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• On a Decentralized Active Sensing Strategy using Mobile Sensor Platforms in a Network  + (In this paper, we consider the problem of … In this paper, we consider the problem of active</br>sensing using mobile sensor nodes that are jointly estimating</br>the state of a dynamic target as a sensor network. We propose</br>a gradient search-based decentralized algorithm that demonstrates</br>the benefits of distributed sensing. We then examine the</br>task of tracking multiple targets. We use a greedy algorithm</br>for associating sensors with targets along with the gradientsearch</br>strategy for sensor vehicle motion planning. Simulation</br>results show that these simple decentralized strategies perform</br>quite well and the sensor nodes exhibit interesting cooperative</br>behavior. exhibit interesting cooperative behavior.)
• The Effect of Sensor Health on State Estimation  + (In this paper, we consider the problem of … In this paper, we consider the problem of state estimation</br>using the standard Kalman filter recursions which takes</br>account of the available sensor health information. Given</br>a stochastic description of the sensor health, we are able</br>to show that the expected error covariance converges to a</br>unique value for all initial values, while the available</br>previous work only showed the upper bound of the expected</br>error covariance converges. Our approach provides both</br>theoretical value to the analysis as well as the potential</br>to get tighter upper bound. Our results provide a criterion</br>of evaluating the sensor measurement. In the multisensor</br>fusion problem, depending on the system error tolerance</br>levels, it can then be determined whether to fuse a</br>particular sensor measurement or not. Examples and</br>simulations are provided to assist the theory.lations are provided to assist the theory.)
• An Iterative Abstraction Algorithm for Reactive Correct-by-Construction Controller Synthesis  + (In this paper, we consider the problem of … In this paper, we consider the problem of synthesizing correct-by-construction controllers for discrete-time dynamical systems. A commonly adopted approach in the literature is to abstract the dynamical system into a finite transition system (FTS) and thus convert the problem into a two player game between the environment and the system on the FTS. The controller design problem can then be solved using synthesis tools for general linear temporal logic or generalized reactivity(1) (GR1) specifications. In this article, we propose a new abstraction algorithm. Instead of generating a single FTS to represent the system, we generate two FTSs, which are underand over-approximations of the original dynamical system. We further develop an iterative abstraction scheme by exploiting the concept of winning sets, i.e., the sets of states for which there exists a winning strategy for the system. Finally, the e�ciency of the new abstraction algorithm is illustrated by numerical examples.ithm is illustrated by numerical examples.)
• Sensor Scheduling Algorithms Requiring Limited Computation  + (In this paper, we consider the scenario wh … In this paper, we consider the scenario where many sensors</br>co-operate to estimate a process. Only one sensor can take</br>a measurement at any time step. We wish to come up with</br>optimal sensor scheduling algorithms. The problem is motivated</br>by the use of sonar range-finders used by the vehicles</br>on the Caltech Multi-Vehicle Wireless Testbed. We see that</br>this problem involves searching a tree in general and propose</br>and analyze two strategies for pruning the tree to keep</br>the computation limited. The first is a sliding window strategy</br>motivated by the Viterbi algorithm, and the second one</br>uses thresholding. We also study a technique that employs</br>choosing the sensors randomly from a probability distribution</br>which can then be optimized. The performance of the</br>algorithms are illustrated with the help of numerical examples.rated with the help of numerical examples.)
• Receding Horizon Control for Temporal Logic Specifications  + (In this paper, we describe a receding hori … In this paper, we describe a receding horizon scheme that satisfies a class of linear temporal logic specifications sufficient to describe a wide range of properties including safety, stability, progress, obligation, response and guarantee. The resulting embedded control software consists of a goal generator, a tra jectory planner, and a continuous controller. The goal generator essentially reduces the tra jectory generation problem to a sequence of smaller problems of short horizon while preserving the desired system-level temporal properties. Subsequently, in each iteration, the tra jectory planner solves the corresponding short-horizon problem with the currently observed state as the initial state and generates a feasible tra jectory to be implemented by the continuous controller. Based on the simulation property, we show that the composition of the goal generator, tra jectory planner and continuous controller and the corresponding receding horizon scheme guarantee the correctness of the system. To handle failures that may occur due to a mismatch between the actual system and its model, we propose a response mechanism and illustrate, through an example, how the system is capable of responding to certain failures and continues to exhibit a correct behavior.d continues to exhibit a correct behavior.)
