Protocol for potential energy-based bifurcation analysis, parameter searching, and phase diagram analysis of noncanonical bistable switches

Abstract

Summary: We have explored the design principles of noncanonical bistable switches using high-throughput bifurcation analysis of positive feedback loops under dual signaling. Here, we present a protocol to carry out bifurcation analysis using pseudo-potential energy of the dynamical system. We also describe steps to perform automated parameter searching for canonical and noncanonical switches and multi-parameter phase diagram analysis of these switches.For complete details on the use and execution of this protocol, please refer to Das et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Biophysics
• Systems Biology
• Biotechnology and Bioengineering
• Computer Sciences