Erik Poppleton
@floppleton.bsky.social
Postdoc working on RNA Nanotech & MD simulations @uniheidelberg.bsky.social & MPIP. GROMACS wrangler, oxDNA developer, @molpigs.bsky.social podcast host, and all around weird lil guy.
Has been known to post about music and neat bugs found in the woods.
Has been known to post about music and neat bugs found in the woods.
Pinned
Erik Poppleton
@floppleton.bsky.social
· Nov 11
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...
bsky.app/profile/flop...
Reposted by Erik Poppleton
Up to 15-fold improvement in protein labeling for DNA-PAINT 🧬🔬. We are excited to present our latest work published in @angewandtechemie.bsky.social!
onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com/doi/10.1002/...
Dynamic Binder Exchange Improves Protein Labeling Efficiency in DNA‐PAINT up to 15‐Fold
Dynamic Binder Exchange (DyBE) leverages transient binder–target interactions to enhance labeling efficiency by up to 15-fold in super-resolution microscopy. DyBE maps nanoscale receptor tyrosine kin...
onlinelibrary.wiley.com
February 7, 2026 at 8:52 AM
Up to 15-fold improvement in protein labeling for DNA-PAINT 🧬🔬. We are excited to present our latest work published in @angewandtechemie.bsky.social!
onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Erik Poppleton
🧪🧬 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....
chemrxiv.org/doi/full/10....
February 8, 2026 at 3:02 AM
🧪🧬 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....
chemrxiv.org/doi/full/10....
Challenge: be normal about Alex Hall
Difficulty: ImpossibHOWDOESHEALWAYSLANDSOCLEAN??? SHOW THESE EUROPEANS THAT THE GREATEST SNOW ON EARTH ALSO MEANS THE GREATEST FLIPS ON EARTH
Difficulty: ImpossibHOWDOESHEALWAYSLANDSOCLEAN??? SHOW THESE EUROPEANS THAT THE GREATEST SNOW ON EARTH ALSO MEANS THE GREATEST FLIPS ON EARTH
with the Olympics coming up, I cannot recommend enough just picking random sports and getting really into them at a moment's notice
did I know anything about women's foil before the last Olympics? I did not
did I become the world's biggest Lee Kiefer fan immediately? absolutely I did
did I know anything about women's foil before the last Olympics? I did not
did I become the world's biggest Lee Kiefer fan immediately? absolutely I did
February 7, 2026 at 2:51 PM
Challenge: be normal about Alex Hall
Difficulty: ImpossibHOWDOESHEALWAYSLANDSOCLEAN??? SHOW THESE EUROPEANS THAT THE GREATEST SNOW ON EARTH ALSO MEANS THE GREATEST FLIPS ON EARTH
Difficulty: ImpossibHOWDOESHEALWAYSLANDSOCLEAN??? SHOW THESE EUROPEANS THAT THE GREATEST SNOW ON EARTH ALSO MEANS THE GREATEST FLIPS ON EARTH
The plot thickens in the sponges-vs-ctenophores-as-animal-outgroup drama…
February 6, 2026 at 9:37 AM
The plot thickens in the sponges-vs-ctenophores-as-animal-outgroup drama…
This is an excellent article on the non-linearities in weaning ourselves off fossil fuels! As the number of extraction/refining/consumption points decrease, the system grows more susceptible to individual failures, which will cause problems unless proactively predicted and protected against.
New from @gruberte.bsky.social and I in @science.org: The energy transition is at risk, and energy models are missing the threat. Fossil energy networks from oil to coal to gas have minimum viable scales of operation, and those thresholds are closer than we think:
www.science.org/doi/epdf/10....
💡🔌
www.science.org/doi/epdf/10....
💡🔌
Fossil energy minimum viable scale
Unseen infrastructural threats to safety and decarbonization may arise as fossil energy systems are phased out
www.science.org
January 30, 2026 at 11:25 PM
This is an excellent article on the non-linearities in weaning ourselves off fossil fuels! As the number of extraction/refining/consumption points decrease, the system grows more susceptible to individual failures, which will cause problems unless proactively predicted and protected against.
Structures of mRNA come to life thanks to some innovative use of DNA-PAINT 🧬
I’m happy to share the main result of my PhD, which you can find on bioRxiv www.biorxiv.org/content/10.6.... If you are interested in learning about a new way to perform DNA-PAINT multiplexing, which we call Combi-PAINT, or if you are interested in the study of mRNA conformation, keep reading! 1/10
January 26, 2026 at 9:10 PM
Structures of mRNA come to life thanks to some innovative use of DNA-PAINT 🧬
Reposted by Erik Poppleton
Our paper on the mysterious Devonian organism Prototaxites has now finally been published! See the paper here (www.science.org/doi/10.1126/...) and our explainer thread below!
Prototaxites reconstruction by Matt Humpage
Prototaxites reconstruction by Matt Humpage
January 21, 2026 at 7:25 PM
Our paper on the mysterious Devonian organism Prototaxites has now finally been published! See the paper here (www.science.org/doi/10.1126/...) and our explainer thread below!
