Skip to main content

The Molecular Workbench Software: An Innovative Dynamic Modeling Tool for Nanoscience Education

  • Chapter
  • First Online:

Part of the book series: Models and Modeling in Science Education ((MMSE,volume 6))

Abstract

Nanoscience and nanotechnology are critically important in the twenty-first century (National Research Council, 2006; National Science and Technology Council, 2007). This is the field in which major sciences are joining, blending, and integrating (Battelle Memorial Institute & Foresight Nanotech Institute, 2007; Goodsell, 2004).

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Notes

  1. 1.

    http://www.design-simulation.com/ip/index.php

  2. 2.

    http://www.algodoo.com

  3. 3.

    http://www.crayonphysics.com

  4. 4.

    For instance, see Gromacs: http://www.gromacs.org

  5. 5.

    “We have become quantum mechanics – engineering and exploring the properties of quantum states. We’re paving the way for the future nanotechnicians.” — Donald M. Eigler, IBM Fellow

  6. 6.

    http://molecularworkbench.blogspot.com/2010/02/mwscript-javascript-interaction.html

References

  • American Chemical Society (2008). Statement on computer simulations in academic laboratories. Washington, DC.

    Google Scholar 

  • Amirouche, F. M. L. (2006). Fundamentals of multibody dynamics: Theory and applications. Berlin: Springer.

    Google Scholar 

  • Battelle Memorial Institute & Foresight Nanotech Institute (2007). Productive nanosystems: A technology roadmap. Menlo Park, CA.

    Google Scholar 

  • Borgman, C. L., Abelson, H., Dirks, L., Johnson, R., Koedinger, K. R., Linn, M. C., et al. (2008). Fostering learning in the networked world: The cyberlearning opportunity and challenge. Arlington, TX : National Science Foundation.

    Google Scholar 

  • Bourg, D. M. (2001). Physics for game developers. O’Reilly Media. Sebastopol, CA.

    Google Scholar 

  • Cass, M. E., Rezepa, H. S., & Rezepa, D. R. (2005). The use of the free, open-source program Jmol to generate an interactive web site to teach molecular symmetry. Journal of Chemical Education, 82(11), 1736–1740.

    Article  Google Scholar 

  • Catto, E. (2007). Box2D. http://www.box2d.org. Accessed 4 Dec 2010.

  • Chang, R. P. H. (2006). A call for nanoscience education. Nano Today, 1(2) , 2.

    Google Scholar 

  • Colella, V. S., Klopfer, E., & Resnick, M. (2001). Adventures in modeling: Exploring complex, dynamic systems with StarLogo. New York: Teachers College Press.

    Google Scholar 

  • Drexler, K. E. (1988). Studying nanotechnology foresight briefing #1. From http://www.foresight.org/Updates/Briefing1.html. Accessed 4 Dec 2010.

  • Drexler, K. E. (1992). Nanosystems: Molecular machinery, manufacturing, and computation (1st ed.). New York: Wiley.

    Google Scholar 

  • Feurzeig, W., & Roberts, N. (1999). Modeling and simulation in science and mathematics education. New York: Springer.

    Google Scholar 

  • Finkelstein, N. D., Adams, W. K., Keller, C. J., Kohl, P. B., Perkins, K. K., Podolefsky, N. S., et al. (2005). When learning about the real world is better done virtually: A study of substituting computer simulations for laboratory equipment. Physical Review Special Topics - Physics Education Research, 1(1), 010103–010110.

    Article  Google Scholar 

  • Goodsell, D. S. (2004). Bionanotechnology: Lessons from nature. New York: Wiley.

    Google Scholar 

  • Greenberg, A. (2009). Integrating nanoscience into the classroom: Perspectives on nanoscience education projects. ACS Nano, 3(4), 762–769.

    Article  Google Scholar 

  • Isralewitz, B., Gao, M., & Schulten, K. (2001). Steered molecular dynamics and mechanical functions of proteins. Current Opinion in Structural Biology, 11, 224–230.

    Article  Google Scholar 

  • Jensen, J. (2010). Simulations in teaching physical chemistry: thermodynamics and statistical mechanics. Molecular modeling basics. http://molecularmodelingbasics.blogspot.com/2010/12/simulations-in-teaching-physical.html. Accessed on December 4, 2010.

  • José, T. J., & Williamson, V. M. (2005). Molecular visualization in science education: An evaluation of the NSF-sponsored workshop. Journal of Chemical Education, 82(6), 937–942.

    Article  Google Scholar 

  • Kafai, Y., & Resnick, M. (1996). Constructionism in practice: Designing, thinking, and learning in a digital world. New Jersey: Lawrence Erlbaum Associates.

    Google Scholar 

  • Lacoursière, C. (2007). Ghosts and machines: Regularized variational methods for interactive simulations of multibodies with dry frictional contacts. Umeå: Umeå University.

    Google Scholar 

  • Leach, A. R. (2001). Molecular modeling: Principles and applications (2nd ed.). Pearson Education. Upper Saddle River, NJ.

    Google Scholar 

  • Liu, G. R., & Liu, M. B. (2003). Smoothed particle hydrodynamics: A meshfree particle method. Singapore: World Scientific Publishing Company.

