Publications

UC Davis (since July 1, 2022)

1. Mac Kevin, E. Braza, Özlem Demir, Surl-Hee Ahn, Clare K. Morris, Carla Calvó-Tusell, Kelly L. McGuire, Bárbara de la Peña Avalos, Michael A. Carpenter, Yanjun Chen, Lorenzo Casalino, Hideki Aihara, Mark A. Herzik Jr., Reuben S. Harris, and Rommie E. Amaro. "Regulatory interactions between APOBEC3B N-and C-terminal domains." Journal of Chemical Information and Modeling 65. 7 (2025): 3593. DOI: https://doi.org/10.1021/acs.jcim.4c02272

2. Yanxiao Han, John R.D. Dawson, Kevin R. DeMarco, Kyle C. Rouen, Khoa Ngo, Slava Bekker, Vladimir Yarov-Yarovoy, Colleen E. Clancy, Yang K. Xiang, Surl-Hee Ahn †, and Igor Vorobyov †. “Molecular simulations reveal intricate coupling between agonist-bound β-Adrenergic Receptors and G Protein.” iScience 28.2 (2025): 111741. DOI: https://doi.org/10.1016/j.isci.2024.111741

3. Siddharth Sonti, Chenghan Sun, Zekun Chen, Robert Michael Kowalski, Joseph S. Kowalski, Davide Donadio, Surl-Hee Ahn †, and Ambarish R. Kulkarni †. “Stability and Dynamics of Zeolite-Confined Gold Nanoclusters.” Journal of Chemical Theory and Computation 20.18 (2024): 8261-8269. DOI: http://doi.org/10.1021/acs.jctc.4c00978

4. Xandra Nuqui, Lorenzo Casalino, Ling Zhou, Mohamed Shehata, Albert Wang, Alexandra L. Tse, Anupam A. Ojha, Fiona L. Kearns, Mia A. Rosenfeld, Emily Happy Miller, Cory M. Acreman, Surl-Hee Ahn, Kartik Chandran, Jason S. McLellan & Rommie E. Amaro. “Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens.” Nature Communications 15.1 (2024): 7370. DOI: https://doi.org/10.1038/s41467-024-50976-9

5. Dennis Plotnikov and Surl-Hee Ahn †. “Optimization of the resampling method in the weighted ensemble simulation toolkit with parallelization and analysis (WESTPA)"  The Journal of Chemical Physics 161.4 (2024): 046101. DOI: https://doi.org/10.1063/5.0197141

6. Christian Seitz, Surl-Hee Ahn * †, Haixin Wei, Matson Kyte, Gregory M. Cook, Kurt L. Krause, and J. Andrew McCammon. "Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase." Journal of Chemical Information and Modeling 64.13 (2024): 5232-5241. DOI: https://doi.org/10.1021/acs.jcim.4c00344

7. Khoa Ngo, Diego Lopez Mateos, Yanxiao Han, Kyle C. Rouen, Surl-Hee Ahn, Heike Wulff, Colleen E. Clancy, Vladimir Yarov-Yarovoy, and Igor Vorobyov. “Elucidating molecular mechanisms of protoxin-II state-specific binding to the human NaV1.7 channel.” Journal of General Physiology 156.2 (2024): e202313368. DOI: https://doi.org/10.1085/jgp.202313368

8. Anupam A. Ojha, Saumya Thakur, Surl-Hee Ahn, and Rommie E. Amaro. “DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced kinetic and thermodynamic sampling.” Journal of Chemical Theory and Computation 19.4 (2023): 1342-1359. DOI: https://doi.org/10.1021/acs.jctc.2c00282

9. Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, Sofia Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christiansen, Daniel G.A. Smith, Zhuoran Qiao, Sai Krishna Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel Zuckerman, Adrian Muholland, Thomas Miller III, Shantenu Jha, Arvind Ramanathan, Lillian Chong, and Rommie E Amaro. “#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol.” The International Journal of High Performance Computing Applications 37.1 (2023): 28-44. DOI: https://doi.org/10.1177/10943420221128233

10. Surl-Hee Ahn * †, Gary A. Huber, and J. Andrew McCammon. “Investigating intrinsically disordered proteins using Brownian dynamics.” Frontiers in Molecular Biosciences 9 (2022): 898838. DOI: https://doi.org/10.3389/fmolb.2022.898838

Before UC Davis

1. Surl-Hee Ahn * †, Anupam A. Ojha, Rommie E. Amaro, and J. Andrew McCammon. “Gaussian accelerated molecular dynamics with the weighted ensemble method: a hybrid method improves thermodynamic and kinetic sampling.” Journal of Chemical Theory and Computation 17.21 (2021): 7938-7951. DOI: https://doi.org/10.1021/acs.jctc.1c00770 Journal Cover Art

