The Role of Environmental Assumptions in Failures of DNA Nanosystems

Abstract

Many failures arise from complex and imperfectly understood interactions of a computational system with aspects of the environment in which it operates. By environment we mean the computational system's broader context, also called the problem world. In this work, we propose a new analysis technique called failure frames, a variation of Jackson's problem frames, to identify and model classes of environmental assumptions whose violation is known from experience to have prevented the requirements from being satisfied. We use instances of failure frames, called failure diagrams, to make explicit in the requirements model the environmental assumptions that contributed to past failures. Developers want to reuse such knowledge of past failures to prevent failures in similar, new systems. We show that failure frames and failure diagrams can capture environmental assumptions that developers need to check in order to prevent recurrence of certain failures in similar application areas. The new failure frame approach that we describe arose from our work in molecular programming of DNA nanosystems. Inaccurate assumptions about the environment are a source of many failures in DNA nanosystems and can be extremely challenging to resolve. We describe the structure of a failure catalog for DNA nanosystems that we have prototyped for use by molecular programmers. We hypothesize that the failure frame approach and catalog can be broadly useful for reducing failure recurrence in other large, distributed applications with autonomous or nondeterministic behavior that must operate in uncertain environments.

Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community

“…It will be important to unravel the assembly kinetics at the single oligonucleotide level within a DNA construct in order to avoid or even harness such hybridization events . To this end, computational modeling , and resources cataloging common failures could vastly simplify and assist structural optimization without the need of iterative experimental work. For instance, software that can predict a library of potential DNA structures from a set of staple strands along with the probability of assembly of each possible structure would contribute to optimizing the design step, thereby mitigating unwanted byproducts.…”

Runtime Fault Detection in Programmed Molecular Systems

“…Environmental assumptions are statements about the system's operational context that are accepted as true by the developers [59]. The proposed MWT will be made of DNA strands and will operate, both literally and figuratively, in a fluid, molecular environment.…”

Modeling technologies and methods for DNA origami

“…As defined in Tun et al (2015), we further separate our failures into one of three failure types: Component, Interaction, and Compound. Component failures happen due to an incorrect specification, i.e., an observed, undesired property does not match a specified property.…”

“…The following contains work done in collaboration with Thein Tun, Robyn Lutz, Yijun Yu, Divita Mathur and Bashar Nuseibeh(Tun et al (2015)). …”