“Structural biology is all about the architecture of molecules. Three-dimensional (3D) functionality completes the students’ understanding of how they work,” explains George Phillips, the Ralph and Dorothy Looney Professor of BioSciences at Rice University. “The arrangement of the atoms determines the biological activity of the molecule. In architecture, form follows function—same with molecules, they do what they do with a shape that is matched to their function. It is true integration of form and function.”
Taught every spring, Phillips’ BIOS 482 course helps students learn the basic connections between molecular structure and biological function. “The challenge grows gradually through the course,” he says, “beginning with why these structures are interesting and how you determine them, how to create illustrations on a physical printed page, then going to computer graphics, then to graphics in the visualization cave, and culminating in the 3D printed models.
Communicating by touching and turning models
To help students get their minds around 3D models, Phillips points them to a database that has the atomic locations for all the atoms. “My research has to do with determining the structure of the models, and 3D printing is a way of communicating results to others. The protein database is just a bunch of numbers — the 3D rendering methods we use render the data in a way others can understand.” Students determine the story they want to tell about a particular protein, download the file from the protein database, and use 3D software to choose colors and styles to highlight points about specific elements in each structure.
“Before we do the 3D printing, they have already learned about 3D rendering in our graphics cave with the 3D glasses,” Phillips said. The cave is a repurposed office, housing a large projection space and computers loaded with modeling software like PyMOL. In the cave, students dim the lights and don 3D glasses to explore their gently rotating and unfurling illustrations of atoms from 360-degree perspectives, including interior paths and chambers. After perfecting their models in the cave, students send their files to the 3D powder-based printer and pick up their models at the Mudd Lab Operations Center in a day or two, depending on the complexity of the model and the number of files sent to the printer.
Phillips continues, “The cave is open to everyone, I want people to get excited about 3D modeling. I’m an experimentalist — I’m in the business of creating these files of coordinates, and I’ve submitted about 500 of them to the protein database. The students are already accustomed to 3D modeling through the computer, but nothing compares to the tactile experience.” At the end of the course, students demonstrate their molecular observations in class presentations featuring slides and models of their structures.
Usually, this cross-listed course is evenly split between graduate students and undergraduate seniors in Chemistry, BCB and CHBE. Graduate students are required to produce and present two different models over the course of the semester, and undergraduates create one. All the students print two copies – one for Phillips and one to keep—and everyone is impressed with the opportunity to create 3D models.
“I have taught this class for three years, but 2015 was the first year we included 3D models,” recalled Phillips. “It took a while to convince the university to invest in this technology, but I had access to a printer like this at the University of Wisconsin-Madison and knew it would impact student learning.” The powder printer at Wisconsin was part of an NSF grant, purchased for the purpose of teaching molecular and structural biology courses by David Nelson, a famous biochemistry textbook author.
Rapid delivery of new fossil casts
Recently, Professor Susan McIntosh of the Department of Anthropology has just used the printer to produce detailed color casts of skull and jaw fragments from an extinct species of hominin. The discovery of Homo naledi, was first announced on September 10, 2015 by Professor Lee Berger of Wits University in South Africa. Berger’s team captured casts of the new fossils with 3D scanners and published the files on a public database. Six weeks after the discovery was announced to the world, McIntosh had successfully printed four casts from Berger’s files. Less than two months after the initial announcement out of South Africa, Rice students in McIntosh’s Intro to Physical Anthropology class (ANTH 203) were matching jaw and tooth casts of the fossils to diagrams of various species and learning for themselves how the discovery is shedding light on possible origins of our own human species.
“As soon as I heard the casts were published on a public database, I started looking for a 3D printer,” said McIntosh. “Carrie Masiello in Earth Science told me that the Shared Equipment Authority had a 3D printer and then George [Phillips] offered to shepherd the entire process.” Students have handled casts before; McIntosh has been collecting commercial and museum casts of fossils for 25-30 years. But the freshly printed Rice models feel almost as if the students are handling the real fossil. One engineering student exclaimed, “Look at the quality of the cast —and the color is fantastic!”
McIntosh envisions endless possibilities for the 3D printer. “Imagine talking about an artifact, a stone tool. Instead of getting a table of measurements and trying to imagine the tool, we can download a 3D file, print it and actually hold the tool!”
Powder makes a difference in 3D printing
Rice has more than one 3D printer. Others may use ultraviolet (UV) light to pulverize a compound, use lasers to cut aluminum parts, or drop goo on a board to build models on top of a base. Phillips explained, “Unlike the others, the 3D powder printer is a full color printer. And it is not designed to make working parts; it’s designed to make models [out of thin air]. The way this one works, it creates a fine white layer of polymeric powder then sprays four colors of glue across different parts of the powder — it colors and glues the powder to create hollow or solid shapes before all the unglued powder is sucked away, revealing your object. These are visual illustrations and prototypes, not working machines. If you drop them, they break.”
Phillips said, “The Shared Equipment Authority (SEA) purchased the printer and will physically maintain it if it needs repair, etc. But operating the printer requires expert, skilled operators —which is why the partnership with the Office of Information Technology (OIT) Infrastructure group is so important. They can train operations center staff to use it.” This part of the partnership is led by Shelby Simms at the Data Center and Edwin Martinez at Mudd.
Printing 3D models takes longer than pressing ink on paper. When a student submits a poster to print, they can usually go collect it in 15-30 minutes —unless the plotters are busy during an Architecture charrette or an Engineering design competition. But it takes hours for 3D powder models to finish. On the other hand, the 3D powder printer can print any kind of computerized object and the possibilities get Phillips excited. “I hope people will think up a variety of things to print. My hope is that this is not just a cool tool in bioscience, but that students would see it and think of cool uses for it in humanities, the arts, architecture, engineering, whatever. You could actually print bubble-head dolls of your friends. You have to be willing pay for the materials, but you can work through the SEA to do the actual printing. It costs more than a glossy poster but for what you get it’s pretty reasonable.”
Contact the SEA to learn more about printing your own 3D model: http://sea.rice.edu/.