Prototaxites reconstruction by Matt Humpage
Prototaxites reconstruction by Matt Humpage
Neat paper! Boosting to the MP feed 🧬
Construction of complex and diverse DNA sequences using DNA three-way junctions
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Construction of complex and diverse DNA sequences using DNA three-way junctions - Nature
Sidewinder enables high-fidelity DNA assembly by separating the information that guides assembly from the final assembled sequence.
doi.org
January 22, 2026 at 1:20 PM
Neat paper! Boosting to the MP feed 🧬
Reposted by Erik Poppleton
Megan is, in addition to being a brilliant physicist, one of the most gifted communicators about complex topics in our field. Don’t miss our latest edition of the Molpigs podcast!
🧬
🧬
We just released the latest episode of the Molpigs podcast! This time with Megan Engel, a professor at the University of Calgary who is who uses machine learning to build better molecular models. 🧬
Links to the episode on all major feeds can be found on our website:
podcast.molpi.gs/media/engel-...
Links to the episode on all major feeds can be found on our website:
podcast.molpi.gs/media/engel-...
molpigs Podcast | Megan Engel: Harnessing Machine Learning to Build Better Molecular Models
Join us for a conversation with Professor Megan Engel from the University of Calgary about what it takes to build better physical models of molecules. Her work is inspired by the challenges faced by t...
podcast.molpi.gs
January 19, 2026 at 5:33 PM
Megan is, in addition to being a brilliant physicist, one of the most gifted communicators about complex topics in our field. Don’t miss our latest edition of the Molpigs podcast!
🧬
🧬
Megan is, in addition to being a brilliant physicist, one of the most gifted communicators about complex topics in our field. Don’t miss our latest edition of the Molpigs podcast!
🧬
🧬
We just released the latest episode of the Molpigs podcast! This time with Megan Engel, a professor at the University of Calgary who is who uses machine learning to build better molecular models. 🧬
Links to the episode on all major feeds can be found on our website:
podcast.molpi.gs/media/engel-...
Links to the episode on all major feeds can be found on our website:
podcast.molpi.gs/media/engel-...
molpigs Podcast | Megan Engel: Harnessing Machine Learning to Build Better Molecular Models
Join us for a conversation with Professor Megan Engel from the University of Calgary about what it takes to build better physical models of molecules. Her work is inspired by the challenges faced by t...
podcast.molpi.gs
January 19, 2026 at 5:33 PM
Megan is, in addition to being a brilliant physicist, one of the most gifted communicators about complex topics in our field. Don’t miss our latest edition of the Molpigs podcast!
🧬
🧬
An interesting discussion on English time-words in the 1600s that I don’t remember being covered in @englishhistpod.bsky.social
Had an intriguing editorial discussion recently: how did people in the past talk about 'minutes' when they didn't have watches or standardised times? How does that affect your thinking?
Come down an Elizabethan/Jacobean rabbit hole with me.
1/
Come down an Elizabethan/Jacobean rabbit hole with me.
1/
January 17, 2026 at 10:15 PM
An interesting discussion on English time-words in the 1600s that I don’t remember being covered in @englishhistpod.bsky.social
Reposted by Erik Poppleton
As an enthusiast of both DNA origami and phage, this work is so exciting to see! Check out this article about "Bacteriophage-Mimetic DNA Origami Needle" from the laboratory of Kurt Gothelf. I love the concept, idea, and execution! 🧬🦠💉
advanced.onlinelibrary.wiley.com/doi/10.1002/...
advanced.onlinelibrary.wiley.com/doi/10.1002/...
January 16, 2026 at 12:16 PM
As an enthusiast of both DNA origami and phage, this work is so exciting to see! Check out this article about "Bacteriophage-Mimetic DNA Origami Needle" from the laboratory of Kurt Gothelf. I love the concept, idea, and execution! 🧬🦠💉
advanced.onlinelibrary.wiley.com/doi/10.1002/...
advanced.onlinelibrary.wiley.com/doi/10.1002/...
Developments in one of the long-running questions in DNA origami diagnostics/therapeutics: how folded is your structure after exposure to biology 🧬
Our new paper is out! Tracking the stability of DNA origami in-vivo is typically done with fluorescence, but are they still attached to intact DNA nanostructures? Here we introduce PLASTIQ, a method to quantify the structure of DNA nanostructures using tiny blood samples, ligations and PCRs!
January 16, 2026 at 12:05 PM
Developments in one of the long-running questions in DNA origami diagnostics/therapeutics: how folded is your structure after exposure to biology 🧬
Reposted by Erik Poppleton
I am very excited to share our pre-print that was just released on the bioRxiv entitled "Biomolecular Condensates Dictate the Folding Landscape of Proteins" doi.org/10.64898/202...
Very grateful for @jerelleaj.bsky.social and the members of the Joseph Group for their support on this project! (1/4)
Very grateful for @jerelleaj.bsky.social and the members of the Joseph Group for their support on this project! (1/4)
January 14, 2026 at 9:10 PM
I am very excited to share our pre-print that was just released on the bioRxiv entitled "Biomolecular Condensates Dictate the Folding Landscape of Proteins" doi.org/10.64898/202...
