using escience to calibrate our tools: parameterisation of quantum mechanical calculations with grid...
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![Page 1: Using eScience to calibrate our tools: parameterisation of quantum mechanical calculations with grid technologies Kat Austen Dept. of Earth Sciences, University](https://reader035.vdocument.in/reader035/viewer/2022070306/5515ee1e550346d46f8b5295/html5/thumbnails/1.jpg)
Using eScience to calibrate our tools: parameterisation of
quantum mechanical calculations with grid
technologies
Kat AustenDept. of Earth Sciences, University of Cambridge
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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
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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
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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
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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
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Kat Austen, Dept. of Earth Sciences, University of Cambridge
What is already done: PCDDs
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Kat Austen, Dept. of Earth Sciences, University of Cambridge
PCBs: Structure
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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
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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)
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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
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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
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Kat Austen, Dept. of Earth Sciences, University of Cambridge
Box size convergence
150 Ry
250 Ry 350 Ry
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Kat Austen, Dept. of Earth Sciences, University of Cambridge
Torsion angle calculations
Basis Set 1Automatic Basis SetAutomatic Basis Set
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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
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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
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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
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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