Protocol for potential energy-based bifurcation analysis, parameter searching, and phase diagram analysis of noncanonical bistable switches
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 d...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723006329 |
| _version_ | 1797648397193183232 |
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| author | Debashis Barik Soutrick Das |
| author_facet | Debashis Barik Soutrick Das |
| author_sort | Debashis Barik |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T15:31:37Z |
| format | Article |
| id | doaj.art-e20604b6adf3482b89e6d6da3cd8853d |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-11T15:31:37Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-e20604b6adf3482b89e6d6da3cd8853d2023-10-27T04:24:42ZengElsevierSTAR Protocols2666-16672023-12-0144102665Protocol for potential energy-based bifurcation analysis, parameter searching, and phase diagram analysis of noncanonical bistable switchesDebashis Barik0Soutrick Das1School of Chemistry, University of Hyderabad, Central University P.O., Hyderabad, Telangana 500046, India; Corresponding authorSchool of Chemistry, University of Hyderabad, Central University P.O., Hyderabad, Telangana 500046, IndiaSummary: 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.http://www.sciencedirect.com/science/article/pii/S2666166723006329BiophysicsSystems BiologyBiotechnology and BioengineeringComputer Sciences |
| spellingShingle | Debashis Barik Soutrick Das Protocol for potential energy-based bifurcation analysis, parameter searching, and phase diagram analysis of noncanonical bistable switches STAR Protocols Biophysics Systems Biology Biotechnology and Bioengineering Computer Sciences |
| title | Protocol for potential energy-based bifurcation analysis, parameter searching, and phase diagram analysis of noncanonical bistable switches |
| title_full | Protocol for potential energy-based bifurcation analysis, parameter searching, and phase diagram analysis of noncanonical bistable switches |
| title_fullStr | Protocol for potential energy-based bifurcation analysis, parameter searching, and phase diagram analysis of noncanonical bistable switches |
| title_full_unstemmed | Protocol for potential energy-based bifurcation analysis, parameter searching, and phase diagram analysis of noncanonical bistable switches |
| title_short | Protocol for potential energy-based bifurcation analysis, parameter searching, and phase diagram analysis of noncanonical bistable switches |
| title_sort | protocol for potential energy based bifurcation analysis parameter searching and phase diagram analysis of noncanonical bistable switches |
| topic | Biophysics Systems Biology Biotechnology and Bioengineering Computer Sciences |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723006329 |
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