Fatty polymers and water, with and without soap

This is an attempt at simulating the effect of soap, by comparing a simulation including only "fat" and water molecules with another one, in which part of the molecules have a polar end, modeling soap. It is a very simplified model of the real process, and I don't claim the result to be particularly convincing, though it seems the molecules mix slightly better in the presence of soap. Feel free to propose improvements if you are knowledgeable about how soap works.
Water and fat do not easily mix. This is related to the fact that water molecules are polar, while fats are not. Soap molecules consist of a hydrophobic and lipophilic "tail", that tends to mix with fat molecules, and a hydrophilic and lipophobic "head", that tends to mix with water molecules. This helps mixing fat and water, and therefore cleaning objects, and people from fatty dirt particles.
This simulation shows a simple model for soap molecules, interacting with water molecules. The soap molecules consist in a tail made of ten neutral atoms, and a head consisting of two atoms of opposite charge. The soap molecules tend to latch on the oxygen atoms in water molecules. There are periodic boundary conditions, and the temperature is controlled by a thermostat with slowly decreasing temperature.
This simulation has two parts, showing the evolution with and without "soap" molecules:
Without soap: 0:00
With soap: 1:43
The particles' color depends on their type. The background indicates the local charge density, slightly averaged over space and time. In the second part, the particles' color hue depends on their kinetic energy.
To save on computation time, particles are placed into a "hash grid", each cell of which contains between 3 and 10 particles. Then only the influence of other particles in the same or neighboring cells is taken into account for each particle.
The temperature is controlled by a thermostat, implemented here with the "Nosé-Hoover-Langevin" algorithm introduced by Ben Leimkuhler, Emad Noorizadeh and Florian Theil, see reference below. The idea of the algorithm is to couple the momenta of the system to a single random process, which fluctuates around a temperature-dependent mean value. Lower temperatures lead to lower mean values.
The Lennard-Jones potential is strongly repulsive at short distance, and mildly attracting at long distance. It is widely used as a simple yet realistic model for the motion of electrically neutral molecules. The force results from the repulsion between electrons due to Pauli's exclusion principle, while the attractive part is a more subtle effect appearing in a multipole expansion. For more details, see en.wikipedia.org/wiki/Lennard...
Render time: Part 1 - 15 minutes 54 seconds
Part 2 - 16 minutes 11 seconds
Compression: crf 23
Color scheme: Turbo, by Anton Mikhailov
gist.github.com/mikhailov-wor...
Music: Finding the Balance by Kevin MacLeod is licensed under a Creative Commons Attribution 4.0 licence. creativecommons.org/licenses/...
Source: incompetech.com/music/royalty-...
Artist: incompetech.com/
Reference: Leimkuhler, B., Noorizadeh, E. & Theil, F. A Gentle Stochastic Thermostat for Molecular Dynamics. J Stat Phys 135, 261-277 (2009). doi.org/10.1007/s10955-009-97...
www.maths.warwick.ac.uk/~theil...
Current version of the C code used to make these animations:
github.com/nilsberglund-orlea...
www.idpoisson.fr/berglund/sof...
Some outreach articles on mathematics:
images.math.cnrs.fr/_Berglund...
(in French, some with a Spanish translation)
#molecular_dynamics #ions #soap

[@garywhite2050]

LOVE THE TUNE WITH THIS ONE! And I NEVER use caps! 😂

[@claytoncoffman2951]

Why did you put a positive and a negative together in the head group? I know anionic surfactants like the ones used in shampoo have a fatty tail with a sulfate anion "head" - it's just a negative charge. There are also cationic and neurtral surfactants. Putting the posisitve and negative together I think is really blunting the effect though as the positive and negative are going to cancel out and cause weak and inspecific bonding.
I agree it's not that convincing, but I think that's because you're missing a key force. The evolution of oil droplet formation is stochastic, so for it to come to pass that the "fat" or rather oil molecules are more likely to stick together when they collide with each other. In nature there are like 4 intermolecular forces, two of which are important. The electromagnetic is the strongest, that's just positive negative attracting and repelling, you've got that. The next most important for this is going to be van der Waals force, which is a weak force that's between all molecules, it's strongest when they are touching but fades very quickly. This will allow "flat" molecules like your oils tend to stick together along each other's lengths more strongly than they interact with the water molecules. This force also increases with molecular weight, and since your oils are "heavier" than your water molecules, this should be even stronger between them. Over time these structures will grow larger and their maximum size determined by temperature. The higher the temperature the more likely the molecules are to "shake apart".
On a whole it seems like your attractive forces are on the whole too weak, and your temperature is too high or your repulsive force is too strong, I've seen sims like this before and the molecules clump very readily with just charge alone. I think the key will be having the ratio of your "positive-negative" attractions and you "universal, weaker, and biased to higher molecular weight molecules" forces in the right ratio.
I used to be a science teacher and I always wanted a nice sim like this to illustrate intramolecular forces work. There isn't one that's *perfect* though.
Check out:
mw.concord.org/nextgen/interactives/#charged-neutral-atoms
mw.concord.org/nextgen/interactives/#dipole-dipole-london-dispersion
mw.concord.org/nextgen/interactives/#oil-water

[@frostfox8813]

Интересно ^^

[@victor_anik]

too much rotation