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
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
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/
Reposted by Erik Poppleton
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....
Analytical Chemistry (open access article)
doi.org/10.1021/acs....
November 1, 2025 at 1:59 PM
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....
Analytical Chemistry (open access article)
doi.org/10.1021/acs....
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! 🧬
Reposted by Erik Poppleton
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.
Sounds like editing an anthology would be worth it for those sorts of interactions alone.
October 25, 2025 at 6:32 PM
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.
Reposted by Erik Poppleton
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/...
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
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/...
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/...
Reposted by Erik Poppleton
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
- 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
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
- 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
Reposted by Erik Poppleton
This is why we fund scientists to study things like oyster slobber even if you don’t think it sounds important
⚠️ Chinese researchers have invented bone glue that mimics how oysters stick to surfaces underwater.
The adhesive can reportedly repair orthopedic fractures in 2-3 minutes, even in blood-rich environments, and is bioabsorbable.
interestingengineering.com/science/chin...
The adhesive can reportedly repair orthopedic fractures in 2-3 minutes, even in blood-rich environments, and is bioabsorbable.
interestingengineering.com/science/chin...
China's oyster-inspired 'bone glue' bonds fractures in minutes
A new oyster-inspired Bone-02 adhesive can revolutionize bone repair without metal fasteners.
interestingengineering.com
September 30, 2025 at 10:35 PM
This is why we fund scientists to study things like oyster slobber even if you don’t think it sounds important
Some really nice fundamental biophysics of DNA base stacking 🧬!
Well, it's been a minute but we have a new preprint to share! Final project in our lab by @jibinpunnoose.bsky.social, investigating strand polarity in base stacking. We measured experimentally with centrifuge force microscope and computationally with MD.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
September 26, 2025 at 2:00 PM
Some really nice fundamental biophysics of DNA base stacking 🧬!
Reposted by Erik Poppleton
Anyway, learning another language is good for you because you die a thousand deaths of embarrassment and then you come out more humble and even more aware of your various human failings
September 26, 2025 at 1:19 PM
Anyway, learning another language is good for you because you die a thousand deaths of embarrassment and then you come out more humble and even more aware of your various human failings
This is sad news… it was such a cool museum when everything was working properly (which as you can read in the piece, it often wasn’t). I particularly liked the “living art” in the atrium.
After nearly 15 years of operating in Salt Lake City, The Leonardo science and art museum has announced it is permanently closing.
Here’s why The Leonardo museum in Salt Lake City says it’s closing for good
After nearly 15 years of operating in Salt Lake City, The Leonardo science and art museum has announced it is permanent closing.
www.sltrib.com
September 25, 2025 at 7:23 PM
This is sad news… it was such a cool museum when everything was working properly (which as you can read in the piece, it often wasn’t). I particularly liked the “living art” in the atrium.
Reposted by Erik Poppleton
I get that the news cycle is packed right now, but I just heard from a colleague at the Smithsonian that this is fully a GIANT SQUID BEING EATEN BY A SPERM WHALE and it’s possibly the first ever confirmed video according to a friend at NOAA
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
September 24, 2025 at 8:30 PM
I get that the news cycle is packed right now, but I just heard from a colleague at the Smithsonian that this is fully a GIANT SQUID BEING EATEN BY A SPERM WHALE and it’s possibly the first ever confirmed video according to a friend at NOAA
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
Reposted by Erik Poppleton
Postdoc position available in the BioEmu team at @msftresearch.bsky.social AI for Science - Berlin DE or Cambridge UK. Looking for candidates with backgrounds in #MachineLearning #AI Biophysics or Bioinformatics
jobs.careers.microsoft.com/global/en/jo...
jobs.careers.microsoft.com/global/en/jo...
September 24, 2025 at 1:06 PM
Postdoc position available in the BioEmu team at @msftresearch.bsky.social AI for Science - Berlin DE or Cambridge UK. Looking for candidates with backgrounds in #MachineLearning #AI Biophysics or Bioinformatics
jobs.careers.microsoft.com/global/en/jo...
jobs.careers.microsoft.com/global/en/jo...
Reposted by Erik Poppleton
Really happy to see this published in its final form @jacs.acspublications.org! 🧬 In this paper, we introduce a new class of biomimetic receptors to host functionality in synthetic cell membranes
Elita Peters @dianatanase.bsky.social @dimichelelab1.bsky.social
pubs.acs.org/doi/10.1021/...
Elita Peters @dianatanase.bsky.social @dimichelelab1.bsky.social
pubs.acs.org/doi/10.1021/...