Very grateful for @jerelleaj.bsky.social and the members of the Joseph Group for their support on this project! (1/4)
Very grateful for @jerelleaj.bsky.social and the members of the Joseph Group for their support on this project! (1/4)
Reposted by Erik Poppleton
My latest on Substack -- a write-up of the talk I gave at NeurIPS in December.
aiguide.substack.com/p/on-evaluat...
aiguide.substack.com/p/on-evaluat...
On Evaluating Cognitive Capabilities in Machines (and Other "Alien" Intelligences)
(Apologies for the length of this post, which means it gets cut off in the email version.
aiguide.substack.com
January 14, 2026 at 6:43 PM
My latest on Substack -- a write-up of the talk I gave at NeurIPS in December.
aiguide.substack.com/p/on-evaluat...
aiguide.substack.com/p/on-evaluat...
Important thread for people who don’t know about/use Bluesky’s powerful feed curation features:
Announcing Thread 1 of a series on how to design an interesting feed for yourself on Bluesky, and getting started with posting so that you aren't screaming into an empty void. I'll number these threads and tag them #BlueskyHacks.
HACK NUMBER 1: finding & pinning interesting feeds.
1/
HACK NUMBER 1: finding & pinning interesting feeds.
1/
January 12, 2026 at 4:30 PM
Important thread for people who don’t know about/use Bluesky’s powerful feed curation features:
Excellent discussion on funding, bureaucracy, and the economics of basic research!
“The system of funding science is fundamentally broken. In some respects, it’s been an unmitigated disaster. It was a house of cards, and it’s not surprising that it’s now falling apart.”
-Mike Lauer, former director of extramural research 🧪
www.statecraft.pub/p/whats-wron...
-Mike Lauer, former director of extramural research 🧪
www.statecraft.pub/p/whats-wron...
What’s Wrong with NIH Grants?
“Science is fundamentally different than remodeling a kitchen”
www.statecraft.pub
January 10, 2026 at 6:44 AM
Excellent discussion on funding, bureaucracy, and the economics of basic research!
New year, new benchmark structure prediction tool! 🧬
Happy new year! A step change in RNA structure prediction, powered by top Kaggle-ers in a collaboration lead by Stanford University and NVIDIA
Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
January 4, 2026 at 2:49 AM
New year, new benchmark structure prediction tool! 🧬
Reposted by Erik Poppleton
Happy new year! A step change in RNA structure prediction, powered by top Kaggle-ers in a collaboration lead by Stanford University and NVIDIA
Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
January 2, 2026 at 1:19 AM
Happy new year! A step change in RNA structure prediction, powered by top Kaggle-ers in a collaboration lead by Stanford University and NVIDIA
Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
Reposted by Erik Poppleton
And we found something chemically heretical:
Spatially organized pH gradients within single organelles. 8/n
Spatially organized pH gradients within single organelles. 8/n
December 17, 2025 at 12:46 AM
And we found something chemically heretical:
Spatially organized pH gradients within single organelles. 8/n
Spatially organized pH gradients within single organelles. 8/n
Looking forward to the workshop and already have a long list of potential projects for the hackathon! 🧬
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/oxdnaworkshop/
OxDNA Conference and Workshop 2026 | February 16-20
sulcgroup.github.io
December 14, 2025 at 10:02 AM
Looking forward to the workshop and already have a long list of potential projects for the hackathon! 🧬
Reposted by Erik Poppleton
New to RNA design? Please try pyFuRNAce! Looking forward to your feedback 🧬
PyFuRNAce is an intuitive browser-based RNA design tool.
@monari-luca.bsky.social @kgoepfrich.bsky.social @uniheidelberg.bsky.social realized the largest cotranscriptionally folded RNA nanostructures to date. #BiotechNatureComms
www.nature.com/articles/s41...
@monari-luca.bsky.social @kgoepfrich.bsky.social @uniheidelberg.bsky.social realized the largest cotranscriptionally folded RNA nanostructures to date. #BiotechNatureComms
www.nature.com/articles/s41...
PyFuRNAce: an integrated design engine for RNA origami - Nature Communications
RNA nanotechnology creates structural and functional RNA architectures for biomedicine, synthetic biology and beyond. Here, the authors introduce pyFuRNAce, an intuitive browser-based RNA design tool....
www.nature.com
December 7, 2025 at 4:39 PM
New to RNA design? Please try pyFuRNAce! Looking forward to your feedback 🧬
Reposted by Erik Poppleton
We are recruiting a tenure track professor in the broader area of molecular biology @zmbh.uni-heidelberg.de at Heidelberg University! www.nature.com/naturecareer... Please share and apply!
Tenure Track Professorship (W1 with Tenure Track to W3) in “Molecular Biology" (f/m/d) - Heidelberg job with Universität Heidelberg | 12850668
The Center for Molecular Biology of Heidelberg University (ZMBH) and the Faculty of Biosciences invite applications for a Tenure Track Professors...
www.nature.com
December 9, 2025 at 6:11 PM
We are recruiting a tenure track professor in the broader area of molecular biology @zmbh.uni-heidelberg.de at Heidelberg University! www.nature.com/naturecareer... Please share and apply!