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Show Notes
In the third episode of our ‘Lab Pigs’ series, which highlights the research and journeys of early career researchers in our field, we talked with Erik Poppleton. Erik researches the use of computational modeling in informing the design of molecular machines. 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. We talked about his research, his experience writing academic software, and the relationship between geology and molecular programming.
Biography
Erik Poppleton’s research is focused on how to use computational modeling to inform the design of molecular machines. As part of Petr Šulc’s and Hao Yan’s research groups at the Biodesign Institute of Arizona State University, 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 degradation and distribution in deep soil.
Core Simulation Tools
- Main oxDNA documentation
- Current stable release (being retired soon)
- Bleeding edge release (has Python bindings!)
- The model is also available as part of LAMMPS, documentation can be found here
Useful tutorials
- A textbook chapter covering how to relax and simulate origamis
- A textbook chapter covering the details of molecular simulation
- Example input files
Useful tools
- TacoxDNA, converters from design software to oxDNA
- oxView, a visualizer and editor for oxDNA
- oxView documentation
- oxdna_analysis_tools, a library of python scripts for basic simulation analysis
- oxdna.org, a public webserver for running simulations
- ox-serve, run interactive simulations in your web browser using a Google Colab GPU
Of course, if you find these tools useful, please remember to cite us! The citations for each tool can be found in its documentation (oxdna.org paper coming soon!)