Load Capacity Improvements in Nucleic Acid Based Systems Using Discrete-Time Feedback Control

Hamidreza Jafarnejadsani, Jongmin Kim, Vishwesh Kulkarni, Naira Hovakimyan

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Kim and Winfree have synthesized a well-known network of transcriptional oscillators in vitro using a modular architecture of synthetic gene analogues and a few enzymes that, in turn, could be used to drive a variety of downstream circuits and nanodevices. However, these oscillators are sensitive to initial conditions and downstream load processes. Furthermore, the oscillations are not sustained since the inherently closed design suffers from enzyme deactivation, NTP fuel exhaustion, and waste product build up. Recently, we had shown that a partially open architecture in which a continuous-Time L1 adaptive controller, implemented inside an in silico computer that resides outside the wet-lab apparatus, can ensure sustained tunable oscillations in two specific designs of the Kim-Winfree oscillator networks. Here, we present its discrete-Time version. As before, we consider two broad cases of operation: (1) the oscillator network operating in isolation, and (2) the oscillator network driving a DNA tweezer subject to a variable load. In both scenarios, our simulation results show a significant improvement in the tunability and robustness of these oscillator networks. Our approach can be easily adopted to improve the loading capacity of a wide range of synthetic biological devices.

Original languageEnglish
Title of host publication2018 5th International Conference on Control, Decision and Information Technologies, CoDIT 2018
Pages1-6
Number of pages6
ISBN (Electronic)9781538650653
DOIs
StatePublished - 22 Jun 2018
Event5th International Conference on Control, Decision and Information Technologies, CoDIT 2018 - Thessaloniki, Greece
Duration: 10 Apr 201813 Apr 2018

Publication series

Name2018 5th International Conference on Control, Decision and Information Technologies, CoDIT 2018

Conference

Conference5th International Conference on Control, Decision and Information Technologies, CoDIT 2018
Country/TerritoryGreece
CityThessaloniki
Period10/04/1813/04/18

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