Membranes, macro-molecules and passive/active transport across membranes

[BrainAnnex]

With the recently-released Beta 12 version, Life123 has by now established a substantial amount of the infrastructures for data science, software management and visualization, for diffusion and (single binding site) reactions.

It's now time to shift into a higher gear with the modeling... and start by introducing elements that have been on the table from the very inception of the project:

- membranes
- macro-molecules (with multiple binding sites)
- passive/active transport across membranes

One guiding criterion to model membranes is the great disparity between the puny thickness of biological membranes (around 4-5 nm) vs. the overwhelmingly larger size of cells (diameters around 0.1 to 5 μm for prokaryotes and some 10-100 μm for eukaryotes.)

We're talking about ratios (of membrane thickness to cell diameter) of some 1:20 to 1:25,000!

A handy source of typical biological values can be found on this site.

[BrainAnnex]

The newest release, Beta 13, rolled out a full implementation of the data structure in 1D, designed to be biologically relevant and extendable to 2D and 3D, plus functions for data management, visualization and reactions.

Diffusion across membranes (passive transport) is expected to be implemented in a few cycles of Beta releases. Membranes in 1-D can be done fairly easily, but the philosophy of the Life123 project is to look ahead at higher dimensions... and strive to do implementations that are conducive to being generalized to 2D and 3D.

A new page on membranes got added to the project's website: https://life123.science/membranes

[BrainAnnex]

Time for an update : it turned out that the initial design - envisioning membranes splitting system bins in 2 parts - seemed promising in 1D, but not easily scalable to 2D, and very hard to scale to 3D.

The project priority shifted to reactions in uniform compartments, including support for enzymatic reactions and a much-improved management of variable time steps.

But now, with the upcoming version RC3 (Release Candidate 3), the time is ripe for a return to membranes! A new way to model membranes is as entities placed in-between system bins rather than cutting thru them. So far, the outlook for the new approach is that it should be scalable to 2D and 3D - and also it appears it will be easier to combine the modeling of transport across membranes with diffusion in the membrane-surrounded organelles.

On the visualization front, as detailed in another thread, the Plotly library has risen to the occasion to display membranes in 1D and 2D : no need to turn to lower-level custom implementations :)