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© 2017 by Ursula Florjanczyk

Visualizing Michaelis-Menten Dynamics through Animation

MASTER'S RESEARCH PROJECT

Committee

Derek Ng | BSc., MScBMC, PhD, Assistant Professor, Master of Science in Biomedical Communications Program, Department of Biology, University of Toronto Mississauga

Stavroula Andreopoulos | BSc, MSc, PhD, Associate Professor, Department of Biochemistry, University of Toronto

Jodie Jenkinson |BA, MScBMC, PhD, Assistant Professor, Master of Science in Biomedical Communications Program, Department of Biology, University of Toronto Mississauga

Audience

Undergraduate biochemistry students

Format

3D and 2D animation

Expected Completion Date

July 2017

About the Project

The Michaelis-Menten model of enzyme kinetics is an invaluable predictive tool used in numerous scientific fields. Unfortunately, the daunting mathematical language can be confusing for undergraduate chemistry students who struggle to link together representations of molecular phenomena at the macro- and micro-scopic level. We proposed to create an introductory animation on Michaelis-Menten dynamics that would help create visual context and employ visual metaphors to facilitate undergraduate student comprehension.

This animation looks at the activity of acetaldehyde dehydrogenase, an enzyme in our livers that helps in the conversion of acetaldehyde to acetate, a step in metabolism of ethanol. The activity of this enzyme is used to link key concepts of enzyme kinetics to physiological symptoms. The animation employs a humorous and engaging tone to maintain audience interest.

General Process

This is my final animation. Click here to see my progress on the 3D scenes.

Research Proposal

​​​​As part of the Research Methods course in BMC, I audited existing visual resources for enzyme kinetics and common chemistry teaching techniques. I found that most teaching tools for Michaelis-Menten dynamics were in a lecture style with little to no visuals.

 

Pre-production

After creating an animatic of my script, I reworked both the script and animatic multiple times until the storyline felt cohesive and the content was understandable and clear. Here are some screenshots from my final animatic, which was used to plan the 3D assets I would need to create my final animation. I made a conscious choice to avoid establishing an aesthetic at this stage.

 

Production

Protein structures were pulled from RCSB PDB, 3D models were created and rigged. Camera movement and assets were animated and then textured, lit, and rendered.

Post-production

Rendered sequences were brought into After Effects to have post-production effects added (including aesthetic fixes, labels, re-timing of scenes etc). Transitions were added, sound effects were created and audio and video was synced in Adobe Premiere Pro.

Going from the above, clockwise:

A scene of our protein of interest against a molecular backdrop

A 2D segment on how known inhibitors of our protein can result in unpleasant symptoms

A scene for a factory metaphor, with robots acting as enzymes

For a more in-depth breakdown of my process work, click here.