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Dunaliella salina algae are trapped and studied using dual-fiber optical tweezers based on nano-imprinted Fresnel lenses. Different forms of cyclic motion of living algae inside the optical trap are observed and analyzed. A characteristic periodic motion in the 0–35 Hz frequency region reflects the algal flagella activity and is used to estimate the algal vitality, by photomovement. The trap stiffness and optical forces are measured for the case of a dead algal cell. It is shown that the dual-fiber optical tweezers can be used to study the vitality (or viability) property of single cells, a property that is essential and can be scaled up to other applications, such as sperm analysis for fertility tests.

Upscaling motor protein activity to perform work in man-made devices has long been an ambitious goal in bio-nanotechnology. The use of hierarchical motor assemblies, as realized in sarcomeres, has so far been complicated by the challenges of arranging sufficiently high numbers of motor proteins with nanoscopic precision. Here we suggest an alternative approach based on actomyosin cortex-like force production, allowing low complexity motor arrangements in a contractile meshwork that can be locally activated by ATP. The design is reminiscent of a motorized exoskeleton coating and thereby actuating soft protein-based polymer structures from the outside. This readily supports the connection and assembly of micro-3D printed modules into larger structures, thereby scaling up mechanical work. We provide an analytical model of force production in these systems and demonstrate the design flexibility by 3D printed units performing complex mechanical tasks, such as micro-arms and hands that perform sign language and wave.

Optical trapping is the science of holding and immobilizing particles and cells, for further manipulation and spectroscopic studies. Enhancing the application of optical trapping is limited by size and flexibility of this tool, mostly limited to high numerical aperture objectives. In this work, we show the potential of using structured light to further enhance the capabilities of optical fibres as optical tweezers, to be used for applications in which space and throughput are of importance. Using femtosecond two photon direct laser writing, we produce accurately designed micro-optic probes at the tip of optical fibres to enhance the light field for trapping single particles as well as single live cells. Enhanced trapping efficiency, ease of transporting trapped particle, and potential of performing wide spectrum spectroscopy on the trapped entity are the advantages of the present approach.

To advance microfluidic integration, we present the use of two-photon additive manufacturing to fold 2D channel layouts into compact free-form 3D fluidic circuits with nanometer precision. We demonstrate this technique by tailoring microfluidic nozzles and mixers for time-resolved structural biology at X-ray free-electron lasers (XFELs). We achieve submicron jets with speeds exceeding 160 m s−1, which allows for the use of megahertz XFEL repetition rates. By integrating an additional orifice, we implement a low consumption flow-focusing nozzle, which is validated by solving a hemoglobin structure. Also, aberration-free in operando X-ray microtomography is introduced to study efficient equivolumetric millisecond mixing in channels with 3D features integrated into the nozzle. Such devices can be printed in minutes by locally adjusting print resolution during fabrication. This technology has the potential to permit ultracompact devices and performance improvements through 3D flow optimization in all fields of microfluidic engineering., There is a need for more robust sample delivery methods for serial crystallography. Here the authors present the design and characterization of ultracompact 3D microfluidic devices that can be printed, which require less sample, have a lower background signal and allow 3D mixing for time resolved experiments.

Methods are described for processing XFEL data from individual crystalline fibrils. The methods are applied to data collected at the Linac Coherent Light Source from an amyloid-forming oligopeptide from the adenovirus shaft., Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. The advantages of this technique should allow structural studies of fibrous systems in biology that are inaccessible using existing techniques.

