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

Devices for safety-critical molecular programmed systems

The behavior of matter at the molecular level can be programmed to create nanoscale molecular components that accomplish desired tasks. Many molecular components are developed with intended uses that are safety-critical, such as medical applications. Ensuring the correctness and fault tolerance of such devices is paramount. Techniques to develop robustly correct programs have been widely studied in software systems and many devices have been constructed to aid in the safe operation of systems. We seek to demonstrate the effectiveness of software and safety engineering techniques in the molecular programming domain. In this thesis, we present the design of five new devices to aid in the development of safetycritical molecular programmed systems. We introduce a Runtime Fault Detection device (RFD) to robustly detect faults and initiate recovery actions in response to a failed system. We present the Concentration Monitor, a device that can detect changes, major and minor, in concentrations in real-time and demonstrate its utility. We also describe methods for constructing chemical reaction networks that can robustly simulate any combinational logic gate. Finally, we present two devices to log the state of a molecular program, where the first device logs a state upon receiving a request, and the second device ensures that the current state meets a defined validity property before allowing a log to be taken. All devices have been formally verified using model checking, simulations, or formal proof techniques. The methods used to construct and verify these devices can be adapted to the design of future molecular systems to assist in ensuring their correctness

Designing a molecular watchdog timer for safety critical systems

The programming of matter (molecular programming) is often realized through DNA strand displacement (DSD). Computations and algorithms using DNA strand displacement are often modeled using chemical reaction networks (CRN) that abstract away DNA specific reactions and terminology. These CRNs can yield complex behavior similar to computer programs. If these molecular programs are further used in vivo to effect cell change or fight disease, the molecular program becomes a safety critical system. In this paper we propose and analyze a molecular watchdog timer, based on a software component often used to monitor the health of a critical system. Using goal-oriented requirements engineering and a stochastic CRN model (SCRN) we design a watchdog timer using two components, a delay clock and a threshold detector. The models are directed, informed, and verified by use of a probabilistic model checker. Analyzing requirements and the design uncovered several defects that were addressed in subsequent iterations. During each phase, the system was modeled using formal verification tools and simulations to verify correctness of the model. It was found that this iterative methodology with verification was potent at illuminating requirement and design flaws. In addition, the final verified model helped determine specific parameters and molecules for initial biological experiments

Design and operation of automated ice-tethered profilers for real-time seawater observations in the polar oceans

An automated, easily-deployed Ice-Tethered Profiler (ITP) has been developed for deployment on perennial sea ice in polar oceans to measure changes in upper ocean temperature and salinity in all seasons. The ITP system consists of three components: a surface instrument that sits atop an ice floe, a weighted, plastic-jacketed wire-rope tether of arbitrary length (up to 800 m) suspended from the surface instrument, and an instrumented underwater unit that profiles up and down the wire tether. The profiling underwater unit is similar in shape and dimension to an ARGO float except that the float's variable-buoyancy system is replaced with a traction drive unit. Deployment of ITPs may be conducted either from ice caps or icebreakers, utilizing a self contained tripod/winch system that requires no power. Careful selection of an appropriate multiyear ice floe is needed to prolong the lifetime of the system (up to 3 years depending on the profiling schedule). Shortly after deployment, each ITP begins profiling the water column at its programmed sampling interval. After each acquired temperature and salinity profile, the underwater unit (PROCON) transfers the data and engineering files using an inductive modem to the surface controller (SURFCON). SURFCON also accumulates battery voltages, buoy temperature, and locations from GPS at specified intervals in status files, and queues that information for transmission at the start of each new day. At frequent intervals, an Iridium satellite transceiver in the surface package calls and transmits queued status and CTD data files onto a WHOI logger computer, which are subsequently processed and displayed in near-real time at http://www.whoi.edu/itp. In 2004 and 2005, three ITP prototypes were deployed in the Arctic Ocean. Each system was programmed with accelerated sampling schedules of multiple one-way traverses per day between 10 and 750-760 m depth in order to quickly evaluate endurance and component fatigue. Two of the ITPs are continuing to function after more than 10 months and 1200 profiles. Larger motor currents are observed at times of fast ice floe motion when larger wire angles develop and drag forces on the profiler are increased. The CTD profile data so far obtained document interesting spatial variations in the major water masses of the Beaufort Gyre, show the double-diffusive thermohaline staircase that lies above the warm, salty Atlantic layer, and many mesoscale eddys. Deployed together with CRREL Ice Mass Balance (IMB) buoys, these ITP systems also operate as part of an Ice Based Observatory (IBO). Data returned from an array of IBOs within an Arctic Observing Network will provide valuable real time observations, support studies of ocean processes, and facilitate numerical model initialization and validation.Funding was provided by the National Science Foundation under Contract Nos. OCE-0324233 and ARC-0519899

