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Molecular Simulation via Web-Based Instruction

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  1. 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

  2. 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 Collaborators

  3. 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

  4. 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

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

  6. Preprocessor Equation processing (TeX  gif) Glossary tags Bibliography tags Streamlining Run-time processor User configurable Formatting Level of presentation Web-Text Design Author contribution Compiled text Preprocessor Run-time processor Reader

  7. 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

  8. 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/

  9. 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!

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

  11. 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

  12. 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 Etomica Class Structure

  13. 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

  14. 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)

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

  16. 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/applets.html • High-school workshop on computational chemistry • www.ccr.buffalo.edu/Workshop00/index-ws00.htm