A NERC’s e Science testbed project

1. Environment from the Molecular Level A NERC’s eScience testbed project A virtual research organization enabled by eMinerals minigrid:An integrated study of the transport andimmobilization of arsenic species in the environmentZhimei DuSeptember 2006

2. Environment from the Molecular Level A NERC’s eScience testbed project Components of eMinerals minigrid History The aim: Incorporate grid technologies with computer simulations to tackle complex environmental problems. Phase 1: Establish eMinerals minigrid and a functional virtual organisation. Phase 2: Fully explore the established infrastructure to perform simulations of environmental processes.

3. Environment from the Molecular Level A NERC’s eScience testbed project Team People: Scientists, Code developers,escientists Institutions: University of Bath, Birkbeck College London, UCL, The Royal Institution, Cambridge, the CCLRC Daresbury, Reading www.eminerals.org

4. Environment from the Molecular Level A NERC’s eScience testbed project Problem • A pressing environmental issue: the contamination of groundwater sources by arsenic. • Rise massive human health problems. • The scale: millions people worldwide at risk. The scale of this environmental disaster has never been seen before. • It has become a worldwide catastrophe.

5. Environment from the Molecular Level A NERC’s eScience testbed project Global arsenic occurrence

6. Environment from the Molecular Level A NERC’s eScience testbed project Arsenic occurrence in Asia

7. Environment from the Molecular Level A NERC’s eScience testbed project Solution • Possible way: selective adsorption. • Promising adsorbents: iron-bearing minerals. • A computational approach: A comprehensive study of the capabilities of different iron-bearing minerals.

8. Environment from the Molecular Level A NERC’s eScience testbed project Challenge Needs • Simulations at different levels. • Various methodologies • Many iron-bearing minerals. • People • Techniques • Infrastructures • Workflows, high-throughput, • Data management, computing resources. A real challenge !!!!

9. Environment from the Molecular Level A NERC’s eScience testbed project Grid techniques • Communication tools • AG meeting: • acting as a valuable management tool. • for members contributingtheir ideas to collaborative papers. • Wiki: • exchange ideas, deposit news, edit collaborative papers. • disadvantage: not support instant communication. • Instant message • useful for members of the project developing new tools.

10. Environment from the Molecular Level A NERC’s eScience testbed project Grid environment support for workflow Job submission: using my_condor_submit (MCS) ---a meta-scheduling job submission tool , where Condor’s DAGman functionality and storage resource brokers (SRB) are used. Workflow in three steps: download input from SRB MCS decides where to run job  upload output to SRB. Our practice has shown: the SRB is of prime importance for data management in such collaboration.

11. Environment from the Molecular Level A NERC’s eScience testbed project Benefits of grid techniques for scientific studies Example: Quantum mechanical studies of the structures of Goethite, Pyrite and Wüstite Problem: The electronic and magnetic structures of many iron-bearing minerals are not very well represented by traditional density functional theory. Minerals: Goethite, Pyrite and Wüstite. Task: Compare GGA and hybrid-functional calculations with experimental data to decide the best way to describe these minerals. Magnetic structures: Ferric iron (3+): AFM, FM Ferrous iron (2+): AFM, FM, NM Maria Alfredsson

12. Environment from the Molecular Level A NERC’s eScience testbed project Example (continue): Calculations needed: • 5-10 different hybrid-functionals for each mineral • 10 to 20 runs needed for each mineral. • These are compute intensive calculations !!!! • All calculations are independent of each other. • Performed on UCL Condor-pool (> 1000 processors) using the MCS job submission tool. • Calculations are completed within a couple of months Prior to this eScience technology, this type of study might have taken a year or longer

13. Environment from the Molecular Level A NERC’s eScience testbed project Science outcomes Computational methods used: • Quantum mechanical calculations(e.g.DFT) • Interatomic Potential Methods • Static lattice energy minimisation • Molecular dynamics simulations Bulk calculations Surface stabilities Hydration processes

14. Environment from the Molecular Level A NERC’s eScience testbed project Incorporation mechanism of arsenic in pyrite (FeS2) • Pyrite plays an important role in the transport of arsenic. • Experiment: • Arsenic substitutes for sulphur, forming AsS di-anion groups rather than As2 groups • Arsenic substitutes for iron. • Using first-principles calculations • How As incorporated ?? • Where it sits in the lattice?? • At Fe or S sites?? Marc Blanchard

15. Environment from the Molecular Level A NERC’s eScience testbed project • DFT (CASTEP code): • The AsS configuration is the most energetically favourable when pyrite precipitates or is stable. • Incorporation of arsenic as a cation is energetically unfavourable in pure pyrite.

16. Environment from the Molecular Level A NERC’s eScience testbed project (a) {100} {100} {111} {011} {011} {101} {101} {001} {010} {101} {101} {012} {100} {111} {001} {110} Structures and stabilities of iron (hydr)oxide mineral surfaces • Iron (hydr)oxide minerals: promising adsorbents to immobilise active arsenic and other toxic species in groundwater. • A large number of simulations required to examine the surface structures and stabilities of these minerals. (b) (c) Calculated bulk structures and the dry (bottom left) and hydrated (bottom right) thermodynamic morphologies of (a) Hematite, (b) Goethite, (c) pure iron hydroxide. Zhimei Du

17. Environment from the Molecular Level A NERC’s eScience testbed project Calculated surface energies for three iron (hydr)oxide minerals, including both dry and hydroxylated surfaces • Surface energies of Fe(OH)2, are lower compared to those of Fe2O3 and FeOOH due to the open layered structure of Fe(OH)2. • In general, the hydroxylated surfaces are more stable than corresponding dry surfaces.

18. Environment from the Molecular Level A NERC’s eScience testbed project ARNALD Molecular dynamics simulations of aqueous solution/goethite interfaces • Immobilisation processes concern the adsorption from solution, but the exact structure of aqueous solutions in contact with surfaces is not yet completely elucidated. • Reasons: • The distribution and local concentration of the various species is difficult to observe experimentally. • Expensive ab initio calculations are unable to cope with the amount of water required. Arnaud Marmier

19. Environment from the Molecular Level A NERC’s eScience testbed project • In pure water, layering water structure formed near the surface. • Layering structures appear near the surface for both sodium and chloride ions. • There is a clear build up of negative charge near the surface. • Reason: the adsorption of chloride ions.

20. Environment from the Molecular Level A NERC’s eScience testbed project Conclusions Our experience showed that • With the support of grid technologies it is very promising to solve complex scientific problems. • We can achieve our goals in a much quicker, more comprehensive and detailed way.

21. Environment from the Molecular Level A NERC’s eScience testbed project Acknowledgement The work was funded by NERC via grants NER/T/S/2001/00855, NE/C515698/1 and NE/C515704/1.