Brian Camley

@diffusiveblob.bsky.social

1363 Followers 1005 Following

Computational biophysics, cell motility, collective motion, soft matter, horses, cats. Associate Prof at Johns Hopkins Physics+Biophysics departments.

for _ in tqdm.tqdm(range(1000), desc="Active dynamics"):
diag = sim.build()
forces = diag["forces"]

active_velocity = v0 * np.column_stack((np.cos(theta), np.sin(theta)))

pts += (mu * forces + active_velocity) * dt

# Gaussian white noise
theta += np.sqrt(2 * Dr * dt) * np.random.randn(N)

sim.update_positions(pts)

Movie S3 from the linked preprint, showing a region of high density moving in a circle in a region where friction is patterned as a spiral

Derivation of the Green's function for an oscillator from Srednicki's QFT textbook, https://web.physics.ucsb.edu/~mark/ms-qft-DRAFT.pdf - discussion from Eq. 7.12 to 7.14 in that PDF

screenshot of nature's search feature that shows you can only enter "start page / article no."

Model showing SNR predicted to switch sign as a function of distance along a device so cells to the left are attracted and cells to the right are repelled, leading to a stable equilibrium

Fig. 4B of the preprint shows SNR is mostly positive if CCR7 cannot internalize

Fig. 4A of the preprint shows SNR switches from positive to negative to positive as a function of ligand concentration [L]mid in a linear gradient from 0 to 2 [L]mid

Description of Fig. 3 AB from the text: "The form of Eq. (11) as a ratio of two nonlinear functions can lead to multiple switches between chemorepulsion and attraction. We show an example in Fig. 3A in which I undergoes a rapid transition between its basal level and a high level as pb increases (i.e. a large hI), and A slowly saturates as pb increases. We see that at small pb, I does not change much, while A increases – leading to an increase in R = A/I. Then, at the transition point where pb ≈ KI, I increases rapidly with pb, leading to a decrease in R. Then, as I saturates, while A continues to increase, R will increase again. We plot dR/dpb for this case in Fig. 3B, seeing that we have chemoattraction at small pb and large pb, but in the intermediate range
where dR/dpb is negative, there will be chemorepulsion; this
chemorepulsive region is shaded in blue throughout Fig. 3."

Nonlinear feedforward loop with bound receptor activating A, I nonlinearly, and A activating R, I inhibiting R, and R the response - sets the direction the cell travels

Fig 1AB of the paper, 1A showing the model for ligand-dependent internalization, Fig 1B showing how the % surface receptor decreases with time in model and experiment

Crop from Movie S2 from Malet-Engra et al. Current Biology 2015, doi: 10.1016/j.cub.2014.11.030 . Left panel: JVM3 cells are attracted to CCL19 gradients in 0-100 ng/mL gradient. Right panel: JVM3 cells are repelled from CCL19 in 0-500 ng/mL gradient. In both cases large clusters of cells are attracted to CCL19.

$When ligand concentration c is changed, allosteric protein responds, and this leads the fraction of receptors bound to adapt back to 0.5$

$Diagram of feedback mechanism: G, which can bind to the receptor, switches to G*, which cannot. This switch is promoted by the bound receptor fraction, and the reverse by the unbound receptor fraction.$

Diagram of "ternary complex" model with receptor switching between unbound, ligand-bound, ligand+allosteric protein bound, and only allosteric protein bound states

J. Chem. Phys. article with ad "Download to use extension (Free)" that presumably links to malware

Output showing we are at 299% of our file quota of 2,048,000

ChatGPT transcript - also shows the code generated:

What's 8.8-8.11?

ChatGPT said:
8.8
−
8.11
=
−
0.31
8.8−8.11=−0.31

You said:
Can you write some code to check that and run it?

ChatGPT said:
The code shows that
8.8
−
8.11
=
0.69
8.8−8.11=0.69, not
−
0.31
−0.31.
I made a sign mistake earlier — 8.8 is larger than 8.11, so the difference is positive.

You said:
How many bs are in blueberry?

ChatGPT said:
There are 2 “b”s in “blueberry.”
(and it did this by generating code to count them)

Streamlines showing the direction cells exposed to two competing signals (A and B) travel

Clip of Google scholar entry for paper "Emergent collective chemotaxis without single-cell gradient sensing" falsely claiming it's published in Biophysical Journal

Movie showing HL-60 cell with fluorescently labeled protein, with the protein redistributing after a field is applied, leading to the cell turning and following the field