XVIVO's Latest Collaboration with Harvard's BioVisions Reveals the Dense, Chaotic World at the Center of our Personal Universes

Harvard University's Department of Molecular and Cellular Biology developed BioVisions, a collaborative lab of scientists, teaching faculty, students and multimedia experts, to better visualize—and virtualize—the biological processes their students were learning about in the classroom. Their first project, "The Inner Life of the Cell," created with the scientific animation company XVIVO, went viral in 2006, mesmerizing all who saw it with an elegant combination of veritas and sheer novelty. Conceived and engineered with copious amounts of scientific data by Alain Viel, director of undergraduate research for the department, and Robert A. Lue, the lab founder and director of BioVisions, the video largely succeeded in demonstrating what happens inside an immune cell for what it left out: the majority of the visually distracting protein molecules that quiver, jostle and move inside every cell in our bodies.

"These cellular processes, and protein packing in particular, are hard concepts to convey in 3D because there really isn't any space inside the cell," says XVIVO founder and creative director Michael Astrachan. "They are all being pushed about by imperceptible water molecules that are moving and diffusing through the cell, absorbing that energy and creating these perpetual, seemingly random interactions."

The leukocyte extravasation process demonstrated in the first video was also deliberately shown in a kind of suspended animation to better emphasize the action. Advances in cellular research and computing power up to that point allowed the BioVisions and XVIVO team to accurately visualize and render the shape and movement of the lumbering kinesin protein inside a white blood cell that appears to amble, step by deliberate step, down a braided cellular cable. But the choice to frame their subject in isolation and slow things way down were creative decisions that the team agreed worked best for the video's educational purpose.

XVIVO created a second video in 2010, "Powering the Cell: Mitochondria," about the creation of adenosine triphosphate molecules. Then, in 2012, BioVisions and XVIVO, under Astrachan's creative direction, began work on an updated version of the original video, taking advantage of continuing advances in render speed and compute power to fill in many of the details they originally left out. Called "Protein Packing," it took nearly two years to complete and features lead animation by Michael Smith and additional animation by Helena Martin and Tony Bexley. Rosalyn Quinton-Bonesteel headed production and Leana and Mickey Reisman provide the haunting piano and violin soundtrack.

"The chaotic motion in this version features a lot more real particle simulations as well as algorithms and programming that we developed," says Astrachan. "Rendering, caching and instancing issues were all huge concerns this time around. We really had to thank the render gods on this one." To handle the rendering load, Smith used Autodesk 3Ds Max to script a custom instanced system that was only called up at render time. "[Smith] wrote a new engine for IK, for example, so objects could change pivots on the fly," Astrachan explains. "There were so many objects and so much geometry in every scene that it was an extremely heavy and computer-taxing animation to put together."

Lacking any point of practical color reference—the molecules inside the cell, after all, are smaller than a single wavelength of light—XVIVO and the BioVisions team chose an intensified, multicolor palette that would highlight each layer of this density without muddying the waters. "Harvard wanted it very colorful, with teaching in mind. We pumped up the colors significantly from the first version so you can better follow the movements of so many things at once."  

The Harvard team's ability to grab even more available data this time around gave the new video its more realistically jerky, electrified aesthetic. "If you look at the 'walk' of the kinesin molecule in this version, it's a lot more random and less intentional," says Astrachan. "It's based on the latest data of how we think it moves, pushed and pulled by the energy reflected off these invisible water molecules." But this more layered, intensified rendering only tells part of the story. "Of course, there would be many, many more molecules quivering and hovering around that one kinesin molecule. We still had to strip many of those out so you could see how it works. We wanted to better convey the densely packed cellular environment, and this gets a little closer to that than the first video, for all its beauty, ever did."


All imagery © Harvard University

Getting each and every simulation to work organically took copious amounts of patience, adds Astrachan. "While some of this stuff could have easily been faked and end up looking identical, we didn't do that," he says. "We made the simulations behave and do what they were supposed to do. Because of the technology we had available to us this time around, this version is more of a true simulation and the first is more of an artistic impression of what happens inside of a cell. I also think the first one was more human. We put more of ourselves into it—the idea that we exist with intentional purpose, despite the chaos that surrounds us. And maybe that made it so relatable. You may start at the chaotic molecular level, but when you pull back to the cellular level, it doesn't seem so chaotic. This new video gets back into the chaotic, crowded center of it all." 

Although he admits that an exact simulation tracking one of these molecules moving from a nucleus to the surface of the cell in under a second would be a blurry mess beyond human perception, the science in "Protein Packing" reflects a complex set of biological systems we are getting closer and closer to visualizing with authority. "It can get infinitely more complex the more data you throw at it, and we still had to pull a lot of things out to bring it to a level the human eye can appreciate," he says. "It's really mind-boggling that what we are seeing here even exists at all. To get one step closer to an understanding of the chaos that's within us all, which we have absolutely no clue about, is pretty mind-bending in itself."

To watch the video with Harvard's detailed narration, visit the BioVisions website here: http://multimedia.mcb.harvard.edu/