• An In Silico Modeling Toolbox for Rapid Prototyping of Circuits in a Biomolecular “Breadboard” System  + (In this paper, we develop an experimentall … In this paper, we develop an experimentally val- idated MATLAB software toolbox as an accompaniment to an in vitro cell-free biomolecular “breadboard” system. The toolbox gives insight into the dynamics of unmeasured states in the cell-free system, accounting especially for the resource usage. Parameter lumping and the reduced order modeling are used to maintain computational tractability and to avoid ill-conditioning. The toolbox allows for most applications to be implemented with standard set of commands for ease of use. Due to the breadboarding nature of the underlying cell-free sys- tem, the toolbox provides a general framework for experiment planning and predictive modeling for synthetic biomolecular circuits cell-free systems, accelerating our capacity to rationally design circuits from well characterized parts.gn circuits from well characterized parts.)
• Trajectory generation for the N-trailer problem using Goursat normal form  + (In this paper, we develop the machinery of … In this paper, we develop the machinery of exterior differential forms, more particularly the Goursat normal form for a Pfaffian system, for solving nonholonomic motion planning problems, i.e., motion planning for systems with nonintegrable velocity constraints. We use this technique to solve the problem of steering a mobile robot with n trailers, We present an algorithm for finding a family of transformations which will convert the system of rolling constraints on the wheels of the robot with n trailers into the Goursat canonical form. Two of these transformations are studied in detail. The Goursat normal form for exterior differential systems is dual to the so-called chained-form for vector fields that has been studied previously. Consequently, we are able to give the state feedback law and change of coordinates to convert the N-trailer system into chained form. Three methods for planning trajectories for chained-form systems using sinusoids, piecewise constants, and polynomials as inputs are presented.</br>The motion planning strategy is therefore to first convert the N-trailer system into Goursat form, use this to find the chained-form coordinates, plan a path for the corresponding chained-form system, and then transform the resulting trajectory back into the original coordinates. Simulations and frames of movie animations of the N-trailer system for parallel parking and backing into a loading dock using this strategy are included.ing dock using this strategy are included.)
• Consensus problems in networks of agents with switching topology and time-delays  + (In this paper, we discuss consensus proble … In this paper, we discuss consensus problems for a network of dynamic agents with fixed and switching topologies. We analyze three cases: i) networks with switching topology and no time-delays, ii) networks with fixed topology and communication time-delays, and iii) max-consensus problems (or leader determination) for groups of discrete-time agents. In each case, we introduce a linear/nonlinear consensus protocol and provide convergence analysis for the proposed distributed algorithm. Moreover, we establish a connection between the Fiedler eigenvalue of the information flow in a network (i.e. algebraic connectivity of the network) and the negotiation speed (or performance) of the corresponding agreement protocol. It turns out that balanced digraphs play an important role in addressing average-consensus problems. We introduce disagreement functions that play the role of Lyapunov functions in convergence analysis of consensus protocols. A distinctive feature of this work is to address consensus problems for networks with directed information flow. We provide analytical tools that rely on algebraic graph theory, matrix theory, and control theory. Simulations are provided that demonstrate the effectiveness of our theoretical results. effectiveness of our theoretical results.)
• Resource Competition as a Source of Non-Minimum Phase Behavior in Transcription-Translation Systems  + (In this paper, we explore how resource lim … In this paper, we explore how resource limitations can lead to coupling interactions between orthogonal com- ponents in a transcription-translation system and the effect those interactions have on its dynamical behavior. To illustrate these ideas, we present a motivating example featuring a classical network motif: the signal cascade. We show that through coupling interactions arising from competition for limited resources, the system exhibits a non-minimum phase step response. These observations lead us to identify a key network motif with the potential to introduce right half plane zeros into the system transfer function. We characterize the parametric conditions under which the network motif produces a non-minimum phase transfer function and illustrate with two examples how resource limitations can 1) introduce the network motif through these coupling interactions, 2) satisfy the parametric conditions sufficient to produce a right half plane zero.icient to produce a right half plane zero.)
