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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 Web text Peter Cummings Hank Cochran Juan de Pablo

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molecular simulation via web based instruction
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

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

  • 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
project aims
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
web text guidelines
Web-Text Guidelines
  • Reader
    • Configurable and dynamic
  • Author
    • Minimal formatting burden permits focus on writing
  • Web technician
    • Adaptable to evolving web standards
web text design

Equation processing (TeX  gif)

Glossary tags

Bibliography tags


Run-time processor

User configurable


Level of presentation

Web-Text Design

Author contribution

Compiled text


Run-time processor


electronic features in web text
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
web text status
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
simulation modules
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!
module composition
Module Composition
  • Dynamic, interactive molecular simulation
  • Supplemental material
    • Lecture notes
    • Example and homework problems
    • Narrative description
  • Evaluation
  • Click here for sample of interface
simulation module construction
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
etomica class structure

Organization and reference


1-D, 2-D, 3-D, lattice, etc.

Vector, Tensor, Boundary


Container of molecules


Molecule data structure


Molecule interactions


Protocol for simulation


Generation of configurations


Property measurement


Changing of parameters


Presentation of data


Interaction with simulation


Units, Iterators, Atom types, Actions, Color schemes, Constants, Defaults, Configurations

Etomica Class Structure
web module status
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
applications of etomica considering only suny buffalo activities
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)
  • National Science Foundation
    • CRCD (Web text)
    • CCD (Web modules)
  • SUNY-Buffalo Educational Technology Fund
  • ITC group at the University of Tennessee
additional information
Additional Information
  • CACHE Molecular Modeling Task Force
  • WWW-based textbook
  • Sample modules
  • High-school workshop on computational chemistry