Erik Poppleton
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floppleton.bsky.social
Erik Poppleton
@floppleton.bsky.social
1K followers 930 following 750 posts
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.
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floppleton.bsky.social
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...
Reposted by Erik Poppleton
jaeseunghahn.bsky.social
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/...
January 16, 2026 at 12:16 PM
floppleton.bsky.social
Developments in one of the long-running questions in DNA origami diagnostics/therapeutics: how folded is your structure after exposure to biology 🧬
bjornhogberg.bsky.social Björn Högberg @bjornhogberg.bsky.social · 1d
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
Reposted by Erik Poppleton
nathanieldhess.bsky.social
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)
January 14, 2026 at 9:10 PM
Reposted by Erik Poppleton
melaniemitchell.bsky.social
My latest on Substack -- a write-up of the talk I gave at NeurIPS in December.

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
floppleton.bsky.social
Important thread for people who don’t know about/use Bluesky’s powerful feed curation features:
drsurekhadavies.bsky.social Dr Surekha Davies, Historical Monster Consultant (she/her) @drsurekhadavies.bsky.social · 5d
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/
Alt: Screenshot of the Bluesky homepage described in the thread.
January 12, 2026 at 4:30 PM
floppleton.bsky.social
Excellent discussion on funding, bureaucracy, and the economics of basic research!
kawillis.bsky.social Kris Willis @kawillis.bsky.social · 7d
“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...
What’s Wrong with NIH Grants?
“Science is fundamentally different than remodeling a kitchen”
www.statecraft.pub
January 10, 2026 at 6:44 AM
floppleton.bsky.social
New year, new benchmark structure prediction tool! 🧬
chaitjo.bsky.social Chaitanya K. Joshi @chaitjo.bsky.social · 15d
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)
January 4, 2026 at 2:49 AM
Reposted by Erik Poppleton
chaitjo.bsky.social
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)
January 2, 2026 at 1:19 AM
Reposted by Erik Poppleton
floppleton.bsky.social
Is the AotY list mostly the big melodeath releases from this year? Yeah, call me basic. Was it a good year for melodeath? Also yes.

Can’t get the texture of the guitar on the Amorphis album out of my head.
#metalSky #AotY2025
Top-12 album list: Återstod - ÅTERSTOD + Meißel split Amorphis - Borderland Blackbraid - Blackbraid III Shadow of Intent - Imperium Delirium Allegaeon - The Ossuary Lens The Halo Effect - March Of The Unheard Grief Ritual - Collapse Aephanemer - Utopie Lorna Shore - I Feel The Everblack Festering Within Me Rivers of Nihil - Rivers of Nihil Eluveitie - Anv Unreqvited - A Pathway to the Moon
December 28, 2025 at 7:43 PM
floppleton.bsky.social
Is the AotY list mostly the big melodeath releases from this year? Yeah, call me basic. Was it a good year for melodeath? Also yes.

