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Global Dynamical Structure Reconstruction from Reconstructed Dynamical Structure Subnetworks: Applications to Biochemical Reaction Networks

Yeung, Enoch and Kim, Jongmin and Gonçalves, Jorge M. and Murray, Richard M. (2015) Global Dynamical Structure Reconstruction from Reconstructed Dynamical Structure Subnetworks: Applications to Biochemical Reaction Networks. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200205-081111268

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Abstract

In this paper we consider the problem of network reconstruction, with applications to biochemical reaction networks. In particular, we consider the problem of global network reconstruction when there are a limited number of sensors that can be used to simultaneously measure state information. We introduce dynamical structure functions as a way to formulate the network reconstruction problem and motivate their usage with an example physical system from synthetic biology. In particular, we argue that in synthetic biology research, network verification is paramount to robust circuit operation and thus, network reconstruction is an invaluable tool. Nonetheless, we argue that existing approaches for reconstruction are hampered by limited numbers of biological sensors with high temporal resolution. In this way, we motivate the global network reconstruction problem using partial network information and prove that by performing a series of reconstruction experiments, where each experiment reconstructs a subnetwork dynamical structure function, the global dynamical structure function can be recovered in most cases. We illustrate these reconstruction techniques on a recently developed four gene biocircuit, an event detector, and show that it is capable of differentiating the temporal order of input events.


Item Type:Report or Paper (Discussion Paper)
ORCID:
AuthorORCID
Yeung, Enoch0000-0001-7630-7429
Kim, Jongmin0000-0002-2713-1006
Gonçalves, Jorge M.0000-0002-5228-6165
Murray, Richard M.0000-0002-5785-7481
Additional Information:This work was supported by the Engineering and Physical Sciences Research Council, the Luxembourg National Research Foundation, Air Force Office of Scientific Research, Grant FA9550-14-1-0060, the Defense Advanced Research Projects Agency, Grant HR0011-12-C-0065, the National Science Foundation, Grant 1317291, and the John and Ursula Kanel Charitable Foundation.
Funders:
Funding AgencyGrant Number
Engineering and Physical Sciences Research Council (EPSRC)UNSPECIFIED
Luxembourg National Research FoundationUNSPECIFIED
Air Force Office of Scientific Research (AFOSR)FA9550-14-1-0060
Defense Advanced Research Projects Agency (DARPA)HR0011-12-C-0065
NSFCCF-1317291
John and Ursula Kanel Charitable FoundationUNSPECIFIED
Record Number:CaltechAUTHORS:20200205-081111268
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200205-081111268
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:101131
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:06 Feb 2020 18:01
Last Modified:11 Nov 2020 20:48

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