Wednesday, July 18, 2012

Molecular Workbench used at University of Ottawa Medical School to teach molecular simulations

The Molecular Workbench software has been widely used in middle and high schools. It is relatively unknown that many colleges and universities around the world use it in their classrooms as well.

Recently, the software was used in the Summer School in the Systems Biology of Neurodegenerative Disease offered by the Ottawa Institute of Systems Biology. Students in this Summer School learned about the basics of molecular dynamics simulations using tools including our "intuitive" Molecular Workbench. They then applied their new knowledge to either model and simulate bilayer membranes made of various lipid species or strictly model a lipid using three different approaches.

For the Molecular Workbench, we have developed a set of unique simulation techniques that can render a dynamic cartoon view of biomolecular processes that are usually too complicated to show all the fine details (see the images to the right for a cartoonized simulation of micelle formation in water and oil, respectively). This capability turns what used to be static illustrations in a biology textbook dynamic and interactive and provide opportunities of exploration to students. This is the key why the coarse-grain modeling techniques developed for MW based on soft body dynamics and particle dynamics looks so promising for the current wave of digitization of chemistry and biology textbooks.

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