Constraint checking during error recovery

The system-level software onboard a spacecraft is responsible for recovery from communication, power, thermal, and computer-health anomalies that may occur. The recovery must occur without disrupting any critical scientific or engineering activity that is executing at the time of the error. Thus, the error-recovery software may have to execute concurrently with the ongoing acquisition of scientific data or with spacecraft maneuvers. This work provides a technique by which the rules that constrain the concurrent execution of these processes can be modeled in a graph. An algorithm is described that uses this model to validate that the constraints hold for all concurrent executions of the error-recovery software with the software that controls the science and engineering activities of the spacecraft. The results are applicable to a variety of control systems with critical constraints on the timing and ordering of the events they control

Automated requirements analysis for a molecular watchdog timer

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 to create the molecular watchdog timer. During the requirements-design iterations, simulation, model checking, and analysis are used to verify the system. Using this methodology several incomplete requirements and design flaws were found, and the final verified model helped determine specific parameters for biological experiments

Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks

We show that very simple molecular systems, modeled as chemical reaction networks, can have behaviors that exhibit dramatic phase transitions at certain population thresholds. Moreover, the magnitudes of these thresholds can thwart attempts to use simulation, model checking, or approximation by differential equations to formally verify the behaviors of such systems at realistic populations. We show how formal theorem provers can successfully verify some such systems at populations where other verification methods fail

Automated caching of behavioral patterns for efficient run-time

Run-time monitoring is a powerful approach for dy- namically detecting faults or malicious activity of software systems. However, there are often two obsta- cles to the implementation of this approach in prac- tice: (1) that developing correct and/or faulty be- havioral patterns can be a difficult, labor-intensive process, and (2) that use of such pattern-monitoring must provide rapid turn-around or response time. We present a novel data structure, called extended action graph, and associated algorithms to overcome these drawbacks. At its core, our technique relies on ef- fectively identifying and caching specifications from (correct/faulty) patterns learnt via machine-learning algorithm. We describe the design and implementa- tion of our technique and show its practical applicabil- ity in the domain of security monitoring of sendmail software

Experiences Using Formal Methods for Requirements Modeling

This paper describes three cases studies in the lightweight application of formal methods to requirements modeling for spacecraft fault protection systems. The case studies differ from previously reported applications of formal methods in that formal methods were applied very early in the requirements engineering process, to validate the evolving requirements. The results were fed back into the projects, to improve the informal specifications. For each case study, we describe what methods were applied, how they were applied, how much effort was involved, and what the findings were. In all three cases, the formal modeling provided a cost effective enhancement of the existing verification and validation processes. We conclude that the benefits gained from early modeling of unstable requirements more than outweigh the effort needed to maintain multiple representations

Probing the Security of DNA Origami

DNA origami is a method used to program the self-assembly of nanoscale computational systems. The contribution of this paper is to probe the security of a canonical DNA origami that is often reused. The paper describes the techniques we used to design probes whose input targets the origami systems’ integrity. Experimental results show that the probes successfully caused up to a third of the systems to fail. Moreover, our approach identified a single, small input whose addition was able to cause the failure of a quarter of the systems. Extending such probes to other DNA origami systems may aid in understanding how to enhance their reliability

Organic matter characteristics of a rapidly eroding permafrost cliff in NE Siberia (Lena Delta, Laptev Sea region)

Organic carbon (OC) stored in Arctic permafrost represents one of Earth’s largest and most vulnerable terrestrial carbon pools. Amplified climate warming across the Arctic results in widespread permafrost thaw. Permafrost deposits exposed at river cliffs and coasts are particularly susceptible to thawing processes. Accelerating erosion of terrestrial permafrost along shorelines leads to increased transfer of organic matter (OM) to nearshore waters. However, the amount of terrestrial permafrost carbon and nitrogen as well as the OM quality in these deposits is still poorly quantified. We define the OM quality as the intrinsic potential for further transformation, decomposition and mineralisation. Here, we characterise the sources and the quality of OM supplied to the Lena River at a rapidly eroding permafrost river shoreline cliff in the eastern part of the delta (Sobo-Sise Island). Our multi-proxy approach captures bulk elemental, molecular geochemical and carbon isotopic analyses of Late Pleistocene Yedoma permafrost and Holocene cover deposits, discontinuously spanning the last ~52 kyr. We showed that the ancient permafrost exposed in the Sobo-Sise cliff has a high organic carbon content (mean of about 5 wt %). The oldest sediments stem from Marine Isotope Stage (MIS) 3 interstadial deposits (dated to 52 to 28 cal ka BP) and are overlaid by last glacial MIS 2 (dated to 28 to 15 cal ka BP) and Holocene MIS 1 (dated to 7–0 cal ka BP) deposits. The relatively high average chain length (ACL) index of n-alkanes along the cliff profile indicates a predominant contribution of vascular plants to the OM composition. The elevated ratio of iso and anteiso-branched fatty acids (FAs) relative to mid- and long-chain (C�20) n-FAs in the interstadial MIS 3 and the interglacial MIS 1 deposits suggests stronger microbial activity and consequently higher input of bacterial biomass during these climatically warmer periods. The overall high carbon preference index (CPI) and higher plant fatty acid (HPFA) values as well as high C=N ratios point to a good quality of the preserved OM and thus to a high potential of the OM for decomposition upon thaw. A decrease in HPFA values downwards along the profile probably indicates stronger OM decomposition in the oldest (MIS 3) deposits of the cliff. The characterisation of OM from eroding permafrost leads to a better assessment of the greenhouse gas potential of the OC released into river and nearshore waters in the future