Point-of-care testing (POCT) in low-resource settings requires tools that can operate independent of typical laboratory infrastructure. Due to its favorable signal-to-background ratio, a wide variety of biomedical tests utilize fluorescence as a readout. However, fluorescence techniques often require expensive or complex instrumentation and can be difficult to adapt for POCT. To address this issue, we developed a pocket-sized fluorescence detector costing less than $15 that is easy to manufacture and can operate in low-resource settings. It is built from standard electronic components, including an LED and a light dependent resistor, filter foils and 3D printed parts, and reliably detected less than 10 nM fluorescein concentrations (with a lower limit of detection of ≈6.8 nM), which is sufficient to follow typical biochemical reactions used in POCT applications. All assays are conducted on filter paper, which allows for a flat detector architecture to improve signal collection. We validate the device by quantifying in vitro RNA transcription and also demonstrate sequence-specific detection of target RNAs in the nanomolar range using a Cas13a-based fluorescence assay. Cas13a is a RNA-guided, RNA-targeting CRISPR effector with promiscuous RNase activity upon recognition of its RNA target. Cas13a sensing is highly specific and adaptable and in combination with our detector represents a promising approach for nucleic acid POCT. Furthermore, our open-source device architecture could be a valuable educational tool that integrates hardware, software and biochemistry concepts.

We demonstrate a novel multilayer polydimethylsiloxane (PDMS) device for selective storage and release of single emulsion droplets. Drops are captured in a microchannel cavity and can be released on-demand through a triggered surface acoustic wave pulse. The surface acoustic wave (SAW) is excited by a tapered interdigital transducer (TIDT) deposited on a piezoelectric lithium niobate (LiNbO3) substrate and inverts the pressure difference across the cavity trap to push a drop out of the trap and back into the main flow channel. Droplet capture and release does not require a flow rate change, flow interruption, flow inversion or valve action and can be achieved in as fast as 20 ms. This allows both on-demand droplet capture for analysis and monitoring over arbitrary time scales, and continuous device operation with a high droplet rate of 620 drops per s. We hence decouple long-term droplet interrogation from other operations on the chip. This will ease integration with other microfluidic droplet operations and functional components.

Scientific Reports 7: Article number: 44628; published online: 16 March 2017; updated: 21 June 2017. In this Article, Henry N. Chapman is incorrectly listed as being affiliated with ‘Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA’ and an additional affiliation was omitted.

The alignment step in fabricating multi-height photoresist masters is a critical and time-consuming process. SU8 masters that combine very thin and thick layers can be difficult to align because of low contrast visibility. We increase visual contrast by selectively developing alignment marks to ease fabrication of masters with thick resist layers deposited on much thinner ones. In addition, we use a vernier calliper based alignment mark to achieve high precision alignment.

Total internal reflection fluorescence (TIRF) microscopy is a commonly used method for studying fluorescently labeled molecules in close proximity to a surface. Usually, the TIRF axial excitation profile is assumed to be single-exponential with a characteristic penetration depth, governed by the incident angle of the excitation laser beam towards the optical axis. However, in practice, the excitation profile does not only comprise the theoretically predicted single-exponential evanescent field, but also an additional non-evanescent contribution, supposedly caused by scattering within the optical path or optical aberrations. We developed a calibration slide to directly characterize the TIRF excitation field. Our slide features ten height steps ranging from 25 to 550 nanometers, fabricated from a polymer with a refractive index matching that of water. Fluorophores in aqueous solution above the polymer step layers sample the excitation profile at different heights. The obtained excitation profiles confirm the theoretically predicted exponential decay over increasing step heights as well as the presence of a non-evanescent contribution. (c) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

Objective: We present a formal approach and methodology for the analysis and generation of user interfaces, with special emphasis on human-automation interaction. Background: A conceptual approach for modeling, analyzing, and verifying the information content of user interfaces is discussed. Methods: The proposed methodology is based on two criteria: First, the interface must be correct — that is, given the interface indications and all related information (user manuals, training material, etc.), the user must be able to successfully perform the specified tasks. Second, the interface and related information must be succinct — that is, the amount of information (mode indications, mode buttons, parameter settings, etc.) presented to the user must be reduced (abstracted) to the minimum necessary. Results: A step-by-step procedure for generating the information content of the interface that is both correct and succinct is presented and then explained and illustrated via two examples. Conclusions: Every user interface is an abstract description of the underlying system. The correspondence between the abstracted information presented to the user and the underlying behavior of a given machine can be analyzed and addressed formally. Applications: The procedure for generating the information content of user interfaces can be automated, and a software tool for its implementation has been developed. Potential application areas include adaptive interface systems and customized/personalized interfaces.

