NDLI: Engineering and verifying requirements for programmable self-assembling nanomachines

Content Provider	IEEE Xplore Digital Library
Author	Lutz, R. Lutz, J. Lathrop, J. Klinge, T. Henderson, E. Mathur, D. Sheasha, D.A.
Copyright Year	2012
Description	Author affiliation: Department of Computer Science, Iowa State University, Ames, IA 50011 USA (Lutz, R.; Lutz, J.; Lathrop, J.; Klinge, T.; Sheasha, D.A.) \|\| Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA (Henderson, E.; Mathur, D.)
Abstract	We propose an extension of van Lamsweerde's goal-oriented requirements engineering to the domain of programmable DNA nanotechnology. This is a domain in which individual devices (agents) are at most a few dozen nanometers in diameter. These devices are programmed to assemble themselves from molecular components and perform their assigned tasks. The devices carry out their tasks in the probabilistic world of chemical kinetics, so they are individually error-prone. However, the number of devices deployed is roughly on the order of a nanomole (a 6 followed by fourteen 0s), and some goals are achieved when enough of these agents achieve their assigned subgoals. We show that it is useful in this setting to augment the AND/OR goal diagrams to allow goal refinements that are mediated by threshold functions, rather than ANDs or ORs. We illustrate this method by engineering requirements for a system of molecular detectors (DNA origami “pliers” that capture target molecules) invented by Kuzuya, Sakai, Yamazaki, Xu, and Komiyama (2011). We model this system in the Prism probabilistic symbolic model checker, and we use Prism to verify that requirements are satisfied, provided that the ratio of target molecules to detectors is neither too high nor too low. This gives prima facie evidence that software engineering methods can be used to make DNA nanotechnology more productive, predictable and safe.
Starting Page	1361
Ending Page	1364
File Size	499038
Page Count	4
File Format	PDF
ISBN	9781467310666
ISSN	02705257
e-ISBN	9781467310673
e-ISBN	9781467310659
DOI	10.1109/ICSE.2012.6227079
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-06-02
Publisher Place	Switzerland
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	DNA Self-assembly Nanobioscience Shape Probabilistic logic Nanoscale devices molecular programming Requirements engineering validation and verification safety DNA nanotechnology
Content Type	Text
Resource Type	Article
Subject	Software

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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