KCNMA1-linked channelopathy | Master's Research

the project

the details

The aim of the study is to find out if a specific visual style of representing molecular structures ("realistic" VS "schematic") in animations,  proves to be educationally more beneficial than the other.

 

The deliverables for this project are two versions of the of the same animation, one with a realistic representation of its elements and one with more schematic representations. The animations are otherwise identical, sharing the same content, narration, music and sound effects, so that only the impact of the visual style in the learning process is tested. 

Audience: People with basic biology knowledge

Software: VMD, ZBrush, 3ds Max, tyFlow, VRay, After  Effects, Red Giant Trapcode Particular, Audacity

Format: 3D animation

Content Expert: Dr. Andrea Meredith, Professor at University of Maryland School of Medicine

Advisor: Dr. Isabel Romero Calvo (UIC)

Committee members: Dr. Evelyn Maizels,

Rex Twedt

research

One of the current challenges in teaching molecular biology is the way it is visualized. However, there is little literature regarding the educational impact of different animation visual styles on biomedical students so that we can direct the production of visual aids towards their visual needs.

 

KCNMA1-linked channelopathy is a rare disease affecting less than 1 in 100,000 people. KCNMA1 gene encodes a protein participating in the large conductance voltage- and calcium-activated potassium channels also known as BK (for Big K+) channels. Parents of children carrying rare diseases are a special population as they usually take the roles of the expert caregiver and care coordinator, roles that often bring with them a need for scientific knowledge. However, their visual needs are highly understudied as well.

 

KCNMA1-linked channelopathy provides an opportunity to understand how different molecule representation styles affect the educational outcome of a complex molecular biology topic in such  populations. Having this knowledge will allow for better decision-making in the design process of future animations which aim to educate people with a basic science knowledge.

script

storyboard

Working closely with my content expert, Dr. Meredith, we established learning goals and  developed a script that was revised multiple times based on feedback from Dr. Meredith  and my committee members.

Similarly to the script, the storyboard underwent a few iterations to perfectly match the style and the flow of the story. A particular challenge of this project was to achieve the fine balance of being scientific without getting into a lot of molecular details.  

production

After the pre-production work was done, I started creating all my 3D assets for the animation. Then, I aligned the KCNMA1 channel in the membrane.

To create the schematic representation of KCNMA1 channel, I modelled an abstract shape in ZBrush following the form of its subunits. 

The neuron models were built using neuronal reconstruction data from the NeuroMorpho database (Hamad lab entries) and by using the NeuroBuild script (created by Nicholas Woolridge) to import the data into ZBrush for further refinement. 

For the main KCNMA1 scene I used a couple of tyFlow particle systems in order to have control over the membrane and the ions.

After a couple of failed test renders and some required tweaking, I was ready to render out my sequences and move on to the next phase.  

post-production

Once I had all my footage rendered out I went into After Effects to composite my scenes, make the transitions, create some effects and add the sound effects. You can see some before and after compositing below. I always enjoy so much the process of giving life to the renders by doing the post-production work.

final product

A beloved professor of mine used to use the phrase per aspera ad astra  (meaning "through hardships to the stars") in his programming lectures. And it's true that this project had a lot of hardships due to the consequences of the pandemic.  However, it made me realize how much I love animating and how eager I am to grow more on this track of biomedical visualization. Below you can see the two different versions of the animation; the "realistic" and the "schematic". 

realistic

schematic

I want to thank Dr. Meredith, Isabel, Evelyn and Rex for their continuous support and resourcefulness over the course of this year's work, and Ben, Katie, Maria and Trakis who contributed to this project in so many ways.