Can’t get the texture of the guitar on the Amorphis album out of my head.
#metalSky #AotY2025
Top-12 album list: Återstod - ÅTERSTOD + Meißel split Amorphis - Borderland Blackbraid - Blackbraid III Shadow of Intent - Imperium Delirium Allegaeon - The Ossuary Lens The Halo Effect - March Of The Unheard Grief Ritual - Collapse Aephanemer - Utopie Lorna Shore - I Feel The Everblack Festering Within Me Rivers of Nihil - Rivers of Nihil Eluveitie - Anv Unreqvited - A Pathway to the Moon
December 28, 2025 at 7:43 PM
Reposted by Erik Poppleton
krishnanyamuna.bsky.social
And we found something chemically heretical:
Spatially organized pH gradients within single organelles. 8/n
December 17, 2025 at 12:46 AM
floppleton.bsky.social
Looking forward to the workshop and already have a long list of potential projects for the hackathon! 🧬
petrsulc.bsky.social Petr Šulc @petrsulc.bsky.social · Dec 14
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/
OxDNA Conference and Workshop 2026 | February 16-20
sulcgroup.github.io
December 14, 2025 at 10:02 AM
Reposted by Erik Poppleton
kgoepfrich.bsky.social
New to RNA design? Please try pyFuRNAce! Looking forward to your feedback 🧬
December 7, 2025 at 4:39 PM
Reposted by Erik Poppleton
kgoepfrich.bsky.social
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
Reposted by Erik Poppleton
andrew.heiss.phd
Some closing thoughts for my students this semester on LLMs and learning #rstats datavizf25.classes.andrewheiss.com/news/2025-12...
Will you incorporate LLMs and AI prompting into the course in the future? No. Why won’t you incorporate LLMs and AI prompting into the course? These tools are useful for coding (see this for my personal take on this). However, they’re only useful if you know what you’re doing first. If you skip the learning-the-process-of-writing-code step and just copy/paste output from ChatGPT, you will not learn. You cannot learn. You cannot improve. You will not understand the code. In that post, it warns that you cannot use it as a beginner: …to use Databot effectively and safely, you still need the skills of a data scientist: background and domain knowledge, data analysis expertise, and coding ability. There is no LLM-based shortcut to those skills. You cannot LLM your way into domain knowledge, data analysis expertise, or coding ability. The only way to gain domain knowledge, data analysis expertise, and coding ability is to struggle. To get errors. To google those errors. To look over the documentation. To copy/paste your own code and adapt it for different purposes. To explore messy datasets. To struggle to clean those datasets. To spend an hour looking for a missing comma. This isn’t a form of programming hazing, like “I had to walk to school uphill both ways in the snow and now you must too.” It’s the actual process of learning and growing and developing and improving. You’ve gotta struggle. This Tumblr post puts it well (it’s about art specifically, but it applies to coding and data analysis too): Contrary to popular belief the biggest beginner’s roadblock to art isn’t even technical skill it’s frustration tolerance, especially in the age of social media. It hurts and the frustration is endless but you must build the frustration tolerance equivalent to a roach’s capacity to survive a nuclear explosion. That’s how you build on the technical skill. Throw that “won’t even start because I’m afraid it won’t be perfect” shit out the window. Just do it. Just start. Good luck. (The original post has disappeared, but here’s a reblog.) It’s hard, but struggling is the only way to learn anything. You might not enjoy code as much as Williams does (or I do), but there’s still value in maintaining codings skills as you improve and learn more. You don’t want your skills to atrophy. As I discuss here, when I do use LLMs for coding-related tasks, I purposely throw as much friction into the process as possible: To avoid falling into over-reliance on LLM-assisted code help, I add as much friction into my workflow as possible. I only use GitHub Copilot and Claude in the browser, not through the chat sidebar in Positron or Visual Studio Code. I treat the code it generates like random answers from StackOverflow or blog posts and generally rewrite it completely. I disable the inline LLM-based auto complete in text editors. For routine tasks like generating {roxygen2} documentation scaffolding for functions, I use the {chores} package, which requires a bunch of pointing and clicking to use. Even though I use Positron, I purposely do not use either Positron Assistant or Databot. I have them disabled. So in the end, for pedagogical reasons, I don’t foresee me incorporating LLMs into this class. I’m pedagogically opposed to it. I’m facing all sorts of external pressure to do it, but I’m resisting. You’ve got to learn first.
December 9, 2025 at 8:17 PM
Reposted by Erik Poppleton
qchengx1e3.bsky.social
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...
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 1, 2025 at 6:46 PM
Reposted by Erik Poppleton
colincarlson.bsky.social
"are you enjoying duo mobile" does a hamburger enjoy being made of quarks. does a fish enjoy linear time. does the mountain enjoy the first taste of a cup of hot chocolate when you get back to the ski lodge. your question means nothing to me. i couldn't enjoy duo mobile even if i tried
December 3, 2025 at 7:36 PM
floppleton.bsky.social
Enumerating possible pseudoknots that a sequence can form with nearest-neighbor models is an NP-hard problem. Even evaluating these structures is challenging, let alone designing them. So it’s great to see data-based models starting to crack the RNA structural design problem! 🧬🧪
chaitjo.bsky.social Chaitanya K. Joshi @chaitjo.bsky.social · Dec 3
Introducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀

