📣There is still time to nominate someone for a #BPS theory and computation subgroup award! See more details here: drive.google.com/file/d/17aUc...
@pilarcossio.bsky.social
In 2017 I co-organized a BPS thematic meeting on Conformational Ensembles from Experimental Data and Computer Simulations We're back in Berlin Aug 2027 with Biomolecular Dynamics: Integrating Experiments and Computation with a great line-up (to be revealed soon) www.biophysics.org/upcoming-the...
🧨🥵🥵Don’t miss the deadline for the @biophysicalsoc.bsky.social Theory & Computation Awards Sept 15! 🥵🥵🚀 The award will recognize outstanding Postdocs, Early Career and Mid-Career scientists in the field of computational biophysics. www.biophysics.org/Awards-Funding
Very excited to share my first blog post with @minhuanli.bsky.social @emilthomasen.bsky.social 🎉 Can we capture an ensemble? Lessons learned from averages and single-molecule measurements in structural biology. rs-station.github.io/2026/08/31/a...
Are We Capturing the Ensemble? | RS Station
rs-station.github.io
⚡ Time is running out! ⚡ The deadline for the @biophysicalsoc.bsky.social Theory & Computation Awards is Sept 15! 🧬💻 Recognizing outstanding research across: 🎓 Postdocs 🌱 Early Career 🚀 Mid-Career Nominate a student or colleague! 🧪✨ 👇 Details: www.biophysics.org/Awards-Fundi...
Subgroup Awards - The Biophysical Society
biophysics.org
1/ We're excited to announce that @rs-station.bsky.social is joining the Open Molecular Software Foundation @omsf.io!
*Preprint Alert*: How do we measure resolution when biomolecules won't sit still? 🔬 Estimating it for a static cryo-EM reconstruction is standard. But what about a conformational ensemble? arxiv.org/abs/2606.14449 with the amazing henryhmattingly.bsky.social and @lukeevanshandle.bsky.social #cryoEM
@flatironinstitute.org senior research scientist Pilar Cossio builds crucial tools to reveal how environmental changes alter the behavior of RNA: https://bit.ly/48rCAg2 #science #biology
Pilar Cossio: Reconstructing RNA’s Shapeshifting Behavior
Flatiron Institute researcher Pilar Cossio builds tools to analyze experimental measurements and reveal how environmental changes alter the behavior of RNA molecules.
bit.ly
Very excited to share MIMIC: check it out! An amazing team effort!
Samuel Sledzieski@samsl.io · 5mo agoIntroducing MIMIC: a new foundation model trained natively across DNA, RNA and proteins. MIMIC is multimodal and generative: it can use structure, regulation, evolution, and experimental context to infer missing biology or design new sequences. 🧵⬇️
Excited so share our theoretical work on cryo-EM vitrification and recovering ensemble distributions!!
Miro Astore@miroastore.bsky.social · 5mo agoWe just preprinted one of my favorite studies @FlatironInst . I was lucky to be part of an amazing team studying the effects of rapid cooling to preserve samples in cryoEM. Read on to learn about the limits of cryoEM for biophysics and how to overcome them www.biorxiv.org/content/10.6...
*postdoc job alert* Are you interested in theory and experiment for time-resolved cryo-EM? If so see below 👇 a collaboration between the Crick and the Flatiron Institutes 💻🔬
Sonya@sonyahanson.bsky.social · 5mo agoExcited to announce this postdoc position at the intersection of experiment and computation for time-resolved cryo-EM! It's a collaboration between the Enchev group at the Crick and myself and @pilarcossio.bsky.social at the Flatiron Institute! Plz share. crick.wd3.myworkdayjobs.com/External/job...
#FlatironCCM researchers have developed a new tool called ROCKET that extends the capabilities of AlphaFold by directly learning from raw experimental data: https://bit.ly/4dUTZkG #science #math
Introducing ROCKET: An Upgrade to AlphaFold That Learns From Raw Experimental Data
Introducing ROCKET: An Upgrade to AlphaFold That Learns From Raw Experimental Data on Simons Foundation
simonsfoundation.org
Celebrating #BiophysicsWeek T&C partnered with Phase Space Invaders podcast: Robert Best @sonyahanson.bsky.social @xuhuihuangchem.bsky.social and host @milosz-wieczor.bsky.social Episode 32: Driving the Future of Biophysics: What’s Next in Theory and Computation? www.buzzsprout.com/2313153/epis...
Episode 32 - Robert Best, Sonya Hanson, Xuhui Huang: Driving the Future of Biophysics. What’s Next in Theory and Computation? - Phase Space Invaders (ψ)
With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're ...
buzzsprout.com
How can we extract unbiased transition rates from ligand-unbinding Random Acceleration MD (RAMD) simulations? Our new paper lays out the theoretical framework behind RAMD. Take a look! doi.org/10.1063/5.03... @benoitroux.bsky.social @yiweiding.bsky.social & Alessia Ghidini #MD #drugdiscovery
A theoretical framework for random acceleration molecular dynamics simulations
The dissociation of a ligand bound to a receptor is a rare event occurring on a timescale that is far longer than can be afforded by standard simulation methodo
doi.org
@benoitroux.bsky.social · 7mo agoWe developed a simple theory and showed that Random Acceleration Molecular Dynamics (RAMD) is consistent with a Smoluchowski equation with an effective temperature and diffusion coefficient that depend quadratically on the magnitude of the random force. pubs.aip.org/aip/jcp/arti...
