#27 · Systems biology

ATP level and phosphorylation free energy set trigger-wave speed and nucleus size

The three preprints share a modeling stance in which an explicit parameter is varied and its effect on a dynamical output is characterized within a constrained theoretical framework. The reaction-diffusion study presents a thermodynamically consistent description in which ATP level and phosphorylation free energy modulate trigger-wave speed, direction, and critical nucleus size. The synaptic crowding study derives an exact in-degree solution for a minimal wiring rule, showing that it yields small-world structure and shapes attractor basins in threshold network dynamics. The breast cancer study analyzes an NF-kB-centered gene regulatory network with HER2+ and TNBC attractors, linking phase-space distance and bifurcation structure to phenotypic plasticity. What is distinctive is the use of thermodynamic or analytically tractable formulations so that descriptor values trace back to model structure. These thread-level claims remain provisional pending review.