Erik Poppleton

The molpigs Podcast

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, of the Biodesign Institute at Arizona State University. 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.

Core Simulation Tools
- Main oxDNA documentation: https://dna.physics.ox.ac.uk/index.php/Main_Page
- Current stable release (being retired soon): https://sourceforge.net/projects/oxdna/files/
- Bleeding edge release (has Python bindings!): https://github.com/lorenzo-rovigatti/oxDNA
- The model is also available as part of LAMMPS, documentation can be found here: https://lammps.sandia.gov/doc/Packages_details.html#pkg-user-cgdna

Useful tutorials
- A textbook chapter covering how to relax and simulate origamis: https://arxiv.org/pdf/2004.05052.pdf
- A textbook chapter covering the details of molecular simulation: https://www.public.asu.edu/~psulc/myimages/chapter.pdf
- Example input files: https://github.com/sulcgroup/oxdna_analysis_tools/tree/master/example_input_files

Useful tools
- TacoxDNA, converters from design software to oxDNA: http://tacoxdna.sissa.it/
- oxView, a visualizer and editor for oxDNA: https://sulcgroup.github.io/oxdna-viewer/
- oxView documentation: https://github.com/sulcgroup/oxdna-viewer
- oxdna_analysis_tools, a library of python scripts for basic simulation analysis: https://github.com/sulcgroup/oxdna_analysis_tools
- oxdna.org, a public webserver for running simulations: oxdna.org
- ox-serve, run interactive simulations in your web browser using a Google Colab GPU: https://colab.research.google.com/drive/1nFC9zy-wEwwl8vlJZAbQZZofavP4PXvL#scrollTo=C_8TB2t5gxDg

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!)

---
Find more information at the episode page here:
https://podcast.molpi.gs/media/poppleton-e-d83cc0825a805d2e/