Molecular Workbench

Regularly updated resource features great simulations and modules

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Subjects & Skills

Creativity, Critical Thinking, Science

Price: Free
Platforms: Mac, Windows, Linux

Pros: Wide range of topics and ability levels make complex info accessible for a wide range of learners.

Cons: The visual style has limited appeal, and some modules can be confusing without instructional support.

Bottom Line: For teachers with the time to prepare, these are great resources for just about any science classroom.

There are many ways teachers can use this program, depending on level of experience and time devoted to it. Beginners (or teachers with little time) can look through the library of topics and find something that matches what they're already teaching. They can then direct students to that simulation. Additionally, if teachers have some knowledge of scripting (or are willing to learn), they can modify existing modules or create brand-new ones that do exactly what the teacher wants. These modules can support a wide range of instructional strategies, including problem-based, inquiry-based, and discovery-based learning.

There are two parts to Molecular Workbench: the website, which contains a library of hundreds of simple simulations that illustrate topics that have already been taught in class; and the desktop app, which combines the simulations with longer, more detailed curriculum modules. Both tools are continually updated by teachers and professionals, and the content on offer includes lessons on physics, chemistry, biology, biotechnology, and nanotechnology.  Each subject is broken down into topics and then into individual simulations. For example: In physics, the instructor can choose anything from a simple pendulum in mechanics all the way up to low-energy electron diffraction in quantum physics. 

The modules are useful for students who want to go beyond simple simulations and conduct more in-depth observational studies. With the desktop application, teachers and students can view the curriculum modules or (if they have the programming and scripting know-how) they can create their own simulations to extend the experience.  This desktop application not only allows for the viewing of the curriculum modules, it also lets teachers (or students) with programming and scripting knowledge create their own simulations. Keep in mind that the Web-based simulations run on plug-ins, so an updated version of Java is required. Also, the application itself requires a lot of computing power (see the Tech Notes).

When used correctly, this website and desktop application are a wonderful way for students to see and manipulate concepts, objects, and substances that are hard to describe in textbooks. Animated simulations (like the one that illustrates how chemical reactions form) offer more detail and insight than still pictures on a page ever could. 

That being said, just turning students loose on the website isn't recommended. The simulations range from middle school level all the way to advanced content that might even stump upper-level undergraduates. Unless students know what they're looking at, or looking for, navigating and searching the site could be intimidating and confusing. Teachers will absolutely find the site useful, but only after they understand how it works and how they want to use it.

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Overall Rating

While the graphics aren't especially flashy or slick, the modules give excellent visualizations of scientific concepts that are hard to describe in a textbook, making tough concepts accessible and appealing for students at all levels.


Learning potential here is solid, but teachers should plan to front-load instruction for many of the modules, which aren't set up for self-direction or individual exploring. 


The FAQ page, blog, and in-depth user manual help teachers think strategically about integrating these modules into the science classroom. 

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