Publications

Google Scholar

  1. Monroe, J. I. Reweighting configurations generated by transferable, machine learned models for protein sidechain backmapping. Molecular Systems Design & Engineering. 2025, 10, 298-313. https://doi.org/10.1039/D4ME00198B.
  2. Burton, H. G. A.; Dong, S. S.; Ghosh, S.; Gu, B.; Jackson, N. E.; Keefer, D.; Lu, Y.; Monroe, J. I.; Peng, B.; Pieri, E.; Spackman, P. R.; Vacher, M.; Vuckovic, S.; Williams-Young, D.; Yang, Z. J.; Yue, S.; Zerze, G. H.; Zhu, T. JCTC Early Career Board Selects. J. Chem. Theory Comput. 2024, 20 (14), 5785–5787. https://doi.org/10.1021/acs.jctc.4c00787.
  3. Monroe, J. I.; Thamaraiselvan, C.; Wickramasinghe, R. R. Grand challenges in membrane transport, modeling and simulation. Frontiers in Membrane Science and Technology. 2024, 2, 1357625. https://doi.org/10.3389/frmst.2023.1357625.

Prior to University of Arkansas

  1. Mahynski, N. A.; Monroe, J. I.; Sheen, D. A.; Paul, R. L.; Chen-Mayer, H. H.; Shen, V. K. Classification and authentication of materials using prompt gamma ray activation analysis. Journal of Radioanalytical and Nuclear Chemistry. 2023, 332, 3259-3271. https://doi.org/10.1007/s10967-023-09024-x.
  2. Monroe, J. I.; Krekelberg, W. P.; McDannald, A.; Shen, V. K. Leveraging Uncertainty Estimates and Derivative Information in Gaussian Process Regression for Efficient Collection and Use of Molecular Simulation Data. J. Chem. Phys. 2023, 158 (16), 164110.
  3. Mahynski, N. A.; Monroe, J. I.; Sheen, D. A.; Paul, R. L.; Chen-Mayer, H. H.; Shen, V. K. Classification and Authentication of Materials Using Prompt Gamma Ray Activation Analysis. J Radioanal Nucl Chem. 2023, 332 (8), 3259–3271.
  4. Monroe, J. I.; Shen, V. K. Systematic Control of Collective Variables Learned from Variational Autoencoders. J. Chem. Phys. 2022, 157, 094116.
  5. Monroe, J. I.; Shen, V. K. Learning Efficient, Collective Monte Carlo Moves with Variational Autoencoders. J. Chem. Theory Comput. 2022.
  6. Moon, H.; Collanton, R.; Monroe, J. I.; Casey, T.; Shell, M. S.; Han, S.; Scott, S. Evidence for Entropically-Controlled Interfacial Hydration in Mesoporous Organosilicas. Journal of the American Chemical Society 2022, 144 (4) 1766-1777.  
  7. Jiao, S.; DeStefano, A.; Monroe, J. I.; Barry, M.; Sherck, N.; Casey, T.; Segalman, R. A.; Han, S.; Shell, M. S. Quantifying Polypeptoid Conformational Landscapes through Integrated Experiment and Simulation. Macromolecules 2021, 54, 11, 5011-5021.
  8. Monroe, J. I.; Jiao, S.; Davis, J. R.; Robinson Brown, D.; Katz, L. E.; Shell, M. S. Affinity of Small-Molecular Solutes to Hydrophobic, Hydrophilic, and Chemically Patterned Interfaces in Aqueous Solution. Proceedings of the National Academy of Sciences 2021, 118 (1), e2020205118.
  9. Monroe, J. I.; Hatch, H. W.; Mahynski, N. A.; Shell, M. S.; Shen, V. K. Extrapolation and Interpolation Strategies for Efficiently Estimating Structural Observables as a Function of Temperature and Density. J. Chem. Phys. 2020, 153, 144101.
  10. Monroe, J.; Barry, M.; DeStefano, A.; Gokturk, P. A.; Jiao, S.; Robinson-Brown, D.; Webber, T.; Crumlin, E. J.; Han, S.; Shell, M. S. Water Structure and Properties at Hydrophilic and Hydrophobic Surfaces. Annu. Rev. Chem. Biomol. Eng. 2020, 11 (1), annurev-chembioeng-120919-114657.
  11. Khanna, V.; Monroe, J. I.; Doherty, M. F.; Peters, B. Performing Solvation Free Energy Calculations in LAMMPS Using the Decoupling Approach. J. Comput. Aided Mol. Des. 2020.
  12. Monroe, J. I.; Shell, M. S. Decoding Signatures of Structure, Bulk Thermodynamics, and Solvation in Three-Body Angle Distributions of Rigid Water Models. J. Chem. Phys. 2019, 151 (9), 094501.
  13. Braun, E.; Gilmer, J.; Mayes, H. B.; Mobley, D. L.; Monroe, J. I.; Prasad, S.; Zuckerman, D. M. Best Practices for Foundations in Molecular Simulations [Article v1.0]. LiveCoMS 2019, 1 (1).
  14. Monroe, J. I.; Shell, M. S. Computational Discovery of Chemically Patterned Surfaces That Effect Unique Hydration Water Dynamics. Proceedings of the National Academy of Sciences 2018, 115 (32), 8093–8098.
  15. Schrader, A. M.; Monroe, J. I.; Sheil, R.; Dobbs, H. A.; Keller, T. J.; Li, Y.; Jain, S.; Shell, M. S.; Israelachvili, J. N.; Han, S. Surface Chemical Heterogeneity Modulates Silica Surface Hydration. Proceedings of the National Academy of Sciences 2018, 201722263.
  16. Stock, P.*; Monroe, J. I.*; Utzig, T.; Smith, D. J.; Shell, M. S.; Valtiner, M. Unraveling Hydrophobic Interactions at the Molecular Scale Using Force Spectroscopy and Molecular Dynamics Simulations. ACS Nano 2017, 11 (3).
  17. Robinson, M. K.*; Monroe, J. I.*; Shell, M. S. Are AMBER Force Fields and Implicit Solvation Models Additive? A Folding Study with a Balanced Peptide Test Set. J. Chem. Theory Comput. 2016, 12 (11).
  18. Monroe, J. I.; Shirts, M. R. Converging Free Energies of Binding in Cucurbit[7]Uril and Octa-Acid Host-Guest Systems from SAMPL4 Using Expanded Ensemble Simulations. Journal of Computer-Aided Molecular Design 2014, 28 (4).
  19. Monroe, J. I.; El-Nahal, W. G.; Shirts, M. R. Investigating the Mutation Resistance of Nonnucleoside Inhibitors of HIV-RT Using Multiple Microsecond Atomistic Simulations. Proteins 2013, No. May, 1–15.

*Indicates equal contributions