Jessica Nash is a Software Scientist and the Education Lead at The Molecular Sciences Software Institute. She completed her PhD at North Carolina State University in Materials Science and Engineering, where she studied DNA nano-materials using molecular dynamics simulations. Since joining MolSSI in 2017, her work has focused on the development and improvement of software in the computational molecular sciences. She currently works as the lead developer for the web dashboard for MolSSI’s project SEAMM (Simulation Environment for Atomistic and Molecular Simulation). As Education Lead for the Institute, she develops educational materials for researchers which enhance their capabilities to write code and use computational molecular science software.
What sparked your interest in DNA nano-materials during your PhD?
I first started getting involved with research in an analytical chemistry lab during my undergrad at UNC Chapel Hill. I worked in an analytical chemistry lab for about one and a half years doing traditional bench research, for chemistry. During that time, I was also interested in learning how to program. I also really liked physical chemistry and physics, and more mathematical things. I ended up doing research for a polymer theorist, Michael Rubenstein. That kind of computational research had a lot of different aspects in it that I was interested in learning more about. When I went to grad school I got interested in DNA as a biopolymer. That’s how I got into DNA and DNA nanomaterials. During my PhD, I did molecular dynamics simulations and analysis of nucleic acid structures.
Could you tell us about your work for MolSSI?
One thing you will see if you use scientific software is that when you’re working on a scientific problem, it can be hard to figure out what software to use and how to use it. There is this huge need for maintaining and improving research software, particularly non-commercial research software. During my PhD, after being on the user end of academic research software, I became interested in making it better. That’s why I started working at the Molecular Sciences Software Institute after finishing my PhD.
At MolSSI, I work on improving the usability and accessibility of molecular science software. I’ve recently been working on the Descriptor Libraries project at MolSSI. It is a collaboration with the Center for Computer-Assisted Synthesis, where we make different molecular libraries available for synthetic chemists.
My other important job is leading the education program at the institute. I’m in charge of all of our workshops and tutorials. We do workshops for the full range of careers of career levels that you can have for molecular science: undergraduates, graduate students, postdocs, faculty, and industry scientists.
I’m also excited about a new project for the institute called ACT-CMS (Accelerating Curricular Transformation in the Computational Molecular Sciences). Our goal is to provide open reusable curricular modules for molecular science to help educators who implement programming and computation into for-credit courses.
Could you tell us about your course you teach for MSSE?
In Chem 274A, our students learn about Python and C++, and the features of these different programming languages we can utilize when making software. For the lab portion of this class, we get hands-on experience doing calculations with molecular science software, for example, running a molecular dynamics simulation or some quantum chemistry calculations. We get to analyze the software we’ve used in the context of what we’ve learned about programming languages. Students experience examples of software that is difficult to use because of the way it was designed. What we try to link in the class is what we’re learning about programming languages and the actual use of the software as someone would experience it.
In terms of software engineering, what are some of the most important considerations when designing tools for computational molecular science researchers?
The first things that I think about if I’m designing tools for Molecular Sciences researchers is who my end users are, what kind of skills they’re going to have, and how they’re going to interact with the software. That’s one of the biggest considerations. Do I want to make this into a Python library, do my end users know how to program? That would determine if I want to make a Python library or something with a graphical interface. You also want to be thinking about how you’re going to distribute it in a way that people can get it and write documentation so that people can use it. Those are the big things when making a tool that other people can use.
How do you think the field of computational molecular sciences will change in the coming years?
The big thing that’s happening right now is all these advancements in AI. I think with machine learning there’s been an emergence of this new paradigm shift of molecular science calculations, of using more machine learning.
The emergence of all these large language models has already revolutionized a lot of a lot of industries, and I think they might have a really big effect in the molecular science field. I think large language models are also having an impact on programming and software development that we’re seeing evolve right now.
What skills do you believe are essential for students pursuing a career in molecular science and software engineering today?
The big skill is always going to be problem-solving, and it’s something I really try to teach to my students. It is so important to be able to take a problem, break it down into its different parts, and figure out a plan for solving a large problem. You have to understand the tools available for solving those problems and the type of information that you would think about when you’re thinking about problems in a particular discipline. The tools in the industry will change but that part will always be constant.
What is the most exciting part of your work at MolSSI?
The most exciting part is being able to work with a broad range of researchers in different fields of molecular science. I love getting to work with incredibly smart people on exciting problems all the time. It’s so exciting to get a broad scope of what’s going on in molecular science, research, and software right now. I love talking to different researchers about their work and specialties. I also love getting to work with students such as through the MSSE program!