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Full-Text Articles in Genetics and Genomics
Automated Requirements Analysis For A Molecular Watchdog Timer, Samuel J. Ellis, Eric R. Henderson, Titus H. Klinge, James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Divita Mathur, Andrew S. Miner
Automated Requirements Analysis For A Molecular Watchdog Timer, Samuel J. Ellis, Eric R. Henderson, Titus H. Klinge, James I. Lathrop, Jack H. Lutz, Robyn R. Lutz, Divita Mathur, Andrew S. Miner
Robyn Lutz
Dynamic systems in DNA nanotechnology are often programmed using a chemical reaction network (CRN) model as an intermediate level of abstraction. In this paper, we design and analyze a CRN model of a watchdog timer, a device commonly used to monitor the health of a safety critical system. Our process uses incremental design practices with goal-oriented requirements engineering, software verification tools, and custom software to help automate the software engineering process. The watchdog timer is comprised of three components: an absence detector, a threshold filter, and a signal amplifier. These components are separately designed and verified, and only then composed …
Requirements Analysis For A Product Family Of Dna Nanodevices, Robyn R. Lutz, Jack H. Lutz, James I. Lathrop, Titus H. Klinge, Divita Mathur, D. M. Stull, Taylor G. Bergquist, Eric R. Henderson
Requirements Analysis For A Product Family Of Dna Nanodevices, Robyn R. Lutz, Jack H. Lutz, James I. Lathrop, Titus H. Klinge, Divita Mathur, D. M. Stull, Taylor G. Bergquist, Eric R. Henderson
Robyn Lutz
DNA nanotechnology uses the information processing capabilities of nucleic acids to design self-assembling, programmable structures and devices at the nanoscale. Devices developed to date have been programmed to implement logic circuits and neural networks, capture or release specific molecules, and traverse molecular tracks and mazes. Here we investigate the use of requirements engineering methods to make DNA nanotechnology more productive, predictable, and safe. We use goal-oriented requirements modeling to identify, specify, and analyze a product family of DNA nanodevices, and we use PRISM model checking to verify both common properties across the family and properties that are specific to individual …
Engineering And Verifying Requirements For Programmable Self-Assembling Nanomachines, Robyn Lutz, Jack Lutz, James Lathrop, Titus Klinge, Eric Henderson, Davita Mathur, Dalia Abo Sheasha
Engineering And Verifying Requirements For Programmable Self-Assembling Nanomachines, Robyn Lutz, Jack Lutz, James Lathrop, Titus Klinge, Eric Henderson, Davita Mathur, Dalia Abo Sheasha
Robyn Lutz
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 …