Simulations of biomolecule condensation for Stanford BIOC/BIOP/SBIO/BIOE 241

(C) R. Das, Stanford University 2019

What this is

This is a tiny sandbox for quickly modeling condensation of particles in a box to illustrate and understand some cool basic behaviors of biomolecular condensation:

• Ultrasensitivity
• Buffering [to do]

You need MATLAB to run it.

How to run it

There are a couple of useful tools in here...

simple_landscape_analysis

This computes the number of particles that remain free (vs. in a condensate) just assuming a simple model where:

• free particles (but not multimers) get a special loner_energy bonus (-2.0 kT)
• particles going into larger and larger multimers get a probability weight proportional to K^n where K is like an equilibrium constant for going into the condensate and n is the multimer stoichiometry.

If you just type at MATLAB

>> simple_landscape_analysis

You'll see a sharp transition as K increases, when the total number of particles is N = 100:

You can see a less sharp transition if N is reduced to 20 (check out alternative parameters in simple_landscape_analysis.m)

simulate_box

Actually simulate the grid of particles.

Just type in MATLAB

>> simulate_box

The default parameters simulate a 15x15 box, increasing the bond strength. Completing all 19 simulations takes about 10 minutes on a MacBook Pro (2.9GHz, i7).

Figure 1 show snapshots of the simulations as they are running.

After completion,

• Figure 1 shows the snapshot of the last simluation (which should be totally condensed)
• Figure 2 shows a scan of num_free with increasing bond strength. Should see a reasonably sharp transition:
• Figure 3 shows snapshots of all the different simulatios with increasing bond strength:
• Figure 4 is used to make a movie for K = 20. [Check the code for how to get other movies]