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Faculty


Maria C. Nagan, Professor of Practice

Associate Dean for Curriculum, College of Arts and Sciences

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B.S. 1997, Grinnell College (Grinnell, IA)
Ph.D. 2001, University of Minnesota – Twin Cities

435 Chemistry, 631-632-5793
Email: maria.nagan@stonybrook.edu  

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RESEARCH

The Nagan lab employs computational methods to understand how chemical functional groups affect RNA  structure and recognition. 

Visit The Nagan Group Website

UNDERGRADUATE RESEARCH Programs

Chemistry REU Site (PI) - supported by NSF CHE-2050541

Velay Program (PI) - supported by the Panaphil Foundation

SUNY SOAR (co-PI) - supported by the SUNY Chancellor

REsearch Leadership

Amber Molecular Dynamics Software  Executive Committee

REcent ROLES

ACS COMP Co-chair Programming, Mercury Executive Committee

AWARDS

Fellow of the American Chemical Society, Godfrey Excellence in Teaching Award,  McNair Mentor Hall of Fame, Walker and Doris Allen Fellowship for Faculty Excellence

SELECTED PUBLICATIONS

1. Lauren E. RaguetteSarah S. GunasekeraRebeca I. Diaz VenturaEthan AminovJason T. LinzerDiksha ParwanaQin WuCarlos Simmerling, and  Maria C. Nagan* Adjusting the Energy Profle for CH-O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simualtions. J. Chem. Phys. B. , 2024, 128 (33), 7921-7933. doi.org/10.1021/acs.jpcb.4c01910
2. Jason T. Linzer, Ethan Aminov, Aalim S. Abdullah, Colleen E. Kirkup, Rebeca I. Diaz Ventura, Vinay R. Bijoor, Jiyun Jung, Sophie Huang, Chi Gee Tse, Emily Á lvarez Toucet, Hugo P. Onghai, Arghya P. Ghosh, Alex C. Grodzki, Emilee R. Haines, Aditya S. Iyer, Mark K. Khalil, Alexander P. Leong, Michael A. Neuhaus, Joseph Park, Asir Shahid, Matthew Xie, Jan M. Ziembicki, Carlos Simmerling, and Maria C. Nagan* Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment. J. Chem. Inf. Model, 2024, 64, 6092-6104. doi.org/10.1021/acs.jcim.4c00756
3. Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti,Gerardo Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Goëtz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala Mehmet C. Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matias R. Machado, Hai Minh Nguyen, Kurt A. O’Hearn, Alexey Onufriev, Feng Pan, Sergio Pantano,Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan,s Jason Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao,Qiang Zhu, Daniel R. Roe, , Darrin M. York, David A Case, Thomas E. Cheatham, III, Adrian Roitberg,C.L. Simmerling, Maria C. Nagan* and Kenneth M. Merz, Jr.*, AmberTools23, J. Chem. Inf. Model, 2023, 63 (20), 6183-6191. doi.org/10.1021/acs.jcim.3c01153.
4. Anderson, K., Arradondo, S., Ball, K.A., Bruce, C., Gomez, M.A., He, K., Hendrickson, H., Madison, L., Ringer McDonald, A., Nagan, M.C., Scott, C.E., Soto, P., Tomlinson, A., Varner, M. and Parish, C. “The Impacts of the Molecular Education and Research Consortium in Undergraduate Computational Chemistry on the Careers of Women in Computational Chemistry” J. Chem. Inf. Model, 2022,62(24), 6316-6322. doi.org/10.1021/acs.jcim.2c00566
3. Maddula, V., Rotenberg, S. A. and Nagan, M.C. “Computational Studies of the α/ß-Tubulin Heterodimeric Interface in Microtubules: The Impact of Phosphorylation of Ser165 in α-Tubulin” Biochemistry, 2022, 61(14), 1508-1516. Cover. doi.org/10.1021/acs.biochem.2c00154 
5. Nagan, M.C. “Using a Lab Wiki for Longevity and Knowledge Transfer in Undergraduate Research” International Journal of Quantum Chemistry, 2020,120 (20), e26262. doi.org/10.1002/qua.26262
6. 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, 4061-4062. doi.org/10.1021/acs.jcim.9b00643
6. Witts, R.N.;Hopson, E.C.; Koballa, D.E.; Van Boening, T.A.; Hopkins, N.H.; Patterson, E.V. and Nagan, M.C. “Backbone-Base Interactions Critical to Quantum Stabilization of Transfer RNA Anticodon Structure” J. Phys. Chem. B, 2013, 117, 7489-7497. doi.org/10.1021/jp400084p
7. Michael, L.A.; Chenault, J.A.; Miller III, B.R.; Knolhoff, A.M. and Nagan, M.C. “Water, Shape-Recognition, Salt Bridges and Pi-Cation Interactions Differentiate Peptide Recognition of the HIV Rev-Responsive Element” J. Mol. Biol.  2009, 392, 774-786. doi.org/10.1016/j.jmb.2009.07.047
8. McCrate, N.E.; Varner, M.E.; Kim, K.I. and Nagan, M.C. “Molecular Dynamics Simulations of Human tRNALys,3UUU: The Role of Modified Bases in mRNA Recognition” Nucleic Acids Res.2006, 34, 5361-5368. doi.org/10.1093/nar/gkl580