• Frequency-Weighted Model Reduction with Applications to Structured Models  + (In this paper, we generalize a recently pr … In this paper, we generalize a recently proposed</br>method for model reduction of linear systems to the frequencyweighted</br>case. The method uses convex optimization and can be</br>used both with sample data and exact models. We also derive</br>simple a priori bounds on the frequency-weighted error. We</br>combine the method with a rank-minimization heuristic, to</br>approximate multi-inputÂmulti-output systems. We also present</br>two applications  environment compensation and simpli�cation</br>of interconnected models  where we argue the proposed</br>methods are useful. we argue the proposed methods are useful.)
• Consensus Protocols for Networks of Dynamic Agents  + (In this paper, we introduce a consensus pr … In this paper, we introduce a consensus protocol for a network of dynamic </br>agents that allows the agents to reach </br>a decision in a distributed and cooperative </br>fashion. We consider both linear and nonlinear protocols as well as </br>the characteristic function of the communication links in the network. </br>This includes links with delay and (possible) distortion/filtering effects. </br>It turns out that for a number of protocols, the convergence properties </br>and the decision-value obtained via this protocol is strongly related </br>to connectivity and algebraic graph theoretic properties of the information </br>flow in the network of decision-making agents. Standard </br>tools from multivariable control and linear control theory such as Nyquist </br>plots appear naturally for convergence analysis of the obtained linear </br>protocols. For the analysis of the nonlinear protocols, certain </br>disagreement costs are constructed that are minimized by the consensus </br>protocols in a distributed way. Simulation results are provided for attitude </br>alignment of a group of 20 dynamic agents.alignment of a group of 20 dynamic agents.)
• Synthesis of Static Test Environments for Observing Sequence-like Behaviors in Autonomous Systems  + (In this paper, we investigate formal test- … In this paper, we investigate formal test-case generation for high-level mission objectives, specifically reachability, of autonomous systems. We use Kripke structures to represent the high-level decision-making of the agent under test and the abstraction of the test environment. First, we define the notion of a test specification, focusing on a fragment of linear temporal logic represented by sequence temporal logic formulas. Second, we formulate the problem of test graph synthesis to find a test configuration for which the agent must satisfy the test specification to satisfy its mission objectives. We an algorithm, based on network flows, for synthesizing a test graph by restricting transitions, represented by edge deletions, on the original graph induced by the Kripke structures. The algorithm synthesizes the test graph iteratively using an integer linear program. We prove completeness for our algorithm, and we show that the edge deletions in each iteration maintain feasibility of the integer linear program in the subsequent iteration. We formalize the notion of a minimally constrained test graph in terms of maximum flow, and prove the synthesized test graph to be minimally constrained. We demonstrate our algorithm on a simple graph and on gridworlds.rithm on a simple graph and on gridworlds.)
• Pre-orders for Reasoning about Input-to-State Stability Properties of Hybrid Systems  + (In this paper, we investigate pre-orders f … In this paper, we investigate pre-orders for reasoning about input-to-state stability properties of hybrid systems. We define the notions of uniformly continuous input simulations and bisimulations, which extend the notions in previous work to include inputs. We show that uniformly con- tinuous input bisimulations preserve incremental input-to-state stability of hybrid systems, and thus provide a basis for constructing abstractions for verification. We show that Lyapunov function based input-to-state stability analysis can be cast in our framework as constructing a simpler one-dimensional system, using a uniformly continuous input simulation, which is input-to-state stable, and thus, inferring the input-to-state stability of the original system.to-state stability of the original system.)
