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Formalizing Modularization and Data Hiding in Synthetic Biology

Lookup NU author(s): Dr Harold Fellermann, Professor Natalio Krasnogor

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Abstract

Biological systems employ compartmentalization and other co-localization strategies in order to orchestrate a multitude of biochemical processes by simultaneously enabling "data hiding" and modularization. This article presents recent research that embraces compartmentalization and co-location as an organizational programmatic principle in synthetic biological and biomimetic systems. In these systems, artificial vesicles and synthetic minimal cells are envisioned as nanoscale reactors for programmable biochemical synthesis and as chassis for molecular information processing. We present P systems, brane calculi, and the recently developed chemtainer calculus as formal frameworks providing data hiding and modularization and thus enabling the representation of highly complicated hierarchically organized compartmentalized reaction systems. We demonstrate how compartmentalization can greatly reduce the complexity required to implement computational functionality, and how addressable compartments permit the scaling-up of programmable chemical synthesis.


Publication metadata

Author(s): Fellermann H, Hadorn M, Fuchslin RM, Krasnogor N

Publication type: Article

Publication status: Published

Journal: ACM Journal on Emerging Technologies in Computing Systems (JETC)

Year: 2014

Volume: 11

Issue: 3

Print publication date: 01/12/2014

ISSN (print): 1550-4832

ISSN (electronic): 1550-4840

Publisher: ACM

URL: http://dx.doi.org/10.1145/2667231

DOI: 10.1145/2667231


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