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??
@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?
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
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. Gล, 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.
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