tom

🧮

[kasra @kasratweets]

oh my god he's right lol. it looks like a regular topology textbook with standard diagrams except every few pages you just have a random full-page drawing??

[tom @atomgardner]

@delta_skeltah is there an 'old men smile unkindly' makeup?

[tom @atomgardner]

@mahlenr what were the lies you almost told but didn't? do you have a sense of their relative temptation? reckon there's a link between a lie's temptation and its bent to change your crossing number?

[tom @atomgardner]

@delta_skeltah this is disorder. cheese belongs in your mouth

[tom @atomgardner]

@0bNARA bōluó

[tom @atomgardner]

got my friend with sev zero ai psychosis saying "estimator" now. maybe i've cured him?

[tom @atomgardner]

@joey_f6 busy busy busy

[21 @twentyone21___]

Everlasting
-2024-

[Curiosity @CuriosityonX]

This single-celled protozoan passing though another one under a microscope

[Spirochrome @spirochrome]

Mesmerizing light sheet imaging of neutrophils swarming at a yeast target!

The neutrophils were labeled with SPY650-DNA (yellow) and a calcium dye (blue).

This movie is part of the recent manuscript by
Evelyn Strickland that we highly recommend reading! https://t.co/U6tn4sfogZ

[Fernando 🌺🌌 @zetalyrae]

Login codes are the worst thing to happen to human civilization.

[陈东成 @fncischen]

ngl the Greater Bay Area (GZ, HK, SZ) region is probably my favorite place in the world right now lol

[Markus J. Buehler @ProfBuehlerMIT]

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 understood without motion, mechanism, and scale. Gō, Brooks & others showed that proteins possess characteristic collective motions - low-frequency normal modes that capture how whole molecules bend, breathe, and fluctuate. Frauenfelder then sharpened the picture further: proteins are not static objects occupying a single minimum, but dynamic ensembles traversing rugged energy landscapes.

And yet the modern AI revolution in protein science has been, above all, a revolution in structure. In our new paper in Matter, @_Bo_Ni and I ask a different question: not what structure will this sequence adopt? but what sequence will realize a prescribed pattern of motion?

VibeGen inverts the conventional design paradigm. Rather than treating dynamics as a consequence to be analyzed after the fact, it makes dynamics the design objective from the outset. Using a language diffusion model with two cooperating agents - a designer that proposes sequences and a predictor that critiques them against the target motion profile - the system converges on de novo proteins with tailored vibrational behavior.

One of the most intriguing results is a form of functional degeneracy - distinct sequences and distinct folds can satisfy the same target dynamical specification. For a given functional pattern of motion, evolution may have sampled only a small region of the physically realizable design space. The space of viable molecular mechanics may be far larger than the repertoire biology happened to discover.

We have made "vibe" into a cultural metaphor - something intuitive, affective, subjective. But at the molecular scale, vibe is not metaphor: It is physics. For a protein, the vibe is the pattern of motion itself; the fluctuations, resonances, and collective displacements that determine what the molecule can do.

[JP Aumasson @veorq]

plot twist: polytime classical factoring algorithm before any working Shor; would be hilarious

[Codetaur @codetaur]

prototype of a recursive time helix calendar/history, with nested coils from centuries -> decades -> years -> days -> hours -> minutes -> seconds. labels need some work but it's the start of something. based almost entirely on @tr_babb 's sketch/idea. in threejs/webgpu

[Tom Moore @mooreth42]

If this is your first time seeing the molecular sorter I hope it instills the same feelings it did, and still does, me.

[Figs From Plums @FigsFromPlums]

Agnes Denes - Absolutes and Intermediates

[conrad house @DlSPUTED]

Rosaire Appel.

[Sam Zeloof @szeloof]

Be careful what you work for