All Stories

  1. Accelerating Free Energy Exploration Using Parallelizable Gaussian Accelerated Molecular Dynamics (ParGaMD)

    Article • Journal of Chemical Theory and Computation, June 2026, American Chemical Society (ACS)

    Surl-Hee Ahn

  2. D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes

    Article • Proceedings of the National Academy of Sciences, May 2026, Proceedings of the National Academy of Sciences

    Surl-Hee Ahn

  3. Ligand Dissociation Pathways from Membrane Receptors Revealed by Weighted Ensemble Simulations

    Article • The Journal of Physical Chemistry B, October 2025, American Chemical Society (ACS)

    Surl-Hee Ahn

  4. Ancestral evolution of oxidase activity in a class of (S)-nicotine and (S)-6-hydroxynicotine-degrading flavoenzymes

    Article • Journal of Biological Chemistry, July 2025, Elsevier

    Surl-Hee Ahn

  5. Accelerating free energy exploration using parallelizable Gaussian accelerated molecular dynamics (ParGaMD)

    Article • May 2025, American Chemical Society (ACS)

    Surl-Hee Ahn

  6. Regulatory Interactions between APOBEC3B N- and C-Terminal Domains

    Article • Journal of Chemical Information and Modeling, March 2025, American Chemical Society (ACS)

    Surl-Hee Ahn

  7. Molecular simulations reveal intricate coupling between agonist-bound β-adrenergic receptors and G protein

    Article • iScience, February 2025, Elsevier

    Surl-Hee Ahn

  8. Regulatory interactions between APOBEC3B N- and C-terminal domains

    Article • December 2024, Cold Spring Harbor Laboratory Press

    Surl-Hee Ahn

  9. Stability and Dynamics of Zeolite-Confined Gold Nanoclusters

    Article • Journal of Chemical Theory and Computation, September 2024, American Chemical Society (ACS)

    Surl-Hee Ahn

  10. Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens

    Article • Nature Communications, August 2024, Springer Science + Business Media

    Surl-Hee Ahn

  11. Optimization of the resampling method in the weighted ensemble simulation toolkit with parallelization and analysis (WESTPA)

    Article • The Journal of Chemical Physics, July 2024, American Institute of Physics

    Surl-Hee Ahn, Surl-Hee Ahn

  12. The Stability and Dynamics of Zeolite-Confined Gold Nanoclusters

    Article • June 2024, American Chemical Society (ACS)

    Surl-Hee Ahn

  13. Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase

    Article • Journal of Chemical Information and Modeling, June 2024, American Chemical Society (ACS)

    Surl-Hee Ahn

  14. Harnessing molecular simulations to design stabilized SARS-CoV-2 S2 antigens

    Article • Biophysical Journal, February 2024, Elsevier

    Surl-Hee Ahn

  15. Elucidating molecular mechanisms of protoxin-II state-specific binding to the human NaV1.7 channel

    Article • Journal of General Physiology, December 2023, Rockefeller University Press

    Surl-Hee Ahn

  16. Elucidating the Fluxionality and Dynamics of Zeolite-Confined Au Nanoclusters Using Machine Learning Potentials

    Article • November 2023, American Chemical Society (ACS)

    Surl-Hee Ahn

  17. A Glycan Gate Controls Opening of the SARS-CoV-2 Spike Protein

    Article • July 2023, Taylor & Francis

    Surl-Hee Ahn

  18. Elucidating Molecular Mechanisms of Protoxin-2 State-specific Binding to the Human NaV1.7 Channel

    Article • March 2023, Cold Spring Harbor Laboratory Press

    Surl-Hee Ahn

  19. DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling

    Article • Journal of Chemical Theory and Computation, January 2023, American Chemical Society (ACS)

    Surl-Hee Ahn

  20. #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

    Article • The International Journal of High Performance Computing Applications, October 2022, SAGE Publications

    Dr Matteo Turilli, Surl-Hee Ahn

  21. Investigating Intrinsically Disordered Proteins With Brownian Dynamics

    Article • Frontiers in Molecular Biosciences, June 2022, Frontiers

    Surl-Hee Ahn

  22. DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced kinetic and thermodynamic sampling

    Article • March 2022, American Chemical Society (ACS)

