Jafarnejadsani, Hamidreza, Kim, Jongmin, Hovakimyan, Naira and Kulkarni, Vishwesh V. (2016) Load capacity improvements in transcriptional systems using discrete-time L1-adaptive control. In: 8th International Workshop on Bio-Design Automation, Newcastle-upon-Tyne, UK, 16-18 Aug 2016. Published in: Proceedings of 8th International Workshop on Bio-Design Automation pp. 75-76.

PDF WRAP_syntheticbioloading-IWBDA2016abstract.pdf - Accepted Version - Requires a PDF viewer. Download (563Kb)

Request Changes to record.

Abstract

DNA-based circuits relying on predictable thermodynamics and kinetics of DNA strand interactions impart flexibility in synthesizing synthetic biological constructs and in coupling these circuits to in vivo processes [1, 2, 6, 7]. Here, we focus on the synthetic Kim-Winfree oscillator network, illustrated in Fig. 1(i), which is a simple but effective coupled oscillator system in which two DNA switches SW1 and SW2 are coupled through activator and inhibitor blocks realized by RNA signals and auxiliary DNA species (see [3]). A typical experimental realization is closed in the sense that once the operation starts, we do not either add any chemicals, especially NTP fuel, externally into the wet-lab apparatus or remove any chemicals, especially waste products, from the apparatus. Within the closed system, the oscillations are bound to die out sooner or later diminishing NTP fuel eventually stops supporting the production of RNA signals and accumulating waste products clog down the toeholds and, as a result, adversely affect the signal propagation. Furthermore, the oxidation effects and the pH variations tend to deactivate the enzymes. Loading poses an additional challenge since it increases the order and the uncertainty of the system indeed, these oscillators have recently been used in [8] to drive conformational changes of a DNA nanomechanical device called DNA tweezers. We show how L1-adaptive control can be used to mitigate these effects.

Item Type:	Conference Item (Poster)
Subjects:	Q Science > QK Botany Q Science > QP Physiology T Technology > TA Engineering (General). Civil engineering (General)
Divisions:	Faculty of Science, Engineering and Medicine > Engineering > Engineering
Library of Congress Subject Headings (LCSH):	Bioengineering, Biosynthesis, DNA, RNA
Journal or Publication Title:	Proceedings of 8th International Workshop on Bio-Design Automation
Official Date:	17 August 2016
Dates:	Date Event 17 August 2016 Published 10 June 2016 Accepted 24 March 2016 Submitted
Page Range:	pp. 75-76
Status:	Peer Reviewed
Publication Status:	Published
Date of first compliant deposit:	1 December 2016
Date of first compliant Open Access:	1 December 2016
Conference Paper Type:	Poster
Title of Event:	8th International Workshop on Bio-Design Automation
Type of Event:	Workshop
Location of Event:	Newcastle-upon-Tyne, UK
Date(s) of Event:	16-18 Aug 2016

Request changes or add full text files to a record

Repository staff actions (login required)

View Item

Downloads