Driving Discovery and Innovation Through Biofilms: A Conversation with Andrew Jones

The NSF-Simons National Institute for Theory and Mathematics in Biology is composed of investigators at the forefront of innovative research at the interface of mathematics and biology. NSF-Simons NITMB Affiliate Members each bring unique perspectives vital for developing new mathematics and inspiring biological discovery. One such NITMB Affiliate Member expanding our understanding of collective cell behavior is Andrew Jones.  

Andrew Jones, assistant professor of Civil and Environmental Engineering, Duke University. 

Andrew Jones is an assistant professor of Civil and Environmental Engineering, with a secondary appointment in mechanical engineering and materials science, at Duke University. He is also associated with the Duke Materials Initiative, the Duke Microbiome Center, and the Duke Integrated Toxicology and Environmental Health Program. Professor Jones leads the Systems for Engaging the Environment Lab, where his team solves global challenges in water and health using engineering and policy analysis.  

We spoke with Andrew Jones to learn more about the applications of his research in mathematics, biology, medicine, and everyday life. 

What is a big question you’ve been asking throughout your research? 

“I study biofilms. Biofilms are like plaque on your teeth or slime on a river. The big question that relates to NITMB is how bacteria biofilms respond to stress and how we can mathematically model that from both a control theory perspective as well as a dimensional analysis perspective, and then a little from a transport phenomenon perspective. One of the major publications to come out of my lab in the last two years was a better model for how charged nanomaterials migrate through biofilms. If we are trying to design a new drug delivery system for antibiotics to treat biofilms and try to get rid of them, how can those things migrate into the biofilm? A biofilm is resistant to chemical assault by design. The reason we brush our teeth is because we want to mechanically abrade in addition to the chemicals because chemicals alone are not enough. One of the points I like to bring up is that, if we think of bacteria having evolved during early Earth, that meant they were dealing with much harsher chemical conditions than we exist in right now. They figured out how to deal with that, and some of those genes exist, conserved across species. A biofilm is structured to deal with harsh chemicals that we would toss at it like alcohol, bleach, or antibiotics. Antibiotics come from bacteria-fungi warfare, which means they are well designed to deal with those diseases. We’re trying to find out how we can improve the penetration of those chemicals into a biofilm because in some places we can’t get mechanical abrasion. One of the complications with knee surgeries and hip replacements is infections that exist on medical devices. Needing to have a patient come back in, cut up their leg, and scrape out the biofilm structure isn’t what we want to do to a patient. We want to be able to give them a drug that will cure this. We’re trying to develop new systems, which means developing new mathematical models.” 

What disciplines does your research integrate? 

“Microbiology, fluid dynamics, and transport phenomena. Dimensional analysis crosses both of these spaces. I’m a mechanical engineer by training, I’ve been in a chemical engineering department, and I’m now an environmental engineer. We do materials engineering occasionally because we’re trying to interpret results of what these biofilms look like.” 

Where do you find inspiration? 

“I take inspiration from physical-chemical systems, generally biological systems. One of the projects we’re working on right now is simulating and then trying to improve flow in a P-trap, the joint underneath your sink. It prevents sewer gases from blowing in your face anytime you turn on your faucet, but the P-trap collects stagnant water, skin cells, nutrients, oils, bacteria, etc. It sits for a while, grows bacteria, and grows biofilms which then get ejected back into your face or into a hospital room, which is not what you want. Some of the inspiration we took from there is the design of the ascending aorta, one of the main arteries of your heart that ejects fluid rapidly at turbulent flow that in most cases would damage tissues. Instead, your body and heart are designed to twist the flow in a helical pattern in the ascending aorta, washing off plaque. One potential use of that is to wash off biofilm. If we take geometry or similar physics and shove it underneath your sink so that the fluid takes a twist and washes off the biofilm in the P-trap. There are a lot of random pieces of biological inspiration we use in our lab as we do bio-inspired design.” 

What aspects of your research could be interesting to mathematicians or applied to biology? 

“I’d say the control theory is probably the most interesting part. Trying to figure out what feedback loops dictate biofilm growth. Being able to apply that to a system, like a biofilm where you have cell death and chemical stress and mechanical stress, and in the body immune system stress, and understand a system with so many different things changing. Immunology, for example, uses the language of control theory, but it doesn’t use the mathematical tools of it as much for looking at the microbiome. That’s one I like, and I joined NITMB for that reason. I think this is a cool problem to wrap my head around, and hanging out with other mathematicians that might think in the same space seems useful.” 

What about the NITMB do you find exciting? 

“As a former math major, I find the entire concept exciting. I was attracted to the idea of applying mathematics to biological problems. That’s what I do in my lab, and I try to simplify and reduce problems down to something that I can solve. I try to figure out what governing physical factors can I shove into a very simple linear relationship, or figure out when the linear relationship fails. I think joining NITMB will help me figure out where my knowledge of complexity stops and where somebody else’s might start, where I need to collaborate with other NITMB faculty and share my work with other NITMB faculty.” 

What career achievement are you most proud of? 

“I got a young investigator award from the Center for Biofilm Engineering. I still talk about that one because that was the place where all my biofilm heroes I was reading about as a PhD student were. And to get that award while I was a postdoc meant I got to meet everybody who did this work and present at the space where most of our knowledge of biofilms came from. Another success of my career so far was getting the Postdoc Mentor of the Year award in 2023. Reading through those comments, and thinking about what my team thought of me, I feel like I’ve transitioned into being a mentor well, and I’m treating my people with the respect that they deserve and trying to help grow new scientists. Watching my research tech go from having no research to publishing a paper in a year and seven months, joining grad school, and having that paper converted into a patent application, felt good. I’m very proud of her success and progress.” 

Outside of your research, what other interests do you have? 

“I had hobbies, I had things I used to do. I am now a runner and a parent, and that is about it. I used to do improv and cook to make people happy. I once cooked for 300 people, and it was awesome. But I don’t do that anymore because I have no time. I go from the lab to pick up my kid, and then I get to spend time with my kid. My kid is an interest of mine, he’s fun to spend time with and watch learn and progress.” 

What are you hoping to work on in the future? 

“I’m excited to get into the controls modeling. Next year I will be working with a prominent microbiome immunology researcher and trying to take all his longitudinal data and start figuring out how to map the controls theory that we know for either biological systems or other non-biological systems onto this microbiome immunology system. That’s one project I’m excited to start sinking my teeth into for the next six months to a year. And then there’s wrapping up a whole lot of the projects that we’re working on right now in the lab, things like redesigning the P-trap. We’re working on a synthetic biofilm so we can study transport a lot better. I have a paper that should hopefully be submitted soon about how we can use scaling tools to work on biological problems and compare them between labs and experimental platforms. To keep pushing that work forward, there was a paper in 2022 that talked about how a large part of biofilm research is either useful for industry or useful for academia, but not both. That paper shows mathematical modeling as the only thing really at the center between industry usefulness and scientific usefulness. Let’s take that and extend it to make it really useful. That’s a lot of what we’re going to be pushing forward in the next year to five years.” 

Is there anything else you would like the NITMB community to know about you? 

“My existing NIH funding was largely geared towards developing new tools to study biofilms. So, if anybody has a mathematical model they feel like tossing at a biofilm, or that they might have data for, or vice versa, let me know. I’m excited to work in this space. Customer discovery and design is one of the things that they train mechanical engineering undergrads in. I still love carrying that with me and working with new people to find new problems and challenges.” 

More information on Andrew Jones and his lab’s work is available on his website and Google Scholar.