Grad student Tyler Earnest, Image of Research semifinalist

Physics Illinois PhD student Tyler Earnest won an honorable mention award in the Image of Research contest, put on by the University of Illinois Graduate College and the Scholarly Commons of the University Library.

Earnest’s poster, titled, “Building Ribosomes from Computational LEGO,” is based on research he performed under Zaida Luthey-Schulten, the William and Janet Lycan Professor of Chemistry, with an affiliate appointment in the Department of Physics.

For his research, Earnest simulated the system of biogenesis of the ribosomal small unit in Escherichia coli. The study took about a year and a half to complete, and the results were published last year in Biophysical Journal (doi:10.1016/j.bpj.2015.07.030).

Earnest said the project combined two of his great fascinations—creating computer simulations and studying how ribosomes function.

 “Ribosomes are pretty much the most fundamental unit of life. They’re found in all domains of life,” he remarks.

Understanding how ribosomes work allows humans to learn a lot about the origins of life and evolution, Earnest adds. It’s also important in terms of bacterial resistance to antibiotics. A lot of antibiotics target the ribosome, so if people know how ribosomes are assembled, researchers can come up with new ways to work with that.

Earnest notes that the vast majority of computer simulations aimed at understanding the biological processes that constitute life are concerned with very small time and length scales, but he took a different approach.

"The types of simulations that I study trade this fine level of detail for the ability to study whole cells instead of single molecules, and hours of simulated time versus nanoseconds,” he explains. “Instead of working with molecules whose behavior is governed by the relative motion of their atoms, we work with populations of different molecules whose behavior is governed by how they interact with each other through chemical reactions and how they move through space through diffusion.

“This is sort of like zooming out the ‘computational microscope’ so that the collective behavior of the whole cell can be studied instead of focusing on a single biomolecule,” he continues. “We no longer can make out the exact details of how a particular mechanism works, but instead can see how these mechanisms work together to compose a biological function.”

Earnest’s computational model shed light on how the small subunit assembly and the production of components interact with each other within the environment of a cell.

“I designed a simple model of the construction of the smaller half of the ribosome, the small subunit, starting from its components,” he notes. “I then combined it with a model which describes how all of the components themselves are made, and placed it into a spatial model of the whole cell and simulated it over a whole cell cycle.”

Another component of Earnest’s research image is a simplified model of how DNA folds up within a bacterium, represented by the “rainbow spaghetti” in the image. Knowing the conformation of the DNA illuminates where each gene is found inside the cell; its location in turn informs how often that gene is used by the cell.

“It is hard to see, but each bend in the tube represents 10 base pairs of DNA. E. coli's genome contains 4.6 million base pairs. The color indicates the position along the DNA strand,” Earnest clarifies. “This work is still in progress, and is not currently connected directly with the cell simulation work. However I intend to combine the two in some way in the near future.”

Earnest’s plans to further pursue this line of research, working toward a whole cell model of E. coli that builds in other processes, such as metabolism, cell division and DNA replication. He has been at the University of Illinois at Urbana-Champaign for eight years. He earned his undergraduate degree from the South Dakota School of Mines and Technology.

This research was funded by the National Science Foundation under grants PHY1026550 and MCB-1244570. A portion of this research was sponsored by the DOE/BER (ORNL 4000134575) as part of the Adaptive Biosystems Imaging Focus at ORNL. Computation was performed on the NSF-supported Blue Waters supercomputer. The conclusions presented are those of the scientists and not necessarily those of the funding agency.

 

The Image of Research is a multidisciplinary competition celebrating the diversity and breadth of graduate student research at the University of Illinois at Urbana-Champaign. Entries are judged on several criteria, including originality; the connection between the research, text and image; and visual impact. A gallery of past and current-year entries is available online.

Earnest and the other semifinalists were honored at a reception at the Illini Union on April 6, 2016.