Automatic control program creation using concurrent Evolutionary Computing

Over the past decade, Genetic Programming (GP) has been the subject of a significant amount of research, but this has resulted in the solution of few complex real -world problems. In this work, I propose that, for some relatively simple, non safety -critical embedded control applications, GP can be used as a practical alternative to software developed by humans. Embedded control software has become a branch of software engineering with distinct temporal, interface and resource constraints and requirements. This results in a characteristic software structure, and by examining this, the effective decomposition of an overall problem into a number of smaller, simpler problems is performed. It is this type of problem amelioration that is suggested as a method whereby certain real -world problems may be rendered into a soluble form suitable for GP. In the course of this research, the body of published GP literature was examined and the most important changes to the original GP technique of Koza are noted; particular focus is made upon GP techniques involving an element of concurrency -which is central to this work. This search highlighted few applications of GP for the creation of software for complex, real -world problems -this was especially true in the case of multi thread, multi output solutions. To demonstrate this Idea, a concurrent Linear GP (LGP) system was built that creates a multiple input -multiple output solution using a custom low -level evolutionary language set, combining both continuous and Boolean data types. The system uses a multi -tasking model to evolve and execute the required LGP code for each system output using separate populations: Two example problems -a simple fridge controller and a more complex washing machine controller are described, and the problems encountered and overcome during the successful solution of these problems, are detailed. The operation of the complete, evolved washing machine controller is simulated using a graphical LabVIEWapplication. The aim of this research is to propose a general purpose system for the automatic creation of control software for use in a range of problems from the target problem class -without requiring any system tuning: In order to assess the system search performance sensitivity, experiments were performed using various population and LGP string sizes; the experimental data collected was also used to examine the utility of abandoning stalled searches and restarting. This work is significant because it identifies a realistic application of GP that can ease the burden of finite human software design resources, whilst capitalising on accelerating computing potential

Distributed network of meteostations with LoRa

Současná práce analyzuje možnosti nasazení distribuované sítě meteostanic v městském prostředí. Cílem této práce je návrh a implementace zařízení s důrazem na jednoduchost instalace, minimální spotřebu, bezdrátový přenos dat a využití alternativního zdroje energie. V rámci této práce byl také implementován algoritmus založený na architektuře neuronové sítě LSTM, schopný generovat předpověď měřených parametrů. Kromě toho na hostingu Amazon byla nasazena infrastruktura, která kombinuje centralizovaný sběr dat ze všech zařízení, předpovídání měřených parametrů, sdílení dat s komunitními projekty monitorování počasí a navíc bylo poskytnuto webové rozhraní pro zobrazování měřených a předpovězených dat. Vyvinutý systém byl úspěšně otestován v reálných klimatických podmínkách. Nakonec byla provedena srovnávací analýza vyvinutého zařízení a komerčních analogů ze stejné a vyšší cenové kategorie. Výsledkem této práce je systém, který má komerční potenciál a je schopen konkurovat populárním stávajícím řešením.The present work analyzes the possibilities of deploying a distributed network of meteostations in an urban environment. The aim of this work is the design and implementation of a device with an emphasis on the simplest possible installation, minimum power consumption, wireless data transmission and the use of alternative power source. Also, within the framework of this work, an algorithm based on the LSTM neural network architecture has been implemented, capable of generating a forecast of the measured parameters. In addition, an infrastructure was deployed on Amazon hosting, combining both centralized data collection from all devices, predicting measured parameters, sharing data with community weather monitoring projects, and, moreover, the web interface was implemented displaying both device data along with measured and predicted parameters. The developed system has been successfully tested in real climatic conditions. Finally, a comparative analysis of the developed device and commercial counterparts from the same and premium price segments was carried out. The result of the present work is a system with commercial potential and the ability to compete with popular existing solutions

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

MEASUREMENT AND MODELING OF HUMIDITY SENSORS

Humidity measurement has been increasingly important in many industries and process control applications. This thesis research focus mainly on humidity sensor calibration and characterization. The humidity sensor instrumentation is briefly described. The testing infrastructure was designed for sensor data acquisition, in order to compensate the humidity sensor’s temperature coefficient, temperature chambers using Peltier elements are used to achieve easy-controllable stable temperatures. The sensor characterization falls into a multivariate interpolation problem. Neuron networks is tried for non-linear data fitting, but in the circumstance of limited training data, an innovative algorithm was developed to utilize shape preserving polynomials in multiple planes in this kind of multivariate interpolation problems