Cation-Controlled Assembly, Activity, and Organization of Biomimetic DNA Receptors in Synthetic Cell Membranes
Biological cells use cations as signaling messengers to regulate a variety of responses. Linking cations to the functionality of synthetic membranes is thus crucial to engineering advanced biomimetic agents such as synthetic cells. Here, we introduce bioinspired DNA-based receptors that exploit noncanonical G-quadruplexes for cation-actuated structural and functional responses in synthetic lipid membranes. Membrane confinement grants cation-dependent control over receptor assembly and, when supplemented with hemin cofactors, their peroxidase DNAzyme activity. Cation-mediated control extends to receptor lateral distribution to localize DNA-based catalysis within phase-separated membrane domains of model synthetic cells, imitating the localization of multimeric membrane complexes to signaling hubs in living cells. Our modular strategy paves the way for engineering from the bottom-up cation-responsive pathways for sensing, signaling, and communication in synthetic cellular systems.
pubs.acs.org
September 8, 2025 at 11:19 AM
Really happy to see this published in its final form @jacs.acspublications.org! 🧬 In this paper, we introduce a new class of biomimetic receptors to host functionality in synthetic cell membranes
Elita Peters @dianatanase.bsky.social @dimichelelab1.bsky.social
pubs.acs.org/doi/10.1021/...
Elita Peters @dianatanase.bsky.social @dimichelelab1.bsky.social
pubs.acs.org/doi/10.1021/...
Reposted by Erik Poppleton
So excited to see our newest study out in print! Led by the brilliant @jgezelle.bsky.social and @sophiekorn.bsky.social, we discovered how viruses from highly divergent families converge on a shared RNA structure mechanism to inhibit cellular nucleases. #RNAsky #LoveVirology
Our study from the Steckelberg lab is out now in @narjournal.bsky.social !! We dove into a new nuclease-blocking viral #RNA structure important for viral infection, which provided evidence of similar structure-based strategies across diverse viral families. academic.oup.com/nar/article/...
A conserved viral RNA fold enables nuclease resistance across kingdoms of life
Abstract. Viral exoribonuclease-resistant RNA (xrRNA) structures block cellular nucleases to produce subgenomic viral RNAs during infection. High sequence
academic.oup.com
September 4, 2025 at 8:54 PM
So excited to see our newest study out in print! Led by the brilliant @jgezelle.bsky.social and @sophiekorn.bsky.social, we discovered how viruses from highly divergent families converge on a shared RNA structure mechanism to inhibit cellular nucleases. #RNAsky #LoveVirology
Zotero has dark mode now?!?!
The last blinding window on my desktop has gone dark in a huge win for cave-gremlin science.
The last blinding window on my desktop has gone dark in a huge win for cave-gremlin science.
September 4, 2025 at 8:53 AM
Zotero has dark mode now?!?!
The last blinding window on my desktop has gone dark in a huge win for cave-gremlin science.
The last blinding window on my desktop has gone dark in a huge win for cave-gremlin science.
Reposted by Erik Poppleton
🧵How to write and manage your first research budgets
The point of funding is to convert it into quality research. A well-spent research budget should fund the idea it was raised on, plus revision experiments, plus preliminary data for the next grant. So you need to spend, while avoiding waste.
The point of funding is to convert it into quality research. A well-spent research budget should fund the idea it was raised on, plus revision experiments, plus preliminary data for the next grant. So you need to spend, while avoiding waste.
September 3, 2025 at 4:03 PM
🧵How to write and manage your first research budgets
The point of funding is to convert it into quality research. A well-spent research budget should fund the idea it was raised on, plus revision experiments, plus preliminary data for the next grant. So you need to spend, while avoiding waste.
The point of funding is to convert it into quality research. A well-spent research budget should fund the idea it was raised on, plus revision experiments, plus preliminary data for the next grant. So you need to spend, while avoiding waste.
Excellent work on dynamic droplet segregation by @wverstraeten.bsky.social!
Something about this paper stimulated even more discussion than usual in group meetings, very interesting dynamics, both socially and under the microscope. 🧬🧪
Something about this paper stimulated even more discussion than usual in group meetings, very interesting dynamics, both socially and under the microscope. 🧬🧪
RNA droplets that grow and segregate by ribozyme catalysis. Check out our latest preprint www.biorxiv.org/content/10.1101/2025.08.29.673008v1
September 2, 2025 at 7:14 AM
Excellent work on dynamic droplet segregation by @wverstraeten.bsky.social!
Something about this paper stimulated even more discussion than usual in group meetings, very interesting dynamics, both socially and under the microscope. 🧬🧪
Something about this paper stimulated even more discussion than usual in group meetings, very interesting dynamics, both socially and under the microscope. 🧬🧪
Super detailed look at charge distribution on DNA helices producing alignment between similar sequences! 🧬
It turns out sDNA 🧬 interacts selectively! Andy Stannard measured these interactions very (very) precisely, and Ehud Haimov, @drjonhedley.bsky.social, Alexei Kornyshev worked out how it all works. It has to do with charge correlation... Check it out here
chemrxiv.org/engage/chemr...
chemrxiv.org/engage/chemr...
Detection and quantification of counterion-mediated homologous recognition in double-stranded DNA
Stretches of double-stranded DNA sharing the same sequence can recognise each other in cells. This phenomenon, known as homologous recognition, is essential for DNA recombination and repair. Yet, its ...
chemrxiv.org
September 2, 2025 at 6:51 AM
Super detailed look at charge distribution on DNA helices producing alignment between similar sequences! 🧬
Reposted by Erik Poppleton
🧪 #RNAsky
If you aren’t using RNAcanvas to draw your RNA structures and explore alternative structures, you are missing out! 56 citations in a year, with multiple ones in top journals like Nature, Science & Cell. Easy to use and packed with unique features! Try it!
academic.oup.com/nar/article/...
