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Chemotactic cells working together balance sensing and signal modulation, showing how shared information speeds and stabilizes collective search for targets.

From the article:

Optimality Theory of Stigmergic Collective Information Processing by Chemotactic Cells
Masaki Kato and Tetsuya J. Kobayashi
PRX Life 3, 043005 (2025)

ARTICLES

Eco-Evolutionary Constraints for the Endemicity of Rapidly Evolving Viruses

David Soriano-Paños

PRX Life 3, 043001 (2025) - Published 2 October, 2025

An eco-evolutionary framework including evolution in infectiousness and antigenic features reveals that mildly infectious viruses might be more likely to become endemic that those with higher infectiousness.

Cyclo-Stationary Distributions of mRNA and Protein Counts for Random Cell Division Times

Syed Yunus Ali, Aditya Saran, Ashok Prasad, Abhyudai Singh, and Dibyendu Das

PRX Life 3, 043002 (2025) - Published 7 October, 2025

The study examines noise contributions from random cell division times, extending beyond the effects of gene expression and partitioning noise, and presents the resulting analytical cyclo-stationary distributions of mRNA and protein counts.

Phase Transitions in in vivo or in vitro Populations of Spiking Neurons Belong to Different Universality Classes

Braden A. W. Brinkman

PRX Life 3, 043003 (2025) - Published 9 October, 2025

Scaling theories differ for spike response models of in vitro and in vivo circuits — representing different universality classes that both exhibit anomalous scaling at a critical balance of inhibition and excitation.

Diverse Mean-Field Dynamics of Clustered, Inhibition-Stabilized Hawkes Networks via Combinatorial Threshold-Linear Networks

Caitlin Lienkaemper and Gabriel Koch Ocker

PRX Life 3, 043004 (2025) - Published 14 October, 2025

Networks of stochastically spiking neurons can be reduced to combinatorial threshold-linear networks, representing a new tool for analyzing neural networks with clustered connectivity.

Optimality Theory of Stigmergic Collective Information Processing by Chemotactic Cells

Masaki Kato and Tetsuya J. Kobayashi

PRX Life 3, 043005 (2025) - Published 15 October, 2025

Chemotactic cells working together balance sensing and signal modulation, showing how shared information speeds and stabilizes collective search for targets.

bioSBM: A Random Graph Model to Integrate Epigenomic Data in Chromatin Structure Prediction

Alex Chen Yi Zhang, Angelo Rosa, and Guido Sanguinetti

PRX Life 3, 043006 (2025) - Published 21 October, 2025

A graph-based generative model designed to capture long-range chromatin interaction patterns from Hi-C data reveals a latent structure of chromatin interactions in the GM12878 lymphoblastoid cell line that strongly align with known biological annotations.

Mathematical Framework for Hierarchical Cell Identity Control by Collective Enhancer Dynamics

Anton Grishechkin, Abhirup Mukherjee, and Omer Karin

PRX Life 3, 043007 (2025) - Published 23 October, 2025

Hierarchical cell identity emerges from the dynamic interplay between competition among enhancers for the recruitment of epigenetic readers and cooperation among enhancers in activating shared transcriptional programs.

Cell Divisions Imprint Long Lasting Elastic Strain Fields in Epithelial Tissues

Ali Tahaei, Romina Piscitello-Gómez, S. Suganthan, Greta Cwikla, Jana F. Fuhrmann, Natalie A. Dye, and Marko Popović

PRX Life 3, 043008 (2025) - Published 5 November, 2025

Inferring division-induced force dipoles from tissue strain fields quantifies mechanical forces of cell division and their impact on tissue mechanics.

Morphogen Patterning in Dynamic Tissues

Alex M. Plum and Mattia Serra

PRX Life 3, 043009 (2025) - Published 6 November, 2025

A mathematical framework reveals how morphogenesis mediates morphogen transport and compartmentalization, formalizes cell-cell interaction ranges in dynamic tissues, and provides new nondimensional numbers to assess when tissue deformation affects patterning.

Connection between Hebbian Unlearning and Steady States Generated by Nonequilibrium Dynamics

Agnish Kumar Behera, Matthew Du, Uday K. Jagadisan, Srikanth Sastry, Madan Rao, and Suriyanarayanan Vaikuntanathan

PRX Life 3, 043010 (2025) - Published 12 November, 2025

Active persistent dynamics are shown to mimic some aspects of Hebbian unlearning — suggesting that nonequilibrium dynamics can provide an alternative way to improve associative recall in neural network models.

