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Petr Šulc @petrsulc.bsky.social · 01/10/2026

Happy to see our preprint on design of mRNA origami out! See summary of the results below:

Petr Šulc @petrsulc.bsky.social · 15/07/2026

Beyond fundamental self-assembly, these open-framework crystals are predicted to possess interesting optical properties, including photonic band gaps, making them promising candidates for future photonic materials. Preprint :https://chemrxiv.org/doi/full/10.26434/chemrxiv.15004426/v1

chemrxiv.org

Programmable selection of tetrahedral crystal lattices from a single nanoscale scaffold | ChemRxiv

Open tetrahedral lattices span diamond polymorphs, ice frameworks, zeolites and clathrates, and many are predicted to support complete photonic band gaps. Yet selectively assembling a chosen tetrahedr...

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Petr Šulc @petrsulc.bsky.social · 15/07/2026

We then experimentally validated all three crystal lattices using small-angle X-ray scattering and electron microscopy. This work demonstrates a new way of thinking about materials design.

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Petr Šulc @petrsulc.bsky.social · 15/07/2026

To make this possible, we developed a computational “competition aware” design pipeline that doesn't just search for interaction rules that build the desired crystal: it also actively eliminates competing structures that could form instead, using our #SATassembly method.

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Petr Šulc @petrsulc.bsky.social · 15/07/2026

These are highly coveted materials with promising applications in photonics, among other applications. The key insight is that we never change the shape of the building block. Instead, we simply reprogram the DNA "sticky ends" that determine which particles can bind to one another.

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Petr Šulc @petrsulc.bsky.social · 15/07/2026

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.

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Petr Šulc @petrsulc.bsky.social · 08/02/2026

The work has occupied a large fraction of my lab for past two years, included both huge modeling effort (by students/postdocs J Evans, M Sample S Roy, M Matthies) and experiments (H Liu and T Diep) We also worked iwth J Hihath and Y Ke's lab for help with carbon nanotube scaffolding

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Petr Šulc @petrsulc.bsky.social · 08/02/2026

Finally, the cubes can have multiple applications in nanoscale manufacturing. For example, they can be used to create 3D carbon nanotube circuits, as shown below where a cube is used to scaffold a 3D carbon nanotube junction for scaling up nanoelectronics manufacturing to 3D:

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Petr Šulc @petrsulc.bsky.social · 08/02/2026

and it can also be used to design dynamic reconfigurable structures, using "cube displacement" reaction, a 3D analogue of the often-used DNA strand displacement used for molecular computing:

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Petr Šulc @petrsulc.bsky.social · 08/02/2026

The platform can also be used to make crystals, such us the Sponge crystal:

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Petr Šulc @petrsulc.bsky.social · 08/02/2026

Our modeling platform finds "minimal assembly kit", the smallest number of cubic shaped DNA origami blocks, interacting with single-stranded overhangs, that are needed to reliably assemble into target prescribed 3D shape. To demonstrate of our platform we build Menger cube (1.9 GDa) fractal:

Menger cube in oxDNA (left) and experimental characterization with SEM (scale bar 100 nm)

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Petr Šulc @petrsulc.bsky.social · 08/02/2026

🧪🧬 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....

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Petr Šulc @petrsulc.bsky.social · 23/12/2025

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...

youtube.com

SUPER SATaCLAUSE: Patchy Man is looking for a home

YouTube video by Sapienza soft matter group

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Petr Šulc @petrsulc.bsky.social · 14/12/2025

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/

sulcgroup.github.io

OxDNA Conference and Workshop 2026 | February 16-20

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Reposted by Petr Šulc

Benjamin D. Greenbaum @bengrbm.bsky.social · 09/10/2025

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!

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Petr Šulc @petrsulc.bsky.social · 04/10/2025

While this work presents a first step towards 'decoding the repeatome' in human genome, it also presents a fast an accessible framework to assess stimulatory potential of transcripts coming from various experimental datasets.

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Petr Šulc @petrsulc.bsky.social · 04/10/2025

Complementary to this hypothesis, it is also possible that maintaining these patterns is also beneficial for the repeat families, as we argue in the case of the highly studied family of LINE-1 repeats, where high CpG content might help prevent their deleterious effect on organism's fitness.

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Petr Šulc @petrsulc.bsky.social · 04/10/2025

We argue that these repeats might have been co-opted to trigger innate immune system response upon translational dysregulation, such as in cancer cells. We checked experimentally that repeat transcripts that we marked as anomalous do bind to pattern recognition receptors of innate immune system.

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Petr Šulc @petrsulc.bsky.social · 04/10/2025

It allows us to quantify how anomalous given sequence is with respect to what one would expect from a typical transcript from human genomes. The two chosen motifs, CpG content and double-stranded regions,are hallmarks of RNA viruses and our immune system recognizes them as immunostimulatory targets.

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Petr Šulc @petrsulc.bsky.social · 04/10/2025

In our work, we instead focus on developing statistical mechanics-based framework to identify anomalous sequence (CpGf) and structure (long double-stranded segment) motifs in transcripts of these regions, which are known to be recognized by innate immune system receptors.

