How do you build different crystal structures from the same nanoscale building block? That's the question we set out to answer in our latest work. We designed a DNA origami tetrahedron that can self-assemble into three distinct crystal lattices:diamond cubic, hexagonal diamond and the ice0.

🧪🧬 You can now play Minecraft with DNA nanotechnology! In our latest preprint we introduce DNA polycubes platform: A modeling driven system, where we use SAT-solvers+multiscale simulations to design 3D finite-size structures that assemble in high yield chemrxiv.org/doi/full/10....

As has become our yearly tradition with John Russo and his team at Sapienza University, there is always a Christmas-themed video based on current patchy self-assembly problem that we work on. The problems (and the videos!) get more sophisticated every year: www.youtube.com/watch?v=keZI...

SUPER SATaCLAUSE: Patchy Man is looking for a home

YouTube video by Sapienza soft matter group

youtube.com

We are happy to announce the oxDNA workshop 2026 at Arizona State University in February 16th - 20th . It will be a three day conference followed by a two-day hackathon of coding up new features in oxDNA and associated tools, as well as tutorials on its usage: sulcgroup.github.io/oxdnaworkshop/

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!

Memorial Sloan Kettering Cancer Center@mskcancercenter.bsky.social · 10mo ago

Dr. @bengrbm.bsky.social has tried to shed light on the innate immune system and how it affects cancer cells as they evolve. Now Dr. Greenbaum’s lab has been taking a deep dive into modeling viral mimicry, trying to understand how this could shape cancer cells’ development process. bit.ly/3VWadA8

🧪 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:⬇️

Repeats mimic pathogen-associated patterns across a vast evolutionary landscape

An emerging hallmark of disease is transcription of pathogen-associated molecular patterns from within the genome–known as viral mimicry. We propose a statistical physics framework to measure “selecti...

cell.com

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! 🧬

Erik Poppleton@floppleton.bsky.social · 2y ago

Are there any other scientists from molecular programming here? That's self-assembly, chemical computation, rational design et al. I made a mol pro feed which works like the Science (🧪) feed. Let me know, I add you to the list, you post with a 🧬 emoji. Let's assemble! bsky.app/profile/flop...

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

Molpigs@molpigs.bsky.social · last yr.

Podcast drop🧬! As part of the Molecular Programming Flightplan, we assembled a panel discussion on collaboration! The panel is now available as two podcasts, each with half the panel, and a bonus interview with @programmablematter.bsky.social. Links to all major feeds here: podcast.molpi.gs

🧪🧬 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🧵

Controlling DNA–RNA strand displacement kinetics with base distribution | PNAS

DNA–RNA hybrid strand displacement underpins the function of many natural and engineered systems. Understanding and controlling factors affecting D...

pnas.org

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

Aidin Lak@laklab-tubs.bsky.social · last yr.

Very excited to introduce mismatch-assisted toehold exchange (MATE) concept for the first time, our new magnetic diagnostics cascades: biorxiv.org/content/10.1... Excellent work by Rebecca, "Metrology4life" 2nd PhD student and Great collaboration with @petrsulc.bsky.social

🧬 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/...

How We Simulate DNA Origami

This tutorial provides a detailed step-by-step description on how to import DNA origami designs into the oxDNA model and characterize the origami's properties (such as equilibrium shape and flexibili...

onlinelibrary.wiley.com

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...

Ceny Neuron 2024: Seznamte se s letošními laureáty | Nadace Neuron

Věda je plná emocí a práce vědce představuje rébus, hru, touhu po poznání, vášeň, radost i lásku. Prozkoumejte krásu těchto emocí prostřednictvím laureátů Ceny Neuron.

nadaceneuron.cz

🧪🧬 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

Automating Blueprints for the Assembly of Colloidal Quasicrystal Clusters

One of the frontiers of nanotechnology is advancing beyond the periodic self-assembly of materials. Icosahedral quasicrystals, aperiodic in all directions, represent one of the most challenging target...

pubs.acs.org

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...

SATa CLAUSE: When magic snow falls, a enchanted meadow blossoms

YouTube video by Sapienza soft matter group

youtube.com

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...

Starter packs

BIOLOGY General Science community https://go.bsky.app/HVYAMEA Research Institutions in Life Sciences https://go.bsky.app/LxXpcvJ LGBTQIA+ in STEM https://go.bsky.app/BFc4wgf LGBTQIA+ in STEM 2 h...

docs.google.com

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

Elisa Franco@francolab.bsky.social · 2y ago

To accelerate the X-odus, I created a DNA & RNA nanotech starter pack :) Comment if you want to be added! go.bsky.app/7LUeJ61

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.

Combination of Coevolutionary Information and Supervised Learning Enables Generation of Cyclic Peptide Inhibitors with Enhanced Potency from a Small Data Set

Computational generation of cyclic peptide inhibitors using machine learning models requires large size training data sets often difficult to generate experimentally. Here we demonstrated that sequent...

pubs.acs.org

🧪 🧬 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...

Evolving to find optimizations humans miss: using evolutionary computation to improve GPU code for bioinformatics applications | ACM Transactions on Evolutionary Learning and Optimization

GPUs are used in many settings to accelerate large-scale scientific computation, including simulation, computational biology, and molecular dynamics. However, optimizing codes to run efficiently on GP...

doi.org

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...

Nucleic acid junctions and lattices

It is possible to generate sequences of oligomeric nucleic acids which will preferentially associate to form migrationally immobile junctions, rather …

sciencedirect.com

Molpigs@molpigs.bsky.social · 2y ago

We've organized two reading groups on classic papers in molecular programming: - A celebration of the late Ned Seeman, the founder of DNA nanotechnology - Foundations of DNA computing Let's talk about some of the great papers we've read! Each discussion will start as a quote of this post. 🧬