The Molecular Workbench™ Platform

July 14, 2010 at 10:16 am 6 comments

The most interesting software that my educational technology class discovered this last Spring was the Molecular Workbench from the Concord Consortium.  The enormous range of material and the power of their modeling package (used in teaching chemistry, biology, and physics) is impressive.  Unfortunately, it doesn’t work on the iPad, and there’s not really much there for mathematics or computer science learning.  It does serve as an interesting standard for what these kinds of tools might look like.  The Molecular Workbench aims to be a medium for science learning.

MW is not just a collection of simulations–do not be deceived by first glance. While it presents many existing simulations that are ready to use in classroom, it is, however, also a modeling tool for teachers and students to create their own simulations and share them with collaborators. There are very sophisticated modeling capacities hidden behind its simple user interface that empower you to create new simulations and even explore the unknowns.

via The Home Page of the Molecular Workbench™ Software.

Entry filed under: Uncategorized. Tags: , .

Google as champion of user-as-creator CMU launches robot-based CS-STEM Program

6 Comments Add your own

  • 1. Charles Xie  |  July 15, 2010 at 11:50 am

    The Molecular Workbench is written in Java, which is unfortunately not supported by iPad. It focuses on science. However, it is a system that supports (most) Java applets, which means one can plug in anything they want, math or science.

    The Molecular Workbench isn’t just for chemistry modeling, as its name might suggest. It did start with a molecular dynamics engine, but it has incorporated a quantum dynamics engine and a computational fluid dynamics engine recently. The idea behind it is to exploit computational methods scientists and engineers have developed to solve fundamental equations in physics, such as Newton’s equation, the Schrodinger equation, the Navier-Stokes equation, the Maxwell equations, and so on, and transform them into interactive computational tools that students can use to learn the science through the visualizations of the results.

    Unlike other science visualization tools that only provide simulations designed by instruction designers, MW supports both instructionism and constructionism. Students can learn by going through curriculum modules created by educators, or by creating their own models and simulations to solve a problem or answer a question. I have seen some very amazing results from classroom tests using the constructionist pedagogy. When students are given such a powerful tool to imagine and create, their creativity is completely unleashed. But I cannot say the same thing based on the field tests of the materials using the instructionist approach. It is harder to assess student learning in that case.

  • 2. Rachel Kannady  |  July 15, 2010 at 3:16 pm

    While my students are not going to be doing higher level computational formulas, the MW does provide them with a realtime visualization of things such as cellular respiration. For students who would only have the “pictures in the book” this demonstration albeit somewhat cartoon in nature, does give them a way to understand the things happening inside the cell in a way that even the most creative and exciting lecture cannot.

    Your discussion of the use of this program is helpful to those of us without extensive background in the world of Java script.

    • 3. Charles Xie  |  July 15, 2010 at 8:57 pm

      Hi Rachel:

      There is no need to do higher level computational formulas in MW. The key is to use the fundamental laws in physics to build virtual worlds of electrons, atoms, molecules, or fluids so that their behaviors are closest possible to reality. The fundamental equations are only used by the software developer to create the virtual world. A computational engine built using first principles has maximal intelligence. Hence, the software can be used to create any model allowed by them and the model will likely to be a good approximation of some real problem.

      This shifts the learning focus from mathematics to physics or chemistry. Computer science in this case plays a very important role of making this happen. Before that, theoretical physics relies on mathematics.

      The instructionist and constructionist pedagogies supported by MW have nothing to do with Java or JavaScript or any programming language. The nice thing about MW is that it is a platform that allows us to explore modeling and simulation for science education without having to worry about how to program a simulation. The engines and the GUIs of the software have done a large part of the job for us. All we need to do is to configure the structures, set the initial conditions and boundary conditions, and perhaps add some customized behaviors.

    • 4. Charles Xie  |  July 16, 2010 at 8:36 am

      MW is not meant to teach research-grade computational methods. The idea is to use them to create virtual worlds which are governed by fundamental laws (instead of some arbitrarily determined “game rules”). Thus, we hope to shift learning from mathematics to physics or chemistry.

      Another way to put it is these virtual worlds give students tools way more powerful than calculators or spreadsheets. They are much better “brain extension” tools.

      A strength of MW is in fact in its ability to design somehow cartoonized simulations. This is a major difference between MW and research simulation tools. MW allows more “coarse-grained” models to not only save computational time but also simplify the views. To some extent, it can be regarded as a tool that makes the illustration in textbooks “live” and yet preserves some basic scientific correctness. The active transport model you mentioned is an example. It conveys an important message, that organized biochemical activities arise from random, chaotic motion of atoms and molecules. I think this is a very powerful feature that makes it useful for education.

      In general, scientific visualizations such as those in MW can deliver the Wow’s, but not necessarily the Aha’s. Take a 3D view of a benzene molecule as an example. You see a hexagonal arrangement of six carbon and six hydrogen atoms, and you can rotate the view to see the molecule from different angles. If you have never seen this before, you may give it some wow’s. But exactly what more do you learn from this kind of activity, compared with a static image printed in your chemistry textbook?

      Making these whole things move (e.g. a dynamic model) seems to improve a bit. For example, in teaching gas laws, a molecular dynamics simulation seems to be able to do a better job than a static illustration, because students can adjust the pressure on a piston and see the gas volume goes up and down. This allows them to explore the causality better.

      But ultimately, it is constructionism that will result in the aha’s. In creating a working simulation to explain something, students must delve into the details and figure out the how-to’s. In this process, they will have to ACTIVELY learn the fundamental principles embodied in the simulation system. There may be many steps in creating a successful simulation, each of which must be done correctly and creatively to make the whole thing work impressively. Each step will result in an aha moment.

  • […] Molecular Workbench: “…is not just a collection of simulations–do not be deceived by first glance. While […]

  • […] have written before about Molecular Workbench.  It’s pretty cool that it can now be made all-in-the-browser. Molecular Workbench is […]


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Trackback this post  |  Subscribe to the comments via RSS Feed

Enter your email address to follow this blog and receive notifications of new posts by email.

Join 9,005 other followers


Recent Posts

Blog Stats

  • 1,879,148 hits
July 2010

CS Teaching Tips

%d bloggers like this: