2025/03/03 by Aleksandra Nelson, Peter G. Wolynes, Nelson, Aleksandra +3
Biochemistry, Genetics and Molecular Biology · #Biological Physics (physics.bio-ph) #FOS: Physical sciences #Gene Regulatory Network Analysis #Mesoscale and Nanoscale Physics (cond-mat.mes-hall) #RNA and protein synthesis mechanisms #Soft Condensed Matter (cond-mat.soft) #Statistical Mechanics (cond-mat.stat-mech)
paper · pdf · doi:10.48550/arxiv.2503.01717
openalex publication_date 2025/03/03 · openalex created_date 2025/10/12 · openalex updated_date 2026/07/30
Complex gene regulatory networks often display emergent simple behavior. Sometimes this simplicity can be traced to a nearly equivalent energy landscape, but not always. Here, we show how a topological theory for stochastic and biochemical networks can predict phase transitions between dynamical regimes, where the simplest landscape paradigm would fail. We demonstrate the utility of this topological approach for a simple gene network, revealing a new oscillatory regime in addition to previously recognized multimodal stationary phases. We show how local winding numbers predict the steady-state locations in the single-mode and bimodal phases, and a flux analysis predicts the respective strengths of the steady-state peaks.