Inside this Issue

• Bioinformatics
• Next Generation Tsunami Modeling
• Space Weather Forecasting
• Navigating Information Space
• Imagining Without Constraints
• Internal Tides of the Ocean
• High-Flying at Mach 8

Story by Leone Thierman

Engaging students’ imaginations and unleashing the power of their discovery and learning can be a challenge for any instructor, especially when teaching an introductory course in organic chemistry and biochemistry to liberal arts majors. In the past, one way to entice students to participate in a hands-on learning experience was to have them create models of chemical compounds using such everyday items as foam balls, marshmallows, gum drops, pipe cleaners, toothpicks or pencils.

But today’s demonstration techniques are somewhat more sophisticated, especially for Dr. Kelly Drew’s Beginnings in Biochemistry class at the University of Alaska Fairbanks. Drew has been working with Dr. Roger Edberg, Arctic Region Supercomputing Center (ARSC), to transform learning about proteins, amino acids and molecules into a bigger-than-life interactive experience.

Using ARSC’s Discovery Lab, Edberg has managed to make the tidy, symmetrical diagrams we see in textbook illustrations leap off the page into a three-dimensional virtual world. Students can step into it and experience for themselves the complex structures associated with chemical compounds like proteins.

“Form is function is a recurrent theme in the course,” says Drew, “and the very confusing structure of stereoisomers, particularly on paper in 2D, is difficult for students to grasp.”

Most illustrations in a chemistry textbook show the 20 amino acids common to proteins as stick figures with straight lines connected to other straight lines. Students are asked to memorize the names and structures of these stick figures, but what they don’t see in those diagrams is that the atom structure doesn’t really form a straight line.

“Stereochemistry can be a very difficult concept to visualize, so the 3D version provided in the Discovery Lab helps bring it into a form that is accessible and even fun,” says Edberg.

Modeling in virtual reality offers unprecedented power to imagine without constraints. Students can actually walk inside the structure of molecules generated in a room that combines high-resolution stereoscopic projection technology and 3-D computer graphics to create the illusion of a complete sense of presence in a virtual environment. They can interact and navigate through the structure with the help of a wireless wand. Using stereoscopic shutter glasses, this technology allows multiple users to immerse themselves fully in the same 3D virtual environment at the same time.

“I didn’t know much about the potential of using the Discovery Lab for teaching,” says Drew, “until Lesa Hollen, a graduate student in neurosciences and an enthusiastic supporter of the facility, brought it to my attention.” Drew is looking at expanding its use beyond just structure modeling to include reactions and electron density models for her Spring 2005 class. Edberg says there is increasing interest from other chemistry professors at UAF to work with ARSC to create 3D visualizations for their classes, as well.

Cross-Cultural Virtual World

As part of the Japanese program at UAF, all Japanese Studies majors complete advanced language training in exchange programs with universities in Nagoya and Hokkaido, Japan. Spending a month living in a Japanese home enables students to learn more about Japanese culture by immersing themselves in an environment where they can improve their language skills.

To further prepare students for this experience, Miho Aoki, joint appointee with ARSC and the UAF Art Department, has been working with Yoko Collier-Sanuki, Assistant Professor of Japanese, UAF, to create a highly-realistic accurate 3D model of a Japanese home for display in the Discovery Lab.

“Having a 3D model is very suitable for the Japanese studies class,” says Aoki. “The Discovery Lab is great because everyone can experience the 3D space as a class.”

Starting with a floor plan of an apartment from a Japanese textbook, Aoki worked this summer with Erhardt Graeff, a student from Rochester Institute of Technology who participated in ARSC’s Alaska Research Summer Challenge intern program. Graeff and Aoki developed a 3D model of various rooms in a Japanese house. The rooms contain furniture and appliances with their controls written in Japanese. Students can use this simulation as preparation for their month-long home-stay in Japan.

“My interest is making education more visual,” says Aoki, “especially because the Japanese writing system is very visual and difficult to learn.” Her hope is that one day Hokkaido University could build a 3D model of an American home for their students.

Aoki sees this project as an opportunity to create stronger ties with Hokkaido University. As the most northern island in Japan, there are many similarities with UAF. Hokkaido University offers northern studies research activities in similar fields such as: polar meteorology and oceanography, physical properties of snow and ice, and observations and modeling of atmospheric and oceanic processes in polar regions.

Future Plans

Along with further development and expansion of the 3D Japanese home model, Collier-Sanuki is very interested in exploring the possibility of using ARSC’s Access Grid Node (AGN) as another tool for future collaborations with Hokkaido University. The Grid allows for simultaneous communications between remote sites via high-bandwidth networking.

Aoki made use of this technology in April 2004 when she took part in a series of events in which artists and participants from around the world experimented with a collaborative art program performed over the Grid.

ARSC is committed to testing and expanding the boundaries of visualization technology at UAF, and to open new doors in understanding the nature of science, art and language.