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Petr Šulc @petrsulc.bsky.social · 04/10/2025

A majority of our genome does not code for proteins nor has any established regulatory function. These regions are sometimes called 'junk DNA'. Their function, or lack of, is a very active topic of research.

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Petr Šulc @petrsulc.bsky.social · 04/10/2025

🧪 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:⬇️

cell.com

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...

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Reposted by Petr Šulc

Erik Poppleton @poppleton.phd · 25/08/2025

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! 🧬

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Petr Šulc @petrsulc.bsky.social · 17/07/2025

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

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Petr Šulc @petrsulc.bsky.social · 07/06/2025

The predictions were verified experimentally. Our results have implications for DNA/RNA molecular computing, design of DNA computing systems that interface with RNA triggers, and as we show in our presented model, it can also have implications for predicting the kinetics in CRISPR-based systems.

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Petr Šulc @petrsulc.bsky.social · 07/06/2025

It shows that just by permuting the distribution of bases in the duplex (while keeping AT / CG base pair number constant), the kinetics of the reaction can be altered by orders of magnitude, stemming from the details of differences in stability between hybrid and canonical bases in DNA/RNA systems.

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Petr Šulc @petrsulc.bsky.social · 07/06/2025

It is also of importance for biological systems like CRISPR-Cas9. In this collaboration, Eryk Ratajczyk supervised by Louis, Doye and Turberfield groups from Oxford, uses our new oxDNA-oxRNA hybrid coarse-grained model to study the strand displacement RNA invades DNA duplex.

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Petr Šulc @petrsulc.bsky.social · 07/06/2025

🧪🧬 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🧵

pnas.org

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...

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Petr Šulc @petrsulc.bsky.social · 26/04/2025

Great work by our student Navraj and Subhajit, building on top of the ground work of previous database by @floppleton.bsky.social and Michael Matthies

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Petr Šulc @petrsulc.bsky.social · 26/04/2025

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

nanobase.org

Nanobase

A repository for DNA/RNA nanotechnology

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Petr Šulc @petrsulc.bsky.social · 08/04/2025

4/4: Our crystal example thus provides a falsifiability test for classical nucleation theory, showing need for also taking into account structural fluctuations. Excellent work by Camilla Beneduce and Diogo Pinto from John Russo's group in Rome!

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Petr Šulc @petrsulc.bsky.social · 08/04/2025

3/4 However, we find that one of the three possible crystal phases is strongly preferred, due to the crystal lattice ordering being similar to the local ordering in the liquid phase.

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Petr Šulc @petrsulc.bsky.social · 08/04/2025

2/4: The assumptions of CNT rely on the free energy difference between bulk phase and the melt, and the interfacial free energy. In this work, we look at a two component system that forms a polymorph: it can nucleate into three different lattices with same interfacial and bulk free-energy.

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Petr Šulc @petrsulc.bsky.social · 08/04/2025

🧪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.

journals.aps.org

Falsifiability Test for Classical Nucleation Theory

Classical nucleation theory (CNT) is built upon the capillarity approximation, i.e., the assumption that the nucleation properties can be inferred from the bulk properties of the melt and the crystal....

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Petr Šulc @petrsulc.bsky.social · 24/03/2025

Thank you Ulrich, it was a pleasure visiting Heidelberg and meeting you. Many thanks to the amazing group of @kgoepfrich.bsky.social for hosting me!

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Petr Šulc @petrsulc.bsky.social · 17/03/2025

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

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Petr Šulc @petrsulc.bsky.social · 05/02/2025

If you change something in the candano file, it has to be loaded again from scratch into oxview. The scadnano tool has recently been expanded to also allow for visualization in embedded oxview window. Having an interactive cadnano-like interface inside oxView is currently on our TBD wishlist

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Petr Šulc @petrsulc.bsky.social · 05/02/2025

🧬 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/...

onlinelibrary.wiley.com

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...

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Petr Šulc @petrsulc.bsky.social · 20/01/2025

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...

nadaceneuron.cz

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.

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Petr Šulc @petrsulc.bsky.social · 22/12/2024

🧪🧬 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

pubs.acs.org

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...

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Petr Šulc @petrsulc.bsky.social · 13/12/2024

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...

youtube.com

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

YouTube video by Sapienza soft matter group

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Petr Šulc @petrsulc.bsky.social · 25/11/2024

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

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Petr Šulc @petrsulc.bsky.social · 23/11/2024

Hello, I am an associate professor in chemistry, would like to be added to the feed. Thank you! My homepage: www.public.asu.edu/~psulc/ Departmental profile: search.asu.edu/profile/3160... Google scholar: scholar.google.com/citations?hl... ORCID: orcid.org/0000-0003-15...

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Petr Šulc @petrsulc.bsky.social · 22/11/2024

🙋‍♂️ me too please

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Petr Šulc @petrsulc.bsky.social · 20/11/2024

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.

pubs.acs.org

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...

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