Work

Topology of the simplest gene switch

Year: 2025

Type: article

Abstract: 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.

Source: Physical Review Research

DOI: 10.1103/rr6n-fn82

Authors: Aleksandra Nelson, Peter Wolynes, Evelyn Tang

Institutions: Center for Theoretical Biological Physics, Rice University

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,625

Funders: National Science Foundation, Welch Foundation