Using eScience to calibrate our tools: parameterisation of quantum mechanical calculations with grid technologies Kat Austen Dept. of Earth Sciences, University of Cambridge

Kat Austen, Dept. of Earth Sciences, University of Cambridge Interesting Aspects for Investigation Surface structure Surface-solution interactions Structure of species in solution - Arsenic V - PCBs Effect of water

Kat Austen, Dept. of Earth Sciences, University of Cambridge Molecular Modelling of Interfaces Achieve: Solvation Energies Adsorption Energies Solvation Structures Geometries Mesoscale: Retardation Factors Remediation of polluted environments

Kat Austen, Dept. of Earth Sciences, University of Cambridge Polychlorinated biphenyls (PCBs) Do not degrade either in the environment or metabolically Cause illness in humans and animals - respiratory illness; reproductive problems; skin conditions; liver, stomach and thyroid problems No natural sources - entirely a product of human activity, mainly through industrial manufacture of heat insulating materials

Kat Austen, Dept. of Earth Sciences, University of Cambridge Methods of remediation and modelling the system Trap on soil particles / minerals to remove from the environment Bioremediation Modelling of the interaction of PCBs with surfaces of environmentally prevalent minerals, as already done with PCDDs / PCDFs -> adsorption energies and adsorption geometries

Kat Austen, Dept. of Earth Sciences, University of Cambridge What is already done: PCDDs

Kat Austen, Dept. of Earth Sciences, University of Cambridge PCBs: Structure

Kat Austen, Dept. of Earth Sciences, University of Cambridge Methods Density Functional Theory (DFT) calculations using SIESTA* Initially need to parametrise model to ensure accurate description of both surface and adsorbate Torsion angle very important in approach of the molecule to the surface *Soler et al. J. Phys. Condensed Matter 2002 (14) p2745

Kat Austen, Dept. of Earth Sciences, University of Cambridge eScience for Job Submission Used eMinerals parameter sweep scripts that: automatically generate, upload to SRB and submit lots (hundreds) of jobs from a simple configuration file and template input file Vary across n-dimensional parameter space Ties in with our auto-visualisation tools (if youre here youve probably missed Toby OH Whites talk on this!) Using my_condor_submit (Richard P. Bruin, 11:35 Rm 3)

Kat Austen, Dept. of Earth Sciences, University of Cambridge eScience for Collaboration Run across the eMinerals minigrid resources Using AgentX within MCS to extract metadata SRB for storage of data, TobysSRB for visualisation (Toby OH White, 16:50 on Tuesday) Use Rcommands and Metadata Manager to search metadata and identify relevant dataset, then find it on the SRB (Poster) Access Grid weekly meetings Blogbooks on the eMinerals wiki

Kat Austen, Dept. of Earth Sciences, University of Cambridge Combinatorial Aspect Box size convergence -> need to find the minimum box size around the molecule in the gas phase minimises computational expense lower limit for the size of the surface cell scan over 10x10 Angstroms -> 121 calculations Scan over torsion angle in 5 degree increments -> 72 calculations 209 different PCB molecules, test at least 418 different geometries at the clay surface

Kat Austen, Dept. of Earth Sciences, University of Cambridge Box size convergence 150 Ry 250 Ry 350 Ry

Kat Austen, Dept. of Earth Sciences, University of Cambridge Torsion angle calculations Basis Set 1 Automatic Basis Set

Kat Austen, Dept. of Earth Sciences, University of Cambridge Optimised Basis Set Barrier to rotation decreases by half between automatic and optimised basis sets

Kat Austen, Dept. of Earth Sciences, University of Cambridge Collaboration Cambridge DFT sweeps for PCBs - box size and torsion angle Bath use Cambridge data in parameterisation of empirical potentials Bath sweeps of configurational space within defined box size Cambridge calculations using Baths optimised geometries

Kat Austen, Dept. of Earth Sciences, University of Cambridge Further work... etc. BSSE - found to be unimportant due to collaborative effort and use of XML! Molecules on surfaces - combinatorial sweeps of different surfaces: organics on carbonates and clays; arsenic on pyrite Assessment of importance of dispersion within molecule - high level calculations of torsion angles Develop potentials - collaboration with Bath

Kat Austen, Dept. of Earth Sciences, University of Cambridge Acknowledgements Toby White (Cambridge) Richard Bruin (Cambridge) Arnaud Marmier (Bath) Martin Dove (Cambridge) Emilio Artacho (Cambridge) eMinerals, NERC