Video: Under the Hood of Molecular Workbench

June 15th, 2012 by The Concord Consortium

It takes a lot of computation to model the atomic and molecular world! Fortunately, modern Web browsers have 10 times the computational capacity and speed compared with just 18 months ago. (That’s even faster than Moore’s Law!) We’re now taking advantage of HTML5 plus JavaScript to rebuild Molecular Workbench models to run on anything with a modern Web browser, including tablets and smartphones.

Director of Technology Stephen Bannasch describes the complex algorithms that he’s been programming behind the scenes to get virtual atoms to behave like real atoms, forming gases, liquids and solids while you manipulate temperature and the attractive forces between atoms. See salt crystallize and explore how the intermolecular attractions affect melting and boiling points. Imagine what chemistry class would have been like (or could be like today) if the foundation of your chemical knowledge started here.

Technology and Curriculum Developer Dan Damelin goes on to describe how open source programming opens up possibilities. For instance, Jmol is a Java-based 3D viewer for chemical structures that we were able to incorporate into Molecular Workbench to allow people to easily build activities around manipulation of large and small molecules, and to make connections between static 3D representations and the dynamic models of how molecules interact. We’re planning to build a chemical structure viewer that won’t require Java and will extend another open source project based on JavaScript and WebGL to visualize molecules in a browser.

Interested in this innovative programming? Great! We’re looking for software developers.

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2 Responses to “Video: Under the Hood of Molecular Workbench”

  1. Chrissy Jacobs Says:

    I’m wondering if you have any sense of when this rebuild will be ready for public use – I’m running into problems with Java because our main platform is currently iPads and the laptops we have available for students have been Java disabled for security reasons… But I just discovered your cellular respiration and diffusion modules and would LOVE to have them as a permanent feature of my unit planning!

    [Reply to this Comment]

    Dan Damelin Reply:

    Hi Chrissy,

    We are happy to hear you found some of our materials helpful. There are two things which may be helpful:
    – Many places that have disabled Java in the web-browser retain the ability to run Java applications. So you will likely be able to still run the Java version of the Molecular Workbench. There is some information here about running it locally without launching from a web-page.
    http://mw.concord.org/modeler/download.html#installwithoutjws
    – We are actively creating similar activities in the NextGen/HTML5 version. Diffusion is one of the ones we are working on in the near term. Cellular respiration is one of our most complex models and is likely a long way off (on the order of months). There may be a chance that with our current funding we might not be able to port all of that particular activity. However, hearing from users what is most important to them will influence where we put our efforts, so thank you for letting us know. We will consider your comments.

    -Dan Damelin (from the NextGen team)

    [Reply to this Comment]

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