Specialties
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Biography
InterestsMy research interests are focused on the development and application of computational methods for studying the structure, function, folding, and dynamics of proteins. We work on problems involving the interplay between computational models in structural biology and experiments at different levels of resolution and different time scales from femtoseconds to seconds or longer. Using computational statistical mechanics as a framework, we study solvation effects in chemistry and biophysics, and develop methods and effective potentials for simulating these systems. Our recent work is focused on the development of novel free energy methods for modeling protein-ligand binding, allosteric conformational changes of proteins, and studying their energy and evolutionary landscapes.
Select PublicationsCavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals.
Zhang, Bin W., Nobuyuki Matubayasi, and Ronald M. Levy (2020). The Journal of Physical Chemistry B, X. DOI: 10.1021/acs.jpcb.0c02721. Mi3-{GPU}: {MCMC}-based inverse Ising inference on {GPUs} for protein covariation analysis. Haldane, Allan and Ronald M. Levy (2020). Computer Physics Communications, X, 107312. DOI: https://doi.org/10.1016/j.cpc.2020.107312. Insights into the energy landscapes of chromosome organization proteins from coevolutionary sequence variation and structural modeling. Levy, Ronald M. (2020). Proceedings of the National Academy of Sciences, 117(5), 201921727. DOI: 10.1073/pnas.1921727117. PMCID: PMC7007567. Epistasis and entrenchment of drug resistance in {HIV}-1 subtype B. Biswas, Avik, Allan Haldane, Eddy Arnold, and Ronald M Levy (2019). {eLife}, 8. DOI: 10.7554/eLife.50524. PMCID: PMC6783267. The Relationship Between Solvation Thermodynamics from IST and DFT Perspectives. Levy, Ronald M., Di Cui, Bin W. Zhang, and Nobuyuki Matubayasi. The Journal of Physical Chemistry B, 121(15), 3825-3841 (2017). DOI: 10.1021/acs.jpcb.6b12889. Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness. Levy, Ronald M., Allan Haldane, and William F. Flynn. Current Opinion in Structural Biology, 43, 55-62 (2017). DOI: 10.1016/j.sbi.2016.11.004. Inference of epistatic effects leading to entrenchment and drug resistance in HIV-1 protease. Flynn, William F., Allan Haldane, Bruce E. Torbett, and Ronald M. Levy. Molecular Biology and Evolution, 34(6), 129 (2017). DOI: 10.1093/molbev/msx095. |
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