Hello and welcome back to the molpigs newsletter! Feel free to hang out at the molpigs Forum! All the past podcasts and tutorial can be found here. You can also now find our podcasts on Apple Podcasts, Spotify, Stitcher, TuneIn, and more (as well as manually in your favorite podcast client with our RSS feed)! Enjoy!

1. Podcast with Erik Poppleton and useful tools
2. New events coming–Chat with Prof. Kate Adamala!
3. Interested in helping out, sharing something interesting, or have an idea for something we could do?

1. Podcast with Erik Poppleton and useful tools, tutorials

We chatted with Erik Poppleton about oxDNA and his experience as being both a wet lab researcher and a software developer. Check it out here!

Erik Poppleton’s research is focused on how to use computational modeling to inform the 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 degradation and distribution in deep soil.

Erik and the oxDNA team also shared the following resources about oxDNA. (If you find these tools useful, please remember to cite them! The citations for each tool can be found in its documentation.)

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: https://oxdna.org/ (oxdna.org paper coming soon!)
• 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

2. New events coming–Chat with Prof. Kate Adamala!

We will soon talk with Prof. Kate Adamala!

Kate Adamala is a biochemist building synthetic cells. Her research aims at understanding chemical principles of biology, using artificial cells to create new tools for bioengineering, drug development, and basic research. The interests of her lab span questions from the origin and earliest evolution of life, using synthetic biology to colonize space, to the future of biotechnology and medicine.

She received a MSc in chemistry from the University of Warsaw, Poland, studying synthetic organic chemistry. In grad school, she worked with professor Pier Luigi Luisi from University Roma Tre and Jack Szostak from Harvard University. She studied RNA biophysics, small peptide catalysis and liposome dynamics, in an effort to build a chemical system capable of Darwinian evolution. Kate’s postdoctoral work in Ed Boyden’s Synthetic Neurobiology group at MIT focused on developing novel methods for multiplex control and readout of mammalian cells. Her full first name spells Katarzyna; she goes by Kate for the benefit of friends speaking less consonant-enriched languages.

If you have any questions about Kate or the work her group is doing, please send them here!

3. Interested in helping out, sharing something interesting, or have an idea for something we could do?

If so, please get in touch with us! Shoot us an email at contributions AT <this domain>, there are loads of ways you can get involved, and many we haven’t even thought of, but here’s a few ideas of what you could do:

• Be a guest on our podcast series: you can talk about anything vaguely related to the field, whether it’s comments on life as a student/researcher, some thoughts you’ve had about the field, some interesting work you want to share, or if you want to speak out about something like mental health, this is the perfect place to do it!
• Present a poster-podcast! This is something we’re very excited to try out, and we hope you feel the same: the idea is to try to explain something (it doesn’t have to be your own work) within a 20-30 minute podcast, with the challenge that all reference material needs to fit into a poster format.
• Want to advertise something on our newsletter? Perhaps you’ve just passed your thesis defence, or are looking for a team for a hackathon, or have a job posting to share, or have just written a blog post you think might be of interest; whatever the case we’d love to help you share the good news!
• We’re also open to more conventional seminar-esque things like talks or journal clubs.

We’re looking forward to getting to hear from you, and getting to know you better!