Computer graphics scientist Ivan Viola is fascinated by life at the nanoscale. In September 2021, he used the summer internship program for high school children of KAUST residents (known as WISE) to develop an opportunity that he hoped “was not only fun, but provided an experience where the students could gain new knowledge and a new skill — an intellectually enriching entertainment experience, or ‘edutainment’.”
The research focus of Viola’s Nanovisualization Research Group is designing very tiny, nanoscale computer graphics and 3D visualization algorithms and techniques. Their research outcomes include research software prototypes, one of which is MesoCraft, a tool for rapid modeling of molecular assemblies.
The idea of running a student internship program began after a discussion with the high school’s head of Life Sciences, Emma Nason. The researchers wondered if some of the students who love biology or 3D modeling would be keen to work with them.
Following an oversubscribed application process, the researchers described how they “had four great young minds to help us define the spatial rules for assembling the complex bacteriophage model.” While Viola oversaw the internship, its organization fell to Deng Luo with the help of Ngan Nguyen, both Ph.D. students in the group.
The internship gave the students a chance to create a challenging mesoscale structure to showcase the type of bio-assemblies that can be modeled using the team’s software prototype. But the benefits flowed both ways: the internship also gave the research team a group of real users who could test MesoCraft, it helped the team answer questions about the utility of the tool. Questions like: Is it stable enough? When does it crash? Is it easy and intuitive to use? How much support does a user need to become proficient?
the benefits flowed both ways: the internship also gave the research team a group of real users who could test MesoCraft, it helped the team answer questions about the utility of the tool.
The program began with briefing the students about the digital data used to represent structural biology on a nanoscale level. They were then trained in modeling by research scientist Ondrej Strnad and specifically in the use of the KAUST MesoCraft software prototype.
Once they had mastered this, Luo described the T4 bacteriophage model, including a literature review of current knowledge of T4 bacteriophages and their ultrastructure. Luo devised this suite of information with collaborator David Goodsell, renowned computational biologist and artist from Scripps Research Institute.
Next came the modeling that was at the crux of the internship. The students were given basic structural building blocks (proteins) and then tasked with working out the rules that led to the assembly of the desired structural part.
“I was quite impressed by the students’ 3D modeling skills and knowledge of biology from high school classes, and their artistic minds and ability to rapidly master MesoCraft,” says Luo.
Viola was impressed he was that the internship produced such a meaningful outcome. “The students, along with Deng and Ngan, actually managed to model T4 within the four-week timeframe of the internship,” he says. “It is a very complex structure to model, plus rule-based modeling requires a lot of quite logical thinking. Nevertheless, during the internship we got the entire structure modeled. That really surprised me.”
While the students learned a lot, so did the researchers. “Through this, we acquired new knowledge, new skills, test reports for our software prototype performance and, last but not least, the first scientifically accurate model of T4 that is publicly accessible and available for everyone to use or analyze,” says Viola.
the first scientifically accurate model of T4
that is publicly accessible
Luo describes how now, “with the model on hand, we can visualize it in a color scheme, print it out, or even animate it”, and this animation will be the next step of his research. “Developing the first scientifically accurate model of the well-studied but little-communicated bacteriophage T4 will better guide us, and others. Being able to visualize it means we can communicate better and disseminate knowledge faster, and thus educate deeper and more broadly.”
“Also gratifying was that all of the students really liked the internship and were genuinely excited and proud of the outcome of their hard work,” Viola says. “We made an offer to the students that when they have a school break and would like to model another biological entity, we will be happy to work with them again.”