Generic Temperature Response of Large Biochemical Networks

Julian B. Voits and Ulrich S. Schwarz

PRX Life 3, 043011 (2025) - Published 13 November, 2025

Combining concepts from stochastic dynamics, statistical physics and graph theory, a new theoretical study shows that large biochemical networks should have a quadratic Arrhenius plot, as seen in developmental processes.

Cellular Flow Architecture Exposes the Hidden Mechanics of Biological Matter

Tianxiang Ma, Valeriia Grudtsyna, Robin V. Bölsterli, and Amin Doostmohammadi

PRX Life 3, 043012 (2025) - Published 18 November, 2025

Lagrangian coherent structures precede and drive long-term intercellular stress reorganization and are physically governed by the mechanical properties of intercellular junctions — revealing how cell motion can be used to infer biomechanical metrics.

Stabilization of Active Tissue Deformation by a Dynamic Signaling Gradient

Muhamet Ibrahimi and Matthias Merkel

PRX Life 3, 043013 (2025) - Published 19 November, 2025

Oriented tissue deformation (convergent extension) is unstable when signaling-gradient-controlled active stresses contract the tissue along the gradient direction, even for large diffusion, but it can be stable when active stresses extend the tissue in gradient direction.

Physical Confinement Regulates Transitions in Nematode Motility

M Sreepadmanabh, Saheli Dey, Sayan Kundu, Ashitha B. Arun, Sandhya P. Koushika, Shashi Thutupalli, Duncan Hewitt, and Tapomoy Bhattacharjee

PRX Life 3, 043014 (2025) - Published 24 November, 2025

Within viscoelastic 3D granular matrices, C. elegans transition from inefficient thrashing under low confinement to efficient crawling under high confinement - a response dictated by the worm’s physical interaction with its environment, without involving soft-touch mechanosensation.

3D Agent-Based Modeling without Chemical Signaling Recreates Collective Behaviors seen in Myxococcus xanthus Colonies

Katherine Copenhagen, Matthew Black, and Joshua W. Shaevitz

PRX Life 3, 043015 (2025) - Published 1 December, 2025

Motility changes during starvation preserve nematic order but intensify defect-driven flows, promoting aggregation in Myxococcus xanthus.

Single Cells Can Resolve Graded Stimuli

Mirna Kramar, Lauritz Hahn, Aleksandra M. Walczak, Thierry Mora, and Mathieu Coppey

PRX Life 3, 043016 (2025) - Published 2 December, 2025

By quantifying the information transmitted from receptor to ERK, the study shows that individual cells can resolve graded stimuli, transmitting over 2 bits of information even with brief, sparse inputs.

Energy Injection in an Epithelial Cell Monolayer Indicated by Negative Viscosity

Molly McCord and Jacob Notbohm

PRX Life 3, 043017 (2025) - Published 4 December, 2025

Negative effective viscosity in epithelial monolayers marks regions wherein cells expend more metabolic energy and move faster, hence quantifying the flow of energy in tissues.

Compositional Control of Aging Kinetics in TDP-43 Condensates

Nuria H. Espejo, Alejandro Feito, Ignacio Sanchez-Burgos, Adiran Garaizar, Maria M. Conde, Antonio Rey, Eduardo Pedraza, Alejandro Castro, Rosana Collepardo-Guevara, Andres R. Tejedor, and Jorge R. Espinosa

PRX Life 3, 043018 (2025) - Published 11 December, 2025

While arginine-rich peptides accelerate the nucleation of inter-protein beta-sheet structures in TDP-43, RNA and HSP70 slow their emergence — revealing the importance of client biomolecules in the stability and aging kinetics of RNA binding proteins.

Noninvasive, Label-Free Imaging of Freely Moving C. elegans Nematodes

Rongbiao Tang, Feixiang Wang, Ke Li, and Yanan Fu

PRX Life 3, 043019 (2025) - Published 17 December, 2025

By combining ultrafast phase-contrast X-ray imaging and phase-contrast computed tomography imaging, this study details a way to simultaneously visualize nematode locomotion and obtain precise, whole-organism morphometric measurements.

REVIEW ARTICLES

Quantum Computing for Genomics: Conceptual Challenges and Practical Perspectives

Aurora Maurizio and Guglielmo Mazzola

PRX Life 3, 047001 (2025) - Published 30 October, 2025

This review article on quantum computing applications in genomics highlights its realistic potential for the field, theoretical limitations, and the conditions that a problem and an algorithm must satisfy to benefit from quantum speedup.

ERRATA

Erratum: Uncovering universal characteristics of homing paths using foraging robots [PRX Life 2, 033007 (2024)]

Somnath Paramanick, Arup Biswas, Harsh Soni, Arnab Pal, and Nitin Kumar

PRX Life 3, 049901 (2025) - Published 24 December, 2025

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