Join Our Team!

If you came directly to this page and want to learn more about our research topics, look at videos of some of our presentations, or our YouTube channel. Also check the “Research” section of this site.

STUDENTS/TRAINEES: We are actively seeking new undergraduate and graduate students to join our research group!

In 2024, We are particularly seeking students with strong math & Comp Sci skills who are interested in applications of AI/deep learning to biomolecular modeling. in addition to math/CS skills, knowledge of chemistry is preferred.

Currently we are only considering students for in-person, year-round research (not summer-only or virtual experiences). Contact us if you have questions about ongoing research in our lab after reading the information on our web site.

How to apply:

First - let’s clarify our policy on the use of AI in writing your application. Generative AI can be a useful tool, especially for people that are less comfortable with written communication in English. However, part of our goal in reading your letter will be to get a sense of who you are, and how you communicate. If your writing isn’t your own, we won’t learn about you, we’ll learn about something or someone else. While we don’t always check your writing using AI-detection tools, it tends to be pretty clear in an in-person interview if someone’s communication style or knowledge of the relevant information is not consistent with their application. If we invite you for an interview based on an AI-written application, and then find that this doesn’t represent you well, it will be a waste of our time and of yours. Summary: take the time to write your application by yourself, using information that you understand.

What to include:

Interested students should email carlos.simmerling@stonybrook.edu after reading all of the information below. Make sure to mention in your email why you’re interested in our lab in particular, and describe any experience that you have with chemistry, computer programming (Python, C, etc), Unix/Linux, and/or biomolecular structure. These skills aren’t strictly needed to work with us, but it gives us an idea of your interests and where you’d be able to start. If these things are missing, we will not be able to evaluate your application.

Please attach pdf files for your resume/CV and transcript (unofficial is ok).

In addition, please read the section below that is appropriate to your education level:

  • PhD-track graduate students:

    • Fall 2024: Learn about our Ph.D. program and graduate school life just a short distance from New York City from current Ph.D. students and faculty. Learn about how to apply and about our fee waivers for international students. No GRE required. We have two info sessions scheduled for this year on Tuesday, November 12, 6-7:30 pm EST and Wednesday, November 13, 8-9:30 am EST.

    • If you are already accepted to a Stony Brook graduate program, contact us as outlined above, and also provide your graduate program, information about rotation start/end dates, and info on any undergraduate research experience that you have had. You should mention specific aspects of our recent work that you find interesting - do your homework before contacting Prof. Simmerling.

    • If you want to work with us but have not yet joined a graduate program at Stony Brook University, there are many options and you should choose the one(s) that are the best fit to your background. Students in our lab have earned their PhD through many graduate programs such as Chemistry, Molecular & Cellular Pharmacology, Biochemistry & Structure Biology, Applied Mathematics & Statistics, and Molecular & Cellular Biology. More information about requirements and application procedures can be found by clicking the names of the graduate program above.

    • Be aware that there are several fellowship opportunities with deadlines that are much earlier than the graduate application deadline, so you want to apply early! For an example, see the IACS graduate fellowship here. If you are interested in these fellowships, contact Prof. Simmerling in addition to submitting your application to the SBU graduate school.

    • All PhD-track graduate students do several research rotations of ~ 10 weeks each before a decision is made about joining a lab for the PhD. We cannot provide guarantees of funding or acceptance prior to a successful research rotation. The rotations also give you an opportunity to learn more about the lab. Joining the lab for your graduate studies is a joint decision involving both you and Prof. Simmerling.

    • We are unable to host all of the students that desire a rotation with our team. Graduate students interested in a research rotation should contact Prof. Simmerling as described above; this must be done before making any rotation arrangements with your graduate program. Prior to agreeing to host you for a research rotation, Prof. Simmerling may ask you for additional information, or perhaps an individual meeting to discuss your research interests, short- and long-term career goals, and which projects in the lab you find most interesting (and why). You will likely want to look at some of our most recent publications.

  • Masters-track graduate students

    • Master students typically do not do a research rotation, since the MS time period tends to be too short for multiple rotations. Instead, contact Prof. Simmerling as noted above, including the relevant information about your background, research interests, what specifically about our work interests you (giving examples from our recent publications or videos), and the amount of time that you can commit to working with us every week. Note that we do not provide funding to MS students; exceptions can be made but only after one semester of volunteering with the lab. Our grants simply do not provide funding for the training of MS students (again, because the time period is too short). Some MS students transfer to the PhD track in their graduate program; working with us for an MS degree does not guarantee placement in the lab for a PhD, and this should be discussed with Prof. Simmerling as soon as you begin considering the PhD track.

  • Undergraduates:

    • You probably don’t need as much background as you think - students in our group come from a variety of majors, with some from Biology or Chemistry, and others from Engineering or Physics. There are lots of things you can do - we’ve had over 50 undergrads work with us, many starting in their freshman year! See the Alumni tab for a list. Many of our undergrads have co-authored research journal articles from our lab.

    • We usually have several undergrads working with us, and our students from the past few years have gone on to medical schools, STEM jobs, and PhD programs at Yale, U Chicago, UCSF, U Pennsylvania, U Washington and more!

    • If you’re interested, contact us following the info above, and also provide your major and year, and how much time you would be able to devote to research each week.

    • For information about earning SBU undergraduate course credits for doing research, see this page. Note that undergraduate students in our lab typically register for research credit only after their first semester in the lab, when they can do some tutorials and learn more about what we do. This gives you a chance to try out our work and see if it’s a good fit before you commit to a graded course.

    • For information about undergraduate research opportunities in labs other than ours, look at the URECA site and their bulletin board.

  • High school students: we accept students that are affiliated with specific Stony Brook programs, such as the competitive Simons summer program at SBU. Students need official SBU status in order to work with our team.

Other potential research mentors: There are many research labs at Stony Brook working in similar areas of computational structural biology. You can see a list of some of them at the Laufer Center faculty page. You should also consider them as possible mentors for your graduate work, or if you join our lab, they can provide additional training and mentorship. The following faculty carry out biomolecular simulations as part of their research:

  • Ivet Bahar, Department of Biochemistry (bridging molecular structure/dynamics and cell/systems behavior)

  • Ken Dill, Departments of Chemistry and Physics (protein folding, cell networks, water, evolution, and more)

  • Robert Rizzo, Department of Applied Mathematics and Statistics (protein-ligand docking)

  • Maria Nagan, Department of Chemistry (RNA structure and function)

  • Dima Kozakov, Department of Applied Mathematics and Statistics (protein-protein interactions)

  • Iwao Ojima, Department of Chemistry (medicinal chemistry)

  • Markus Seeliger, Department of Pharmacological Sciences (kinase structure and function)

  • David Green, Department of Applied Mathematics and Statistics

  • Dan Raleigh, Department of Chemistry (protein folding and misfolding)

  • Troy Wymore, Department of Chemistry (functional plasticity of enzymes)

  • Jin Wang, Department of Chemistry (nonequilibrum statistical mechanics)

  • Christian Aponte-Rivera, Department of Chemistry (polymer properties of protein )

  • Qun Liu, Brookhaven National Lab Biology Department (membrane protein structural biology, technology development)

    The following faculty do computational chemistry, but not necessarily on biomolecules:

  • Ben Levine, Department of Chemistry (electronically excited materials)

  • Nav Nidhi Rajput, Materials Science and Chemical Engineering (materials design)

  • Marivi Fernandez-Serra, Department of Physics (computational condensed matter physics)

  • also look at other faculty in the SBU Institute for Advanced Computational Science