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

Useful tutorials

Useful tools


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:

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