carlos simmerling

For the Love of Chemistry

A professor inspires his lab team by tapping into his past.

Each Friday Carlos Simmerling asks his lab students what they plan to do for fun that weekend, encouraging them to get away from their work and spend time relaxing. He has a hard time following his own advice, but here he takes a moment to enjoy the warming weather. (Photo by John Griffin)

By Liza N. Burby

Carlos Simmerling, PhD, was one of those kids with a chemistry kit in his basement and tolerant parents who didn’t mind the resulting smoke. When it came time for college, he didn’t hesitate to major in chemistry. However, that was an experiment that at first went awry.

“I wanted to be a chemist. When I took organic chemistry, it was the first time that I really thought about it being three-dimensional, and that was really exciting to me. Because my father was an artist, I understood visualization,” said Simmerling, a Marsha Laufer Endowed Professor of Physical and Quantitative Biology and associate director of the Laufer Center at Stony Brook University. “But then I took the lab and hated the solvents, the spills, the lack of safety equipment. I decided if this was the life of a chemist, it wasn’t for me.”

He quit college and entered the workforce for eight years, becoming a computer store manager. Though Simmerling was financially doing well, it became clear to further his career he needed a college degree. He decided the quickest path was going back to study chemistry but at that point, he was more interested in computers.

His past experiences melded when he realized the overlap of his interest in computers, visualization and chemistry. “I did still love chemistry. It’s just that I wanted to do something more computational,” he said. 

It was his doctoral advisor at the University of Illinois at Chicago who showed him how, encouraging Simmerling to perform early research on methods for computer modeling of biomolecules such as proteins. He went on to a postdoctoral fellowship at University of California, San Francisco, where he became a lead developer of the Amber biomolecular simulation software that is used in thousands of research labs worldwide. His current National Institutes of Health (NIH)- and National Science Foundation (NSF)-funded research focuses on development of improved simulation methods and models and using these tools to study biomolecular recognition mechanisms.

A Résumé of Mentoring Skills
When he joined SBU’s Department of Chemistry in 1998, he brought with him a passion for providing students with the guidance he had initially lacked and the belief that a lab can be like a family. The result is that while Simmerling is known for breakthrough research, he’s also recognized as a dedicated student mentor. He recently won the Gordon Bell Prize for developing a groundbreaking simulation of the COVID-19 virus, analyzing its infectious effect on host cells. But he didn’t do it alone; it was a collaborative approach with his undergraduate and graduate students — an unusual situation in most science research labs, though not for a professor whose students understand that he cares about them and their careers.

Carlos sitting in front of zoom call with students

Simmerling’s team includes seven graduate students and 12 undergrads who are collaborating on a groundbreaking simulation of the COVID-19 virus. Though they’ve all been working remotely because of the pandemic, the project has united them with a common goal. (Photo by Maria Nagan)

Lauren Raguette, a fourth-year, PhD chemistry student, said Simmerling creates a positive atmosphere for all his students and adapts his mentoring style to their individual needs. His interest in her career goals following graduation inspired her to become a chemistry professor.

“He knows that being a graduate student is a steppingstone to get where we want to be, so not only does he go about making these years great, he also makes sure that he’s setting us up for success no matter what we want to do next,” she said, adding that Simmerling helped her find professional development opportunities and allowed her to recruit undergraduates into the lab. 

Another trait his students value is he helps them identify their preferred work mode, whether hands-on or independent, said graduate student Lucy Fallon, who is working on the replication transcription complex of COVID-19 and has been in his lab since 2017. 

To date, Simmerling has mentored six postdoctoral fellows, 29 graduate students, 49 undergraduates and 46 high school students. He’s received the Siemens Foundation Outstanding Mentor award five times. According to Karen Kernan, director of Programs for Research and Creative Activity, Simmerling has also mentored a high school student winner in the Siemens competition as well as a number of semifinalists/finalists in high school research competitions. He’s been supportive of a number of programs/initiatives — including the Simons Summer Research Program and the Undergraduate Research and Creative Activities program.  

“He has dedicated so much time and energy to mentoring students over the years in multiple programs/initiatives,” Kernan said. “I think he’s such a good model for the students because they listen to him. Most of all, I think he just gets across that you need to really like what you’re doing and you need to like working on these difficult problems.”

It’s All About Teamwork
Simmerling said his business experience helped him to recognize the skills required to run a lab and to mentor, like managing a team.

Kelly Chiu

Kelley Chiu joined Simmerling’s lab in 2018. She said because of his support of her project, which is focused on amyloid beta, a protein involved in Alzheimer’s, she was able to have a peer-reviewed paper published when she was a sophomore. “He’s always been so supportive because he just doesn’t view undergrads as only a means to help his own lab, but he really tries to do the extra mile to go out and help undergrads as well…he creates a really supportive environment.” (Photo by Jessica O’Conner)

“Everything is about teamwork in science,” he said. “Your team involves people that are like you, but also people that don’t have your skill set. The best teams are the ones where people have complementary skills. In my lab, we’ve got a graduate student from the molecular and cell biology program, one from applied math, one from pharmacology, and a bunch from chemistry, because that’s our core expertise. Science these days is very interdisciplinary. Interfacing between fields can be the glue that holds projects together. Learning how to talk to biologists and physicists and how to speak both of the languages and solve problems ends up being really important. That’s something I try to teach my students.”

