Erik Poppleton
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poppleton.phd
Erik Poppleton
@poppleton.phd
1.1K followers 1K following 840 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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poppleton.phd
There is only one song powerful enough to make an entire generation start singing with just a single note.

(Blank video, sound up)
May 11, 2026 at 11:21 AM
poppleton.phd
I feel like @aptshadow.bsky.social was binging on Creature posts from @lize.bsky.social while writing the Bug Section of Children of Strife.
Highlight of text from Children of Strife by Adrian Tchaikovsky "This is a good batch," Pil said approvingly. He picked out one specimen with the drone cams. It must have been over a mètre long, with legs twice that-just ridiculously unwieldy legs. It thrashed through the slick foliage as though trying to swim. Its head-or the front end of it, as it didn't have a distinct head section-was studded with clusters of eyes, and half a dozen weaving antennae. These fondled everything in front of it suggestively every time it stopped. Kott looked at it and wondered why it didn't just die of utter horror at its own existence. But, however ill, malformed and generally wrong every generation of bugs down there looked, she couldn't deny them their zest for their horrible, misshapen life.
May 10, 2026 at 3:52 PM
poppleton.phd
I will never get Mambo no. 6 out of my head
Tweet from @corylockwood saying “Someday Lou Bega's gonna drop Mambo number 6 and I hope it kills every single one of us.”
April 2, 2026 at 7:34 AM
poppleton.phd
I ran over 50 µs of molecular dynamics simulations to characterize the dynamics and geometric constraints introduced by the triplexes! Simulations revealed that there is a tradeoff between occupancy in the three triplex sites, and that generally not all of them can be satisfied at the same time.
Analysis of simulation data showing the occupancy of each of the triplex motifs and how it correlates with the angle between the joined helices. Generally, peaks in the triplet probabilities for each triplet corresponds to a discrete peak in the angle distribution.
April 1, 2026 at 9:50 AM
poppleton.phd
And it works! AFM imaging of αKL-containing tiles shows assembly of unbounded stacks of tiles mediated by the loops! We tested 4 different sequence variants based on different biological 23S rRNA sequences and a negative control where U nucleotides replaced the triplex-forming purines.
A gallery of AFM images showing how changing the sequence of the flanking bases affects yields of nanoscale tile assemblies mediated by ails. Changing the A-minor bases to Gs maintains high yields of structures, and any base can be inserted as a spacer between the 4-base loop and the A-minor triplex. Disrupting triplexes by inserting Us leads to poor yield. Additionally, yield of assemblies is dependent on multiple aKLs, revealing the cooperatively of multiple, weak interactions.
April 1, 2026 at 9:50 AM
poppleton.phd
"But that looks so easy!" you say. "Just design a few unpaired bases!" Not so fast! Those bases must be pre-organized into a loop without disrupting the host helix. Thankfully, lead author and RNA wizard Cody Geary developed a nature-inspired triplex strategy which satisfies all the requirements. 🧬
Motif composition of the aKL: Most of the motif is based on the alphaPK from the 23S rRNA subunit, which has a single A-minor triplet and a three-base loop. Cody extended that motif with a motif based on the P4-P6 Group 1 Intron structure from Tetrahymena, which stabilizes a crossover with a G-major and two A-minor triplets. By extending the loop by 1 additional base and modifying the flanking sequences, we generated the aKL, which should be a 4-base loop stabilized by neighboring triplexes.
April 1, 2026 at 9:50 AM
poppleton.phd
Why do we need new motifs? The structure of nucleic acids limits the ways molecular designers can connect helices! When routing a single stranded origami, there's no good way to make sideways connections. The αKL solves this problem by looping out a 4-base sequence, which joins helices side-by-side.
The library of existing single-stranded connectors. 180-degree and 120-degree kissing loops connect two strands loop-to-loop. Branched kissing loops can branch a third strand from a 180-degree kissing loop at a 90-degree angle, but that forces any connections away from the connection because the bKL sequence needs to be long enough to be stable. Paranemic crossovers (PX) can be used to connect helices side-by-side, however they require complete crossover of the strand. The aKL joins neighboring helices by a short loop producing from the side of the helix.
