about me

I’m David Dotson, a research software engineer for the Beckstein Lab in the Center for Biological Physics at Arizona State University. I specialize in developing software tools for answering biological questions with molecular dynamics simulations, and doing so with greater ease and speed. I am a Pythonista, Linux nerd, and a loud-and-proud advocate for the use of open source software in science.

Publications

Y. Huang, W. Chen, D.L. Dotson, O. Beckstein, and J. Shen. Mechanism of the pH-dependent activation of the sodium-proton antiporter NhaA. Nat. Commun. 7 (2016), 12940. doi: 10.1038/ncomms12940.

D.L. Dotson, S.L. Seyler, M. Linke, R.J. Gowers, and O. Beckstein. datreant: persistent, Pythonic trees for heterogeneous data. Proceedings of the 15th Python in Science Conference (2016), 51—61.

R.J. Gowers, M. Linke, J. Barnoud, T.J.E. Reddy, M.N. Melo, S.L. Seyler, J. Domanski, D.L. Dotson, S. Buchoux, I.M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. Proceedings of the 15th Python in Science Conference (2016), 98—105.

M. Coincon, P. Uzdavinys, E. Nji, D.L. Dotson, I. Winkelmann, S. Abdul-Hussein, A.D. Cameron, O. Beckstein, and D. Drew. Crystal structures reveal the molecular basis of ion-translocation in sodium/proton antiporters. Nature Struct. Mol. Biol. (2016). doi: 10.1038/nsmb.3164

C. Lee, S. Yashiro, D.L. Dotson, P. Uzdavinys, S. Iwata, M.S.P. Sansom, C. von Ballmoos, O. Beckstein, D. Drew, and A.D. Cameron. Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights. J. Gen. Physiol. 144 (2014), 529—544. doi: 10.1085/jgp.201411219

C. Lee, H.J. Kang, C. von Ballmoos, S. Newstead, P. Uzdavinys, D.L. Dotson, S. Iwata, O. Beckstein, A.D. Cameron, and D. Drew. A two-domain elevator mechanism for sodium/proton antiport. Nature 501 (2013), 573—577. doi: 10.1038/nature12484

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