Thank you @mskcancercenter.bsky.social for highlighting our work on #viralmimicry in our genome, its evolution, the selective forces on it, and its potential role in cancer.

A great years long collaborative effort with @petrsulc.bsky.social, @daniel-decarvalho.bsky.social, & many great colleagues!

🧪 In our new work (just published in Cell Genomics) with Benjamin Greenbaum , John LaCava, Daniel De Carvalho, PhD , Simona Cocco and Remi Monasson labs, we venture into the dark matter of human genome:
www.cell.com/cell-genomic...

🧵A shot thread summary below in comments:⬇️

On this first day of #DNA31, reminder for the mol pro community that I put together this feed which picks up the last 3 days of posts from our community! Enjoy the meeting! 🧬

A great effort to chart possible future paths for the molecular programming field

🧪🧬
Our new paper is just out in PNAS:
www.pnas.org/doi/10.1073/...

It is about nucleic acid strand displacement, which is a key reaction in molecular computation, and part of the success of the oxDNA model comes from the fact it can efficiently simulate this process.

1/4🧵

Just in time for #FNANO conference in Snowbird, UT, our updated and improved version of nanobase.org server is online. Just like the PDB database helped to share protein structures, we want to create a community resource for the DNA/RNA/protein nanotechnology design researchers to share their work

🧪In our new paper (journals.aps.org/prl/abstract...) in collaboration with Russo, Romano, Rovigatti and Sciortino groups in Rome / Venice, we look at Classical Nucleation Theory: a popular model of nucleation process, n is a key phenomena in self-assembly, self-organization and phase transitions.

Great collaboration with @laklab-tubs.bsky.social , simulations carried out by my student Josh Evans

🧬 A new tutorial article from our student Sarah, walking step by step through DNA origami simulation using oxDNA model, with the help of oxview.org and oxdna.org free tools. No prior experience assumed, and also accompanied by a video: youtu.be/5-rgMekX8gE
onlinelibrary.wiley.com/doi/10.1002/...

I am very grateful to Neuron Foundation, considered among the most prestigious awards for Czech Scientists, for awarding me Promising Scientist award in Physics yesterday at a ceremony in Prague. Many thanks goes to my family, collaborators and students: www.nadaceneuron.cz/novinky/ceny...

🧪🧬 New article with J Russo, D. Pinto and F. Sciortino out is @acspublications.bsky.social ACS Nano: pubs.acs.org/doi/10.1021/...
We use our #SAT Assembly method to design particles that assemble into 3D quasicrystal clusters, paving a way to their experimental realization with DNA nanostructures

In our Christmas tradition with John Russo's lab at Sapienza university of Rome, here is a Christmas-themed video highlighting a current research project based on our #SAT-assembly method, this time chiral crystals self-assembly (made by C. Beneduce): www.youtube.com/watch?v=0A7x...

Thank you so much to whoever put this very comprehensive list of #science Bsky starter packs together. This is just amazing: docs.google.com/document/d/1...

Are you working in DNA/RNA nanotech? Add your name to the list!

Our new article on combining ML with experiments to design peptide binders to a target proteins is just out in ACS Central Science: pubs.acs.org/doi/10.1021/... .
We show it is possible to iteratively combine training on small dataset and experiments to achieve higher binding affinity.

🧪 🧬 Can code be evolved? In our collaboration with S. Forrest group, we show that random "mutations" to the code, accepted if they pass unit tests, can actually find changes to CUDA version of oxDNA simulation tool for DNA nanotechnology that lead to a speedup:
doi.org/10.1145/3703...

First up, Ned Seeman's 1982 "Nucleic Acid Junctions and Lattices", published in the Journal of Theoretical Biology. This was the first paper to propose that through sequence design it might be possible to create precisely-defined crystal lattices out of DNA. 🧬

www.sciencedirect.com/science/arti...