential model is able to reproduce the interactions between water and the metal ions regardless of whether they are at the mineral surface or in bulk water. The simulations predict that the free energy of adsorption of water is relatively small compared to the enthalpy of adsorption calculated in previous papers. This suggests a large change in entropy associated with the water adsorption on the surface. We also demonstrate that the free energy profile of a metal ion adsorbing on the surface correlates with the solvent density and that the rate of formation of an innersphere complex depends on overcoming a large free energy barrier, which is mainly electrostatic in nature. Furthermore, comparison among the rates of desorption of magnesium, calcium, and strontium from the calcite surface suggests that magnesium has a much lower rate of desorption due to its strong interactions with both water and the surface.

Free energy of adsorption of water and calcium on the {10 1? 4} calcite surfaceElectronic supplementary information (ESI) available: free energy calculations. See http://www.rsc.org/suppdata/cc/b3/b311928a/

Molecular dynamics simulations of the calcite-water interface have shown that the free energy of adsorption of water is relatively small compared to the previously calculated enthalpy of adsorption implying a large entropy change and that the free energy profile of a calcium adsorbing on the surface correlates with the solvent density; these calculations allow us to begin to address the rates of adsorption and desorption which are essential for studying growth and dissolution.

Synthesis, structure and ionic conductivity in nanopolycrystalline BaF2/CaF2 heterolayers

Atomistic simulations have shown that the calculated conductivity of nano-polycrystalline BaF2/CaF2 heterolayers is considerably higher than the component bulk materials and we predict that grain-boundary diffusion is the key to fast ionic conductivity in these systems.

Encapsulated oxide nanoparticles: the influence of the microstructure on associated impurities within a material

Simulation techniques have been used to explore how the microstructure of a material influences the nature of associated impurities embedded therein. We illustrate this by exploring four systems: BaO and CaO nanoparticles encapsulated within a ("perfect") MgO host lattice and SrO and MgO nanoparticles encapsulated within a ("microstructural") BaO lattice, which comprises a network of screw-edge dislocations. This study uses annealing techniques to generate energetically feasible nanoparticle structures and morphologies, dislocation networks, interfacial boundaries, and strain profiles. Specifically, the different encapsulated nanoparticles exhibit a range of morphologies, expose a variety of facets at the nanoparticle/host lattice interface, and are observed to rotate within the cavity they occupy inside the host lattice. The structure and nature of the nanoparticles reflect the lattice misfit between the nanoparticle and the host lattice. The study suggests also that there exists a "critical nanoparticle size", above which dislocations evolve.

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.