A major challenge in high-resolution x-ray free-electron laser-based coherent diffractive imaging is the development of aerosol injectors that can efficiently deliver particles to the peak intensity of the focused X-ray beam. Here, we consider the use of a simple convergent-orifice nozzle for producing tightly focused beams of particles. Through optical imaging we show that 0.5 μm particles can be focused to a full-width at half maximum diameter of 4.2 μm, and we demonstrate the use of such a nozzle for injecting viruses into a micro-focused soft-X-ray FEL beam.

The paper presents an agent based framework for control of conflict-free scheduling and spacing of airport arrival and approach traffic. The proposed tool incorporates a multi-agent conflict-resolution algorithm that guarantees to arriving aircraft safe approach trajectories, and a dynamic prioritization mechanism that aids in efficient utilization of the available airspace and arrivals runway capacity. The approach can be employed by a central authority or autonomously by the arriving aircraft.

The traditional framework for discrete-event control is extended to include the case of control with active events, in which both the user and the environment have events that they can trigger. A variety of liveness and safety specifications can be considered within this extended framework. A synthesis algorithm of minimally restrictive controllers is outlined. Multiuser systems are also discussed.

Alan Turing, in “The Chemical Basis of Morphogenesis” [Turing AM (1952) Philos Trans R Soc Lond 237(641):37–72], described how, in circular arrays of identical biological cells, diffusion can interact with chemical reactions to generate up to six periodic spatiotemporal chemical structures. Turing proposed that one of these structures, a stationary pattern with a chemically determined wavelength, is responsible for differentiation. We quantitatively test Turing’s ideas in a cellular chemical system consisting of an emulsion of aqueous droplets containing the Belousov–Zhabotinsky oscillatory chemical reactants, dispersed in oil, and demonstrate that reaction-diffusion processes lead to chemical differentiation, which drives physical morphogenesis in chemical cells. We observe five of the six structures predicted by Turing. In 2D hexagonal arrays, a seventh structure emerges, incompatible with Turing’s original model, which we explain by modifying the theory to include heterogeneity.

A formal, model-based approach is proposed for the development and evaluation of the sequences of actions specified in procedures. The approach employs methodologies developed within the discipline of discrete-event and hybrid systems control. We demonstrate the proposed approach through an evaluation of a procedure for handling an irregular engine-start on board a modern commercial aircraft.

In this paper, we study the control of Composite Hybrid Machines (CHMs) subject to safety specifications. CHMs are a fairly general class of hybrid systems modeled in modular fashion as the concurrent operation of Elementary Hybrid Machines (EHMs). The formalism has a well-defined synchronous-composition operation that permits the introduction of the controller as a component of the system. The task of a legal (safety) controller is to ensure that the system never exits a set of specified legal configurations. Among the legal controllers, we are particularly interested in designing a minimally-interventive (or minimally-restrictive) one, which interferes in the system‘s operation only when constraint violation is otherwise inevitable. Thus, a minimally interventive safety controller provides maximum flexibility in embedding additional controllers designed for other control objectives to operate concurrently, while eliminating the need to re-investigate or re-verify the legality of the composite controller with respect to the safety specification. We describe in detail an algorithm for controller synthesis and examine the viability of a synthesized controller as related to the possibility of Zenoness, where the system can undergo an unbounded number of transitions in a bounded length of time.

There have been rapid advances in control and automated driving aids in today's cars, with a concomitant rise in the breadth and complexity of driver interaction. Thus there is a need for a clear, consistent, logical, and holistic design methodology to the design and analysis of the driver-vehicle interaction environment. Such design method should also take into account expected future technological enhancements and advances. In this paper we present some emerging automated driving aids that are currently implemented in modern vehicles and those that are anticipated in the coming years. We focus on three automation features -- adaptive cruise control (ACC), Lane Centering (LC), and Full Speed Range ACC (FSRA). The design methodology is based on formal modeling of the functionality and user interaction of these systems and analysis of their corresponding user interfaces. The approach demonstrated here is valid for a wide range of user interaction systems where operational complexity requires careful and verifiable design.

