From postdoc affiliate to award-winning researcher

When it comes to landing the ideal job, having a great start can make all the difference. When it comes to working in cyberinfrastructure or research computing, there isn’t a much better way to start than working at a state-of-the-art facility staffed by mentors with decades of experience. You don’t necessarily have to work for NCSA to gain experience from the Center that benefits your career trajectory. Sometimes, simply getting the experience of working with advanced research computing resources can make researchers comfortable enough with the technology to keep including it in their research plans, making their research output that much more potent. Combine that with the powerful mentorship that comes from Center staff, and NCSA affiliates and partners gain a host of skills with cyberinfrastructure that can change a career path substantially. To illustrate the power of the NCSA experience, we reached out to professionals whose careers were boosted by their experience at the Center. Here’s the first story in a new series highlighting these professionals’ experiences.

Research to Build a Career On

Jodi Hadden-Perilla, the C. Eugene Bennett Early Career Chair of Chemistry and an assistant professor of chemistry and biochemistry at the University of Delaware (UD), was a postdoc at the University of Illinois at Urbana-Champaign (U. of I.) when she first became involved with NCSA. She was working with the late Professor Klaus Schulten, an NCSA affiliate based at the Beckman Institute. Schulten’s group, the Theoretical and Computational Biophysics Group (TCBG), developed the NAMD/VMD software, a parallel molecular dynamics (MD) code designed for high-performance simulation and analysis of large biomolecular systems, for use on NCSA’s legendary supercomputer, Blue Waters. Hadden-Perilla was a member of Schulten’s group for three years and became quite familiar with Blue Waters during her time as a postdoc.

“A major milestone I contributed to while working for Prof. Schulten was that I performed the world’s first atomistic MD-simulation of the hepatitis B virus capsid,” Hadden-Perilla said. “The capsid is an essential structural component of the virus; it self-assembles to package the viral RNA pre-genome, plays a role in maturation of the RNA to the DNA genome, and is responsible for protecting the genome and trafficking it throughout the host cell – including to and into the nucleus of a newly infected host. The genome is, of course, a genetic blueprint that the virus will use to make copies of itself. My simulation of the empty capsid in explicit solvent encompassed around 6 million atoms and took seven months to equilibrate the system and run one microsecond of production sampling on Blue Waters.”

If I had never had the opportunity to use NCSA resources and benefit from NCSA support, if I had never had the opportunity to explore the dynamics of that first intact capsid, I would not be on the career or research trajectory that I’m on today.

– Jodi Hadden-Perilla

Hadden-Perilla further explained the importance of this work and how impactful this research would be in the field of virology. “Although crystal structures of the capsid have been available since the 1990s, those structures provide only a single snapshot of the capsid that has been artificially symmetrized. So these experimentally-derived structures give the impression that the capsid is this perfectly symmetric, static structure and that the protein-protein interactions captured in the structure represent the only possible state that the capsid exists in. My simulation represented the first time that we got to see the capsid move and explore asymmetric states, and we found that the capsid is remarkably flexible and that so much more happens than is captured in individual experimental structures.”

Hadden-Perilla did more than help create new ways to study viruses. Throughout her career, she has continued to build on her experience working with NCSA resources. “While still at UIUC, I contributed to a paper with Klaus about using MD simulations to examine virus capsids as drug targets, and after I had moved to an independent postdoctoral position at UD, I published a paper on the microsecond-long capsid simulation in memoriam to Klaus,” she said. “This work, enabled by NCSA and Blue Waters, was the platform from which I launched my career. I became faculty at UD in 2019, and over the years have published seven additional papers on simulations of the HBV capsid. Among other things, these simulations have revealed new conformations of the capsid never captured in experimental structures that help to explain how it carries out key functions in the viral life cycle, how mutations can positively or negatively impact those functions, how mutations can confer drug resistance and how all of this motion affects the results of experimental characterizations of the capsid. Looking back, I have not published a single paper on HBV that did not benefit from NCSA resources!” Hadden-Perilla’s most recent work on HBV utilized NCSA’s Delta supercomputer. 

