Environment from the Molecular Level
A NERC eScience testbed project
Science areas in the eMinerals project
Scientific mission of eMinerals
"We will exploit the full potential of the virtual organisation to launch a large integrated study of the transport of pollutants in the environment, focusing on the primary mechanisms by which toxic elements and molecules partition between mineral surfaces, natural organic matter, and solution."
New Methods for New Science
The eMinerals project springs from a long term vision to create a new paradigm for the way that computational sciences carry out increasingly complex studies.
Before eMinerals ... the traditional way of conducting computational studies is for the work to be carried out by individuals. These individuals manage their own computations, workflow, access to resources and data files. With the increase in computational power simulations of ever greater complexity can be run, providing results with a higher degree of realism.
After eMinerals ... large scale calculations have been facilitated by breaking away from traditional working methods. The computational sciences have arrived at the point where large simulations can be performed by collaborations, rather than individuals. eMinerals has developed an infrastructure to support collaborations between simulation scientists and this hassignificantly expand the horizons of molecular-level computer simulations for applications to environmental processes.
The escience technologies developed within the project are detailed in other pages. They have enabled us to do better and more diverse research, discussed below...
So, what is the research focus?
Enabled by eecience technologies, the eMinerals scientific endeavour is heading towards understanding complex envionmental systems through the use of molecular and molecular-scale modelling. The systems of interest of the eMinerals project are, primarily: the adsorbtion of contaminants on mineral surfaces, the mineral-fluid interface and damage to minerals caused by high-level radioactivity. Here is why...
Contaminated land and water resources pose a major remediation challenge to the governments and people of both the developed and the developing world. Strategies to remediate contaminated sites or to protect aquifers require robust models of water catchment, sediment transport, and of ground water flow. Such models need to be able to quantify the rate of water flow and movement of the polluting contaminant (be it a potentially toxic element, an organic compound, etc.). In hydrogeology, the simple picture is that the mobility of the contaminant is related to rate of fluid flow via the retardation factor, R, which is physically linked to the efficiency of the adsorption of the contaminant onto the minerals making up the surface soil, sediments or rocks, and in turn depends upon the partition coefficient, K, of the solute between water and the mineral surface. The retardation factor is used in most reactive transport models to describe the evolution and transport of the contaminant. However, the thermodynamic databases used in reactive transport models are far from complete or perfect, and significant features are based on assumed adsorption mechanisms and ill-constrained mineral-fluid equilibria. Thus, for example, models currently employed for the adsorption of potentially toxic elements (e.g. Cd, As, Cr…) are generally based on the assumption that the ions are bound onto a mineral surface via a single surface site, displacing one proton of hydroxyl ion per site. However, recent experiment and modelling suggest that most cations adhere to mineral surfaces via two or more sites. This means that the partition coefficient will be different between the two cases, leading to a different functional dependence on pH. The use of the inappropriate form of K in reactive transport models will therefore lead to inaccurate predictions of the change of R with chemical conditions, and could result in erroneous prediction of the evolution of regional-scale ground water chemistry.
This example highlights the serious need for a detailed understanding of adsorption, desorption and transport processes at the molecular level, and a significant part of our science programme will work towards developing this understanding together with the creation of a well-constrained thermodynamic database for mesoscale modelling that will rectify the major shortcomings of current data. We use our integrated compute and data grid environment, coupled with new developments in the grid infrastructure and simulation codes to make a “grand challenge” assault on the understanding of the atomic-scale processes involved in the transport of a wide range of contaminants in the environment.
eMinerals Scientific Aims and Objectives
We aim to achieve a detailed understanding of key environmental, interfacial processes. To do this, we must answer some key questions:
- What are the mechanisms involved in adsorption and desorption of contaminants onto mineral surfaces and natural organic matter in soils and rocks, and what is the relative importance of different mechanisms?
- How do contaminants partition between water, mineral surfaces and natural organic molecules?
- How will these processes affect the transport of the contaminants in the environment?
We are using molecular scale modelling to answer these questions. The eScience technologies developed within the eMinerals project allows the collaborators within the eMinerals virtual organisation to investigate an array of different species and surfaces that are representative of typical components of very polluted environments, such as mine tippings, toxic industrial waste dumps and areas affected by agricultural pollution from pesticide run offs. The systems also investigate solutions to long-term storage of radioactive waste, and large-scale natural occurrences of As and F in regional groundwater systems.
What numbers do we want?
Briefly, larger scale models need the following numbers:
- energies and free energies of adsorption processes
- energy barriers for transport
- diffusion rates
- desorption rates
- partition coefficients.
These numbers will provide extensive data sets that can be fed into mesoscale models of the transport of contaminants in environments such as sediments and porous rocks. Up to now, scientific investigations of these issues, both experimental and theoretical, have focused on individual contaminants and individual potential atomic environments. eScience has now created the opportunity to compare different contaminants and systems in a single integrated study.
The solvated species that we are investigating are:
- metal cations and anions, including Cs, As, Pb etc.
- fluorine anions
- chlorinated organic molecules such as PCBs, DDTs and dioxins.
We are investigating the interaction of the above environmental contaminants with a range of mineral surfaces including:
- hydrated and anhydrous surfaces of clays
This study requires a range of molecular simulation methods. There are two important considerations, namely the level of accuracy and sample size, and there is always a trade-off between these since higher accuracy and larger samples both require increased computer power. Highest accuracy can be achieved using quantum mechanical (QM) methods, but the largest samples can only be achieved using empirical models for the forces between atoms. Empirical models are being used to investigate large systems and to supply preliminary data for the more demanding QM calculations. The latter focus in on specific surface sites and molecular functional groups. In addition, the QM calculations are being used to provide the basis for deriving empirical potential parameters, completing a continuuous cycle of improvement in our models.