April 1, 2026 at 9:50 AM
poppleton.phd
In addition to carrying genetic data, DNA and RNA can also be designed to fold into 'molecular breadboards' with nanometer addressability. To enable tightly-packed RNA origami, we developed a new motif, the αKL, which we're excited to share in our preprint!🧬🧪 1/🧵
www.biorxiv.org/content/10.6...
Scientific diagram showing the alphaKL. Left panels shows various atomic force microscope images of structures built using the motif, while the right panel shows a computer rendering of the motif.
April 1, 2026 at 9:50 AM
poppleton.phd
The plot thickens in the sponges-vs-ctenophores-as-animal-outgroup drama…
Screenshot of a Science Magazine headline announcing the retraction of “Integrative phylogenetic positions sponges at the root of the animal tree”
February 6, 2026 at 9:37 AM
poppleton.phd
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
poppleton.phd
Edit of the @dril tweet “turning a big dial taht says "Racism" on it and constantly looking back at the audience for approval like a contestant on the price is right” except racism is crossed out and replaced with worm.
December 16, 2025 at 9:13 PM
poppleton.phd
98% is apparently a very wide percentile in the distribution…
Duolingo year in review showing 36537 XP is also 98%
December 2, 2025 at 5:25 PM
poppleton.phd
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
poppleton.phd
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
poppleton.phd
Why does this keep happening??
Screenshot of a Bluesky post containing a screenshot of a Reddit post saying “The Hatman does NOT respect gender pronouns past 450mg” in a quote post of Melania Trump looming in a hat.
September 17, 2025 at 10:19 PM
poppleton.phd
This is just... not true? His thesis was on sequences which resemble miRNA in the HIV genome which affect CD4 expression. It's an impressive thesis, especially from a globetrotting rockstar. But neither it, nor the associated paper is highly cited, let alone by anything to do with vaccines. 🧪
Screenshot from Google Scholar showing Bryan "Dexter" Holland's publications. The paper has been cited 34 times and the thesis 4 times.
August 1, 2025 at 5:46 PM
poppleton.phd
It should be obvious from the title, but the first 30 pages introduced baroque styles with some historical tales, some deeper cuts from Escher’s catalogue, and the historical/mathematical context of Gödel’s Incompleteness Theorem. Then dropped some AI musings which are still relevant today.
Page 26 from GEB which reads in part: “By the early 1950's, mechanized intelligence seemed a mere stone's throw away; and yet, for each barrier crossed, there always cropped up some new barrier to the actual creation of a genuine thinking machine. Was there some deep reason for this goal's mysterious recession? No one knows where the borderline between non-intelligent behavior and intelligent behavior lies; in fact, to suggest that a sharp borderline exists is probably silly. But essential abilities for intelligence are certainly: to respond to situations very flexibly; to take advantage of fortuitous circumstances; to make sense out of ambiguous or contradictory messages; to recognize the relative importance of different elements of a situation; to find similarities between situations despite differences which may separate them; to draw distinctions between situations despite similarities which may link them; to synthesize new concepts by taking old concepts and putting them together in new ways; to come up with ideas which are novel. Here one runs up against a seeming paradox. Computers by their very nature are the most inflexible, desireless, rule-following of beasts. Fast though they may be, they are nonetheless the epitome of unconsciousness. How, then, can intelligent behavior be programmed? Isn't this the most blatant of contradictions in terms? One of the major theses of this book is that it is not a contradiction at all. One of the major purposes of this book is to urge each reader to confront the apparent contradiction head on, to savor it, to turn it over, to take it apart, to wallow in it, so that in the end the reader might emerge with new insights into the seemingly unbreachable gulf between the formal and the informal, the animate and the inanimate, the flexible and the inflexible.”
June 15, 2025 at 2:03 PM
poppleton.phd
They really hid it in Fig S28-i… looks like a 500-minute doubling time, compared with 200-minute for the parent strain. Also much lower maximum OD600. 🧪
A plot showing growth of the first version of Syn57, which is essentially a flat line (“near unculturable in liquid), vs the second version which has a 500 minute doubling time and saturates around 0.6 OD600. A plot which contains the growth curve of the parent strain which has about a 200 minute doubling time and a maximum OD600 around 1.4
May 2, 2025 at 11:54 PM
poppleton.phd
Wow, this one from @cnn.com might be the worst political graphic I’ve ever seen.