Reliable sample delivery is essential to biological imaging using X-ray Free Electron Lasers (XFELs). Continuous injection using the Gas Dynamic Virtual Nozzle (GDVN) has proven valuable, particularly for time-resolved studies. However, many important aspects of GDVN functionality have yet to be thoroughly understood and/or refined due to fabrication limitations. We report the application of 2-photon polymerization as a form of high-resolution 3D printing to fabricate high-fidelity GDVNs with submicron resolution. This technique allows rapid prototyping of a wide range of different types of nozzles from standard CAD drawings and optimization of crucial dimensions for optimal performance. Three nozzles were tested with pure water to determine general nozzle performance and reproducibility, with nearly reproducible off-axis jetting being the result. X-ray tomography and index matching were successfully used to evaluate the interior nozzle structures and identify the cause of off-axis jetting. Subsequent refinements to fabrication resulted in straight jetting. A performance test of printed nozzles at an XFEL provided high quality femtosecond diffraction patterns. (C) 2016 Optical Society of America

In this paper we discuss a formal approach to the design and analysis of automotive systems, from a human-machine interaction (HMI) point of view. Specifically, we detail the behavior of a generic climate control system, present a statecharts model of this system, and discuss aspects of user interaction analysis. Several general principles for the design of climate control systems are illustrated and discussed. The topic of design patterns, in the context of a formal description of user interaction, is introduced, and two design patterns are illustrated and discussed.

The authors describe an algorithm for navigating a polygonal robot, capable of translational motion, in an unknown environment. The environment contains stationary polygonal obstacles and is bounded by polygonal walls, all of which are initially unknown to the robot. The environment is learned during the navigation process by use of a laser range-finding device, and new knowledge is integrated with previously acquired information. A partial map of the environment, containing parts of the obstacles that were seen by the robot and the free space between them, is obtained. The obstacles in the map are transformed into a new set of expanded polygonal obstacles, allowing the robot to be treated as a point, and the navigation problem is reduced to point navigation among unknown polygonal obstacles. A navigation graph is built from the transformed obstacles and used to search for a piecewise linear path to the destination. The algorithm is proved to converge to the desired destination in a finite number of steps provided a path to the destination exists. >

When a discrele-event system P consists of several subsystems P1,...,Pn which operate concurrently, a natural approach to the supervisory control problem is to synthesize a ‘local’ controller Si , for each subsystem Pi , and operate the individually controlled subsystems Si/Pi concurrently. Such an approach is called concurrent supervisory control and is closely related to decentralized supervisory control as studied by Cieslak et al. (1988) and Lin and Wonham (1988). In the present paper simple and easily computable conditions are developed which guarantee that concurrent supervisory control can achieve the optimal behaviour achievable by a global supervisor. To achieve this, two specific concurrent control strategies are introduced.

Serial femtosecond crystallography (SFX) using X-ray Free-Electron Lasers (XFELs) allows for room temperature protein structure determination without evidence of conventional radiation damage. In this method, a liquid suspension of protein microcrystals can be delivered to the X-ray beam in vacuum as a micro-jet, which replenishes the crystals at a rate that exceeds the current XFEL pulse repetition rate. Gas dynamic virtual nozzles produce the required micrometer-sized streams by the focusing action of a coaxial sheath gas and have been shown to be effective for SFX experiments. Here, we describe the design and characterization of such nozzles assembled from ceramic micro-injection molded outer gas-focusing capillaries. Trends of the emitted jet diameter and jet length as a function of supplied liquid and gas flow rates are measured by a fast imaging system. The observed trends are explained by derived relationships considering choked gas flow and liquid flow conservation. Finally, the performance of these nozzles in a SFX experiment is presented, including an analysis of the observed background.

We propose a distributed multi-agent framework for conflict free navigation in a discrete environment. The two-phased approach, which consists of a 'conflict-resolution' phase followed by an 'agent-accommodation' phase, guarantees maximal capacity utilization under guaranteed safety requirements. The methodology, which is motivated by the free-flight paradigm in air traffic management (ATM), is applicable to autonomous UAVs, various ground transport settings and, with suitable modifications, also to distributed ATM.

