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

Debashis Barik; Soutrick Das

doi:10.1016/j.xpro.2023.102665

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

STAR Protoc. 2023 Dec 15;4(4):102665. doi: 10.1016/j.xpro.2023.102665. Epub 2023 Oct 31.

Authors

Debashis Barik¹, Soutrick Das²

Affiliations

¹ School of Chemistry, University of Hyderabad, Central University P.O., Hyderabad, Telangana 500046, India. Electronic address: dbariksc@uohyd.ac.in.
² School of Chemistry, University of Hyderabad, Central University P.O., Hyderabad, Telangana 500046, India.

Abstract

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.

Keywords: Biophysics; Biotechnology and Bioengineering; Computer Sciences; Systems Biology.

MeSH terms

Signal Transduction*