Movie Mania

Web Extras

Movie: Making a Microscopic Metropolis

Movie: Walking the Line

Movie: Blood Clots Show Their Flex

Just as sound and color revolutionized the film industry, computer technology has changed the way scientists view biology. Researchers today not only can take snapshots of biology, they can animate entire biological processes, thrusting viewers deep into never-before-seen worlds.

»  Scientists Develop Sixth Sense
»  Now Playing on a Computer Near You
»  The Art of Animation

Scientists Develop Sixth Sense

A scientist manipulates plastic models of two proteins while the computer tracks and displays their electrostatic properties, shown here as red and blue clouds.
Credit: Arthur Olson

Thanks to a high-tech tool, scientists just regained their "sixth sense."

Before you think of a certain flick starring Bruce Willis, think about feeling your muscles flex as you push a box across carpet or plunging forward as your car suddenly stops. These physical responses to external cues are what many experts consider the sixth type of sensory experience.

Some scientists lost this sense in the computer age. They no longer used physical models of biological molecules, like proteins or DNA, to see how they fit together. Instead, they used computer-generated models.

"Many scientists stopped working with physical models altogether," says Arthur Olson, a structural molecular biologist. "The nature of spatial perception changes and the kind of understanding you get from interacting with your surroundings were lost when computer graphics took over."

Pick up a nearby object. Rotate it so you see all its sides. Does it feel heavy? What about cold? Smooth? How would you determine these qualities if you only saw the object on a computer screen?

Now, Olson and his team at the Scripps Research Institute in La Jolla, California, have developed a tool that allows them to do both: physically manipulate a model of a biological molecule while watching its chemical and biophysical properties change on a computer screen. Olson says combining the two experiences will let researchers approach and understand biological problems in new ways.

The scientists use special printers that generate plastic or plaster 3-D shapes as easily as other printers produce 2-D pictures. As Olson and others hold and interact with the models, a camera records a close-up shot of the models in motion. A computer program then superimposes graphics, like the arrangement of atoms or the energy between modeled molecules.

Olson combines the model and computer graphics into one image that allows him to study all the different facets of the biological molecule. Olson hopes that one day his interface could double as a video game that lets students explore and play at the molecular level. —EC

Back to Top

Now Playing on a Computer Near You
By David Bochner

The ribosome plays itself in this molecular movie.
Credit: Kevin Sanbonmatsu

Superman is super strong, super fast, and generally super fly. But in a comic book, he's also super flat, leaving many of his superhero feats up to your imagination. But when the comic book turns cinematic, Superman truly comes alive.

Sometimes scientists only get to see the comic book view of biology: Experimental data gives researchers just snapshots of what a biological process looks like at a specific time. Now, computational biologist Kevin Sanbonmatsu at the Los Alamos National Laboratory in New Mexico brings those processes to life.

Sanbonmatsu uses high-performance computers to create movies of a tiny molecular machine present in every living organism. This machine—called the ribosome—builds proteins from the genetic instructions encoded in DNA. Interested in understanding the origin of life, Sanbonmatsu says he studies the ribosome because "it may be the oldest artifact in the cell."

But there's more to it than curiosity. Sanbonmatsu also says that about half of all antibiotics used to treat bacterial infections target the ribosome, meaning that a better understanding of this biological machine could lead to super-strong drugs.

To make his movies, Sanbonmatsu starts with experimental data, like the structure of a ribosome in a particular instance, and generates a storyboard of sorts. Hundreds of connected computer processors—or a supercomputer—then turn the snapshots into an entire movie filled with information scientists couldn't otherwise see or even imagine.

"You can look at static structures of the ribosome," says Sanbonmatsu, "but the only way to watch it in motion is the supercomputer simulation."

His team has created the largest biological simulation ever, bringing new life to characters in the old story of protein synthesis.

Back to Top

The Art of Animation
By Karin Jegalian

An artist's rendering of how chemicals change and move among cells in the brain. Watch the animation.
Credit: Kim Hager

Amid a network of blood vessels and star-shaped support cells, neurons in the brain signal each other. The mists of color show the flow of important molecules, such as glucose, oxygen, and nitric oxide.

This image is a snapshot from a 52-second simulation created by Kim Hager, an animation artist in the Laboratory of Neuro Imaging at the University of California, Los Angeles. The animation, which portrays how chemicals change and move among cells in the brain, took about 300 hours to create. To put it all together, Hager worked closely with Neal Prakash, a neurobiologist in the same lab. Prakash initially asked for a drawing to illustrate a research paper, but the director of the lab suggested producing an animation instead.

Hager, who studied photography, video, and graphic design in college and later earned a graduate degree in media arts, does not draw movies frame-by-frame. Instead, she builds "virtual sculptures" filled with color, light, texture, and motion and then guides the viewer's eye through the scenes.

The lab features this animation, along with dozens of others, on its Web site and also plays it in a state-of-the-art theater during presentations for scientists, students, and other visitors.

Hager says her role is to make the research more accessible to different audiences. "Seeing an animation," she explains, "makes it easier to comprehend what a researcher is saying."

Back to Top