Simmerling is also committed to diversity in his lab and actively recruits underrepresented groups into STEM. “I believe in going to them, not waiting for them to decide on their own about going to graduate school, because a lot of them don’t have the support network with inside knowledge, and they may not have the courage to face it on their own. I tell them that a career in science is a valid option for them, that I support them and will guide them through the process.”

That’s why there are 10 female undergraduates currently working in his lab, he said. “I’m trying to keep the pipeline full and make sure they have someone on their side if things get difficult (and at some point they do, for all of us). It’s what I didn’t have when I was in college, and why I quit. A lot of really talented people need someone like me to encourage them, mentor them and believe in them, especially if they didn’t come from a family or schools that had the experience or resources to do it.”

Simmerling also thinks it’s important his students understand solving hard problems is supposed to be fun. “In graduate school, you might spend a lot of time thinking that you’re not making any progress, but you are, because you’re learning the hard problem-solving skills. It can be really discouraging, so I create an environment where people feel like they’re not alone and they hear that they’re on the right path.”

This positive setting is what Kelley Chiu, a junior information systems major, credits for her ability to have a peer-reviewed paper published when she was a sophomore. She joined Simmerling’s lab as a first year in 2018. 

“Without Professor Simmerling, I would not have been able to do all this because I feel like it’s definitely really difficult to find people like him to support and trust so much with just an undergrad. His lab is made up of grad students and undergrads, but to every single person, he has this personalized attention and he really builds off our strengths.”

The Simmerling Community
Simmerling helps prepare his students beyond his lab as well. Chuan Tian, PhD ’19, who works at Eli Lilly, said he took over Simmerling’s force field development project while working on his doctorate at SBU. “Carlos is a pioneer in this field. And I was a fresh PhD student when I took over the project that he had been doing for almost 20 years. The progress was slow in my first one or two years. But he’s very patient and he taught me a lot. What’s valuable is he really trusted me and gave me the freedom and flexibility to try different things and learn at my own speed.” 

Simmerling even keeps in touch with students after they graduate, said Agnes (He) Huang, PhD ’18, an application scientist at OpenEye Scientific Software. “He maintains a Simmerling Lab Alumni Google group where he shares job postings and news about Stony Brook. Even after we graduate, we feel a part of the Simmerling community. That’s something I really appreciate.”

It was in this community that the COVID project became a group decision. Simmerling said his lab primarily runs computer simulations of biomolecules like proteins, “and we want to understand what their shape looks like, how they interact with other molecules, how something might become drug-resistant because the interactions change.” 

“If we don’t have more women and other underrepresented groups doing research early on, they tend not to go to graduate school. I want them to have that confidence, and to be in an environment where they see people like themselves being successful and say, ‘You know what? I can do this, too.’”

– Carlos Simmerling

When the pandemic hit and students moved to remote learning, they wanted to feel they weren’t helpless. He said the team, which includes seven graduate students and 12 undergraduates, decided they had to find a way to fight back.

“Even if we knew that we weren’t going to solve this problem and cure the disease, it’s the fight that matters and we all have this common goal,” Simmerling said. 

“This project has brought students together,” he continued. “Lots of people work on overlapping and similar things in the group, but this is a huge one where your piece of the project wasn’t going to do anything without everybody else’s piece, and it really helped give us an even greater sense of teamwork and that’s what everybody needs now.” 

He’s also been collaborating with a few teams outside of Stony Brook and other faculty members on this project. Simmerling said that the university’s overall atmosphere makes this approach a natural fit. “Stony Brook has been good at both mentoring me and providing lots of opportunities for collaboration. It makes it very easy to build a team that’s from different areas in the sciences. And that’s what modern science really is about.”

Throughout the pandemic, he has kept in daily contact with his students, sending them a morning email to check in while he has his coffee, and on Fridays reminding them to step away from their work and do something fun. 

“I need these connections as much as they do because the work, while exciting, is hard and can be very isolating during this time,” Simmerling said.  

Ultimately, he said, he loves his job. “I think that was one of the things that I learned from my father was that he worked really hard, but he loved what he did. I feel like that’s success: having a job I care about and loving the outcome.”

View Simmerling’s lab website to learn more about his ongoing work.  Simmerling also appeared on ‘Tuesdays with Melanie: The Comeback Podcast,’ with PhD student Lucy Fallon to talk about ‘Humanizing Science.’

Liza N. Burby is a freelance writer and features editor for Stony Brook University Magazine, as well as a journalism professor.