End of Project Meeting Insight Gained

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End of Project MeetingInsight Gained

• Clay-Poly Project
• Quarterly Meeting September 2004
• H. C. Greenwell UCL

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Contents

• Insight gained.
• Technology development.
• Performing ab initio simulations.
• Performing large-scale MD simulations.
• Visualization and data analysis.
• Database development.
• Communication methods.
• Left overs.

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Introduction

• The project has used a blend of commercial
  software and free open-source software. The
  development of the commercial software is
  restricted to novel use. Licencing and use of
  closed-source binaries restricts the amount of
  software development.
• Insight has been gained into the restrictions
  inherent with many software packages currently
  available. It is also arguable that insight
  gained can be applied to what has been learnt
  about project management.

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Technology Development

• Insight has been gained into
• Lack of commercially available software for very
  large-scale simulations.
• Many open-source codes, which are suitable for
  large-scale simulation are restricted to
  bio-systems.
• Lack of support for freeware, coupled with a lack
  of tools for data analysis means that a
  scientific software writer/administrator needs to
  be closely linked with such a project.
• Critically, there are NO builder environments for
  large-scale materials simulation.

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Ab initio Simulation

• Ab initio simulation can be used to rationalize
  reactivity within organo-clay systems - see J.
  Phys. Chem paper.
• However, thorough experimental analysis must be
  available to allow a hypothetical series of
  reaction steps to be constructed. Close links
  between the synthetic and computational chemist
  are needed.
• Ab initio methods should, ideally, be utilised in
  the initial stages of the project to gain insight
  into reactive sites within the interlayer.
• Ab initio methods should also be used to
  rationalize interesting reactivity not readily
  characterised by conventional methods.

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Large-Scale MD

• Large-scale MD can provide insight into
• The configuration and location of cations,
  monomers, and water in the interlayer region
  (Visualization and 1-D density).
• The nature of inter-molecular interactions in the
  interlayer (Visualization and RDFs).
• The dynamics of molecules within the interlayer
  (Diffusion coefficients).

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Large-Scale MD

• Large-scale MD can provide insight into
• The time-scales needed for obtaining reasonable
  statistics for analysis.
• Rare events that are not observed in smaller
  model systems.
• The effect of the length of periodic boundary
  conditions.
• Configurations to act as starting points for ab
  initio simulations.

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Large-Scale MD

• Large-scale MD has provided insight into
• The importance of hydrophilic/hydrophobic domains
  within the clay interlayer. The amphiphilic
  nature of the interlayer of organo-clays is a
  dominant feature, directing intercalant
  arrangement, and hence reactivity.
• The blocking effect of monomer chain length on
  reactive sites. Star-polymers/rings should be
  better. Short chains may be non-water soluble.
• The interplay of cation/water/monomer on the
  nature of the clay interlayer is very complex.

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Large-Scale MD

• Large-scale MD has provided insight into
• The effect of cation type on the sites that the
  cation may occupy. This is also related to the
  hydrating ability of the cation, and how much
  water is displaced by monomers.
• The very dominating need for cations to maintain
  an inner sphere of coordinating O atoms. Monomer
  backbone oxygens/alcohol groups replace the
  hydration shells of water.
• The interplay between the organic material and
  the organophilic faces of the clay sheets.

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Visualization and Data Analysis

• Insight has been gained into
• The usefulness of visualization to supplement and
  make sense of empirical, bulk property data, e.g.
  atom density plots and RDFs.
• Using visualization as a diagnostic tool to
  identify potential problems with model
  systems/force field parameterisation.
• Converting data into a form readily interpretable
  by non-computational chemists.
• The writing of scientific data analysis tools,
  which are often task-specific

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Data Base

• Insight has been gained into
• Benefits and limitations of using commercial and
  free-ware relational data-base management systems
  (RDBMS).
• Design and implementation of RDBMS.
• The benefit of having a RDBMS implemented at the
  start of the project.
• Data formats and tools for data manipulation and
  analysis.

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Communication

• Insight has been gained into
• Benefits of regular (daily) instant messenger
  sessions for fostering esprit de corps, keeping
  track of ongoing work and rapidly answering
  queries during publication writing.
• The need for minute taking during quarterly
  meetings and follow up on the resulting action
  points at subsequent meetings.
• Limitations of e-mail as a form of communication.

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Performing MD5. Replication
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Performing MD7. Data Analysis
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Performing MD8. Visualization - PEODiAc_Na
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Performing MD8. Visualization - PEG_Li
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Performing MD8. Visualization - PEG_Li
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Performing MD8. Visualization - PEG_K
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Performing MD8. Visualization - PEG_K
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What Next - Periodicity?