Baig, Y. | Search bioRxiv

bioRxiv2023

Anti-Diffusion in an Algae-Bacteria Microcosm: Photosynthesis, Chemotaxis, and Expulsion

In Nature there are significant relationships known between microorganisms from two kingdoms of life, as in the supply of vitamin B12 by bacteria to algae. Such interactions motivate general investigations into the spatio-temporal dynamics of metabolite exchanges. Here we study by experiment and theory a model system: a coculture of the bacterium B. subtilis, an obligate aerobe that is chemotactic to oxygen, and a nonmotile mutant of the alga C. reinhardtii, which photosynthetically produces oxygen when illuminated. Strikingly, when a shaft of light illuminates a thin, initially uniform suspension of the two, the chemotactic influx of bacteria to the photosyn-thetically active region leads to expulsion of the algae from that area. This effect arises from algal transport due to spatially-varying collective behavior of bacteria, and is mathematically related to the "turbulent diamagnetism" associated with magnetic flux expulsion in stars.

biophysics↗

bioRxiv2022

Distributed information encoding and decoding using self-organized spatial patterns

Dynamical systems often generate distinct outputs according to different initial conditions, and one can infer the corresponding input configuration given an output. This property captures the essence of information encoding and decoding. Here, we demonstrate the use of self-organized patterns, combined with machine learning, to achieve distributed information encoding and decoding. Our approach exploits a critical property of many natural pattern-formation systems: in repeated realizations, each initial configuration generates similar but not identical output patterns due to randomness in the patterning process. However, for sufficiently small randomness, different groups of patterns that arise from different initial configurations can be distinguished from one another. Modulating the pattern generation and machine learning model training can tune the tradeoff between encoding capacity and security. We further show that this strategy is applicable to non-biological dynamical systems and scalable by implementing the encoding and decoding of all characters of the standard English keyboard. Significance StatementSelf-organized patterns are ubiquitous in biology. They arise from interactions in and between cells, and with the environment. These patterns are often used as a composite phenotype to distinguish cell states and environment conditions. Conceptually, pattern generation under an initial condition is encoding; discerning the initial condition from the pattern represents decoding. Inspired by these examples, we develop a scheme, integrating mathematical modeling and machine learning, to use self-organization for secure and accurate information encoding and decoding. We show that this strategy is applicable to non-biological dynamical systems. We further demonstrate the scalability of the scheme by generating a complete mapping of the standard English keyboard, allowing encoding of English text. Our work serves as an example of nature-inspired computation.

systems biology↗