For a current list of publications, see my Google Scholar page.

CV

26. R. L. Hayes, C. F. Nixon, S. Marqusee, and C. L. Brooks, III, “Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design,” Proceedings of the National Academy of Sciences of the United States of America 121, e2312029121 (2024).

25. M. T. Robo, R. L. Hayes, X. Ding, B. Pulawski, and J. Z. Vilseck, “Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling,” Nature Communications 14, 8515 (2023).

24. J. Z. Vilseck, L. F. Cervantes, R. L. Hayes, and C. L. Brooks, III, “Optimizing multisite λ-dynamics throughput with charge renormalization,” Journal of Chemical Information and Modeling 62, 1479–1488 (2022).

23. R. L. Hayes, J. Z. Vilseck, and C. L. Brooks, III, “Addressing intersite coupling unlocks large combinatorial chemical spaces for alchemical free energy methods,” Journal of Chemical Theory and Computation 18, 2114–2123 (2022).

22. R. L. Hayes, J. Buckner, and C. L. Brooks, III, “BLaDE: A basic lambda dynamics engine for GPU accelerated molecular dynamics free energy calculations,” Journal of Chemical Theory and Computation 17, 6799–6807 (2021).

21. J. Z. Vilseck, X. Ding, R. L. Hayes, and C. L. Brooks, III, “Generalizing the discrete Gibbs sampler-based λ-dynamics approach for multisite sampling of many ligands,” Journal of Chemical Theory and Computation 17, 3895–3907 (2021).

20. R. L. Hayes, and C. L. Brooks, III, “A Strategy for Proline and Glycine Mutations to Proteins with Alchemical Free Energy Calculations,” Journal of Computational Chemistry 42, 1088–1094 (2021).

19. E. P. Raman, T. J. Paul, R. L. Hayes, and C. L. Brooks, III, “Automated, accurate, and scalable relative protein-ligand binding free energy calculations using lambda dynamics,” Journal of Chemical Theory and Computation 16, 7895–7914 (2020).

18. T. J. Paul, J. Z. Vilseck, R. L. Hayes, and C. L. Brooks, III, “Exploring pH dependent host/guest binding affinities,” Journal of Physical Chemistry B 124, 6520–6528 (2020).

17. J. Z. Vilseck, N. Sohail, R. L. Hayes, and C. L. Brooks, III, “Overcoming challenging substituent perturbations with multisite λ-dynamics: A case study targeting β-secretase 1,” Journal of Physical Chemistry Letters 10, 4875–4880 (2019).

16. A. Mandic, R. L. Hayes, H. Lammert, R. R. Cheng, J. N. Onuchic, “Structure-based model of RNA pseudoknot captures magnesium-dependent folding thermodynamics,” Journal of Physical Chemistry B 123, 1505–1511 (2019).

15. J. R. Widom, Y. A. Nedialkov, V. Rai, R. L. Hayes, C. L. Brooks, III, I. A. Artsimovitch, N. G. Walter, “Ligand modulates cross-coupling between riboswitch folding and transcriptional pausing,” Molecular Cell 72, 541–552 (2018).

14. R. L. Hayes, J. Z. Vilseck, and C. L. Brooks, III, “Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme,” Protein Science 27, 1910–1922 (2018).

13. J. Z. Vilseck, K. A. Armacost, R. L. Hayes, G. B. Goh, and C. L. Brooks, III, “Predicting binding free energies in a large combinatorial chemical space using multisite λ dynamics,” Journal of Physical Chemistry Letters 9, 3328–3332 (2018).

12. X. Ding, R. L. Hayes, J. Z. Vilseck, M. K. Charles, and C. L. Brooks, III, “CDOCKER and λ-dynamics for prospective prediction in D3R grand challenge 2,” Journal of Computer Aided Molecular Design 32, 89–102 (2018).

11. X. Ding, J. Z. Vilseck, R. L. Hayes, and C. L. Brooks, III, “Gibbs sampler-based λ-dynamics and Rao-Blackwell estimator for alchemical free energy calculation,” Journal of Chemical Theory and Computation 13, 2501–2510 (2017).

10. R. L. Hayes, K. A. Armacost, J. Z. Vilseck, and C. L. Brooks, III, “Adaptive landscape flattening accelerates sampling of alchemical space in multisite λ dynamics,” Journal of Physical Chemistry B 121, 3626–3635 (2017).

9. S. Roy, H. Lammert, R. L. Hayes, B. Chen, R. LeBlanc, T. K. Dayie, J. N. Onuchic, and K. Y. Sanbonmatsu, “A magnesium-induced triplex pre-organizes the SAM-II riboswitch,” PLoS Computational Biology 13, e1005406 (2017).

8. R. R. Cheng, O. Nordesjö, R. L. Hayes, H. Levine, S. C. Flores, J. N. Onuchic, and F. Morcos, “Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes,” Molecular Biology and Evolution 33, 3054–3064 (2016).

7. J. K. Noel, M. Levi, M. Raghunathan, H. Lammert, R. L. Hayes, J. N. Onuchic, P. C. Whitford, “SMOG 2: A versatile software package for generating structure-based models,” PLoS Computational Biology 12, e1004794 (2016).

6. R. L. Hayes, J. K. Noel, A. Mandic, P. C. Whitford, K. Y. Sanbonmatsu, U. Mohanty, and J. N. Onuchic, “Generalized Manning condensation model captures the RNA ion atmosphere,” Physical Review Letters 114, 258105 (2015).

5. J. Zimmermann, R. Hayes, M. Basan, J. N. Onuchic, W.-J. Rappel, and H. Levine, “Intercellular stress reconstitution from traction force data,” Biophysical Journal 107, 548–554 (2014).

4. R. L. Hayes, J. K. Noel, P. C. Whitford, U. Mohanty, K. Y. Sanbonmatsu, and J. N. Onuchic, “Reduced model captures Mg²⁺-RNA interaction free energy of riboswitches,” Biophysical Journal 106, 1508–1519 (2014).

3. R. L. Hayes, J. K. Noel, U. Mohanty, P. C. Whitford, S. P. Hennelly, J. N. Onuchic, and K. Y. Sanbonmatsu, “Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch,” Journal of the American Chemical Society 134, 12043–12053 (2012).

2. L. S. Matthews, R. L. Hayes, M. S. Freed, and T. W. Hyde, “Formation of cosmic dust bunnies,” IEEE Transactions on Plasma Science 35, 260–265 (2007).

1. R. Hayes and M. Freed, “The fractal dimension and charging of preplanetary dust aggregates,” Journal of Young Investigators 16 (2007).