    Surl-Hee Ahn

  23. Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling

    Article • Journal of Chemical Theory and Computation, November 2021, American Chemical Society (ACS)

    Surl-Hee Ahn

  24. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

    Article • November 2021, Cold Spring Harbor Laboratory Press

    Surl-Hee Ahn

  25. Data for molecular dynamics simulations of Escherichia coli cytochrome bd oxidase with the Amber force field

    Article • Data in Brief, October 2021, Elsevier

    Surl-Hee Ahn

  26. A glycan gate controls opening of the SARS-CoV-2 spike protein

    Article • Nature Chemistry, August 2021, Springer Science + Business Media

    Surl-Hee Ahn

  27. Gaussian accelerated molecular dynamics with the weighted ensemble method: a hybrid method improves thermodynamic and kinetic sampling

    Article • August 2021, American Chemical Society (ACS)

    Surl-Hee Ahn

  28. Gaussian accelerated molecular dynamics with the weighted ensemble method: a hybrid method improves thermodynamics and kinetics sampling

    Article • August 2021, American Chemical Society (ACS)

    Surl-Hee Ahn

  29. Characterizing protein kinase A (PKA) subunits as macromolecular regulators of PKA RIα liquid–liquid phase separation

    Article • The Journal of Chemical Physics, June 2021, American Institute of Physics

    Huan-Xiang Zhou, Surl-Hee Ahn

  30. Data for Molecular Dynamics Simulations of Escherichia Coli Cytochrome Bd Oxidase with the Amber Force Field

    Article • April 2021, American Chemical Society (ACS)

    Surl-Hee Ahn

  31. AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

    Article • The International Journal of High Performance Computing Applications, April 2021, SAGE Publications

    Dr Matteo Turilli, Surl-Hee Ahn

  32. A glycan gate controls opening of the SARS-CoV-2 spike protein

    Article • February 2021, Cold Spring Harbor Laboratory Press

    Surl-Hee Ahn

  33. SARS-CoV-2 Glycosylated Spike Activation Mechanism - Simulations of the Full Unbiased Pathway

    Article • Biophysical Journal, February 2021, Elsevier

    Surl-Hee Ahn

  34. AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Dr Matteo Turilli, Surl-Hee Ahn

  35. Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach

    Article • Journal of Chemical Information and Modeling, April 2020, American Chemical Society (ACS)

    Surl-Hee Ahn

  36. Ranking of Ligand Binding Kinetics using a Weighted Ensemble Approach and Comparison with Milestoning

    Article • Biophysical Journal, February 2020, Elsevier

    Surl-Hee Ahn

  37. Foldamer Architectures of Triazine-Based Sequence-Defined Polymers Investigated with Molecular Dynamics Simulations and Enhanced Sampling Methods

    Article • The Journal of Physical Chemistry B, October 2019, American Chemical Society (ACS)

    Surl-Hee Ahn

  38. Tamoxifen suppresses pancreatic β-cell proliferation in mice

    Article • PLOS One, September 2019, PLOS

    Surl-Hee Ahn

  39. The multi-dimensional generalized Langevin equation for conformational motion of proteins

    Article • The Journal of Chemical Physics, May 2019, American Institute of Physics

    Surl-Hee Ahn

  40. Erratum: “Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers” [J. Chem. Phys. 149, 072330 (2018)]

    Article • The Journal of Chemical Physics, May 2019, American Institute of Physics

    Surl-Hee Ahn

  41. Tamoxifen Suppresses Pancreatic β-Cell Proliferation in Mice

    Article • March 2019, Cold Spring Harbor Laboratory Press

    Surl-Hee Ahn

  42. Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers

    Article • The Journal of Chemical Physics, August 2018, American Institute of Physics

    Surl-Hee Ahn

  43. Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

    Article • The Journal of Chemical Physics, August 2017, American Institute of Physics

    Surl-Hee Ahn

  44. Building a Coarse-Grained Model Based on the Mori-Zwanzig Formalism

    Article • MRS Proceedings, January 2015, Cambridge University Press

    Surl-Hee Ahn