iiinova — where your digital self keeps evolving

Sam Foley @samuelfoley.com · 01/10/2026

BPS abstract day tradition

Cloudflare error when trying to access www.biophysics.org

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Sam Foley @samuelfoley.com · 29/09/2026

Intruders under the blanket!

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Sam Foley @samuelfoley.com · 25/09/2026

Nicolaas van Kampen's essay on the Gibbs Paradox, in addition to being an insightful, no-nonsense explanation gas entropy and indistinguishability ("Quantum mechanics has no bearing on the question"), opens with some comments on physics education that were ahead of the times for 1984!

Beste Dik,
It is a long time since we both attended the lectures by Mrs de Haas-Lorentz on thermodynamics. They were excellent from a pedagogical point of view since they forced you to figure out almost everything yourself. That is a much better way of learning physics than the spoonfeeding of predigested formalisms which is nowadays regarded as the highest wisdom in education. I remember how puzzled I was by the sudden appearance of the term —kN log N in the entropy. After I figured it out I found that there is still much confusion about it in the literature. That is my excuse for bothering you with such a time-worn subject.

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Sam Foley @samuelfoley.com · 22/09/2026

To add insult to injury, it's full of AI slop images.

A hallucinated man in a suit holding a metal rectangle that has merged with his elbow

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Sam Foley @samuelfoley.com · 13/09/2026

He saw this episode of Star Trek and got confused why we still have two Irelands

Lt. Commander Data brings up "the Irish Unification of 2024" in conversation with Captain Picard

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Sam Foley @samuelfoley.com · 21/08/2026

"How could you do this to me"

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Sam Foley @samuelfoley.com · 19/08/2026

I mean, how can you see a book that's just called "Tubes" and NOT be compelled to read it?

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Sam Foley @samuelfoley.com · 19/08/2026

These are the kinds of diagrams I want in the math books I read Taken from "Tubes", 2nd Ed. by Alfred Gray

Excerpt from "Tubes" 2nd Ed. by Alfred Gray:

"Import Remarks:
(1) If P has a boundary, then
T(P,r) =/= {m in M | distance(m,P) <= r},
because the ends of the set on the right-hand side must be excluded to get the left-hand side"

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Sam Foley @samuelfoley.com · 18/08/2026

Some fun with parallel curves

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Sam Foley @samuelfoley.com · 17/07/2026

Oh boy, I better go find a phone book!

A poster page in the back of a book:
"For more adventures of Star Wars: X-Wing Rogue Squadron, head to your local comic-book specialty store! You'll find it listed under 'comic books' in your local telephone directory!"

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Sam Foley @samuelfoley.com · 12/07/2026

Okay, I admit it, I've been reading SW expanded universe books again. This one is actually quite good so far, despite the title and cover giving the impression that it's a Yoda/Dooku forbidden romance novel.

Cover of "Star Wars: Yoda: Dark Rendezvous"

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Sam Foley @samuelfoley.com · 07/07/2026

Watching a required university training video and... is Sameer here living in Cyberpunk 2077?

A man in the foreground, with a high-tech futuristic apartment in the background with neon lighting and a view of a cityscape from the perspective of a high-rise building.

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Sam Foley @samuelfoley.com · 03/07/2026

Homescreen weather widget was not designed with this weather in mind

Google weather widget cutting off the current temperature as "10" (no units) when it is actually 100°F

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Sam Foley @samuelfoley.com · 27/06/2026

Mesmerizing waves that seem to move in slow motion at a water-cyclosiloxane interface.

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Sam Foley @samuelfoley.com · 18/06/2026

"How was the simulation time step decided?"

Part of a classic "Calvin and Hobbes" comic:

"How do they know the load limit on bridges, dad?"

"They drive bigger and bigger trucks over the bridge until it breaks."

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Sam Foley @samuelfoley.com · 11/06/2026

The article is out now in Physical Review Research and on arXiv! doi.org/10.1103/cnfz... Thanks as always to my mentor @mejohnson81.bsky.social who got me onto this topic through the lab’s excellent work on non-equilibrium self-assembly processes.

Overview of analytical model for self-assembly of a protein coat on the membrane

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Sam Foley @samuelfoley.com · 11/06/2026

This is a super interesting result not just for endocytosis, but for cellular information processing and decision-making in general. You don’t need to spend energy at decision time; you can spend energy to put yourself in a state where equilibrium processes drive decision-making “for free”. (6/7)

Plots of simulation results for equilibrium assembly sizes as well as assembly timescales.

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Sam Foley @samuelfoley.com · 11/06/2026

A related worry is whether or not an equilibrium phase transition is fast enough to accomplish the cell’s goals on physiologic timescales. Based on our non-equilibrium simulations and rough theoretical estimates, the timescale of self-assembly is plenty fast. (5/7)

Plot of loop formation time vs receptor copy number.

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Sam Foley @samuelfoley.com · 11/06/2026

As an illustrative canonical example, we examine a model for the initiation of clathrin-mediated endocytosis. CME wants to take up cargo receptors; if the conditions are right, the self-assembly process itself can make the decision to start endocytosis. (3/7)

Schematic of our simplified coarse-grained self-assembly model for CME, along with a snapshot of an assembled clathrin coat after 60 seconds of simulation time.

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Sam Foley @samuelfoley.com · 11/06/2026

Information processing and decision-making in living cells is usually presented as requiring energy-consuming, switch-like biochemical reactions to ensure sensitive and robust response. We show that equilibrium self-assembly can accomplish similar feats via carefully tuned phase boundaries. (2/7)

Assembly phase diagram figure from the paper, along with plots of how the phase boundary changes with variation of the underlying parameters

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Sam Foley @samuelfoley.com · 11/06/2026

🧪⚛️ Our paper is finally published in Phys Rev Research! doi.org/10.1103/cnfz... Can cells make decisions using equilibrium physical principles, without resorting to irreversible, energy-consuming signaling cascades? We say yes, with the help of self-assembling membrane proteins! 🧵(1/7)

$Plot of fractional response vs receptor concentration, comparing three different "passive sensing mechanisms": direct binding from solution, membrane-assisted binding, and membrane self-assembly.$

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Sam Foley @samuelfoley.com · 10/06/2026

Getting mixed signals here

! High importance
This message was identified as junk.

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Sam Foley @samuelfoley.com · 19/05/2026

Throwback to a similar photo I took during a heat wave two years ago

Squirrel tries to cool off on the cement pedestal of a cat statue on the Johns Hopkins campus

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Sam Foley @samuelfoley.com · 19/05/2026

The squirrelometer is registering very hot today

A squirrel fully splooted on a shaded brick pathway, trying to stay cool in the heat

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Sam Foley @samuelfoley.com · 12/05/2026

Some more accidental art

A 2D matplotlib imshow plot that looks a lot like some kind of phase-separation kinetic coarsening simulation. Unfortunately, the subject matter has absolutely nothing to do with these topics, and the similarity is purely accidental in nature.

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Sam Foley @samuelfoley.com · 05/05/2026

If not for pets, why friend shaped? This fox has become a frequent sight on JHU campus and the adjacent Baltimore Art Museum sculpture garden, which is where I believe it has set up its den.