Ian Kenney | People | Beckstein Lab

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Ian Kenney
May 30

Ian Kenney

Ian is a Postdoctoral Research Scholar working on sustainable and interoperable software for the analysis of molecular simulations in the context of the MDAnalysis MDAKits ecosystem. He graduated with a PhD in Physics from ASU in November 2022. He obtained his BSc in Physics from ASU in 2017 and started his PhD in the same year. During his undergraduate degree he already worked in the Beckstein lab.

Graduate projects

  • quantitative studies of sodium/proton antiporters
  • workflow automation
  • solvation free energy prediction for small and drug-like molecules1.

Undergraduate work

As part of a NSF REU (under the umbrella of the SPIDAL project, which aims to provide Middleware and High Performance Analytics Libraries for Scalable Data Science) he set up and performed large scale molecular dynamics simulations of vesicles2,3. The input files and analysis code are freely available as the GitHub repository github.com/Becksteinlab/vesicle_library.

Ian is also working on methods and protocols to accurately calculate solvation energies of small and drug-like molecules1,4. Solvation free energies (such as the hydration energy) are important physical quantities that determine the partitioning of drugs between the membrane and intra- or extracellular space. Predicting solvation free energies via computer simulations aids in the design of drugs and also serves as a sensitive test for the quality of state-of-the art computer simulation approaches. In order to automate the process of calculating solvation free energies he took over the development of the MDPOW library.

He is interested in computational methods and as part of the outreach project BioXFEL BioVizSim Village: Experiencing Molecules he taught the basics of Linux to highschool students and freshmen undergraduates.

Publications

  1. a b I. M. Kenney, O. Beckstein, and B. I. Iorga. Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field. J Comput Aided Mol Des, 30 (2016) 1045–1058. doi: 10.1007/s10822-016-9949-5.
  2. a Kenney, Ian M.; Beckstein, Oliver (2015): Technical Report: SPIDAL Summer REU 2015: Biomolecular benchmark systems. figshare. doi: 10.6084/m9.figshare.1588804
  3. a R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102 – 109, Austin, TX, 2016. SciPy.
  4. a Selwa, E., Kenney, I.M., Beckstein, O., Iorga, B.I. SAMPL6: calculation of macroscopic pKa values from ab initio quantum mechanical free energies. J Comput Aided Mol Des, 32 (2018) 1203–1216. doi:10.1007/s10822-018-0138-6

Poster Presentations

  1. BioPhest Meeting 2016, University of Arizona, Tucson AZ, Poster: Calculation of small-molecule transfer free energies in various solvents, I.M. Kenney, B.I. Iorga, and O. Beckstein. April 16, 2016
  2. 2015 APS 4CS Meeting, Tempe, AZ, Poster: Towards an automated pipeline for solvation free energy calculations, I.M. Kenney, B.I. Iorga, and O. Beckstein, October 17, 2015.
  3. BioPhest Meeting 2015, Arizona State University, Tempe, AZ, Poster: Towards an automated pipeline for solvation free energy calculations, I.M. Kenney, B.I. Iorga, and O. Beckstein. May 2, 2015

Honors and Awards

  • NSF REU Studentship Summer 2015 (associated with the SPIDAL project)