Mentorship that Matters

Mentorship may sometimes be overshadowed by the technical awe of the hardware NCSA manages and supports, but the Center’s most valuable resource is its people. Center affiliates are chosen in part for their passion, expertise and accomplishments in their field. They often work with students and postdocs, mentoring them not only with their research projects but also by helping to introduce them to the potential that can be found in high-performance computing (HPC) resources. Schulten was a prime example of an affiliate who shared his passion and knowledge with his team.

Hadden-Perilla was struggling with a lot of personal setbacks and losses, including the passing of her mentor, Professor Klaus. “I was a first-generation college student who had a rocky start in academia,” she said, “and there have been a lot of hiccups along the way. I flunked out of college on the first try, struggled with the loss of my dad to cancer during graduate school and lost my postdoctoral mentor, too, just as my research projects in his group were starting to mature.”

Perilla speaks openly about her setbacks on her career journey, including the fact that during her very first year as a faculty member, a global pandemic hit, forcing her to adapt to remote teaching and training. “Having made it so far as to be eligible for tenure is a major milestone in my career. I hope that by being open about challenges we’ve overcome in our past, we can better mentor, guide and support our trainees through the challenges they will face in their own careers.”

This work, enabled by NCSA and Blue Waters, was the platform from which I launched my career.

–Jodi Hadden-Perilla

Hadden-Perilla’s compassion and openness in her mentoring style come in part from her own mentor during her time as a postdoc with Professor Schulten’s team. 

“I learned so much from him,” she said. “He never put any restrictions on me, just gave me access to amazing opportunities and resources and said, ‘Get going!’ The most important thing Klaus taught me was about scientific communication. Not just about presenting my findings in a clear and compelling way but in a way that could convey my own passion for the work and its impact. The scientific communication skills I learned from Klaus, and the opportunities he gave me to participate in proposal writing, have been essential for my success in obtaining research funding and supercomputer access in my independent career. I think about Klaus often and hope he would have been proud.”

Hadden-Perilla’s work continues to flourish. Her next big research project still involves a virus, but this time she’s researching the human papillomavirus (HPV) in the hopes her research will help develop treatments against it.

“We’re currently simulating the intact HPV capsid at atomistic resolution, a calculation that encompasses over 16 million atoms,” she said. “Given all that we’ve learned over the years from our simulations of hepatitis B, I’m very excited to see what we can learn by watching this new, much larger capsid move. It has taken us years to analyze the atomistic simulation of the hepatitis B capsid because the dataset is so rich with information. Beyond simulating HPV, tackling the analysis phase of the project is going to be a big challenge. HPV is, of course, a major cause of cervical cancer, a leading cause of cancer-related deaths among women worldwide. I’m hoping we can discover new aspects of the capsid that present opportunities for novel drug development against it.”

Though Hadden-Perilla’s career continues to climb – she received an NSF CAREER award in 2023 for her work on virus research – she fondly remembers the support she received in those early years. 

“If I had never had the opportunity to use NCSA resources and benefit from NCSA support, if I had never had the opportunity to explore the dynamics of that first intact capsid, I would not be on the career or research trajectory that I’m on today. NCSA – in terms of computing resources and support from the NCSA team as we utilize those resources – has been essential for my success from the time I was a first-year postdoc to now when I am going up for tenure at UD. This fall will represent 10 years that I have depended on NCSA for important aspects of my work!”

ABOUT NCSA
The National Center for Supercomputing Applications at the University of Illinois Urbana-Champaign provides supercomputing, expertise and advanced digital resources for the nation’s science enterprise. At NCSA, University of Illinois faculty, staff, students and collaborators from around the globe use innovative resources to address research challenges for the benefit of science and society. NCSA has been assisting many of the world’s industry giants for over 35 years by bringing industry, researchers and students together to solve grand challenges at rapid speed and scale.