If you aren’t using RNAcanvas to draw your RNA structures and explore alternative structures, you are missing out! 56 citations in a year, with multiple ones in top journals like Nature, Science & Cell. Easy to use and packed with unique features! Try it!
academic.oup.com/nar/article/...
RNAcanvas: interactive drawing and exploration of nucleic acid structures
Abstract. Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. H
academic.oup.com
August 28, 2025 at 10:33 PM
🧪 #RNAsky
If you aren’t using RNAcanvas to draw your RNA structures and explore alternative structures, you are missing out! 56 citations in a year, with multiple ones in top journals like Nature, Science & Cell. Easy to use and packed with unique features! Try it!
academic.oup.com/nar/article/...
If you aren’t using RNAcanvas to draw your RNA structures and explore alternative structures, you are missing out! 56 citations in a year, with multiple ones in top journals like Nature, Science & Cell. Easy to use and packed with unique features! Try it!
academic.oup.com/nar/article/...
On this first day of #DNA31, reminder for the mol pro community that I put together this feed which picks up the last 3 days of posts from our community! Enjoy the meeting! 🧬
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...
August 25, 2025 at 8:12 AM
On this first day of #DNA31, reminder for the mol pro community that I put together this feed which picks up the last 3 days of posts from our community! Enjoy the meeting! 🧬
Reposted by Erik Poppleton
RNA is far more than a messenger.
Its structures regulate, evolve, and catalyze — carrying out functions DNA alone cannot.
But predicting #RNA structure from sequence is still extremely difficult.
In our recently published paper in @narjournal.bsky.social we present a way forward.
🧵 ⤵️
Its structures regulate, evolve, and catalyze — carrying out functions DNA alone cannot.
But predicting #RNA structure from sequence is still extremely difficult.
In our recently published paper in @narjournal.bsky.social we present a way forward.
🧵 ⤵️
August 25, 2025 at 3:02 AM
RNA is far more than a messenger.
Its structures regulate, evolve, and catalyze — carrying out functions DNA alone cannot.
But predicting #RNA structure from sequence is still extremely difficult.
In our recently published paper in @narjournal.bsky.social we present a way forward.
🧵 ⤵️
Its structures regulate, evolve, and catalyze — carrying out functions DNA alone cannot.
But predicting #RNA structure from sequence is still extremely difficult.
In our recently published paper in @narjournal.bsky.social we present a way forward.
🧵 ⤵️
Reposted by Erik Poppleton
RFdiffusion2 is now live!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
August 22, 2025 at 12:51 AM
RFdiffusion2 is now live!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
Reposted by Erik Poppleton
god can you imagine quitting this website for a week. you come back and everyone is like "yeah I think the scold adoption of burrito taxis as a quasi-glonzo issue is negatively polarizing me towards takeout abundance hoxhaism". you'd feel like you're having several concurrent micro-strokes
August 10, 2025 at 3:02 AM
god can you imagine quitting this website for a week. you come back and everyone is like "yeah I think the scold adoption of burrito taxis as a quasi-glonzo issue is negatively polarizing me towards takeout abundance hoxhaism". you'd feel like you're having several concurrent micro-strokes
Reposted by Erik Poppleton
My work on DNA condensates @dimichelelab1.bsky.social is now out! 🧬🎉🍬
A huge thank you to @francolab.bsky.social lab for their invaluable expertise and to everyone in our lab for their insights, feedback, and countless discussions along the way. I’ve learned so much from working with you all!
A huge thank you to @francolab.bsky.social lab for their invaluable expertise and to everyone in our lab for their insights, feedback, and countless discussions along the way. I’ve learned so much from working with you all!
August 13, 2025 at 4:22 AM
My work on DNA condensates @dimichelelab1.bsky.social is now out! 🧬🎉🍬
A huge thank you to @francolab.bsky.social lab for their invaluable expertise and to everyone in our lab for their insights, feedback, and countless discussions along the way. I’ve learned so much from working with you all!
A huge thank you to @francolab.bsky.social lab for their invaluable expertise and to everyone in our lab for their insights, feedback, and countless discussions along the way. I’ve learned so much from working with you all!
Reposted by Erik Poppleton
Building a synthetic cell together - nice common perspective written by many leading scientists who gathered in Shenzhen China for the inaugural ‘SynCell Global Summit’.
Check it out in Nature Comm: www.nature.com/articles/s41...
Check it out in Nature Comm: www.nature.com/articles/s41...
August 13, 2025 at 7:19 AM
Building a synthetic cell together - nice common perspective written by many leading scientists who gathered in Shenzhen China for the inaugural ‘SynCell Global Summit’.
Check it out in Nature Comm: www.nature.com/articles/s41...
Check it out in Nature Comm: www.nature.com/articles/s41...