Requirements analysis for a product family of DNA nanodevices

Abstract

Abstract-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 products. Challenges to doing requirements engineering in this domain include the errorprone nature of nanodevices carrying out their tasks in the probabilistic world of chemical kinetics, the fact that roughly a nanomole (a 1 followed by 14 0s) of devices are typically deployed at once, and the difficulty of specifying and achieving modularity in a realm where devices have many opportunities to interfere with each other. Nevertheless, our results show that requirements engineering is useful in DNA nanotechnology and that leveraging the similarities among nanodevices in the product family improves the modeling and analysis by supporting reuse.

Automated requirements analysis for a molecular watchdog timer

“…This technique challenges the goal graph by identifying candidate obstacles to the satisfaction of the goals, assessing the likelihood and criticality of those obstacles, and controlling or resolving them, e.g., by adding or modifying goals. We found in previous work on a product family of DNA nanopliers that the use of a goal oriented requirements engineering approach, with a focus on early analysis of the risks to satisfying the goals [50], worked well in helping find and remedy missing and unrealistic requirements [33,34].…”

The Role of Environmental Assumptions in Failures of DNA Nanosystems

“…In that case the scientists will not be confident that the nanosystem reliably does what it is supposed to do. We thus focus on environmental failures that are significant enough that they have been reported to prevent a threshold occurrence [6] of the required behavior from occurring in previous nanosystems.…”

“…The new failure frame technique that we describe arose from our recent work in a relatively new field of computation, that of molecular programming [6], [7]. Molecular programming is programming in the literal sense, in that DNA can be programmed to implement computational algorithms, and DNA tile self-assembly is Turing universal [8].…”

Devices for safety-critical molecular programmed systems

“…We specified the system goals for the MWT using an approach introduced in [45,46] based on the KAOS [64] method developed by Axel van Lamsweerde. One of the primary advantages of goal-based approaches is in the refinement process.…”

“…Techniques such as goal oriented requirements engineering [64], a process by which informal system goals are turned into a formal specification, aid in the analysis of a system's intended use for possible faults or failures. Previously, goal oriented requirements engineering has been used to analyze a molecular system and find obstacles that would hinder correct operation [45,46]. Formal methods, specifically model checking, have been shown to be useful in the study of programmed nanodevices [38].…”