1. Party colors are very important in German politics (they often just call CDU “blacks”). You can’t just choose random colors.
2. “22.6% Others” hides two of the big stories: the collapse of FDP and the gains by Linke.
February 24, 2025 at 3:01 PM
poppleton.phd
I bow down to the great Bossett. But also, can anybody explain why Echidna+Quasar had such a low score?? I tried googling the combination but got nothing.
The result of a word association game where you try to get as far apart as possible the words used were Ontology, Camisole, Carburetor, Echidna, Quasi, Melancholy, and Coriander. This gave a score of 94.31 which was higher than 99.92% of people.
February 11, 2025 at 11:44 PM
poppleton.phd
I think I figured out why California can’t build its high-speed rail system! New ETA: 2070
A screenshot from Wikipedia saying: “The California High-Speed Rail Authority's (CHSRA) board approved on 15 November 2017 an early train operator contract with DB Engineering & Consulting USA.[9] The firm is the U.S. arm of Deutsche Bahn AG. As early train operator, DB Engineering & Consulting will assist CHSRA with planning, designing and implementing the state's high-speed rail program.”
February 1, 2025 at 11:17 AM
poppleton.phd
We made the oxView export so we could 3D print structures. The Molecular Nodes visualization is going to be much more flexible as far as blender styling and is also able to load trajectories. Here are some tiny resin prints of Holliday junctions I made for an outreach project.
Tiny resin 3D prints of Holliday junctions, an X-shaped structure made of helical DNA molecules
January 24, 2025 at 1:00 PM
poppleton.phd
This was the year where things I wasn’t expecting absolutely blew me away and much of what I was excited for was meh (except Time II, that slapped). Here’s to more surprises in 2025!

#metalsky #metalsky2024 #AOTY
The Body & Dis Fig - Orchards of a Futile Heaven The album cover shows a mushroom-shaped cloud of fireballs raining from the sky. Linkin Park - From Zero The album cover is an abstract image of pinks and grays that looks like an oil slick. Dvne - Voidkind The album art shows a giant figure clad in red robes with gold filigree, with another figure in white which is also an opening in the chest of the larger figure. A crowd of people enter the smaller figure and there are far too many arms. Thy Shining Curse - Theurgia The art shows two hooded, metal-faced figures facing each other holding skulls.
December 31, 2024 at 7:07 PM
poppleton.phd
Assuming that unpaired scaffolds are actually unpaired is a poor assumption! This is the same conclusion we came to in the Leaf-Spring Nanoengine paper, where a part of the spring, designed to be single-stranded, formed hairpins which stabilized the closed state. 🧬

www.nature.com/articles/s41...
Screenshot of text from a scientific paper: Dynamic reconfiguration was then explored for 2D and 3D voxel shapes (Fig. 4). Similarly to monomers (Fig. 2E), intramonomer interfaces on “vertex” voxels were switched between flexible and rigid states by addition of invader or connector strands. The length of the ssDNA scaffold tether was found to affect yields of possible monomer geometries (fig. S45). The 354-nt tether has a theoretical maximum ssDNA contour length of ~240 nm, but in oxDNA simulations, the tether was predicted to have secondary structure (fig. S10). Experimentally, structures with tether spacings of 7 to 33 nm formed with high yields (Ndesigns = 7, 79 to 89%; figs. S137 and S138). Yields were lower for the 62-nm tether spacing but recovered after addition of short complementary strands to remove secondary structure from the scaffold, increasing the range of possible structural reconfigurations (fig. S46). The part about oxDNA simulations predicting secondary structure is highlighted.
December 2, 2024 at 12:28 PM
poppleton.phd
I finally got around to reading this and Fig 3e is so cute! 🧬
A part of a figure from a scientific paper showing a design schematic for a dinosaur assembled from 'DNA origami voxels'. The dinosaur was then functionalized with flourophores and imaged with DNA-PAINT, resulting in a super-resolution microscope image of blue dots outlining a very small dinosaur.
December 2, 2024 at 9:55 AM