2. Surl-Hee Ahn * †, Christian Seitz, Vinicius Wilian D. Cruzeiro, J. Andrew McCammon, and Andreas W. Goetz. “Data for Molecular Dynamics Simulations of Escherichia Coli Cytochrome bd Oxidase with the Amber Force Field.” Data in Brief 38 (2021): 107401. DOI: https://doi.org/10.1016/j.dib.2021.107401

3. Terra Sztain, Surl-Hee Ahn *, Anthony T. Bogetti, Lorenzo Casalino, Jory A. Goldsmith, Ryan S. McCool, Fiona L. Kearns, Francisco Acosta-Reyes, Suvrajit Maji, Ghoncheh Mashayekhi, J. Andrew McCammon, Abbas Ourmazd, Joachim Frank, Jason S. McLellan, Lillian T. Chong, and Rommie E. Amaro. “A Glycan Gate Controls Opening of the SARS-CoV-2 Spike Protein.” Nature Chemistry 13.10 (2021): 963-968. DOI: https://doi.org/10.1038/s41557-021-00758-3

4. Surl-Hee Ahn *, Sanbo Qin, Jason Z. Zhang, J. Andrew McCammon, Jin Zhang, and Huan-Xiang Zhou. “Characterizing protein kinase A (PKA) subunits as macromolecular regulators of PKA RI⍺ liquid-liquid phase separation.” The Journal of Chemical Physics 154.22 (2021): 221101. DOI: https://doi.org/10.1063/5.0049810 Selected as Editor’s Pick & 2021 Editors’ Choice Collection

5. Lorenzo Casalino, Abigail Dommer, Zied Gaieb, Emilia Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony Bogetti, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian Chong, Carlos Simmerling, David Hardy, Julio Maia, James Phillips, Thorsten Kurth, Abraham Stern, Lei Huang, John McCalpin, Mahidar Tatineni, Tom Gibbs, John Stone, Shantenu Jha, Arvind Ramanathan, and Rommie Amaro. “AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics.” The International Journal of High Performance Computing Applications 35.5 (2021): 432-451. DOI: https://doi.org/10.1177/10943420211006452

6. Surl-Hee Ahn, Benjamin R. Jagger, and Rommie E. Amaro. “Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach.” Journal of Chemical Information and Modeling 60.10 (2020): 5340-5352. DOI: http://doi.org/10.1021/acs.jcim.9b00968

7. Surl-Hee Ahn †  and Jay W. Grate †. “Foldamer Architectures of Triazine-Based Sequence-Defined Polymers Investigated with Molecular Dynamics Simulations and Enhanced Sampling Methods.” The Journal of Physical Chemistry B 123.44 (2019): 9364-9377. DOI: http://doi.org/10.1021/acs.jpcb.9b06067 Journal Cover Art

8. Surl-Hee Ahn, Anne Granger, Matthew M. Rankin, Carol J. Lam, Aaron R. Cox, and Jake A. Kushner. “Tamoxifen Suppresses Pancreatic β-cell Proliferation in Mice.” PLOS ONE 14.9 (2019): e0214829. DOI: http://doi.org/10.1371/journal.pone.0214829

9. Hee Sun Lee, Surl-Hee Ahn, and Eric F. Darve. “The Multi-Dimensional Generalized Langevin Equation for Conformational Motion of Proteins.” The Journal of Chemical Physics 150.17 (2019): 174113. DOI: http://doi.org/10.1063/1.5055573

10. Surl-Hee Ahn † , Jay W. Grate, and Eric F. Darve. “Investigating the Role of Non-Covalent Interactions in Conformation and Assembly of Triazine-Based Sequence-Defined Polymers.” The Journal of Chemical Physics 149.7 (2018): 072330. DOI: http://doi.org/10.1063/1.5024552

11. Surl-Hee Ahn † , Jay W. Grate, and Eric F. Darve. “Efficiently Sampling Conformations and Pathways Using the Concurrent Adaptive Sampling Algorithm.” The Journal of Chemical Physics 147.7 (2017): 074115. DOI: http://doi.org/10.1063/1.4999097

12. Hee Sun Lee, Surl-Hee Ahn, and Eric F. Darve. “Building a Coarse-Grained Model Based on the Mori-Zwanzig Formalism.” MRS Online Proceedings Library Archive 1753 (2015).  DOI: http://doi.org/10.1557/opl.2015.185

† Corresponding author, * Co-first author