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.
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
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! 🧬
Why does this keep happening??
September 17, 2025 at 10:19 PM
Why does this keep happening??
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. 🧪
August 1, 2025 at 5:46 PM
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. 🧪
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.
June 15, 2025 at 2:03 PM
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.
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. 🧪
May 2, 2025 at 11:54 PM
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. 🧪
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.
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
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.
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.
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.
February 11, 2025 at 11:44 PM
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.
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.”](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:nukg7mqku65kfll7cqs6psgt/bafkreigjpukgvvzk63h6cs5mrxkn4yg5np24hgwvvdbe3nu4w3h3cpdxlm@jpeg)
February 1, 2025 at 11:17 AM
I think I figured out why California can’t build its high-speed rail system! New ETA: 2070
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.
January 24, 2025 at 1:00 PM
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.
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
#metalsky #metalsky2024 #AOTY
December 31, 2024 at 7:07 PM
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
#metalsky #metalsky2024 #AOTY
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...
www.nature.com/articles/s41...
December 2, 2024 at 12:28 PM
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...
www.nature.com/articles/s41...
I finally got around to reading this and Fig 3e is so cute! 🧬
December 2, 2024 at 9:55 AM
I finally got around to reading this and Fig 3e is so cute! 🧬
I’m not sure how you would make this more obvious, but this article is a letter to the editor, not a case report or review. Seeing lots of people saying this displays the rot of scientific publishing, and while publishing is rotten to the core, this isn’t it. 🧪
November 23, 2024 at 10:06 AM
I’m not sure how you would make this more obvious, but this article is a letter to the editor, not a case report or review. Seeing lots of people saying this displays the rot of scientific publishing, and while publishing is rotten to the core, this isn’t it. 🧪
This tidbit is amazing! I love these examples where computers start behaving more like biology instead of rigid logic machines.
Also there’s a typo at the top of page 3 in the description of MD, idk if it’s too late to fix for typesetting.
Also there’s a typo at the top of page 3 in the description of MD, idk if it’s too late to fix for typesetting.
November 17, 2024 at 7:46 AM
This tidbit is amazing! I love these examples where computers start behaving more like biology instead of rigid logic machines.
Also there’s a typo at the top of page 3 in the description of MD, idk if it’s too late to fix for typesetting.
Also there’s a typo at the top of page 3 in the description of MD, idk if it’s too late to fix for typesetting.
The Nature cover for those who haven't seen it
November 12, 2024 at 10:19 PM
The Nature cover for those who haven't seen it
I'm over 2 years late doing this, but somebody recently pointed out to me that I never updated the PyPi repository to say that oxDNA Analysis Tools was merged into the oxDNA repository. If you're still using the PyPi version, make sure you update to the new source! 🧬
November 11, 2024 at 6:04 PM
I'm over 2 years late doing this, but somebody recently pointed out to me that I never updated the PyPi repository to say that oxDNA Analysis Tools was merged into the oxDNA repository. If you're still using the PyPi version, make sure you update to the new source! 🧬
From the Wikipedia article on Brazil’s electricity grid, it’s almost all hydro. Pleasantly surprised to see wind and solar in the next two slots too!
en.m.wikipedia.org/wiki/Electri...
en.m.wikipedia.org/wiki/Electri...
November 10, 2024 at 11:22 AM
From the Wikipedia article on Brazil’s electricity grid, it’s almost all hydro. Pleasantly surprised to see wind and solar in the next two slots too!
en.m.wikipedia.org/wiki/Electri...
en.m.wikipedia.org/wiki/Electri...
Another, similar paper provided a fantastic euphemism for “killed by volcano” in science speak. (Some guts too).
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
November 3, 2024 at 11:09 PM
Another, similar paper provided a fantastic euphemism for “killed by volcano” in science speak. (Some guts too).
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
I chose pumpkin as my medium for the Japanese spider crab day of #invertober2024!
October 18, 2024 at 9:38 PM
I chose pumpkin as my medium for the Japanese spider crab day of #invertober2024!
Attention new Bsky users: as the butterfly site, you’re legally required to quote this skeet with an original bug pic you took yourself!
(don’t forget the alt text)
(don’t forget the alt text)
October 17, 2024 at 6:50 AM
Attention new Bsky users: as the butterfly site, you’re legally required to quote this skeet with an original bug pic you took yourself!
(don’t forget the alt text)
(don’t forget the alt text)
Does it matter…? Hmmm, let’s check Project 2025…
And this doesn’t even begin to cover the social effects that Trump’s presence has on science and the international perception of the US as a place that’s good to work.
And this doesn’t even begin to cover the social effects that Trump’s presence has on science and the international perception of the US as a place that’s good to work.
October 7, 2024 at 6:35 PM
Does it matter…? Hmmm, let’s check Project 2025…
And this doesn’t even begin to cover the social effects that Trump’s presence has on science and the international perception of the US as a place that’s good to work.
And this doesn’t even begin to cover the social effects that Trump’s presence has on science and the international perception of the US as a place that’s good to work.
My contribution to days 2-6 of #Invertober2024! I haven’t drawn in years and this is so much fun!
October 6, 2024 at 9:21 PM
My contribution to days 2-6 of #Invertober2024! I haven’t drawn in years and this is so much fun!
Anybody else getting permission denied errors when you try to get a BibTeX citation through Google Scholar? Seems to be happening to my colleagues as well... 🧪
October 1, 2024 at 2:59 PM
Anybody else getting permission denied errors when you try to get a BibTeX citation through Google Scholar? Seems to be happening to my colleagues as well... 🧪
Here, as a demonstration of this I asked Dall-E 3 to draw a hand, and it does fine. It has seen a bunch of images labeled "hand". But then if I ask it to draw an image of a gymnast doing pommel horse, the guy has 4 fingers on one hand and the other is in a silly place.
September 24, 2024 at 9:15 AM
Here, as a demonstration of this I asked Dall-E 3 to draw a hand, and it does fine. It has seen a bunch of images labeled "hand". But then if I ask it to draw an image of a gymnast doing pommel horse, the guy has 4 fingers on one hand and the other is in a silly place.
