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A virtual research organization enabled by eMinerals minigrid:
An integrated study of the transport andimmobilization of arsenic species in the
environment
Zhimei Du
September 2006
A NERC’s eScience testbed project
Environment from the Molecular Level
History
A NERC’s eScience testbed project
Environment from the Molecular Level
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.
Components of eMinerals minigrid
TeamPeople: Scientists, Code developers, escientists
Institutions:
University of Bath, Birkbeck College London, UCL,
The Royal Institution, Cambridge,
the CCLRC Daresbury, Reading
www.eminerals.orgwww.eminerals.org
A NERC’s eScience testbed project
Environment from the Molecular Level
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.
A NERC’s eScience testbed project
Environment from the Molecular Level
Global arsenic occurrence
A NERC’s eScience testbed project
Environment from the Molecular Level
Arsenic occurrence in Asia
A NERC’s eScience testbed project
Environment from the Molecular Level
Solution
• Possible way: selective adsorption.• Promising adsorbents: iron-bearing minerals.
• A computational approach: A comprehensive study of the capabilities of different iron-bearing minerals.
A NERC’s eScience testbed project
Environment from the Molecular Level
Challenge Needs• Simulations at different levels.• Various methodologies • Many iron-bearing minerals. • People• Techniques• Infrastructures• Workflows, high-throughput, • Data management, computing resources.
A NERC’s eScience testbed project
Environment from the Molecular Level
A real challenge !!!!
Grid techniques
Communication tools
AG meeting: acting as a valuable management tool.
for members contributing their 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.
A NERC’s eScience testbed project
Environment from the Molecular Level
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.
A NERC’s eScience testbed project
Environment from the Molecular Level
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
A NERC’s eScience testbed project
Environment from the Molecular Level
Maria Alfredsson
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
A NERC’s eScience testbed project
Environment from the Molecular Level
Science outcomes
Bulk calculationsBulk calculationsSurface stabilitiesSurface stabilitiesHydration processesHydration processes
Computational methods used:Computational methods used: Quantum mechanical calculations(e.g.DFT)
Interatomic Potential Methods
• Static lattice energy minimisation
• Molecular dynamics simulations
A NERC’s eScience testbed project
Environment from the Molecular Level
• 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??
Incorporation mechanism of arsenic in pyrite (FeS2)
Marc Blanchard
A NERC’s eScience testbed project
Environment from the Molecular Level
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.
As in Fe site As in S site
AsS As2 As instead of S2
As in Fe site As in S site
AsS As2 As instead of S2
A NERC’s eScience testbed project
Environment from the Molecular Level
Zhimei Du
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.
{100}
{011}{101}
{100}
{011}{101}{111}
{001}
{010}{101}
{111}
{110}
{001}
{012}
{101}
{100}
(a)
Calculated bulk structures and the dry (bottom left) and hydrated (bottom right) thermodynamic morphologies of (a) Hematite, (b) Goethite, (c) pure iron hydroxide.
(b) (c)
A NERC’s eScience testbed project
Environment from the Molecular Level
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.
Fe2O3
Surface 001 012a 012b 012c 100 101 110 111a 111b Dry surface
energy (Jm-2) 1.78 1.87 2.75 2.35 1.99 2.34 2.02 2.21 2.07
Hydrated surface energy (Jm-2)
0.90 0.38 0.28 0.38 0.27 0.04 0.20 0.33 0.28
FeOOH Surface 010 100 110 001 011 101 111
Dry surface energy(Jm-2)
1.92 1.68 1.26 0.67 1.18 1.72 1.33
Hydrated surface energy (Jm-2)
0.51 1.17 0.68 0.52 0.34 1.32 1.12
Fe(OH)2
Surface 001 010 011 101 110 111 Dry surface
energy (Jm-2) 0.04 0.38 0.35 0.35 0.64 0.60
A NERC’s eScience testbed project
Environment from the Molecular Level
ARNALD
Arnaud Marmier
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.
A NERC’s eScience testbed project
Environment from the Molecular Level
• 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.
A NERC’s eScience testbed project
Environment from the Molecular Level
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.
A NERC’s eScience testbed project
Environment from the Molecular Level
Acknowledgement
The work was funded by NERC via grants NER/T/S/2001/00855, NE/C515698/1 and NE/C515704/1.
A NERC’s eScience testbed project
Environment from the Molecular Level
