Title: LAMMPS Throws Light on the Structure and Materials Properties of Clay-Polymer Nanocomposites and DNA-Intercalated Layered Double Hydroxide Nanomaterial

Speaker: Peter Coveney, Professor of Theoretical Chemistry Director, Centre for Computational Science University College, London, UK

Date/Time: Thursday, June 5, 2008 at 3:00pm

Location: CSRI Building/Room 90 (Sandia NM)

Brief Abstract: Large-scale atomistic simulations (> 100,000 atoms) are becoming more commonplace as the size of available computational resources increases and efficient classical molecular dynamics algorithms are developed. With the recent advances in grid computing methods alongside the advent of petascale resources, it is now possible to easily and effectively simulate large-scale systems, considerably extending the spatial dimensions of clay models that have previously been studied. Grid based methods are especially useful when one is considering an ensemble of different size simulations; each simulation can be run simultaneously on suitable grid resources, thereby significantly reducing turnaround times.

In these large-scale simulation studies, we have observed thermally induced undulatory fluctuations of both anionic and cationic clay sheets: we use these to calculate the materials properties of a range of nanomaterials, which would be difficult to measure experimentally due to the small size of the clay platelets. We have recently performed simulations of various anionic clays intercalated with chloride ions, various organic polymers, and DNA. The structure and stability of DNA at realistic sizes intercalated in-between anionic clay sheets is important for understanding its possible use in gene therapy and drug delivery. The stability of intercalated DNA and RNA is also of importance to origins of life studies, which have yielded evidence that minerals may have played an important role in prebiotic synthesis.

To facilitate this, we have developed and use the Application Hosting Environment (AHE), a lightweight, fully Web services compliant middleware toolkit designed to allow a user to transparently access federated grid resources provided, for example, by the UK National Grid Service and those provided by international grid projects, such as US TeraGrid and DEISA in the EU. AHE simplifies user access to the grid by hiding many of the underlying details that a user typically needs to know in order to run applications on a grid. In AHE, legacy scientific codes are represented by Web services which the user interacts with by means of one or more simple clients. AHE is based around a community model, whereby an expert user installs their scientific application on a set of target grid resources, installs the AHE server, then configures the AHE server with details of the application and resources. End users can then download the AHE client and use it to launch simulations using the shared application, with a much reduced barrier to entry. Using this new technology, we have performed several large-scale molecular dynamics studies of layered silicate nanocomposites and bio-inorganic composites involving full intermolecular interactions using the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) hosted within AHE and deployed across three interoperating high performance computing grids located on two continents.

In summary, with the help of easy-to-use grid middleware federating international high end computing resources, fully atomistic simulations of clay systems now attain dimensions directly comparable to those of the real minerals. This has resulted in new insight into finite-size effects in simulations and real systems, and has facilitated the calculation of hard-to-obtain materials property data, of significant interest in both pure and applied research.

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