Biology subjects

Fahimi, P.

Publications and source records attributed to Fahimi, P..

3 recordsLinked to original sources

bioRxiv2026

Hierarchical Value of Information in Microbial Predator-Prey Interactions

Information is fundamental to biological survival, but the amount of information and its biological value are not equivalent. Shannon information quantifies uncertainty reduction, whereas Volkenstein's value of information measures how information changes the probability of a biologically relevant outcome. Although originally developed for molecular biology contexts, the latter concept has rarely been applied to environmental sensing and ecological interactions. Here we develop a value-of-information framework for microbial predator-prey interactions based on hydrodynamic sensing, in which prey detect fluid disturbances generated by approaching predators. Using a mechanistic model that incorporates sensory thresholds, memory, false alarms, biological benefits and costs, and predator encounter probability, we characterize mutual information from three hierarchical measures of biological value: encounter-conditional value, ecological value, and lifetime fitness value. The framework reveals how small amounts of sensory information can produce disproportionately large survival benefits during predator encounters, generating encounter-level value amplification in which biological value exceeds Shannon information. However, although global sensitivity analysis shows that such amplification is common, it is not universal and becomes progressively diluted at broader ecological and lifetime scales by encounter rarity, background noise, and sensory costs. Across most parameter combinations, the encounter-conditional value exceeded the ecological value, which in turn exceeded the lifetime fitness value. These results demonstrate that environmental sensing should be evaluated not only by how accurately it represents the external world, but by how strongly it changes biologically relevant outcomes. More broadly, the framework extends Volkenstein's concept of information value to ecological interactions and provides a quantitative framework for predicting when environmental information enhances survival and fitness, thereby providing a platform for explaining the evolution, maintenance, diversification, and loss of sensory systems.

ecology↗

bioRxiv2026

Intrinsic electrostatics of ATP synthase modulate the proton motive force across species

ATP synthase functions within a highly structured electrostatic environment, but comparative information on its intrinsic protein electrostatics across species remains limited. Here, we analyze 178 crystallographic and cryo-EM ATP synthase structures from 17 species using a consistent Poisson-Boltzmann workflow. The calculations reveal reproducible species-dependent axial electrostatic asymmetries across the Fo-F1 complex, with plane-averaged potential differences of approximately 10-20 mV between an entry-side axial window (z = -10 to +10 Angstrom) and an exit-side axial window (z = +50 to +70 Angstrom) in several taxa. The five available Homo sapiens structures display a consistent axial electrostatic orientation within this species, whereas broader variation is observed across the full multi-species dataset; these two observations reflect within-species and across-species comparisons, respectively. Membrane-mimicking low-dielectric slabs amplify the profiles and demonstrate the sensitivity of the electrostatic landscape to dielectric boundary conditions. We interpret these quantities as static, structure-derived electrostatic descriptors, not as independent membrane voltages or additive proton-motive-force terms. The results provide a comparative electrostatic atlas of ATP synthase and suggest testable hypotheses concerning local proton-pathway energetics, structural evolution, and inhibitor sensitivity.

biophysics↗

bioRxiv2026

Carbon-to-ATP Ratios Across the Kingdoms of Life

ATP is the major energy-carrying molecule in cells, driving chemical reactions for cell development and growth. A diverse set of metabolically active marine bacteria and unicellular eukaryotes appear to maintain an approximately constant cellular carbon-to-ATP ratio (C:ATP) of 250 (g/g), which has been used as a predictor of marine microbial biomass for about 60 years. We have compiled [~] 400 measurements of ATP and carbon content from more than 80 papers published between 1964 and 2024, spanning organisms from bacteria to animals and plants along with a wide range of tissues. These data show that the carbon-to-ATP ratio varies by a staggering six orders of magnitude, depending not only on physiological and environmental conditions but also on species, completely contradicting the long-standing assumption in the literature. Here we develop a theory for organismal C:ATP content based upon metabolic rate, ATP transportation time within the organism, and ratio of structural to functional carbon within an organism, accentuating why such a deviation from 250 should be expected. Our model predicts both the median and variation in C:ATP ratios across organisms across the tree of life. We find the median C:ATP is typically within a factor of two of 250 for bacteria and unicellular marine eukaryotes. The ratio is notably lower in multicellular animals and higher for leaves and roots of land plants. Eukaryotic photosynthetic organisms have a median C:ATP > 250, which we attribute mainly to the proximity of mitochondria and chloroplasts, both of which tend to be near ATP consumption sites, thereby reducing ATP transport time relative to heterotrophs. Within broad taxonomic groups we predict variation of six orders of magnitude in C:ATP due to differences in biomass-normalized metabolic rate and the amount of non-metabolically active, structural material in organisms.

ecology↗