A token-based air traffic management paradigm is presented that enables the de-coupling of: (1) the air traffic control system (ATCS) task to maintain safety; and (2) airline operational center (AOC) goal to choose optimal flight paths. Under the token-based paradigm, each local area (sector) issues tokens that permit entry to that region of space over an assigned period of time. The number of tokens is limited by the ATCS to guarantee admission and safe passage to the destination point in the sector within a pre-specified time-interval. The token-based paradigm allows AOCs to freely trade the tokens between different aircraft and to choose desirable flight paths by choosing the sequences of sectors (as long as the AOC can procure the needed tokens). Although, the aircraft is forced to fly along established routes in each sector, the flexibility in choice of sectors may meet the AOC's needs for freedom.

The traditional framework for discrete-event control is extended to include the case of control with active events, in which both the user and the environment have events that they can trigger. A variety of liveness and safety specifications can be considered within this extended framework. A synthesis algorithm of minimally restrictive controllers is outlined.

In this paper, we study the control of composite hybrid machines (CHM) subject to configuration-based safety specifications. CHM are a class of hybrid systems modeled in modular fashion as the concurrent operation of elementary hybrid machines (EHM). We recall our algorithm presented previously (1997) for synthesis of minimally-interventive controllers that guarantee constraint satisfaction. The paper focuses on essential questions associated with viability of a synthesized controller as related to the possibility of Zenoness of the controlled system. A hybrid system is Zeno if it can undergo an unbounded number of transitions in a bounded length of time.

This paper discusses a formal and rigorous approach to the analysis of operator interaction with machines. It addresses the acute problem of detecting design errors in human-machine interaction and focuses on verifying the correctness of the interaction in complex and automated control systems. The paper describes a systematic methodology for evaluating whether the interface provides the necessary information about the machine to enable the operator to perform a specified task successfully and unambiguously. It also addresses the adequacy of information provided to the user via training material (e.g., user manual) about the machine's behavior. The essentials of the methodology, which can be automated and applied to the verification of large systems, are illustrated by several examples and through a case study of pilot interaction with an autopilot aboard a modern commercial aircraft. The expected application of this methodology is an augmentation and enhancement, by formal verification, of human-automation interfaces.

In this paper we address the problem of designing systems for human-automation interaction that insure satisfaction of a wide range of performance requirements (such as guaranteeing the safety and liveness of mission critical operations). Our approach is based on formal procedures that focus on the information provided to the user. We propose a formal methodology for constructing interfaces and corresponding user- manuals that is based on performing a systematic abstraction of the behavioral model of the system. The procedure is aimed at achieving two objectives: First, the interface must be correct in that with the given interface the user will be able to perform the specified tasks correctly. Secondly, the interface must be succinct. The paper discusses the underlying concepts and the formal methods for this approach. Two examples are used to illustrate the methodology. The algorithm for constructing interfaces that is proposed in the paper can be automated, and a preliminary software system for its implementation has been developed.

