eMinerals: Applications of GRID enabled science to understand the Environment from the molecular level.
Lead Research Organisation:
University of Cambridge
Department Name: Earth Sciences
Abstract
Dealing with containment of waste and the problem of contaminated land and water resources pose a major 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 quantity the rate of water flow and the rate of movement of the polluting contaminant (be it a toxic metal, an organic compound, etc.). However, the thermodynamic data bases used in reactive flow models are far from complete or perfect, and significant features are based on assumed adsorption mechanisms and ill-constrained mineral-fluid equilibria. We propose, therefore, to establish a collaborative research programme based on atomistic simulation methods to study the way pollutants attach to mineral surfaces and natural organic matter, how they dissolve into water, and how they are carried around the environment. The goal of the study is to tackle many different types of surfaces, interfaces and solutions, and many different pollutants, in order to provide comprehensive data sets and to allowed detailed comparisons to be made. We will also be using a range of simulation methods, each with complementary strengths. This is an ambitious study, and requires the development of a high-level computing and data management infrastructure. We will build on developments coming through the current eMinerals project which allow calculations to be spread across share computing resources, and handle data through web interfaces. This work will link closely with experimental studies carried out in the laboratories of the project partners and their other collaborators. These include field-based studies that identify major pollutants in different settings, and laboratory studies of surfaces and fluid flow that can provide information from the atomic level up to macroscopic length scales. The final goal is to provide complete and accurate data that can be used to provide inputs for modelling of pollutants over larger length scales.
Organisations
Publications
Woodley S
(2007)
New software for finding transition states by probing accessible, or ergodic, regions
in Molecular Simulation
White TO
(2009)
Lessons in scientific data interoperability: XML and the eMinerals project.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Walker AM
(2009)
Integrating computing, data and collaboration grids: the RMCS tool.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Walker A
(2006)
Computer modelling of the energies and vibrational properties of hydroxyl groups in - and -Mg2SiO4 Computer modelling of the energies and vibrational properties of hydroxyl groups in - and -Mg2SiO4
in European Journal of Mineralogy
Walker A
(2007)
Three water sites in upper mantle olivine and the role of titanium in the water weakening mechanism
in Journal of Geophysical Research: Solid Earth
Walker A
(2007)
The origin of the compressibility anomaly in amorphous silica: a molecular dynamics study
in Journal of Physics: Condensed Matter
Trachenko K
(2007)
Logarithmic relaxation in radiation-amorphized zircon
in Physical Review B
Trachenko K
(2007)
Pressure-induced structural transformation in radiation-amorphized zircon.
in Physical review letters
Trachenko K
(2006)
Atomistic simulations of resistance to amorphization by radiation damage
in Physical Review B
Todorov I
(2006)
DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism
in Journal of Materials Chemistry
Todorov I
(2006)
Simulation of radiation damage in gadolinium pyrochlores
in Journal of Physics: Condensed Matter
Todorov I
(2007)
Use of massively parallel molecular dynamics simulations for radiation damage in pyrochlores
in Journal of Materials Science
Stimpfl M
(2006)
An ångström-sized window on the origin of water in the inner solar system: Atomistic simulation of adsorption of water on olivine
in Journal of Crystal Growth
Sola E
(2009)
Equation of state of hexagonal closed packed iron under Earth's core conditions from quantum Monte Carlo calculations
in Physical Review B
Smith W
(2006)
A short description of DL_POLY
in Molecular Simulation
Salje EK
(2009)
eScience for molecular-scale simulations and the eMinerals project.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Peroos S
(2006)
A computer modelling study of the uptake, structure and distribution of carbonate defects in hydroxy-apatite.
in Biomaterials
Ono S
(2008)
Ab initio molecular dynamics simulations for thermal equation of state of B2-type NaCl
in Journal of Applied Physics
Martin P
(2006)
Application of molecular dynamics DL_POLY codes to interfaces of inorganic materials
in Molecular Simulation
Goodwin AL
(2008)
Colossal positive and negative thermal expansion in the framework material Ag3[Co(CN)6].
in Science (New York, N.Y.)
Frame I
(2009)
New tools to support collaboration and virtual organizations.
in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
Fortes A
(2007)
The high-pressure phase diagram of ammonia dihydrate
in High Pressure Research
Du Z
(2006)
Molecular dynamics simulations of hydration, dissolution and nucleation processes at the alpha-quartz (0001) surface in liquid water.
in Dalton transactions (Cambridge, England : 2003)
Dove M
(2006)
Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within the e Minerals escience project
in Molecular Simulation
Cooke DJ
(2006)
Surface structure of (10(-)10) and (11(-)20) surfaces of ZnO with density functional theory and atomistic simulation.
in The journal of physical chemistry. B
Bush I
(2006)
A DAFT DL_POLY distributed memory adaptation of the Smoothed Particle Mesh Ewald method
in Computer Physics Communications
Blanchard M
(2007)
Adsorption of As(OH) 3 on the (001) Surface of FeS 2 Pyrite: A Quantum-mechanical DFT Study
in The Journal of Physical Chemistry C
Blanchard M
(2007)
Arsenic incorporation into FeS2 pyrite and its influence on dissolution: A DFT study
in Geochimica et Cosmochimica Acta
Berry A
(2007)
Titanium substitution mechanisms in forsterite
in Chemical Geology
Austen K
(2008)
Electrostatic versus polarization effects in the adsorption of aromatic molecules of varied polarity on an insulating hydrophobic surface
in Journal of Physics: Condensed Matter