The Virtual Museum of Minerals and Molecules: An educational resource for the twenty-first century IIMMIIMM Cynthia A. Stiles 1, Phillip Barak 1, and Edward A. Nater 2 1 Dept. of Soil Science, University of Wisconsin – Madison, 2 Dept. of Soil, Water and Climate, University of Minnesota – Twin Cities GSA Poster: 8 Nov 2004, Denver; GSA PPT presentation: Dec

Introduction IIMMIIMM The Virtual Museum of Minerals and Molecules (VMMM) is a web-based educational resource presenting interactive, 3D, research-grade molecular models to help visualize the sub-microscopic intricacies of mineral and organic substances. Created in response to an increasingly visual audience attuned to high-quality computer–generated 3D imagery, the VMMM is designed to be not only educational, but also entertaining. Innovations in web- based 3-D visualization are making their way pervasively into the biotechnology and engineering fields – why not use these visualization packages to illustrate the essential building blocks of our living world?

Introduction IIMMIIMM This virtual museum is not bound by physical walls, but actively grows as we seek and identify new materials and innovative ways of presenting information that is readily available to a web- connected audience. Best of all, admission is FREE of charge! VMMM is presently serving over 250K visitors a year and was chosen by the editors of Scientific American as one of the top 50 scientific websites of 2003.

Introduction IIMMIIMM Requirements for viewing this work are commonly available browser software such as MSIE5.5 or better or Netscape 4.7x and free browser plug-ins, principally CHIME (both Windows and OS9 versions downloadable from and any of a number of VRML plugins. Beginning in early 2005, requirements for viewing this work using the Jmol applet will include Safari, Firefox, or Mozilla on OSX and virtually all Windows and Linux graphical browsers, providing that Java has been installed and Javascript is enabled. (Support for OS9 will be discontinued for technical reasons.)

How it works IIMMIIMM The Museum contains 150 displays of minerals and molecules of interest to the earth, soil, and environmental sciences, organized into Mineral and Organic “wings”, further subdivided into galleries and rooms. Coverage ranges from the familiar (such as kaolinite and smectite) to the new and exotic (biomolecules such as the potassium transport channel and aquaporin that allow organisms to interact with their mineral environment).

Ball and Stick Molecular Structure

How it works Each display consists of: a computer-generated chemical model of the mineral or molecule of interest that can be rotated, zoomed, and highlighted; a text page describing the mineral or molecule, its importance in the natural environment, and other salient facts; an atom key that identifies atoms by color; a series of buttons that allow the mineral or molecule to be displayed in stick, ball & stick, or space-filling mode; For minerals, a page describing their classification, composition, and crystallographic axes and angles, space group, and atomic positions, references to the primary data, electron micrographs, and other appropriate instructional aids and materials. IIMMIIMM

How it works Animation scripts can be constructed that flip, rotate, or highlight various features either on load or upon user mouse click; such animations can be used to smoothly move between one molecular visualization mode to another, while still permitting user interactivity with the model during the transition, in a manner that has no physical equivalent. IIMMIIMM

Ball and Stick Molecular Structure

Selection of a molecule from the menu takes the viewer into an interactive screen that allows for highlighting of various features of the molecule. Additional information is often included with the selection to enhance the viewing experience.

Demonstration: Struvite Ball and Stick Molecular Structure

Demonstration: Struvite Ball and Stick Molecular Structure

Demonstration: Struvite

Evolving views – polyhedral to spacefill Methyl tert-butyl ether (MTBE), a commonly studied groundwater contaminant

Evolving views – polyhedral to spacefill Methyl tert-butyl ether (MTBE), a commonly studied groundwater contaminant

Evolving views – polyhedral to spacefill Methyl tert-butyl ether (MTBE), a commonly studied groundwater contaminant

Evolving views – polyhedral to spacefill Methyl tert-butyl ether (MTBE), a commonly studied groundwater contaminant

Evolving views – polyhedral to spacefill Methyl tert-butyl ether (MTBE), a commonly studied groundwater contaminant

Moving Ahead IIMMIIMM Our Future Plans: The VMMM is in the process of migrating from the Chime browser plug-in primarily on MS Windows boxes to a molecular viewer in the form of Java applet that is functional on a wide variety of platforms and will silently download and reside in cache between calls. Due to the open source nature of the Jmol applet, development is expected to permit visualization of *.cif format and polyhedral rendering currently beyond the capabilities of Chime. With these changes, the VMMM will increase the accessibility of its displays to a yet larger audience.

Moving Ahead IIMMIIMM Our Future Plans (cont’d): We continue to improve displays and expand our collection of molecular models We plan to develop an ancillary component with micromorphology of mineral grains and fabrics for realistic views. Planned “Virtual Tours of the Virtual Museum” will allow users to browse through areas of individual interest. We will be enhancing the viewing experience by incorporating stereoscopic 3-D viewing capabilities that make the molecules virtually jump out of the screen at the viewer. And we are adding a “game room” with puzzles and other activities.

Our Sponsor IIMMIIMM Visit us soon at: We gratefully acknowledge MDL for making Chime available to the educational community and to Michael Howard and the open source chemistry community for producing Jmol, the java molecular viewer applet that will be used in future versions of the Virtual Museum. Financial support has been provided by USDA-CREES Higher Education Challenge Grant