Molecular Simulation via WebBased Instruction

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Molecular Simulation via Web-Based Instruction

• Peter T. Cummings
• University of Tennessee-Knoxville
• Oak Ridge National Laboratory
• David A. Kofke
• State University of New York at Buffalo
• Richard Rowley
• Brigham Young University

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Collaborators

• Web text
• Peter Cummings
• Hank Cochran
• Juan de Pablo
• A.Z. Panagiotopoulos
• Richard Rowley
• Doros Theodorou
• David Kofke

• Web modules
• Richard Rowley
• Ariel Chialvo
• Juan de Pablo
• Randy Snurr
• Ed Maginn
• Dan Lacks
• A.Z. Panagiotopoulos
• Phil Westmoreland
• Peter Cummings
• Ron Terry
• David Ford
• David Kofke

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Background

• Expanded use of molecular modeling can advance
  chemical engineering
• CACHE Molecular Modeling Task Force
• Foster integration of molecular modeling in
  chemical engineering curricula
• Initiatives
• WWW based textbook on molecular simulation (NSF
  CRCD)
• Molecular-simulation based teaching modules (NSF
  CCD)
• FOMMS 2000 Triennial conference
• First conference to be held July 2000

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Project Aims

• Web text
• Comprehensive resource for learning molecular
  simulation
• How to program (graduate)
• How to interpret (undergraduate and graduate)
• Web modules
• Simulation used to teach molecular origins of
  macroscopic behavior
• interactive molecular simulation modules with
  supporting material
• Enable persons unknowledgeable in molecular
  simulation to construct working, physically
  correct simulations to illustrate some phenomenon
• Permit someone with programming skill to add new
  functionality efficiently

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Web-Text Guidelines

• Reader
• Configurable and dynamic
• Author
• Minimal formatting burden permits focus on
  writing
• Web technician
• Adaptable to evolving web standards

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Web-Text Design

• Preprocessor
• Equation processing (TeX ? gif)
• Glossary tags
• Bibliography tags
• Streamlining

• Run-time processor
• User configurable
• Formatting
• Level of presentation

Author contribution
Compiled text
Preprocessor
Run-time processor
Reader
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Electronic Features in Web-text

• Color figures animations
• Rasmol presentations of molecule configurations
• Movies from simulations
• Computer source code
• Illustrative Java applets
• Large sample data sets for practicing analysis
• Annotation of text
• glossary mouse-overs
• bibliography mouse-overs
• tangents and asides

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Web-Text Status

• Accomplished
• Core chapters completed or near completion
• Working preprocessor and run-time processor
• Graphics and layout features in place
• Incomplete
• Synthesis and coordination of contributions
• Applets, figures, homework problems
• Tweaking
• Technology keeps changing!
• XML/Java
• Plans and access
• Used in some courses in Spring 2000 use again in
  Fall
• http//w3press.utk.edu/

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Simulation Modules

• Teaching of molecular origins of macroscopic
  behavior
• vapor pressure, viscosity, adsorption, nonideal
  gases, etc.
• Web accessible, platform independent (Java)
• Production of multiple modules
• Infrastructure developed and first modules
  produced by collaborators
• Additional modules to be produced by larger
  community
• Need to provide authoring support!

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Module Composition

• Dynamic, interactive molecular simulation
• Supplemental material
• Lecture notes
• Example and homework problems
• Narrative description
• Evaluation
• Click here for sample of interface

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Simulation Module Construction

• Java-based programming
• Interactive with polished user interface
• Molecular simulation API
• Etomica
• Highly extensible
• Object-oriented, drag-and-drop construction of
  molecular simulation
• Construction tools
• Presently Beanbox, such as VisualCafe,
  JBuilder
• Future Developing our own simulation-construction
  application

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Etomica Class Structure

• Simulation
• Organization and reference
• Space
• 1-D, 2-D, 3-D, lattice, etc.
• Vector, Tensor, Boundary
• Phase
• Container of molecules
• Species
• Molecule data structure
• Potential
• Molecule interactions
• Controller
• Protocol for simulation

• Integrator
• Generation of configurations
• Meter
• Property measurement
• Modulator
• Changing of parameters
• Display
• Presentation of data
• Device
• Interaction with simulation
• Support
• Units, Iterators, Atom types, Actions, Color
  schemes, Constants, Defaults, Configurations

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Web-Module Status

• Accomplished
• Etomica API designed and substantially
  implemented
• Basic documentation (click here for example)
• Many prototype applets
• Specification of prototype modules
• Incomplete
• Construction, testing and deployment of prototype
  modules, with supporting materials
• Etomica as a standalone simulation-construction
  tool
• Continuing activities
• Further API design and development
• Improvements to documentation

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Applications of Etomica(considering only
SUNY-Buffalo activities)

• Summer 1999
• High-school workshop in Computational Chemistry
  at SUNY-Buffalo Center for Computational Research
• Spring 2000
• CE530 Molecular Simulation course at SUNY-Buffalo
• Summer 2000
• Repeat of high-school workshop
• Fall 2000
• CE 526 Statistical Mechanics course at
  SUNY-Buffalo
• Future growth
• Interacting with Buffalo area high-school science
  teachers to examine implementation in high-school
  curricula (NSF ITR proposal pending)

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Acknowledgments

• National Science Foundation
• CRCD (Web text)
• CCD (Web modules)
• SUNY-Buffalo Educational Technology Fund
• ITC group at the University of Tennessee

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Additional Information

• CACHE
• www.cache.org
• CACHE Molecular Modeling Task Force
• zeolites.cqe.nwu.edu/Cache/
• WWW-based textbook
• w3press.utk.edu
• Sample modules
• wings.buffalo.edu/eng/ce/kofke/applets/
• www.cheme.buffalo.edu/courses/ce530/Applets/applet
  s.html
• High-school workshop on computational chemistry
• www.ccr.buffalo.edu/Workshop00/index-ws00.htm