Erik Poppleton
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floppleton.bsky.social
Erik Poppleton
@floppleton.bsky.social
1K followers 930 following 740 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
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 · 14d
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 · 25d
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 · 25d
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
floppleton.bsky.social
For the first time in the history of the universe, it wasn’t, in fact, DNS.
November 19, 2025 at 8:48 AM
floppleton.bsky.social
Pretty sure this would ban every lab I’ve ever been a part of from getting any US government funding…
laurahelmuth.bsky.social Laura Helmuth @laurahelmuth.bsky.social · Nov 14
"Prohibited activities would include joint research, co-authorship & advising a foreign graduate student or postdoc. The language is retroactive, meaning any interactions during the previous 5 years could make a scientist ineligible for future federal funding."
Dictators despise science.
U.S. Congress considers sweeping ban on Chinese collaborations
Researchers speak out against proposal that would bar funding for U.S. scientists working with Chinese partners or training Chinese students
www.science.org
November 14, 2025 at 6:32 PM
Reposted by Erik Poppleton
skwinnicki.bsky.social
Lots of folks captioning aurora photos like "for a few minutes we didn't think about politics"

guess I'm built different, every time I'm out trying to see night sky stuff I frequently think about how much light pollution is entirely preventable with just a tiny bit of regulation
Basic light pollution diagram showing four different streetlight set ups ranging from more light pollution on the left to less light pollution on the right. The most pollution option, labelled "very bad" is a street lamp with a round uncovered bulb on top, making a sphere of light in the air. The next option, labelled "bad" has a tiny cap on top, that limits the upward pollution a bit. The "better" option is mostly uncovered on top, limiting pollution above the streetlight. The final option, labelled "best" has a full shroud overtop, limiting the light to only below the streetlight, where it is needed for pedestrians and vehicles.
November 13, 2025 at 10:03 PM
Reposted by Erik Poppleton
floppleton.bsky.social
I recently pushed an update to the #oxDNA to PDB converter which makes the backmapped structures work out-of-the-box with all-atom simulation tools (the previous version didn't correctly remove the phosphate from the 5' end). Here's a 2-minute demo on how to prepare an oxDNA structure for GROMACS! 🧬
October 28, 2025 at 10:21 AM
Reposted by Erik Poppleton
mpoessel.de
Since hashtags are not really the same kind of thing here as they were on Twitter, I'll use this thread to collect any of the Ozymandias-related gems I come across in my timeline. If the name doesn't ring a bell, here is the original. 1/
Ozymandias
Near them, on the sand, Half sunk a shattered visage lies, whose frown, And wrinkled lip, and sneer of cold command, Tell that its sculptor well those passions read Which yet survive, stamped on these...
www.poetryfoundation.org
October 30, 2025 at 8:25 PM
Reposted by Erik Poppleton
siuzdak.bsky.social
In response to the multiple requests on how MRM generation works (without standards) from the MS/MS data, here it is step by step.
Analytical Chemistry (open access article)
doi.org/10.1021/acs....
November 1, 2025 at 1:59 PM
floppleton.bsky.social
I recently pushed an update to the #oxDNA to PDB converter which makes the backmapped structures work out-of-the-box with all-atom simulation tools (the previous version didn't correctly remove the phosphate from the 5' end). Here's a 2-minute demo on how to prepare an oxDNA structure for GROMACS! 🧬
October 28, 2025 at 10:21 AM
Reposted by Erik Poppleton
jeffvandermeer.bsky.social
try explaining the internet to monks on an island who inexplicably own ebook rights to an obscure translation and think you're pirates trying to steal their gold.
warrencook.bsky.social Warren Cook @warrencook.bsky.social · Oct 25
Sounds like editing an anthology would be worth it for those sorts of interactions alone.
October 25, 2025 at 6:32 PM
Reposted by Erik Poppleton
lize.bsky.social
Biolune is officially coming soon on Steam! 🌳🐌🌲🌘🐁🌲☀️

Play as a little robot fascinated by organic life. Terraform moons, cultivate ecosystems, and build a strange, beautiful home in an uncaring void. Wishlist now! ✨

store.steampowered.com/app/3070190/...
Biolune on Steam
An artificial life simulation about a robot cultivating ecosystems on the moons of a ruined planet. Grow fantastical plants and animals, facilitate their evolution, and gather resources while discover...
store.steampowered.com
October 21, 2025 at 6:21 PM
Reposted by Erik Poppleton
jbenmenachem.com
Wow. Harvard nuking its PhD programs

- Science PhD admissions reduced by more than 75%
- Arts & Humanities reduced by about 60%
- Social Sciences by 50–70%
- History by 60%
- Biology by 75%
- The German department will lose all PhD seats
- Sociology from six PhD students to zero
Harvard FAS Cuts Ph.D. Seats By More Than Half Across Next Two Admissions Cycles | News | The Harvard Crimson
The Faculty of Arts and Sciences slashed the number of Ph.D. student admissions slots for the Science division by more than 75 percent and for the Arts & Humanities division by about 60 percent for th...
www.thecrimson.com
October 21, 2025 at 5:11 PM