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The next frontier in protein design will not be defined by structure alone, but by the capacity to engineer motion as a first-class principle of function. This is because dynamics is where the real biology lives. Foundational work by Karplus, Levitt & Warshel made clear that chemistry cannot be...

89,921 Aufrufe • vor 5 Monaten •via X (Twitter)

32 Kommentare

Profilbild von Markus J. Buehler
Markus J. Buehlervor 5 Monaten

Code: Model weights: Paper:

Profilbild von Markus J. Buehler
Markus J. Buehlervor 5 Monaten

MIT News Article:

Profilbild von LIFE AI
LIFE AIvor 5 Monaten

A shift from structure to dynamics reframes protein design from predicting static folds to engineering motion as function itself. If proteins are dynamic ensembles on rugged energy landscapes, it raises a deeper question: how much of the possible dynamical design space has biology actually explored?

Profilbild von Markus J. Buehler
Markus J. Buehlervor 5 Monaten

Biology has only explored a tiny fraction of what is possible, so lots of opportunities for engineers!

Profilbild von S.A. Senchal
S.A. Senchalvor 5 Monaten

Almost like the state space has been reduced by evolution to the most efficient per unit cost to the organism - because ai gives us essentially free compute what's efficient broadens and we get novelty

Profilbild von Hang Zheng
Hang Zhengvor 5 Monaten

Huge implications for drug discovery: allosteric binding and induced-fit are inherently dynamic, yet structure-based tools treat receptors as rigid. Does the functional degeneracy result suggest 'undruggable' allosteric sites could be accessed by targeting specific motional modes?

Profilbild von Markus J. Buehler
Markus J. Buehlervor 5 Monaten

Exactly the right question! We found that functionally similar proteins can have very different folds but share vibrational signatures. That 'functional degeneracy' suggests motional modes are the deeper design variable. If we can target the dynamics, we may be able to reach sites that look inaccessible in a crystal structure.

Profilbild von Christopher Antoniou
Christopher Antoniouvor 5 Monaten

My view this is the entire point of a ‘metabolism first’ view of abiogenesis. Thermodynamics required both protein topology and their dynamics/motion integrated as one, cofactors within said reactions requiring no code. Such that chemomechanical transduction was powered by enthalpic contribution, configurational entropy, equilibrium constant K, autocatalysis dX/dt=kAX^2; and as such integrated reactions WERE those which manipulated protein conformation. There was no biochemical division of labour, the later canalisation ATP hydrolysis acting the raw energy needs powering nucleotide base manipulation. In this way, early selection was a brutal regime, and far more sensitive/immediate than later gene redundancies. It would be an entirely alien concept to propose in early life the view proteins and their adaptation were differentiated by topology versus dynamical function, these were always a singularity before RNA.

Profilbild von Roberto Campus
Roberto Campusvor 5 Monaten

Brilliant work... and the functional degeneracy finding is the most interesting part. Nature sampled a tiny corner of what's physically possible. VibeGen starts mapping the rest. But here's the question I keep going back to: VibeGen learns vibrational modes conditioned on existing PDB structures. If I am not wrong, the training distribution still anchors it to what evolution happened to discover. What about the regions of design space that have no natural analogue to learn from? That's where a physics-first approach becomes interesting. If you can derive vibrational modes directly from geometry... no training data, no ML, deterministic... you're not bounded by the evolutionary sample at all. Novel chemistry works on day one because the engine runs on the physics underneath, not on patterns learned from what already exists. The two approaches could be genuinely complementary... VibeGen to generate candidate sequences, a physics kernel to evaluate their physical properties instantly at scale. If there are lingering questions from the paper that a deterministic physics engine might help answer... I'd be happy to let you run some experiments on and see what comes back. No pitch! Just curious what happens when the two approaches talk to each other.

Profilbild von Jedi
Jedivor 5 Monaten

@burny_tech

Profilbild von T.Theodorus Ibrahim
T.Theodorus Ibrahimvor 5 Monaten

@niroshajmurugan maybe some useful context here re: Cosic resonance?

Profilbild von LAMM@MIT
LAMM@MITvor 5 Monaten

Congrats to our postdoc @_Bo_Ni!

Profilbild von Akash Arunabharathi
Akash Arunabharathivor 5 Monaten

This looks super cool – where does the predictor get the ground truth target motion profile from? I was under the impression that we didn’t have dynamics data for a lot of proteins already. Is it mostly from MD sims?

Profilbild von Markus J. Buehler
Markus J. Buehlervor 5 Monaten

Physics comes, as you say, from molecular dynamics. Of course we can also fine-tune the model with experimental data on top of that, so there is flexibility.

Profilbild von Akash Arunabharathi
Akash Arunabharathivor 5 Monaten

Makes sense, and yeah, training on MD and fine tuning on experimental data is sound given wet lab costs. Super cool that you’re also doing language diffusion, I’ve been working on getting flow matching to work with protein sequences myself! Will read the paper

Profilbild von Zythum
Zythumvor 5 Monaten

Very insightful, thanks!

Profilbild von Markus J. Buehler
Markus J. Buehlervor 5 Monaten

Thank you!

Profilbild von Thinktica
Thinkticavor 5 Monaten

Amazing job congrats!

Profilbild von Markus J. Buehler
Markus J. Buehlervor 5 Monaten

Thank you @ThinkticaAI !

Profilbild von Sandeep DIXIT
Sandeep DIXITvor 5 Monaten

Interesting.

