Software That Models Atomic-Scale World Wins Science SPORE Award

Growing up in China, Charles Xie did not have much to lure him into the world of science. His only concrete enticement, at least when he was very young, was a few simple books about such world-famous scientists as Thomas Edison and Albert Einstein.

Now, however, Xie is the architect of the Molecular Workbench software, a computational tool that allows students to manipulate live visualizations of atoms and molecules according to the real laws that govern their interaction.

“Think about how many more chemists or physicists can be produced when students who are developing an interest in science experience this,” Xie said.

Because of its ability to draw students into the real world of science, the Molecular Workbench has been selected to win the Science Prize for Online Resources in Education.

The Molecular Workbench team. [Image © Science/AAAS]

The Molecular Workbench team.
[Image © Science/AAAS]

Science magazine developed the Science Prize for Online Resources in Education (SPORE) to promote the best online materials in science education. The acronym SPORE suggests a reproductive element adapted to develop, often in less-than-ideal conditions, into something new. In the same way, these winning projects are seen as the seeds of progress in science education, overcoming considerable challenges to educational innovation. Each month, Science publishes an article by a recipient of the award, which explains the winning project. The article about the Molecular Workbench was published on 24 June.

“We’re trying to advance science education,” said Bruce Alberts, editor-in-chief of Science. “This competition provides much-needed recognition to innovators in the field whose efforts promise significant benefits for students and for science literacy in general. The publication in Science of an article on each Web site will help guide educators around the globe to valuable free resources that might otherwise be missed.”

Work on the Molecular Workbench began in 2000 with an initial three-year grant from the National Science Foundation. Soon after, Xie, who received his Ph.D. in China and had been working on another science curriculum project, came to the Concord Consortium, a nonprofit educational research and development organization. A computational physicist, Xie and his colleagues at the Concord Consortium saw that the computational tools used in molecular modeling research could also be excellent tools for educators.

The learning provided by Molecular Workbench is highly conceptual. The system offers a dynamic picture of atoms or molecules that is not otherwise available to students. Difficult vocabulary, which can put off students before they even get to the actual concepts of science, is not necessary to the presentation of the concepts.




A video tour of molecular self-assembly, one of the Molecular
Workbench’s features.

[Video © and courtesy of The Concord Consortium, Inc.]

“With such a tool, you can bring the conceptual picture up front,” Xie said. “This allows a much larger audience to access the concepts.”

In fact, although most of the users of Molecular Workbench are middle-school and high-school students, even some elementary-school teachers have used it, if only to give students more dynamic representations of atoms and molecules than the ball-and-stick models most adults saw in school. Users have downloaded the classroom-ready interactive online lessons nearly 800,000 times.

Molecular Workbench accurately simulates atomic-scale phenomena using the fundamental laws of molecular dynamics and quantum mechanics. Xie referred to those laws as “the jewels of human knowledge” because they are constant, governing interactions across the sciences, even for instance some of the most fundamental biological processes.

Working with those laws, Xie said, teaches students how different science topics are interrelated, and recognition of this unity offers them a mastery that is difficult to attain through fragmented presentation of the factual knowledge.

“We empower students with those laws, handing them a powerful tool,” Xie said. “They can develop a coherent picture across the sciences. Understanding the unity of science is what is important.”

Many educators see the integration of science learning as crucial to improving science education in U.S. classrooms.

As an example of such integration, the essay about Molecular Workbench in Science explains that, using the software, the three states of matter can be explored using a single computational experiment. Basically, students add particles into a container under a piston, in a way reminiscent of playing a video game. They adjust the properties of the particles to see what happens. They discover that gas particles move freely to fill the entire container, that liquid particles flow to the lowest part of the container, and that solid particles vibrate and assume a fixed volume and shape. If they push the piston, they see that a gas can be compressed, whereas neither a liquid nor a solid can be compressed significantly. Raising the temperature of a solid, they observe how it softens, collapses, melts, evaporates, and expands. They can even adjust the interaction potential among the particles to explore how it is responsible for the formation of each phase.

Because the computational engine of Molecular Workbench is capable of simulating many different phenomena in a dynamic manner, students can interact with the modeled phenomena like real scientists.

“Using the Molecular Workbench software, students are able to actually see accurate approximations of atomic-scale interactions, then to formulate questions, design experiments to explore those questions, and to study and test their results,” said Melissa McCartney, editorial fellow at Science. “This engages them in a very full experience of the scientific process.”

Supporting that ability to conduct an experiment or even to design one “gives the power of creation to students,” Xie said, adding that a tool that supports that kind of creativity helps students to become active learners.

“This kind of tool helps bridge the gap between what is happening on the research frontier and what is in the classroom,” he said. Even professional scientists and engineers use Molecular Workbench, Xie said, to help them think about and especially to visualize the problems they’re exploring.

After Molecular Workbench is presented in Science, it may be that more working scientists will use it. In any case, Xie said, winning the SPORE award “is an honor, especially because it is issued by Science magazine.” Furthermore, he says the essay on Molecular Workbench highlights an important issue. “It is time for the whole nation to look at science education. We cannot delay. Maybe this essay will encourage more scientists to contribute to improving science education.”