Using eScience to calibrate our tools: parameterisation of

quantum mechanical calculations with grid

technologies

Kat AustenDept. of Earth Sciences, University of Cambridge

Kat Austen, Dept. of Earth Sciences, University of Cambridge

Interesting Aspects for Investigation

Surface structureSurface-solution

interactions

Structure of species in

solution - Arsenic V

- PCBsEffect 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

systemTrap 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

MethodsDensity 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 SubmissionUsed 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 you’re here you’ve probably missed Toby OH White’s 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 CollaborationRun 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 AspectBox 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 1Automatic Basis SetAutomatic Basis Set

Kat Austen, Dept. of Earth Sciences, University of Cambridge

Optimised Basis Set

-1

-0.9

-0.8

-0.7

-0.6

-0.5

-0.4

-0.3

-0.2

-0.1

0

-177-162-152-142-132-122-112-101-91-81-66-56-46-35-25 -5 5 15 25 35 46 56 66 76 86 96106117127137157177

Angle / degrees

Energy (+2799.4) / eV

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 Bath’s 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