Reverse engineering cellular decisions for hybrid reconfigurable network modeling

Howard A Blair, Jureepan Saranak, Kenneth W. Foster

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Cells as microorganisms and within multicellular organisms make robust decisions. Knowing how these complex cells make decisions is essential to explain, predict or mimic their behavior. The discovery of multi-layer multiple feedback loops in the signaling pathways of these modular hybrid systems suggests their decision making is sophisticated. Hybrid systems coordinate and integrate signals of various kinds: discrete on/off signals, continuous sensory signals, and stochastic and continuous fluctuations to regulate chemical concentrations. Such signaling networks can form reconfigurable networks of attractors and repellors giving them an extra level of organization that has resilient decision making built in. Work on generic attractor and repellor networks and on the already identified feedback networks and dynamic reconfigurable regulatory topologies in biological cells suggests that biological systems probably exploit such dynamic capabilities. We present a simple behavior of the swimming unicellular alga Chlamydomonas that involves interdependent discrete and continuous signals in feedback loops. We show how to rigorously verify a hybrid dynamical model of a biological system with respect to a declarative description of a cell's behavior. The hybrid dynamical systems we use are based on a unification of discrete structures and continuous topologies developed in prior work on convergence spaces. They involve variables of discrete and continuous types, in the sense of type theory in mathematical logic. A unification such as afforded by convergence spaces is necessary if one wants to take account of the affect of the structural relationships within each type on the dynamics of the system.

Original languageEnglish (US)
Title of host publicationProceedings of SPIE - The International Society for Optical Engineering
Volume8058
DOIs
StatePublished - 2011
EventIndependent Component Analyses, Wavelets, Neural Networks, Biosystems, and Nanoengineering IX - Orlando, FL, United States
Duration: Apr 27 2011Apr 29 2011

Other

OtherIndependent Component Analyses, Wavelets, Neural Networks, Biosystems, and Nanoengineering IX
CountryUnited States
CityOrlando, FL
Period4/27/114/29/11

Fingerprint

reverse engineering
Network Modeling
Reverse engineering
Reverse Engineering
Biological systems
Hybrid systems
Feedback
decision making
Decision making
Topology
Formal logic
mathematical logic
Feedback Loop
Unification
topology
Hybrid Systems
Biological Systems
cells
Algae
Attractor

ASJC Scopus subject areas

  • Applied Mathematics
  • Computer Science Applications
  • Electrical and Electronic Engineering
  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics

Cite this

Blair, H. A., Saranak, J., & Foster, K. W. (2011). Reverse engineering cellular decisions for hybrid reconfigurable network modeling. In Proceedings of SPIE - The International Society for Optical Engineering (Vol. 8058). [80581L] https://doi.org/10.1117/12.884364

Reverse engineering cellular decisions for hybrid reconfigurable network modeling. / Blair, Howard A; Saranak, Jureepan; Foster, Kenneth W.

Proceedings of SPIE - The International Society for Optical Engineering. Vol. 8058 2011. 80581L.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Blair, HA, Saranak, J & Foster, KW 2011, Reverse engineering cellular decisions for hybrid reconfigurable network modeling. in Proceedings of SPIE - The International Society for Optical Engineering. vol. 8058, 80581L, Independent Component Analyses, Wavelets, Neural Networks, Biosystems, and Nanoengineering IX, Orlando, FL, United States, 4/27/11. https://doi.org/10.1117/12.884364
Blair HA, Saranak J, Foster KW. Reverse engineering cellular decisions for hybrid reconfigurable network modeling. In Proceedings of SPIE - The International Society for Optical Engineering. Vol. 8058. 2011. 80581L https://doi.org/10.1117/12.884364
Blair, Howard A ; Saranak, Jureepan ; Foster, Kenneth W. / Reverse engineering cellular decisions for hybrid reconfigurable network modeling. Proceedings of SPIE - The International Society for Optical Engineering. Vol. 8058 2011.
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