📝: tinyurl.com/gRNAde-paper

Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
December 3, 2025 at 10:45 PM
floppleton.bsky.social
An early and authoritative drop on the AOTY lists! I’ve only listened to two of these, so time to see if they have rude words for my tentative list.
posttim.bsky.social Timothy™️ (Not Tim) @posttim.bsky.social · Dec 2
Here it is. The guide you need. The one list to rule them all. Gifted early. I’ll say more below. But: the main event. My 2025 AOTY list. Lovely stuff.
Der Weg einer Freiheit - Innern Pupil Slicer - Fleshwork Thormesis - Nevertheless Astodan - Dirges Ancst - Dominion An Abstract Illusion - The Sleeping City Pothamus - Abur Noctambulist - Noctambulist II: De Droom Mors Principium Est - Darkness Invisible Catharsis - Hope Against Hope Labyrinthus Stellarum - Rift in Reality Ursula - I Don't Like Anything
December 2, 2025 at 6:02 PM
floppleton.bsky.social
The latest from RNA-designer extraordinaire
@monari-luca.bsky.social is out in @natcomms.nature.com. We introduce PyFuRNAce.de, a design tool for RNA origami. It simplifies design with a rich motif library and automatic 2d/3d modeling and routing optimization 🧬

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 2, 2025 at 11:44 AM
Reposted by Erik Poppleton
paolocrosetto.bsky.social
Since AI slop is again all over Scientific Reports, a thread on the economics of grey-zone publishing.

Why does slop keep getting published? What does it mean for science? How can we stop this?

Background readings:
Understand the strain: tinyurl.com/2b6wxx5r
Stop the drain: tinyurl.com/3jfscscy
An obviously AI-generated figure with AI slop and fake text all over it, recently published in Scientific Reports.
November 30, 2025 at 11:10 AM
Reposted by Erik Poppleton
The long-awaited Dipids paper is finally out www.nature.com/articles/s41...! Check out the largest containers ever self-assembled from DNA origami🧬, and the amazing person and story behind it www.linkedin.com/feed/update/... Congrats to Christoph🎉 and thanks for letting me be part of this journey🥹!
Self-assembled cell-scale containers made from DNA origami membranes - Nature Materials
Through the programmable self-assembly of lipid-inspired radially symmetric DNA, porous molecular membranes and cell-sized compartments are formed with applications in bottom-up biology and soft robot...
www.nature.com
November 28, 2025 at 3:32 PM
floppleton.bsky.social
Ahhh, I love the smell of academic fraud in the morning.
erikangner.com Erik Angner @erikangner.com · Nov 27
"Runctitiononal features"? "Medical fymblal"? "1 Tol Line storee"? This gets worse the longer you look at it. But it's got to be good, because it was published in Nature Scientific Reports last week: www.nature.com/articles/s41... h/t @asa.tsbalans.se
Infographic with AI slop published in Nature Scientific Reports
November 27, 2025 at 9:36 PM
Reposted by Erik Poppleton
sltrib.com
Remember last year when we said we would drop The Tribune's paywall if we raised enough money to support the transition to free? About that… 😁
The Salt Lake Tribune will drop its paywall next year, CEO tells donors at NewsMakers gala
After years of requiring people to pay for online news content, The Tribune announced an upcoming change during its 2025 annual NewsMakers Gala.
www.sltrib.com
November 23, 2025 at 8:36 PM
floppleton.bsky.social
I think I’m gonna have to retract this meme I made… 🧬
Strong doge vs weak doge meme where the strong is labeled DNA saying “still readable after being in a dead mammoth for 1.6 million years” and the weak labeled RNA saying “oh no! Is that a hydroxide ion?”
November 20, 2025 at 10:41 PM