Transformative Applications in Education/Molecular Workbench

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Overview of Molecular Workbench[1][edit | edit source]

Molecular Workbench (MW) is a sophisticated modeling platform useful for education at all levels, providing not only an environment for creating interactive simulations, but also an authoring tool for building user interfaces and creating guided learning activities. MW is one of the few software systems that was intentionally designed to support teaching and learning. It is equipped with a report and assessment system for collecting data and measuring learning with models and simulations.

A copy of this open source (and therefore free) software can be downloaded from its home

The Molecular Workbench includes a "Library of Models" and an "Activity Center," which aid both students and teachers in using the program and tailoring it to their own needs. The "Library of Models" contains hundreds of models organized into specific sections on chemistry, biology, physics and nanotechnology, mostly created by staff at the Concord Consortium and their collaborators. The "Activity Center" section of the Molecular Workbench program contains collections of fully-developed, classroom-ready activities in the fields of electron technology, biotechnology, chemistry and biology. These include 2D and 3D interactive models of molecules, bonds and chemical reactions. In addition, there are many non-molecular simulations, such as classic mechanics and quantum mechanics. The Molecular Workbench is a flexible system. It allows anyone to create any type of models and simulations supported by the system, and easily deploy them anywhere on the Internet. Pedagogically, it not only allows students to learn through well-designed, scaffolded activities, but also allows them to learn through open-ended model construction activities, as in the case of Scratch and Phun.

Description of Application[edit | edit source]

This program was developed by the Concord Consortium to help provide secondary school students with concrete models of molecules that they could manipulate in order to enhance their understanding of the foundational principle of structure driving function at all levels, even those that can not be seen with the naked eye. Yet, the depth of coverage of some of the topics makes many of the activities applicable to introductory college courses as well.

MW allows students to interact and experiment with simulations based on real-time molecular dynamics (MD) calculations and visualizations [3]. It is not a set of animations! The molecular visualizations were created using java, and can support other applications, including Jmol (Available at, an open-source Java viewer for chemical structures that is embedded into Molecular Workbench. Jmol images are 3-D virtual models of molecules that can be manipulated by the users as needed to allow for a full exploration of the molecules that can help enhance their understanding of their structures. Users can also pick the type of display (ball & stick, spaced filled, ribbon, etc.) for the various molecules and this capability alone can be helpful in deciphering the interaction of the various atoms within the molecule. Users (both students and teachers) can also author new models as needed.

The "Molecular Workbench" software also contains embedded assessment items and built-in student tracking allowing instructors to follow the work of individual students or groups of students through the various activities. It also allows students to take "snapshots" of their work which can later be incorporated into reports or printed out as needed. These "snapshots" include space for labeling and explaining the particular "snapshot," allowing students to describe the results of their manipulations at various stages as they work with a particular model or go through a specific activity. The snapshots are also seamlessly incorporated into embedded report templates, allowing students to easily create professional-looking reports for self-assessment, peer assessment or assessment by their instructors.

There are also educational games and activities which again can be captured for assessment purposes as well. These embedded assessments can be used either formatively or summatively by both the students and the instructor.

Transformative Potential[edit | edit source]

Science educators are calling for sweeping changes that focus less on facts and more on deep understanding of "big ideas."[2] One of these big ideas in biology and chemistry is that the structure of something affects its function. In other words, how something works is often dependent on its physical aspects. This is true of relatively large structures all the way down to the atomic level. When it comes to trying to understand the hows and whys of chemical reactions and many biological functions, being able to actually see and study the structure of chemicals and structures at the molecular level can create understanding of why it works the way it does. Being able to zoom in on the details of a virtual model, zoom out for an overview or flip it over to view it from a different perspective can all lead to recognition of the similarities of these microscopic structures to models already understood in everyday life. In other words, being able to manipulate virtual molecules can enhance understanding of why these molecules interact with others (react) the way they do. As Wenglinsky put it "activities that concretized or illustrated concepts proved associated with higher student performance."[3]

The types of learning activities offered in this program encourage a constructivist approach to education, thus aiding in the transformation of the student learning experience. Yet it is also important to note that the scaffolding within the authoring part of the program provides instructors' with the tools needed to create and support more constructivist activities in to their classrooms, a move that has been shown to enhance learning and retention in the sciences.[4] Thus this program facilitates the transformation of both teaching and learning.

Sample Activities[edit | edit source]

Visualizations[edit | edit source]

Visualization of a segment of DNA

The program provided user-friendly options for changing this visualization of a segment of DNA (Deoxyribonucleic Acid). Note that in this final version, the two different phosphate-sugar backbones are easily distinguishable from each other, further enhancing the understanding of what is meant by a "double helix."

This is a space-filled version. The other display options include: ball-and-stick, wire frame, stick, Delaunay Triangulation, Voronoi Diagram or Delaunay & Voronoi Overlay. Molecular Workbench contains hundreds of interactive molecular models like this one, that can be easily manipulated by the learners, even the first time they use the program. All they have to do is click on the molecule and drag the mouse.

