Erik Poppleton
2017-now: Biological Design PhD Program, School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
2013-2017: Bachelors of Science in Biology and Geology, College of Arts and Sciences, Tufts University, Medford, MA, USA
Erik Poppleton's research is focused on how to use computational modeling to inform design of molecular machines. As part of Petr Sulc's and Hao Yan's research groups, Erik uses coarse-grained molecular modeling software to identify structural features and rationally iterate designs of DNA and RNA nanostructures, which he can then test in the lab; as part of this, he also develops general-use analysis tools for oxDNA, and conversion tools to integrate the various design and simulation tools in the nucleic acid nanotechnology ecosystem.
His previous research has included using oxidizing agents to accelerate bioremediation of hydrocarbon-contaminated soils, using bacterial collagen-like molecules and synthetic peptides for biophysical characterization of the molecular basis for collagen structure, and using isotope tracking to characterize carbon degridation and distribution in deep soil.
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TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami. Journal of Computational Chemistry (2019). A. Suma, E. Poppleton, M. Matthies, P. Sulc, A. A. Louis, J. P. K. Doye, C. Micheletti, L. Rovigatti
- Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles. ACS Nano (2019). M. Matthies, N. P. Agarwal, E. Poppleton, F. M. Joshi, P. Sulc, T. L. Schmidt.
- Enzymatic Phosphorylation of Ser in a Type I Collagen Peptide. Biophysical Journal (2018). Y. Qiu, E. Poppleton, A Mekkat, H. Yu, S. Banerjee, S. E. Wiley, J. E. Dixon, D. L. Kaplan, Y. Lin, B. Brodsky.
- Root litter decomposition slows with soil depth. Soil Biology and Biochemistry (2018). C. E. H. Pries, B. N. Sulman, C. West, C. O'Niell, E. Poppleton, R. C. Porras, C. Castanha, B. Zhu, D. B. Wiedemier, M. S. Torn.
- Effects of flexibility of the α2 chain of type I collagen on collagenase cleavage. Journal of Structural Biology (2018). A. Mekkat, E. Poppleton, B. An, R. Visse, H. Nagase, D. L. Kaplan, B. Brodsky.