Self-organized computation in the far-from-equilibrium cell

Abstract

Recent progress in our understanding of the physics of self-organization in active matter has pointed to the possibility of spontaneous collective behaviors that effectively compute things about the patterns in the surrounding patterned environment. Here, we describe this progress and speculate about its implications for our understanding of the internal organization of the living cell.

FIG. 1.

Some changes in the spatial coordinates describing the molecules in a cell may involve transport of a macromolecule from one location to another. For example, the coordinate vector $\overrightarrow{X}$ might describe the center of mass of a protein (blue) whose own enzymatic activity might cause it to diffuse more rapidly than other non-catalytic proteins of comparable size and shape (red and green).

FIG. 2.

Two assembly states described by different coordinate values X_A and X_B are separated by a barrier and differ in energy (which increases in the upwards vertical direction). In thermal equilibrium (above), the Boltzmann distribution dictates that probability density should accumulate more at X_B, which has lower energy. However, in the presence of nonequilibrium driving (orange), it is possible for external forcing to pump probability density over the barrier, such that it accumulates in the higher energy state. One possible mechanism for this might be if the assembled structure corresponding to X_B is better at absorbing work energy from the patterned external drive than the assembled structure described by X_A.

FIG. 3.

Some changes in the spatial coordinates describing the molecules in a cell may involve chemical transformations. For example, the coordinate vector $\overrightarrow{X}$ might describe the atomic degrees of freedom of a protein (blue) whose hydrolysis might be catalyzed by a protease (red) either with or without active chemical driving (orange).

FIG. 4.

Some changes in the spatial coordinates describing the molecules in a cell may involve structural transformations. For example, the coordinate vector $\overrightarrow{X}$ might describe the configurational degrees of freedom of a protein with a misfolded (green) and natively folded (blue) conformational states whose native folding might be catalyzed by a chaperone protein (red), usually with the assistance active chemical driving (orange).