Scaffolding, in the form of suggested activities, are provided to prevent learners from simply playing with the models. Be aware that the zoom feature is very fast, causing the viewer to pass by the particular molecule too quickly on some visualizations. Instructors may want to demonstrate this problem and how to "find" the molecule on the computer monitor again if their students "fly by" too quickly.

Close up of the active site of one of the enzymes of glycolysis

Both of these screenshots depict small molecules within their active or binding sites on much larger enzymes. Note the change of perspective that can be seen by choosing two different types of display models. The one on the left is a ball-and-stick molecule of a substrate (DHAP) within the active site of one of the enzymes of glycolysis. The one below is a space-filled shot of a typical cell kinase with cAMP (cyclic Adenosine Monophosphate) in its active binding site. Note the great difference in size between the ball-and-stick model of cAMP and this large enzyme made of globular protein.

cAMP enfolded in the active site of a typical kinase.

Learning Activities[edit | edit source]

Molecular Workbench contains many different learning activities designed for use by secondary students. Many have found the activities useful for post-secondary education as well.

Concept Map on Molecular Energy

The concept map on the left challenges the learner to think of a related concept to fill in the blank. It is just one example of how the collaborative nature of Molecular Workbench leads to the incorporation of a wide variety of technological teaching tools, including ones like concept mapping that are not traditionally used in science education.

The Learning Activities section of Molecular Workbench also contains excellent simulations on a large variety of subjects including membrane transport and protein folding. Unfortunately, these simulations run rather slowly, so in demonstrating them to a classroom of students, be sure to pull the models up earlier and simply minimize them to your desktop.

A limited number of interactive essays (IE's)are also available in the Learning Activities portion of Molecular Workbench. So far these essays have been mostly focused on chemistry, but an IE on osmosis is currently being created. A biology activity for the MIT Museum is also under construction, but almost completed. I especially liked the section on drug discovery, since that process is a key component of the biotechnology industry.

External Links[edit | edit source]

The Concord Consortium[edit | edit source] - homepage of The Concord Consortium a non-profit organization that provides educational research and workforce development.

Affiliated Science Education Sites[edit | edit source] - homepage of the center for Technology Enhanced Learning in Science (part of WISE, see below) - homepage of the Web-Based Inquiry Science Environment (primarily for K-8 education)

Molecular Viewing Programs[edit | edit source] homepage for Jmol, the molecular modeling program used in Molecular Workbench - homepage for Pymol, another open-source molecular modeling program. - homepage for Qutemol, another open-source molecular modeling program. - homepage for Visual Molecular Dynamics, a modeling and bioinfomatics program developed, run by the University of Illinois at Urbana-Champaign - compilation of free molecular modeling programs by The Interactive Library.

Related Programs[edit | edit source] - homepage for Biomolecular Explorer - homepage for the Center for BioMolecular Modeling - Molecular Visualization Freeware - inventoried with a grant from the National Science Foundation (NSF) - listing of the "Top 5" 3D Molecular Visualization Technologies (aka "the MolviZ Top 5") - homepage for Proteopedia collaborative encyclopedia of 3D molecular models.

Discussion[edit | edit source]

History of this Program[edit | edit source]

This program has been developed by the Concord Consortium, with funding provided from the National Science Foundation. The original grant was obtained by Dr. Boris Berenfeld and Dr. Robert Tinker in 2000 to help bring molecular modeling to K-12 science education.

Dr. Charles Xie, a computational physicist, with expertise in molecular dynamics and quantum chemistry, developed this new software, the "Molecular Workbench." This software includes the use of "Jmol" (available at, an open-source Java viewer for chemical structures and allows users to manipulate 3-D models of various molecules and author new models as needed. Dr. Xie has included extensive documentation and tutorials on this aspect of the program, as well as a blog that contains a history page that allows one to search either by the author or the type of molecule created.

Connections[edit | edit source]

The authoring capability creates a library of "draft models" and interactive simulations by pioneering educators across the globe, much like those found within WISE (the Web-based Inquiry Science Education site, available at The program can be easily used within WISE, which helps create a powerful synergy for K-12 educators, when these programs are used together. For example, Dr. Dalit Levy contributed an MW-based activity within the TELS (Technology Enhanced Learning in Science) portion of WISE called "Phases of Matter and Phase Change" for 9-11th graders (see )

References[edit | edit source]

1 ^ Concord Consortium, (n.d.). Molecular Workbench.

 Retrieved April 2, 2009 from

2 ^ Wiggins, G. & McTighe, J. (2005). Understanding by

 Design (2nd Edition).  Alexandria, VA: Association for Supervision and Curriculum

3 ^ Wenglinsky, H. (2005), Using Technology Wisely, New York,

 NY: Teacher's College Press, Columbia University

4 ^ Jonassen, D., Howland, J., Marra, R.M. and Crismond, D.

 (2008). Meaningful Learning with Technology, 3rd Edition, Upper Saddle River, 
 NJ: Pearson Education, Inc.