Grasping the Molecules of Life: Modeling in Three Dimensions

Arthur Olson
Professor, Department of Molecular Biology, The Scripps Research Institute

Videography by Nerine & Robert Clemenzi, Edited by Nerine Clemenzi
Copyright © Philosophical Society of Washington.  All rights reserved.


Biology has become accessible to an understanding of processes that span from atom to organism. As such we now have the opportunity to build a spatio-temporal picture of living systems at the molecular level. Recent work in my laboratory addresses some of the issues that we confront in our attempts to create, interact with, and communicate physical representations of complex molecular environments.

In this talk I will discuss and demonstrate three levels of interaction with protein interactions: 1) human perceptual and cognitive interaction with complex structural information; 2) interaction and integration of multi-scale data sources to construct cellular environments at the molecular level; and 3) interaction of software tools that can bridge the disparate disciplines needed to explore, analyze and communicate the emergent holistic molecular view of living systems.

In order to increase the understanding and interaction with complex molecular structural information we have combined two evolving computational technologies: computer autofabrication, known as solid printing and augmented reality, the technology that combines real-world object with computer generated information. We create tangible models utilizing computer autofabrication. Each molecular model can be custom made, with an ease similar to that of printing an image on a piece of paper. Augmented reality is used to combine computer-generated information with the physical models in the same perceptual space. By real-time video tracking of the models as they are manipulated we can superimpose text and graphics onto the models to enhance the information content and drive interactive computation.

We have recently developed automated technologies to construct the crowded molecular environment of living cells from structural information at multiple levels. We can populate cytoplasm, membranes, organelles and multi-protein complexes within the same structural volume, resulting in three-dimensional representations of cellular environments that synthesize our current best knowledge of such systems, and which can become "community models" that evolve with new information and knowledge.

The communication of such complex structural information requires both extensive scientific knowledge as well as expertise in creating clear visualizations and interactive environments. To this end we have developed a method of combining our existing molecular modeling environment with several professional "Hollywood" grade 3D modeling and animation programs. This gives both molecular scientists and professional scientific illustrators access to the best capabilities of both the science and art of molecular communication. In doing so it brings new, expanded capabilities to both communities.

Arthur Olsen

About the Author:

Arthur Olsen holds the Anderson Endowed Chair in the Department of Molecular Biology at The Scripps Research Institute where he is founder and director of its Molecular Graphics Laboratory. He received his Ph.D. from University of California Berkeley in Physical Chemistry, and went on to Postdoctoral Research at Harvard University where he was involved in solving the first atomic resolution structure of an intact virus capsid in 1977. He returned to Berkeley in 1979 to become Assistant Director of the National Resource for Computation in Chemistry. He has been at Scripps since 1981.

He is a pioneer in the analysis and visualization of biological assemblies His laboratory has developed, applied and distributed a broad range of molecular modeling and visualization software over the past 30 years, including AutoDock, which is the world's most widely used and highly cited drug-discovery docking program. He started the first Internet distributed biomedical computing project, FightAIDS@Home, which is now running on over two million computers worldwide, and for which he was honored by resolution in the California State Legislature. He is the Director of a newly awarded NIH sponsored Center on the Structural Biology of AIDS, involving six institutions nationwide.

He has pioneered many advances in molecular graphics. His latest work focuses on the development of novel and intuitive human interfaces for research and education in structural molecular biology utilizing solid printing and augmented reality technologies. Olson's visualizations and animations have reached a broad audience through public venues such as the Disney EPCOT center, Public television, and a number of art and science museum exhibits around the world.

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