• Bisimulations for Reasoning about Input-to-State Stability Properties of Hybrid Systems  + (In this paper, we investigate pre-orders f … In this paper, we investigate pre-orders for reason- ing about input-to-state stability properties of hybrid systems. We define the notions of uniformly continuous input simulations and bisimulations, which extend the notions in previous work to include inputs. We show that uniformly continuous input bisimulations preserve incremental input-to-state stability of hybrid systems, and thus provide a basis for constructing abstractions for verification. We show that Lyapunov function based input-to-state stability analysis can be cast in our frame- work as constructing a simpler one-dimensional system, using a uniformly continuous input simulation, which is input-to-state stable, and thus, inferring the input-to-state stability of the original system.to-state stability of the original system.)
• Polyhedral Cone Invariance Applied to Rendezvous of Multiple Agents  + (In this paper, we pose the N-scalar agent … In this paper, we pose the N-scalar agent rendezvous</br>as a polyhedral cone invariance problem in the N</br>dimensional phase space. The underlying dynamics of the</br>agents are assumed to be linear. We derive a condition</br>for positive invariance for polyhedral cones. Based on this</br>condition, we demonstrate that the problem of determining a</br>certificate for rendezvous can be stated as a convex feasibility</br>problem. Under certain rendezvous requirements, we show</br>that there are no robust closed-loop linear solutions that satisfy</br>the invariance conditions. We show that the treatment of the</br>rendezvous problem on the phase plane can be extended to</br>the case where agent dynamics are non-scalar. case where agent dynamics are non-scalar.)
• Distributed Cooperative Control of Multiple Vehicle Formations Using Structural Potential Functions  + (In this paper, we propose a framework for … In this paper, we propose a framework for formation stabilization of</br>multiple autonomous vehicles in a distributed fashion. Each vehicle is assumed to</br>have simple dynamics, i.e. a double-integrator, with a directed (or an undirected)</br>information ow over the formation graph of the vehicles. Our goal is to find</br>a distributed control law (with an efficient computational cost) for each vehicle</br>that makes use of limited information regarding the state of other vehicles. Here,</br>the key idea in formation stabilization is the use of natural potential functions</br>obtained from structural constraints of a desired formation in a way that leads to</br>a collision-free, distributed, and bounded state feedback law for each vehicle.unded state feedback law for each vehicle.)
• Voluntary lane-change policy synthesis with reactive control improvisation  + (In this paper, we propose reactive control … In this paper, we propose reactive control impro- visation to synthesize voluntary lane-change policy that meets human preferences under given traffic environments. We first train Markov models to describe traffic patterns and the motion of vehicles responding to such patterns using traffic data. The trained parameters are calibrated using control improvisation to ensure the traffic scenario assumptions are satisfied. Based on the traffic pattern, vehicle response models, and Bayesian switching rules, the lane-change environment for an automated vehicle is modeled as a Markov decision process. Based on human lane-change behaviors, we train a voluntary lane- change policy using explicit-duration Markov decision process. Parameters in the lane-change policy are calibrated through reactive control improvisation to allow an automated car to pursue faster speed while maintaining desired frequency of lane-change maneuvers in various traffic environments.maneuvers in various traffic environments.)
• Distributed Structural Stabilization and Tracking for Formations of Dynamic Multi-Agents  + (In this paper, we provide a theoretical fr … In this paper, we provide a theoretical framework that consists of</br>graph theoretical and Lyapunov-based approaches to stability analysis and </br>distributed control of multi-agent formations. </br>This framework relays on the </br>notion of graph rigidity as a means of identifying the shape variables </br>of a formation. Using this approach, we can </br>formally define formations of multiple vehicles and three types of </br>stabilization/tracking problems for dynamic multi-agent systems. </br>We show how these three problems can be addressed mutually independent of</br>each other for a formation of two agents. Then, we introduce a procedure </br>called dynamic node augmentation that allows construction of a larger </br>formation with more agents that can be rendered structurally stable </br>in a distributed manner from some initial formation that </br>is structurally stable. We provide two examples of formations</br>that can be controlled using this approach, namely, the V-formation</br>and the diamond formation.the V-formation and the diamond formation.)
