Projects
robust methods to sample kinetics
One of the remaining grand challenges in the molecular dynamics simulation field is being able to sample kinetic properties (rate constants, pathways) efficiently. Hence, I have focused my efforts on developing new state-of-the-art methods that will be able to sample kinetics efficiently from molecular dynamics simulations.
Gaussian accelerated molecular dynamics (GaMD) - Weighted ensemble (WE) method: a hybrid method that combines the two for efficient thermodynamic + kinetic sampling
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. https://doi.org/10.1021/acs.jctc.1c00770 Journal Cover ArtConcurrent adaptive sampling (CAS) algorithm: committor function to accelerate reactant to product sampling + Voronoi tessellation to use multi-dimensional progress coordinates
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
† Corresponding author, * Co-first author
pipeline for drug discovery from force fields to virtual screening
Computer-aided drug discovery is another area of interest of mine, and I plan to contribute to this field with my expertise in enhanced sampling methods for molecular dynamics simulations.
Amber force field for heme cofactors in cytochrome bd oxidase, which is implicated in Mycobacterium tuberculosis and E. coli
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
† Corresponding author, * Co-first author
Figure from Safarian et al. Nat Commun 12 (2021): 5236.
simulations as computational microscopes
With the enhanced sampling methods for molecular dynamics simulations, molecular dynamics simulations are closer to being true microscopes that can look into proteins, biomolecules, and materials at an atomic level and unveil their underlying dynamics and mechanisms.
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 (2022). https://doi.org/10.1101/2021.11.12.468428
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
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
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 April (2021). DOI: https://doi.org/10.1177/10943420211006452
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
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
† Corresponding author, * Co-first author
Figure from Casalino et al. The International Journal of High Performance Computing Applications April (2021).