Microprocessors and microcontrollers are now widely used in automobiles. Microprocessor systems contain sources of interrupt and interrupt service routines, which are software components executed in response to the assertion of an interrupt in hardware. A major problem in designing the software of microprocessor systems is the analytical treatment of interrupt latency. Because multiple interrupt service routines are executed on the same CPU, they compete for the CPU and interfere with each other's latency requirements. Here, interrupt latency is defined as the delay between the assertion of the interrupt in hardware and the start of execution of the associated interrupt service routine. It is estimated that 80% of intermittent bugs in small microprocessor software loads are due to improper treatment of interrupts. Until this work, there is no analytic method for analyzing a particular system to determine if it may violate interrupt latency requirements. There is also no reliable empirical method for ruling out the possibility of interrupt latency violations in a particular system, as they may occur under only very specific conditions. We use a newly developed hybrid system approach to solve this interrupt latency compatibility analysis problem. We have developed an efficient algorithm to determine if interrupt latency violations may occur in a particular system. A software tool that implements the algorithm is also being developed. With such software, we can easily check if interrupt latency constraints may be violated under any circumstances. If so, such software may also indicate how to modify the interrupts and interrupt service routines to avoid such violations. INTRODUCTION Microprocessor systems contain interrupt sources (ISs), which can request service from the processor (assert an interrupt), and must always have a software response (the execution of the corresponding software interrupt service routine, or ISR) starting within an interval of time (the maximum allowable interrupt latency, or AIL) after the assertion of the hardware interrupt. Because a processor may execute only one stream of instructions at a time, the execution of one ISR may delay the execution of another ISR until the first has completed. Hence, ISs and their associated ISRs interfere with each other’s interrupt latency requirements and may not be combined arbitrarily in the same microprocessor system without the possibility of the AIL being violated for some or all ISs. As a necessary condition to guarantee that a microprocessor system will always behave as intended, each IS must always be serviced by its corresponding ISR within the AIL. Verifying that the interrupt latency requirement is always satisfied for every IS is the interrupt latency compatibility problem that we address in this paper. The importance of the interrupt latency compatibility problem in microprocessor system design cannot be overstated. A system accidentally constructed so that interrupt latency incompatibilities exist has a high probability of exhibiting serious behavioral defects which are intermittent, because the conditions required to

In this paper, we study the control of Composite Hybrid Machines (CHMs) subject to safety specifications. CHMs are a fairly general class of hybrid systems modeled in modular fashion as the concurrent operation of Elementary Hybrid Machines (EHMs). The formalism has a well-defined synchronous-composition operation that permits the introduction of the controller as a component of the system. The task of a legal controller is to ensure that the system never exits a set of specified legal configurations. Among the legal controllers, we are particularly interested in designing a minimally-restrictive (or minimally-interventive) one, which interferes in the system's operation only when constraint violation is otherwise inevitable. Thus, when composed to operate concurrently with another legal controller, our controller will never interfere with the operation of the other. Therefore, a minimally-restrictive controller provides maximum flexibility in embedding additional controllers designed for other control objectives to operate concurrently, while eliminating the need to re-investigate or re-verify the legality of the composite controller. We describe in detail an algorithm for controller synthesis and examine through several examples questions associated with algorithm termination and controller existence.

We examine a class of hybrid systems called Composite Hybrid Machines (CHMs), that consist of the concurrent (and partially synchronized) operation of Elementary Hybrid Machines (EHMs). Legal behavior is specified by a set of illegal configurations that the CHM may not enter, and is to be achieved by the concurrent operation of the CHM with a suitably designed legal controller. A legal controller is minimally restrictive if, when composed to operate concurrently with another legal controller, it will never interfere with the operation of the other controller. We focus attention on the problem of synthesizing a minimally restrictive legal controller, whenever a legal controller exists. We present an algorithm for the synthesis of minimally restrictive legal controllers for CHMs with rate-limited dynamics, where legal guards are conjunctions or disjunctions of atomic formulas in the dynamic variables (of the type x ≤ x0 or x ≥ x0).

Combat is formulated as a dynamical encounter between two opponents, each of whom has offensive capabilities and objectives. With each opponent is associated a target in the event space in which he endeavors to terminate the combat, thereby winning. If the combat terminates in both target sets simultaneously or in neither, a joint capture or a draw, respectively, is said to occur. Resolution of the encounter is formulated as a combat game; namely, as a pair of competing event-constrained differential games. If exactly one of the players can win, the optimal strategies are determined from a resulting constrained zero-sum-differential game. Otherwise, the optimal strategies are computed from a resulting non-zero-sum game. Since optimal combat strategies frequently may not exist, approximate combat games are also formulated leading to approximate optimal strategies. To illustrate combat games, an example, called the turret game, is considered. This game may be thought of as a highly simplified model of air combat, yet it sufficiently complex to exhibit a rich variety of combat behavior, much of which is not found in pursuit-evasion games.