Travelling between the atomic molecular world and the world visible to our eyes can be an uncomfortable journey. Rules and forces that govern one world are not necessarily critical to the other. For example, random movement belongs more to the molecular world than to the visible one. Gravity, on the other hand, is far more important to large bodies like people and trucks than for small molecules. Yet understanding why many macroscopic phenomena work the way they do requires a degree of comfort with visiting the atomic-scale world.

Many scientists spend their time at the atomic and molecular levels. Physicists focus on atoms, their constituents, and the energy that is transferred within that world. Chemists pay attention to the reactions of molecules. Biologists begin to perk up when the nucleic acids, lipids, proteins, and carbohydrates critical to life processes are mentioned. For many of these scientists, the micro world is inherently interesting. For students, this is usually not the case - they demand that their learning have relevance to their lives. Yet they are rarely given the opportunity to travel between the micro and macro worlds, and so grasp where the real explanations lie for much that occurs in their visible world. Wouldn't it be powerful if students could explore the implications of random movement by experiencing the atomic world where random motion is dominant, and see that changes in the atomic world can cause changes in the visible world? Imagine if they could enter a virtual laboratory and change the salinity bathing a cell, and then enter the atomic level of the cell to see what the changed solution looks like in terms of atoms and molecules.

Molecular Workbench Project
With the National Science Foundation's support, we are conducting research that asks whether exposure to key concepts and new modeling tools at the atomic level can help students understand a wide range of macroscopic phenomena. This work extends the investigations of Paul Horwitz with GenScope and Biologica™ (see article page 1) and builds on our previous modeling work.

Specifically, the Molecular Workbench project is investigating whether computer models can help students understand how the behavior of certain chemical and biological systems emerge from the fundamental behaviors of their atomic and molecular constituents. Which macro themes have the greatest power to connect students with the micro world? And given the kinds of computers students are likely to have access to, what kinds of atomic-scale situations can be simulated best in this environment?

The Modeling Environment
Our objective is to have students learn about the atomic-scale world by interacting with it through a series of learning activities presented by three software packages. The first and most critical is an atomic, molecular, and biomolecular modeling engine, called Oslet (Figure 1). This modeling micro world computes the motion of atoms and molecules from the forces applied to them. Until recently, these computations were so extensive that they required a supercomputer. Now an average desktop computer will allow students to perform experiments on hundreds of atoms.

Students do not need to understand the calculations to learn from these models. By experimenting with simple models, they can see how individual atoms and molecules interact. When hundreds interact the same way, they can see emergent properties.

In Oslet, collections of neutral atoms can illustrate temperature, pressure, gas laws, states of matter, phase change, absorption, latent heats, osmosis, diffusion, heat flow, crystals, inclusions, and annealing. Add bonding, molecules, and photons that can exchange energy with bonds, and Oslet can exhibit chemical equilibria, heat gain and loss in reactions, explosions, stoichiometry, color, spectra, florescence, and chemiluminescence. Add charge and polar molecules, and Oslet can show plasma, surface tension, solutions, hydrophilic and hydrophobic molecules, conformation, binding specificity, and self-assembly. In short, a wide range of physical, chemical, and biological processes can be understood by interacting with Oslet's atomic-scale models.

The second software package, Zoom It (Figures 2 and 3), is a modeling world inspired by the Charles and Ray Eames film Powers of Ten and developed by Parallel Graphics in Moscow, Russia. Zoom It allows students to navigate in 3D and zoom to the atomic world in a series of factor-of-ten steps. Students can zoom from a solar system to an island and then enter a laboratory with a set of rooms and simulations and investigations leading to Oslet.

The third software package is Pedagogica, which pulls Zoom It and Oslet together into a hypermodel (see article, page 1) and uses scripts to control what students see, presents appropriate activities, and monitors student progress. Pedagogica is able to provide multiple ways to enter and use the Molecular Workbench software. While manipulating the model a student might be queried by Pedagogica about the experience, be offered alternative paths, be given more or less complex versions of the same material, or be "followed" for purposes of evaluation.

Teachers will be able to use Molecular Workbench material to enhance existing lessons. But students can work on their own, too. Students can start with an exploration of Oslet's atomic-scale representations and work through a set of activities, or they can pick a case history and follow its implications and discoveries down to the appropriate use of the molecular engine. Such explorations include health themes such as sickle cell anemia, vitamins, and oral rehydration. We believe that all these cases have aspects that can be more easily understood with Oslet's simulated molecular explanations. For example, a student learning about solutions and osmosis can pick up the case of oral rehydration therapy for cholera, enter the laboratory, explore the effect of changing salinity on an erythrocyte, and then zoom into a membrane and arrive at the Oslet model of osmotic pressure.

Oslet's next challenge is moving into 3D, and knitting the movement between 2D and 3D together. Already students can move through crystal lattices built from first principles (see picture, page 1). As Oslet grows in power, our challenge remains to provide students with a motivating and strong but simple way to undertake challenges not only in the sciences, but in the arena of model building itself. As students move to develop models themselves, and to understand the workings of models such as Oslet, they will be better able to use atomic molecular understanding to make sense of their own macro world.

Barbara Tinker is project manager for Molecular Workbench
barbara@concord.org

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Last Updated: April 21, 2001
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