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Title: Formalizing modularization and data hiding in synthetic biology
Authors : Fellermann, Harold
Krasnogor, Natalio
Hadorn, Maik
Füchslin, Rudolf Marcel
Published in : ACM Journal on Emerging Technologies in Computing Systems
Volume(Issue) : 11
Issue : 3/24
Publisher / Ed. Institution : Association for Computing Machinery
Issue Date: 2014
License (according to publishing contract) : Licence according to publishing contract
Type of review: Peer review (Publication)
Language : English
Subject (DDC) : 572: Biochemistry
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.
Departement: School of Engineering
Publication type: Article in scientific Journal
DOI : 10.1145/2667231
ISSN: 1550-4832
Appears in Collections:Publikationen School of Engineering

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