Welcome to the new version of CaltechAUTHORS. Login is currently restricted to library staff. If you notice any issues, please email coda@library.caltech.edu
Published February 6, 2020 | Submitted
Report Open

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


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.

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.

Attached Files

Submitted - ykgm15-cdc_s.pdf


Files (624.3 kB)
Name Size Download all
624.3 kB Preview Download

Additional details

August 20, 2023
August 20, 2023