TU Wien Informatics

Talk: Toward Whole Cell Mesoscale Models

  • 2018-10-05
  • Research

Prof. Arthur Olson, The Scripps Research Institute, USA


The ability to create structural models of cells and cellular components at the molecular level is being driven by advances ranging from proteomics and expression profiling to ever more powerful imaging approaches. It is being enabled by technology leaps in computation, informatics, and visualization. Our CellPACK program is a tool for generating structural models of cellular environments at molecular and atomic level. Recently we have implemented a GPU-based implementation of CellPACK that speeds up the process by orders of magnitude, in what we have termed “instant packing.” This enables interactive exploration and manipulation of components of the packings. Visualization of these models is also enabled by GPU-based efficient representations, renderings and levels of detail. The ability to model complex cellular components such as a bacterial nucleoid and distinct phases is a significant challenge that we continue to work on. Our Lab’s recent lattice-based method for rapidly producing bacterial nucleoids is a prototype for other rule-based generative structure builders. Use of GPU-based physics engines enables real time interaction with dynamic models. Flexx is a real-time constraint solver from NVidia. It is capable of interactive constraint minimization of up to 1 million particles in real time. Such systems can quickly resolve clashes and identify interactions in the crowded cellular environment. In a parallel effort to CellPACK, we have developed CellPAINT, which has its origins in David Goodsell’s watercolor paintings of cellular environments and processes. Cellpaint uses a painting metaphore to enable creation of Goodsell-like images interactively within a Unity game-engine. These images can be animated using a simple Brownian motion-based diffusion model. Recently we have expanded this interactive interface into 3D, and have also implemented it in a Virtual Reality environment.

The talk will include live interactive demonstrations of the current state of our software.


Arthur Olson is the Anderson Research Chair Professor in the Department of Integrative Structural and Computational Biology at The Scripps Research Institute and founder and director of its Molecular Graphics Laboratory. He received his Ph.D. from the University of California, Berkeley in Physical Chemistry developing computational methods in X-ray crystallography. As a Damon Runyon postdoctoral fellow at Harvard he published on the first atomic resolution structure of an intact viral capsid. Before moving to Scripps, he served as Assistant Director of the National Resource for Computation in Chemistry at Lawrence Berkeley National Laboratory.

For over 35 years Olson has pioneered the analysis and visualization of biological assemblies spanning length scales from angstroms to microns. His laboratory has developed AutoDock and AutoDock Vina, which are the world’s most highly cited ligand protein docking programs. Olson served as Director of the NIH funded HIV Interactions and Viral Evolution (HIVE) Center. In 2000 he started the first Internet distributed biomedical computing project, FightAIDS@Home, now running on over two million computers worldwide, and for which he was honored by resolution in the California State Legislature. His work in molecular visualization has focused on the development of novel and intuitive human interfaces for research and education in structural molecular biology including 3D printing and augmented reality technologies. Over the last several years he and his colleagues have developed CellPACK/CellView to model, visualize and interact with intact cellular environments at the molecular level. 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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