The escience challenge
The figure above represents the three-dimensional problem of tacking different pollutants on different minerals urfaces with different simulation methods (level of theory). This challenge is too great for a single laboratory.
The merit of using escience to bring together geographically distributed centres of excellence as a virtual organisation is that collectively the scientists of a virtual organisation can have expertise across the three-dimensional space represented by the figure. This is the strength of the eMinerals project team.
The escience approach, described in more detail elsewhere on this site, is to enable the scientists to work closely together to tackle a wide range of environmental systems.
More specifically, the research aims are:
- Development and testing of empirical models for the forces between organic molecules (e.g. carboxylic acid, dioxins, PCBs), water molecules, mineral surfaces and contaminant elements. We will QM methods to generate a database of forces and energies against which the models will be tuned and tested.
- Calculation of structure and stability of common surfaces of environmentally important minerals (e.g. clay minerals, carbonates, Fe/Mn/Al-oxides/oxyhydroxides, phosphates and sulphides) in contact with aqueous fluids using empirical and QM based methods. The effects of temperature, pH, and surface chemistry will also be assessed giving us a clear idea of the surface composition under a range of conditions.
- Generation of representative models of organic substrates commonly found in soils, comparison of structure and pKa (measure of acid strength) with literature values. This work builds on the success of earlier theoretical work generating small but representative molecules as models for organic substrates (e.g. humic acids etc), as well as much larger molecules that more closely mimic the functionality of species found in soils.
- Adsorption of organics on oxidic minerals as a function of pH and surface charge, in order to produce a reliable understanding of the mechanisms and of the degree of surface coverage under a variety of external conditions.
- Adsorption of metallic ions and light anions onto the minerals listed above and organic substrates in order to investigate the effects of ionic strength, redox, and surface states on adsorption process, calculate the energies for exchanging with surface ions, and compare different modes of speciation and precipitation at the mineral surface. This leads to understanding of the mechanisms for the adsorption modes as a function of aqueous conditions, and of the factors controlling the adsorption rates.
- Generation of models and databases for transport and flow models of the evolution of contaminants in soil and ground water on a local scale. Inappropriate model parameters used in transport models can result in erroneous predictions. We aim to derive models and databases, which can be used by the hydrology community to improve the parameters in their transport models.
What we have achieved so far
There has already been considerable progress in these areas. Please see our Highlights page for more detailed information. Here is a list of our current achievements, relating to our specific aims.
- Potentials have been developed that allow for large scale studies of organic contaminants on clay surfaces, and work is currently underway to diversify to other surfaces. Suites of the different PCB, PCDD and PCDF congeners have been studied. The empirical potential methods, being less computationally expensive, have allowed for a comprehensive sweep of the surface to be carried out, and the minimum position for the molecules have been identified. These results have fed into QM calculations of the adsorption energy at these optimised positions, allowing for tuning of the QM calculations and refinement of the adsorption energy due to the dual-pronged simulation approach.
- The stability of non-stoichiometric oxide surfaces have been studied, and iron hydroxide and quartz surfaces have been studied in the presence of solution.
- Arsenic impurities have been incorportated into iron sulfide minerals using high level QM simulations. Work is now underway to model these impurities at the iron sulfide surfaces.
- Accurate descriptions of the various components of the systems have been achieved through the sharing of scientific knowledge within the eMinerals virtual organisation, using the three different levels of modelling techniques. Highly correlated systems have been modelled using expensive computational techniques and these results will be used for parameterisation of empirical potentials in order to model their behaviour in larger systems.
This science part of the project is being carried out by research staff at Cambridge (radioactive waste, organic molecules, aluminosilicate, clay and carbonate surfaces, water), Bath (carbonate surfaces, water, metal cations, organic molecules), UCL (oxides/hydroxides, sulphides, metal cations), RI (sulphide surfaces, metal ions, fluoride anions), and Birkbeck (carbonate and phosphate surfaces, water, organic molecules, cations).
Many of our publications can be found in our Documents page. Some papers that focus on some of science achievements the eMinerals project can be downloaded as pdf files by clicking on the links below:
Environment from the molecular level: an escience testbed project.
MT Dove, M Calleja, J Wakelin, K Trachenko, G Ferlat, P Murray-Rust, NH de Leeuw, Z Du, GD Price, PB Wilson, JP Brodholt, M Alfredsson, A Marmier, RP Tyer, LJ Blanshard, RJ Allan, K Kleese van Dam, IT Todorov, W Smith, VN Alexandrov, GJ Lewis, A Thandavan, SM Hasan.
Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9) pp 302305
Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated compute and data grid.
M Calleja, R Bruin, MG Tucker, MT Dove, RP Tyer, LJ Blanshard, K Kleese van Dam, RJ Allan, C Chapman, W Emmerich, PB Wilson, JP Brodholt, A Thandavan, VN Alexandrov.
Molecular Simulations 31, 303313, 2005
eMinerals: Science Outcomes enabled by new Grid Tools.
M Alfredsson, E Artacho, M Blanchard, JP Brodholt, CRA Catlow, DJ Cooke, MT Dove, Z Du, NH de Leeuw, A Marmier, SC Parker, GD Price, JMA Pruneda, W Smith, I Todorov, K Trachenko, and K Wright.
Proceedings of All Hands 2005 (ISBN 1-904425-53-4), pp 788795, 2005