Nagan Research Lab
Dr. Maria Nagan
Professor of Practice, Department of Chemistry
Associate Dean for Curriculum, College of Arts and Sciences
Email: maria.nagan@stonybrook.edu
Chemistry Office: 435 Chemistry
Dean's Office: Melville Library E-3320
Welcome to Dr. Nagan's research page!
Students in the Nagan lab are all undergraduate and high school students.
The Nagan lab employs computational methods to examine RNA structure and protein recognition of RNA. We make movies on the computer, collecting structures of molecules throughout time, and then use physical chemistry and mathematical principles to extract meaning out of the data. To join the group, please read more about the Nagan lab projects and then email Dr. Nagan to see about availability of spots.
Undergraduate Research Programs
Dr. Nagan is director of two larger undergraduate research programs at Stony Brook University.
Stony Brook Chemistry REU
Click here to apply for Summer 2024
Open to non-Stony Brook students, Funded by NSF CHE-2050541
Velay Program
Click here to see students' videos from last year
Stony Brook students: Click here to apply for Summer 2024
Funded by the Panaphil Foundation
Leadership in the Computational Community
Amber MD Software Leadership Team
New AmberTools paper:
Case, D. A.; Aktulga, H. M.; Belfon, K.; Cerutti, D. S.; Cisneros, G. A.; Cruzeiro, V. W. D.; Forouzesh, N.; Giese, T. J.; Götz, A. W.; Gohlke, H.; Izadi, S.; Kasavajhala, K.; Kaymak, M. C.; King, E.; Kurtzman, T.; Lee, T.-S.; Li, P.; Liu, J.; Luchko, T.; Luo, R.; Manathunga, M.; Machado, M. R.; Nguyen, H. M.; O’Hearn, K. A.; Onufriev, A. V.; Pan, F.; Pantano, S.; Qi, R.; Rahnamoun, A.; Risheh, A.; Schott-Verdugo, S.; Shajan, A.; Swails, J.; Wang, J.; Wei, H.; Wu, X.; Wu, Y.; Zhang, S.; Zhao, S.; Zhu, Q.; Cheatham, T. E., III; Roe, D. R.; Roitberg, A.; Simmerling, C.; York, D. M.; Nagan*, M. C.; Merz*, K. M., Jr. AmberTools. J. Chem. Inf. Model 2023, 63, 6183-6191.
Dr. Nagan's lab makes advanced techniques accessible to the wider computational community. If you have ideas for Amber user support and tutorials, please contact Dr. Nagan. We welcome contributions from the community.
Mercury Consortium
Dr. Nagan has spent the majority of her career at primarily undergraduate institutions and continues to be committed to involving undergraduate students in research. The Mercury Consortium has been funded by NSF for over 20 years. For articles related to the consortium see:
Shields, G. C., "Twenty years of exceptional success: The molecular education and research consortium in undergraduate computational chemistry ( MERCURY )." International Journal of Quantum Chemistry 2020, 120 (20), e26274. DOI: 10.1002/qua.26274
Anderson, K., Arrandondo, S., Ball, A., Bruce, C., Gomez, M., He, K., Hendrickson, H., Madison, L, McDonald, A., Nagan, M., Scott, C., Soto, P., Tomlinson, A., Varner, M., Parish, C., “The impacts of Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY) on the Careers of Women in Computational Chemistry.” J. Chem. Inf. Model. 2022 https://doi.org/10.1021/acs.jcim.2c00566
Our annual conference is open to all undergraduates conducting computational chemistry research. It is usually held in late July and serves as a friendly, summative experience for undergraduates to give poster presentations. As well, keynote speakers include renowned faculty in computational chemistry, scientists from industry and national labs.
Women Make COMP
In collaboration with Prof. Giulia Palermo (UC-Riverside) and Dr. Kira Armacost (GSK), we created a program in ACS COMP for women graduate students and post-doctoral fellows, to find mentors, and support from prominent women in the field. This is only a small step to creating a vibrant community for the next generation of women in computational chemistry. This Spring 2024, Prof. Palermo and Dr. Anda Trifan are co-hosting the latest Women Make COMP symposium.
Palermo, G., Armacost, K.A. and Nagan, M.C. " Women Make COMP: Mentoring the Next Generation of Women in Computational Chemistry." J. Chem. Inf. Model. 2019, 59, 10, 4061-4062.