#BPS2026 The T&C subgroup is hosting a fun event on Saturday evening, Feb 21st 🎉 Open bar for 2 hours + food! Tickets are selling fast, so sign up soon: www.biophysics.org/2026meeting/...
BPS2026 Annual Meeting Subgroup Dinners| Biophysical Society
biophysics.org
Go use cryojax ! It's awesome! I can't wait to see what people do with it.
Structural Biology@actacrystd.iucr.org · 8mo agoMichael J. O'Brien et al.: CryoJAX: a cryo-electron microscopy image-simulation library in JAX #CryoEM #ImageSimulation #AutomaticDifferentiation @harvard@unewhaven@Cornell...#IUCr https://journals.iucr.org/paper?S2059798326000550
Happy new year!!🎆 & checkout our new preprint exploring optimal transport for cryoEM parameter optimization:
Minhuan Li@minhuanli.bsky.social · 9mo agoCheck our new preprint smoothing rugged Cryo-EM landscapes: shorturl.at/gYs9U We tackle practical hurdles of Optimal Transport (OT) loss—differentiability, cost & noise sensitivity—make it a feasible inference workhorse. W/ G. Woollard, D. Herreros, @pilarcossio.bsky.social, K. Dao Duc 🧵👇 (1/9)
Happy to share our cryoEM Ensemble Optimization method! 🎉It infers optimal structures and their weights directly from individual cryoEM images - no maps just physics! with David Sliva-Sánchez, @erikhthiede.bsky.social & Roy Lederman www.biorxiv.org/content/10.6...
Cryo-electron microscopy ensemble optimization using individual particles and physical constraints
Biomolecules are inherently dynamic, and understanding their conformational ensemble distributions is essential for understanding their dynamics and biological roles. Cryo-electron microscopy (cryo-EM...
biorxiv.org
Checkout our cryo-EM simulator in JAX: paving the way for cryo-EM probabilistic modelling & statistical structural biology #cryoEM with @m0bri3n.bsky.social @miroastore.bsky.social + Harvard, Flatiron & Cornell!
Michael O’Brien@m0bri3n.bsky.social · 10mo agohey bsky! excited to share what i've been working on for a few years now. cryoJAX: A Cryo-EM Image Simulation Library In JAX www.biorxiv.org/content/10.1... cryoJAX is a modular framework for implementing forward models of cryo-EM image formation. these can be used to build powerful data analyses!
**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: pcossio@flatironinstitute.org
Submit your BPS T&C subgroup nominations::!!
Viviana Monje@vmonje.bsky.social · 11mo agoHello @biophysicalsoc.bsky.social Theory & Computation Subgroup! Please consider volunteering as an officer for our subgroup for the 2026-2028 cycle. Submit your nomination(s) by November 17th. Looking forward to seeing you next Annual Meeting in San Francisco next year!!
*Job Alert*: postdoc positions available @flatironinstitute.org in Computational Mathematics: apply.interfolio.com/173401
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
Check out our latest preprint for the first community #cryoEM heterogeneity challenge 🎆🎇 @sonyahanson.bsky.social @miroastore.bsky.social + method developers and participants! @flatironinstitute.org
Miro Astore@miroastore.bsky.social · last yr.That's a wrap! The results of the first #cryoEM heterogeneity challenge are up on biorxiv! biorxiv.org/content/10.110
#BPS2026 submit your nomination for the Theory and computation awards!!!
Viviana Monje@vmonje.bsky.social · last yr.Submit your nominations for the 2026 T&C Subgroup Awards. Recipients get a cash award and speak at the next @biophysicalsoc.bsky.social Annual Meeting in San Francisco, CA. Deadline: August 1, 2025 biophysics.org/awards-fundi...
Check out our recent preprint 👇on counting particles to estimate populations in #cryoem: noise can bias the estimates; with Luke Evans & a great team.
bioRxiv Biophysics@biorxiv-biophys.bsky.social · last yr.Counting particles could give wrong probabilities in Cryo-Electron Microscopy https://www.biorxiv.org/content/10.1101/2025.03.27.644168v1
If you care about how to use cryoEM to estimate conformational ensembles and populations of different states you should read this from @pilarcossio.bsky.social and team ❄️ 🔬
bioRxiv Biophysics@biorxiv-biophys.bsky.social · last yr.Counting particles could give wrong probabilities in Cryo-Electron Microscopy https://www.biorxiv.org/content/10.1101/2025.03.27.644168v1
#APSSummit25 come to our session in generative modeling and machine learning in chem phys! Chaired with @GrantRotskoff and an amazing set of speakers 🎉 starting Thursday 11:30am room 204A
#BPS2025 waiting for the national lecture 🥳 @giuliapalermo.bsky.social @labvanni.bsky.social @sriraksha.bsky.social @sesamedusa.bsky.social
