Professor and Students Study Deformations to Increase Health

People don’t often think of deformation as a good thing.

But when it comes to biofilaments – such as strands of DNA – it’s not only good, it’s necessary for the biofilament to complete its functions. When biofilaments twist, twine, bend or loop in the ways that are correct for them, the result is a normal, healthy organism, be it a cell, an organ or a whole body.

Professor Sachin Goyal, with the School of Engineering, and graduate student Nitish Appanasamy are modeling the “deformation” of certain biofilaments, trying to find ways to predict how such strands react when proteins, enzymes and outside forces are introduced to them.

The goal is to be able to design medications or medical treatments that will encourage biofilaments to deform in ways that cure diseases.

“In principal, it extends to any disease,” Goyal said. “It could work for injuries, too, because what’s really about is tissue damage. Every disease, every injury involves DNA.”

Goyal’s research is a perfect example of UC Merced’s cutting-edge, interdisciplinary research that could change the way medicine is practiced and applied.

Goyal really specializes in mechanical engineering, and was working on the problem of undersea cables that buckle and twist. He soon recognized the similarity between those cables and DNA.

Appanasamy was an undergrad in one of Goyal’s classes in India, and got interested in the biofilament project there. He followed Goyal to UC Merced last year, and has now taken his research into modeling the thermal fluctuations that influence deformations further than anyone else has, Goyal said.

Like others, they can do single-molecule experiments, selecting small pieces of DNA and applying controlled forces so they can examine mechanical reactions.

But to really expand the experiments and the modeling, they need more power for their calculations, and are talking about working with graphical processing units (GPUs) like the ones Professor Christine Isborn uses in the School of Natural Sciences.

The GPUs go into making supercomputer hybrids out of regular computers, and drastically speed up complicated computations.

“We’re trying to create simulations that will speed up the progress of research,” Appanasamy said.

Their work could enhance gene therapy, which has had some success with diseases like cystic fibrosis, sickle cell anemia and hemophilia, but needs much more research, Goyal said.

“We just need more details, more simulations to fill the gaps between what we can and can’t see through experiments,” he said.

Goyal is also applying his research power to the problem of the tremors associated with Parkinson’s disease, examining the biomechanics and trying to build a platform of information from which better treatments than dopamine therapy can be developed.

Additionally, he is researching Dark Matter DNA – what used to be called “junk” DNA. Like many others now, Goyal doesn’t believe the parts of the DNA strand that used to be seen as useless actually are; instead, they are what enable the more obviously active parts to function properly.

He’s also got plans for projects with other faculty researchers looking into cancer treatments and other health issues.

“It’s his kind of fresh perspective on biology that’s going to bring new insights,” Appanasamy said of his mentor.