    Book  Google Scholar 

  • Monroy-Hernández, A., & Resnick, M. (2008). Empowering kids to create and share programmable media. Interactions, March–April, 50–51.

    Article  Google Scholar 

  • National Research Council. (1996). National science education standards. Washington, DC: National Academy Press.

    Google Scholar 

  • National Research Council. (2006). A matter of size: Triennial review of the national nanotechnology initiative. Washington, DC: National Academies Press.

    Google Scholar 

  • National Science and Technology Council. (2007). The national nanotechnology initiative strategic plan. Arlington, VA: National Nanotechnology Coordination Office.

    Google Scholar 

  • NSF Blue Ribbon Panel on SBES. (2006). Simulation-based engineering science: Revolutionizing engineering science through simulation. Washington, DC: NSF.

    Google Scholar 

  • Pallant, A., & Tinker, R. (2004). Reasoning with atomic-scale molecular dynamic models. Journal of Science Education and Technology, 13(1), 51–66.

    Article  Google Scholar 

  • Panoff, R. (2009). Simulations deepen scientific learning. ASCD Express, 4(19) . Retrieved from http://www.ascd.org/ascd_express/vol4/419_panoff.aspx. Accessed 3 Dec 2010.

  • Papert, S. (1991). Situating constructionism. In I. Harel, & S. Papert (Eds.), Constructionism. Norwood, NJ: Ablex Publishing Corporation.

    Google Scholar 

  • Rappaport, D. C. (1997). The art of molecular dynamics simulation. Cambridge: Cambridge University Press.

    Google Scholar 

  • Rieth, M., & Schommers, W. (2006). Handbook of theoretical and computational nanotechnology (1st ed). Los Angeles, CA: American Scientific Publishers.

    Google Scholar 

  • Shipley, E., & Moher, T. (2008). Instructional framing for nanoscale self-assembly design in middle school: A pilot study. Paper presented at the Annual Meeting of the American Educational Research Association, March 24–28, 2008.

    Google Scholar 

  • Stam, J. (2003). Real-time fluid dynamics for games. Paper presented at the Proceedings of the Game Developer Conference. San Jose, CA.

    Google Scholar 

  • Steinberg, R. N. (2000). Computers in teaching science: To simulate or not to simulate?. American Journal of Physics, 68(7), S37–S41.

    Article  Google Scholar 

  • A. E. Sweeney, & S. Seal (Eds.). (2008). Nanoscale Science and Engineering Education. Los Angeles, CA: American Scientific Publishers.

    Google Scholar 

  • Shipley, E., Silva, B. L., Daly S., Wischow, E., Moher, T., & Pellegrino, J. W. (2008, June 23–28). Using construct-centered design to revise instruction and assessment in a nanoscale self-assembly design activity: A case study. Proceedings of the 8th international conference for the learning sciences (Vol. 3). Utrecht, Netherlands.

    Google Scholar 

  • Tinker, R., & Xie, Q. (2008). Applying computational science to education: The molecular workbench paradigm, computing in science and engineering. Computing in Science and Engineering, 10(5), 24–27.

    Article  Google Scholar 

  • Watanabe, N., & Tsukada, M. (2000). Fast and stable method for simulating quantum electron dynamics. Physical Review E, 62(2), 2914–2923.

    Article  Google Scholar 

  • Wieman, C. E., Adams, W. K., & Perkins, K. K. (2008). PhET: Simulations that enhance learning. Science, 322, 682–683.

    Article  Google Scholar 

  • Wilensky, U., & Reisman, K. (2006). Thinking like a wolf, a sheep or a firefly: Learning biology through constructing and testing computational theories – An embodied modeling approach. Cognition & Instruction, 24(2), 171–209.

    Article  Google Scholar 

  • Wilson, E. K. (2003). Computational nanotechnology: Modeling and theory are becoming vital to designing and improving nanodevices. Chemical & Engineering News, 81(17), 27–29.

    Article  Google Scholar 

  • Wong-Ekkabut, J., Baoukina, S., Triampo, W., Tang, I.-M., Tieleman, D. P., & Monticelli, L. (2008). Computer simulation study of fullerene translocation through lipid membranes. Nature Nanotechnology, 3, 363–368.

    Article  Google Scholar 

  • Xie, C., & Pallant, A. (2009). Constructive chemistry: A case study of gas laws. Concord 13(2) , 12–13.

    Google Scholar 

  • Xie, Q., & Tinker, R. (2006). Molecular dynamics simulations of chemical reactions for use in education. Journal of Chemical Education, 83(1), 77–83.

    Article  Google Scholar 

  • Zollman, D., Rebello, N. S., & Hogg, K. (2002). Quantum mechanics for everyone: Hands-on activities integrated with technology. American Journal of Physics, 70(3), 252–259.

    Article  Google Scholar 

Download references

Acknowledgment

This work is supported by the National Science Foundation under grant number DUE-0802532.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Charles Xie .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Xie, C., Pallant, A. (2011). The Molecular Workbench Software: An Innovative Dynamic Modeling Tool for Nanoscience Education. In: Khine, M., Saleh, I. (eds) Models and Modeling. Models and Modeling in Science Education, vol 6. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0449-7_6

Download citation

Publish with us

Policies and ethics