• Agreement Problems in Networks with Directed Graphs and Switching Toplogy  + (In this paper, we provide tools for conver … In this paper, we provide tools for convergence and</br>performance analysis of an agreement protocol for a</br>network of integrator agents with directed information</br>flow. We also analyze algorithmic robustness of this</br>consensus protocol for networks with mobile nodes and</br>switching topology. A connection is established between the Fiedler eigenvalue of the graph Laplacian and</br>the performance of this agreement protocol. We demon-</br>strate that a class of directed graphs, called balanced</br>graphs, have a crucial role in solving average-consensus</br>problems. Based on the properties of balanced graphs,</br>a group disagreement function (i.e. Lyapunov function)</br>is proposed for convergence analysis of this agreement</br>protocol for networks with directed graphs and switching topology.th directed graphs and switching topology.)
• Minimally Constrained Testing for Autonomy with Temporal Logic Specifications  + (In this paper, we study automated test gen … In this paper, we study automated test generation for discrete decision-making modules in autonomous systems. First, we consider a subset of Linear Temporal Logic to represent formal requirements on the system and the test environment. The system specification captures requirements for the system under test while the test specification captures basic attributes of the test environment known to the system, and additional structure provided by a test engineer, which is unknown to the system. Second, a game graph representing the high-level interaction between the system and the test environment is constructed from transition systems modeling the system and the test environment. We provide an algorithm that finds the projection of the acceptance conditions of the system and test specifications on the game graph. Finally, to ensure that the system meets the test specification in addition to satisfying the system specification, we present a framework to construct a minimally constrained test. Specifically, we formulate this as a multi-commodity network flows problem, and present two optimizations to solve for the minimally constrained test. We conclude with future directions on applying these algorithms to constrain test environments in self-driving applications.environments in self-driving applications.)
• Towards a Packet-Based Control Theory - Part I: Stabilization over a Packet-Based Network  + (In this paper, we study the classical prob … In this paper, we study the classical problem</br>of stabilizing a Linear Time Invariant (LTI) system in a</br>packet-based network setting. We assume that the LTI system</br>is unstable but both controllable and observable. The state</br>information is transmitted to the controller over a packetbased</br>network. We also assume that there is a perfect link</br>from the controller to the plant. We give a set of sufficient</br>conditions under which the system can be stabilized for a</br>given data rate C. In particular, these conditions can yield an</br>upper bound on the minimum C for which the system can</br>be stabilized. A recursive encoding-decoding scheme and an</br>associated control law are proposed to achieve stability for</br>rate exceeding this bound. An optimal bit allocation problem</br>is investigated in which we ask about how to allocate the</br>bits in a single packet for a subsystem of a general LTI</br>system such that a minimum upper bound on the data rate is</br>achieved.We then formulate the optimal bit allocation problem</br>as a Linear Matrix Inequality (LMI) optimization problem</br>which can be solved efficiently using standard Semi-definite</br>Programming (SDP) solvers. Examples and simulations are</br>given to demonstrate the results.ions are given to demonstrate the results.)
• Connected Cruise Control Design Using Probabilistic Model Checking  + (In this paper, we synthesize a robust conn … In this paper, we synthesize a robust connected cruise controller with performance guarantee using probabilis- tic model checking, for a vehicle that receives motion informa- tion from several vehicles ahead through wireless vehicle-to- vehicle communication. We model the car-following dynamics of the preceding vehicles as Markov chains and synthesize the connected cruise controller as a Markov decision process. We show through simulations that such a design is robust against imperfections in communication.st against imperfections in communication.)
• Design Space Exploration of the Violacein Pathway in Escherichia coli Based Cell-Free System  + (In this study, an Escherichia coli (E. col … In this study, an Escherichia coli (E. coli) based transcription translation cell-free system (TX-TL) was employed to sample various enzyme expression levels of the violacein pathway. TX-TL enables rapid modifications and prototyping of the pathway without complicated cloning cycles. The violacein metabolic pathway has been successfully reconstructed in TX-TL. Analysis of the product via UV-Vis absorption and liquid chromatography-mass spectrometry detected 4.95 mM of violacein. Expression levels of pathway enzymes were modeled using the TX-TL Toolbox. The model revealed the length of an enzyme coding sequence (CDS) significantly affected its expression level. Finally, pathway exploration suggested an improvement in violacein production at high VioC and VioD DNA concentrations. at high VioC and VioD DNA concentrations.)