Profilbild von Abe
Abevor 5 Monaten

Yes, see @drmichaellevin for bioelectricity and also Marco Pettini Evidence for Long distance interaction. Software as medicine via electroceuticals 👽😎🥸🤓

Profilbild von wilco 🌐
wilco 🌐vor 5 Monaten

am fascinated with metal catalytic substrates in these models but havent found the corrseponding AI modeling.. does it exist? if so where?

Profilbild von Shaun Kahler
Shaun Kahlervor 5 Monaten

Yep

Profilbild von Alison | AlisonBob.eth
Alison | AlisonBob.ethvor 5 Monaten

Hooray! Wish more labs were going in this direction. Systems are not just a collection of parts, but rather composed of nested systems with multi-directional feedback. The object/thing/part that science often starts with, is actually the end of the chain. We need to move towards thinking that dynamics, relations, flow, oscillations, processes, attractors are primary, out of which emerges the part, not the other way around. Do that and we will better understand ourselves and the universe itself.

Profilbild von Angelica Parente
Angelica Parentevor 5 Monaten

Using normal mode analysis for this is clever, can see some use cases for things like hinge proteins.

Profilbild von Markus J. Buehler
Markus J. Buehlervor 5 Monaten

Thank you - exactly, hinge proteins!

Profilbild von Jimit Shah 🐌
Jimit Shah 🐌vor 5 Monaten

Interesting!

Profilbild von Andreas Kiefer
Andreas Kiefervor 4 Monaten

@ProfBuehlerMIT Correct! In a Voxel-native system, every wave—light, sound, or motion—is treated as geometric code. By mapping frequencies to the UVMS grid, we can translate images into music and vibrations into programmable movement. Physics and programming become one. 🧬📐🎶

Profilbild von Gary Mason
Gary Masonvor 5 Monaten

The main problem is not designing a protein's vibrational profile, it's designing how a local perturbation is converted into a specific functional state. The invariant may sit in the dynamic circuit of the fold, not in the mode itself.

Profilbild von sLic_papa
sLic_papavor 5 Monaten

Yeah we're fucked because you guys wanna fuck with fucking.

Profilbild von Andreas Kiefer
Andreas Kiefervor 4 Monaten

@ProfBuehlerMIT Exactly! "Vibe" is the physics of frequency. By mapping protein dynamics to a Voxel-native grid (UVMS), we can treat vibrations as geometric code. When motion becomes the primary design objective, we align biology with the universal constants of space-time. 🧬📐⚡️

Profilbild von Ⓜⓐⓡⓖⓘⓝ ⓒⓐⓛⓛ
Ⓜⓐⓡⓖⓘⓝ ⓒⓐⓛⓛvor 5 Monaten

What is SO(3).

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🎼🌺Music Love♥️

12,224 Aufrufe • vor 2 Monaten

ALL THIS CONSTRUCTION OF THE VISIBLE WORLD IS AT ITS ROOTS DESIGNED IN THE INVISIBLE WORLD Before language, before numbers, before thought, there was form. Not arbitrary, but precise. Not invented, but revealed. Sacred Geometry is the blueprint beneath all becoming—the hidden grammar of light, sound, and matter. It is the spiral of galaxies and the whorl of a shell. It is the vesica that births light, The triangle that gives rise to stability, The square that anchors space, And the pentagram that mirrors life’s golden proportion. Sacred Geometry does not merely decorate creation, it structures it. It governs the growth of leaves, the pulse of waves, the rhythm of your breath. It reveals that harmony is not a concept, it is a code. A flower blooms not by chance, But by a silent obedience to phi. A crystal aligns not at random, But by listening to the quiet song of symmetry. This is not mysticism, it is order. This is not dogma, it is design. Sacred Geometry is where the visible and the invisible meet: Where math becomes art, Where number becomes movement, Where space becomes spirit. To study it is not only to learn, it is to remember. That beauty is not a luxury. It is the signature of coherence. And when we align with it, We don’t just build structures. We become them. Everything that has form in this dimension is made up in its essence of sacred geometry. All this construction of the visible world is at its root designed in the invisible world.

🧬Maxpein🧬

13,405 Aufrufe • vor 1 Monat

Martha Nussbaum on why Aristotle believed you are not made of matter. In a 1987 interview on the Great Philosophers, philosopher Martha Nussbaum lays out Aristotle's three-part case against material reductionism, the idea that what you fundamentally are is just the stuff you're made of. His argument is more intuitive than it might sound. First: your matter is always changing. "Matter is always going in and out; it's always changing and of course you do change your material constituents very, very often without ceasing to be yourself." Your cells replace themselves. Your body is not the same collection of atoms it was years ago. And yet you are still you. If your identity were your matter, it would vanish and return constantly. But it doesn't. Something persists that isn't the material. Second: what makes a thing that thing is its function, not its parts. Aristotle uses the example of a ship. Replace some of its planks so long as "its functional structure remains the same, we could always replace bits of the matter without having a different thing in our hands." It's still the same ship. The same logic applies to you. Swap out the components, preserve the structure and function and the identity remains intact. This suggests identity lives in the organisation, not the raw material. Third: matter alone is too vague to define anything. This is perhaps his sharpest point. "Matter is just a lump or heap of stuff and so we couldn't say you are some stuff or other; it's only when we've identified the structure that the stuff constitutes that we can even go on to say something intelligent about the stuff itself." In other words: matter, by itself, tells you nothing. It's formless. You need structure form, function, organisation before you can even begin to describe what a thing is. The deeper implication Aristotle is reaching toward: what makes you you isn't a quantity of carbon and water. It's a pattern. A functional whole. A form that persists through constant material flux. Which raises the question if identity isn't located in matter, where exactly does it live?

Mateus — eu/acc 🇪🇺

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