Swanson Group

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

BBCB v 4.5 - Registration Form We invite you to a networking event on Friday March 27 at 11:30am ET | 8:30am PT | 5:30pm CET, intended to reconnect former attendees of the “Building Bridges in Computational Biophysics” symposia and...

Come celebrate #BiophysicsWeek with us!
Looking forward to reconnect with our BBCB community & meet new peers.
Register for this upcoming networking event on March 27th 11:30am ET / 8:30am PT:
forms.gle/1gBP3N7aTHSX...

See you at #bps2026!

Congrats, Alex!

#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/...

Opinion | Let the Arms Race Begin

If Congress doesn’t act, the last nuclear arms control treaty between the U.S. and Russia will expire. It would pointlessly wipe out decades of diplomacy, and could spark another arms race that makes the world less safe. This piece is worth the read.

Bacteriocin biophysics: From protein-protein interaction models to navigators of the bacterial cell envelope Bacteriocins are toxins deployed by bacteria to kill their competitors. Here, I reflect on my laboratory’s work on protein bacteriocins and their immunity proteins from Gram-negative bacteria. We unco...

A gift of an article from the inimitable Colin Kleanthous as he says a moving farewell to his laboratory. A brave, unrepentant and scientifically brilliant journey is described - please have a read, friends.

www.jbc.org/article/S002...

From Flux to Function: Extracting Mechanistic Insights from Ion Channels via I–V and I–μ Analyses The molecular origins of ion-channel current–voltage (I–V) relationships are often unclear, obscured by ensemble averaging in experimental analysis and persistent underestimation of single-channel ion currents in simulations. Here, we present a mathematical framework that relates ion channel properties to experimentally measured I–V and current–chemical potential (I–μ) relationships. By accounting for how rates change in response to electrochemical conditions in a multistate kinetic model of systems with sequential binding sites, this approach demonstrates how the spatial arrangement of sites and transition states, together with rate asymmetries in ion uptake, transfer, and release, manifest in distinct open-channel current and conductance profiles. Varying these properties in model systems reveals a molecular basis for understanding rectification and nonohmic open-channel flux. Application to models fit to experimental I–V curves demonstrates that these mechanistic trends hold in heterogeneous systems, suggesting a (potentially) transferable paradigm for open-channel flux in channels and transporters with two or more sequential binding sites. Together, these results establish a theoretical framework for open-channel current and foundation for mechanistically interpreting experimental I–V and I–μ assays.

Electrochemical gradients are a cornerstone of life. Too often, we model these two driving forces interchangeably…but they’re quite different.

Check out how you can use these differences to extract mechanistic insight directly for e-phys assays!

pubs.acs.org/doi/abs/10.1...

Our recent preprint shows that metastable, short-lived PPIs captured by MD and IGME define key design targets for PROTACs, enabling rational discovery of sub-nanomolar RIPK1 degraders.

Great collab w/ Weiping Tang! Congrats to Yue & co-authors!

chemrxiv.org/doi/full/10....
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I'm here outside Speaker Johnson’s office because he is starving families and gutting health care to cover up the Epstein Files.

Change my mind.

Nearly all famines are man-made. Hunger is about controlling something more powerful than you. It’s why lion obeys the lion tamer even though he can rip the lion tamer to shreds in an instant.

The Shutdown of U.S.A.I.D. Has Already Killed Hundreds of Thousands The short documentary “Rovina’s Choice” tells the story of what goes when aid goes.

One analytical model shows that, as of November 5th, the dismantling of U.S.A.I.D. has already caused the deaths of 600,000 people, two-thirds of them children. https://newyorkermag.visitlink.me/jUzNSc

Don’t miss this opportunity to work with a fantastic mentor, a great team, in a beautiful city of France!

‘Extinction level’ cuts coming to NASA, report says NASA’s science programs budget could be slashed by 50 percent in fiscal year 2026, people familiar with the Trump administration’s budget request warn

The Independent outlines how catastrophic the proposed cuts to #NASA 's science budget would be, describing it as 'extinction level' cuts. Please speak up. www.the-independent.com/news/world/a...

Protest outside NIH headquarters in Bethesda opposes possible cuts to healthcare Denna McGrew says her 23-year-old son, Ethan, who died Tuesday, was given another year of life thanks to the NIH Clinical Center.

Around 1,000 people gathered in Bethesda Saturday to express their frustration and fear over possible cuts to Medicare, Medicaid and research at the National Institutes of Health headquarters. Many were doctors worried federal cuts could come for them. www.wusa9.com/article/news...

The House Continuing Resolution budget “adjustments” for NIH are drastic. Here are some examples:

I know right. 😒 So bad…

POSTDOC IN MOL SIMULATIONS AND AI

Open position in my group, apply here:

iit.taleo.net/careersectio...

Looking for motivated candidates. 👍💪🥇

Welcome!

Completely agree. Welcome Bill! Wouldn’t be the same without you.

Substrate interactions guide cyclase engineering and lasso peptide diversification - Nature Chemical Biology How a lasso cyclase ties a lasso peptide into its characteristic knot has remained poorly understood. Here the authors identify key molecular interactions that guide lasso peptide folding and cyclase ...

Congrats on the lovely work!

www.nature.com/articles/s41...

https://www.nature.com/articles/s41589-024-01775-2

It was a pleasure to highlight the latest on lasso peptide folding and substrate–cyclase tolerance from the Shukla, Burk, and Mitchell teams.
t.co/IwJWRDrcoh

Why I have resigned from the Royal Society The Royal Society is a venerable institution founded in 1660, whose original members included such eminent men as Christopher Wren, Robert H...

For those who missed it: Elon Musk, the Royal Society, and me
deevybee.blogspot.com/2024/11/why-...

Love this! Such an honorable move.🏅 Thank you for taking a stand. These are the acts that keep hope alive.

Twitter’s heir apparent isn’t X or Threads — it’s Bluesky The blue bird is dead. Long live the blue sky.

Others have noted it but I will too: The big reason Bluesky is so hot right now is that the people who add value to social media - the frequent posters in specific fields - are here now, talking to each other and creating the "spectator value" that draws users and attention.

It is a reminder that NIH is, at its heart, a collection of dedicated humans - scientists, physicians and staff - all public servants trying their best to advocate for and support the rest of us 🇺🇸

Congrats, Mike!

Who should you nominate as reviewers for your manuscript? After a long chat with a post-grad it appears that there's a lot of misguided advice out there. Thread 👇

That’s awesome! And I think it’s significant that it holds over the voltage curve. Excellent work.