David Dotson
In June 2017, David started a new position in industry and left the Becksteinlab .
David is a former graduate student turned research software engineer. He develops and maintains the lab’s open-source software stack, much of which can be found on GitHub. He also works as the lead system administrator, keeping the lab’s hardware infrastructure running and working for everyone.
When not working on software, David also contributes to projects that involve membrane proteins: molecular machines that serve as gatekeepers to entry and exit of small molecules for the cell. Much is already known about many of these proteins, but the detailed molecular picture for how these dynamic structures perform their tasks remains an unsolved area of intense research.
David obtained his B.S. Physics from the Missouri University of Science and Technology. He began work in the lab in August 2012.
Beginning in 2013, he helped found The Sundial Project. Loosely affiliated with The Compass Project at UC – Berkeley, this program seeks to improve student retention in physics by matching new students with graduate and upper-undergraduate mentors. Sundial also serves as a platform for funding educational and social programs in an effort to build a tangible student community.
In 2015, David became a Software Carpentry instructor. Software Carpentry is a non-profit organization that puts on “bootcamps” at institutions all over the world to teach best practices for building and using software to do science efficiently and reproducibly.
David regularly shares his thoughts on science, software, and education on his blog.
Software projects David actively develops or contributes to can be found on his GitHub profile.
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
Presentations
SciPy 2016, Austin, TX, Talk: datreant: Persistent, Pythonic Trees for Heterogeneous Data D. L. Dotson, S. Seyler, M. Linke, R. Gowers, O. Beckstein, July 13, 2016.
Biophysical Society Annual Meeting 2016, Los Angeles, CA, Poster: High-Resolution Structures and Molecular Dynamics Simulations of Thermus Thermophilus NapA Reveal a Large-Scale Conformational Change For Ion Translocation, D. L. Dotson, M. Coincon, P. Uzdavinys, E. Nji, I. Winkelmann, S. Abdul-Hussein, A. D. Cameron, D. Drew, O. Beckstein, March 2, 2016.
SciPy 2015, Austin, TX, Poster: MDSynthesis: a Python package enabling data-driven molecular dynamics research, D. L. Dotson, O. Beckstein, July 8, 2015.
Biophysical Society Annual Meeting 2015, Baltimore, MD, Talk: Recent Structures and Molecular Dynamics Simulations Offer New Perspective on Na+/H+ Antiporters, D. L. Dotson, C. Lee, S. Yashiro, P. Uzdavinys, C. von Ballmoos, D. Drew, A. D. Cameron, O. Beckstein, February 9, 2015.
BioPhest Meeting 2014, University of Arizona, Tuscon, AZ, Talk: “Study of ion transport in sodium/proton antiporter proteins by molecular dynamics simulations,” D. L. Dotson, C. Lee, D. Drew, A. D. Cameron and O. Beckstein, April 26, 2014.
2013 APS 4CS Meeting, Denver, CO, Poster: Study of ion transport in sodium/proton antiporter proteins by molecular dynamics simulations, D. L. Dotson, C. Lee, D. Drew, A. D. Cameron, O. Beckstein, October 18, 2013.
BioPhest Meeting 2013, Arizona State University, Tempe, AZ, Talk: “Conformational changes in DNA with lesions,” D. L. Dotson and O. Beckstein, April 20, 2013.
Honors and Awards
Summer University Graduate Fellowship, Department of Physics, Arizona State University (2015)
Molecular Imaging Corporation Endowment Fellowship, Department of Physics, Arizona State University (2015)
Education Committee Travel Award, Biophysical Society Annual Meeting (2015)
Travel Award, American Physical Society – Four Corners Meeting (2013)
Graduate Assistance in Areas of National Need, Center for Biological Physics, Arizona State University (2011)