• Estimation schemes for networked control systems using UDP-like communication  + (In this work we consider a class of networked control systems (NCS) when the control signal is sent to the plant via a UDP-like communication protocol, the controller sends a communication packet to the plant across a lossy network but the controller.....)
• An Estimation Algorithm for a Class of Networked Control Systems Using UDP-Like Communication Schemes  + (In this work we consider a class of networ … In this work we consider a class of networked control</br>systems (NCS) when the control signal is sent to the plant</br>via a UDP-like communication protocol. In this case the</br>controller sends a communication packet to the plant across</br>a lossy network, but the controller does not receive any</br>acknowledgement signal indicating the status of the control</br>packet. Standard observer based estimators assume the</br>estimator has knowledge of what control signal is applied</br>to the plant. Under the UDP-like protocol the</br>controller/estimator does not have explicit knowledge</br>whether the control signals have been applied to the plant</br>or not. We present a simple estimation algorithm that</br>consists of a state and mode observer as well as a</br>constraint on the control signal sent to the plant. For</br>the class of systems considered, discrete time LTI plants</br>where at least one</br>of the states that is directly affected by the input is</br>also part of the measurement vector, the estimator is able</br>to recover the fate of the control packet from the</br>measurement at the next timestep and exhibit better</br>performance than other naive schemes. For</br>single-input-single-output (SISO) systems we are able to</br>show convergence properties of the estimation error and the</br>state. Simulations are provided to demonstrate the</br>algorithm and show it's effectiveness.the algorithm and show it's effectiveness.)

• Characterization of minimum inducer separation time for a two-input integrase-based event detector  + (In this work, we present modeling and expe … In this work, we present modeling and experimental characterization of the minimum time needed for flipping of a DNA substrate by a two-integrase event detector. The event detector logic diâµerentiates the temporal order of two chemical inducers. We find that bundling biological rate parameters (transcription, translation, DNA search- ing, DNA flipping) into only a few rate constants in a stochastic model is sufficient to accurately predict final DNA states. We show, through time course data in E.coli, that these modeling predictions are reproduced in vivo. We believe this model validation is critical for using integrase-based systems in larger circuits.ntegrase-based systems in larger circuits.)
• Learning pose estimation for UAV autonomous navigation and landing using visual-inertial sensor data  + (In this work, we propose a robust network- … In this work, we propose a robust network-in-the-loop control system for autonomous navigation and landing of an Unmanned-Aerial-Vehicle (UAV). To estimate the UAV's absolute pose, we develop a deep neural network (DNN) architecture for visual-inertial odometry, which provides a robust alternative to traditional methods. We first evaluate the accuracy of the estimation by comparing the prediction of our model to traditional visual-inertial approaches on the publicly available EuRoC MAV dataset. The results indicate a clear improvement in the accuracy of the pose estimation up to 25% over the baseline. Finally, we integrate the data-driven estimator in the closed-loop flight control system of Airsim, a simulator available as a plugin for Unreal Engine, and we provide simulation results for autonomous navigation and landing.lts for autonomous navigation and landing.)
• Rapid in vitro engineering of 16 two-input logic gates  + (In vitro transcription and translation sys … In vitro transcription and translation systems have been used to rapidly test and debug synthetic circuits, allowing for much faster design-build-test cycles. To demonstrate the power of in vitro prototyping, we designed 16 two-input logic gates using a library of 14 linear DNA constructs. We successfully implemented all 16 gates in an E. coli cell extract prototyping environment (TXTL), going from design to functionality in less than 3 months. In separate tests, each taking less than an hour to set up and less than 8 hours to run, we were able to quickly diagnose functionality of engineered parts, including quantification of promoter leakiness and promoter and repressor strength. In subsequent short tests we determined optimal circuit component ratios and investigated component interactions, including crosstalk and resource loading. To lower the entry barrier to in vitro testing, we also created a cellphone-based fluorescent imager that can be used to measure fluorescent output of paper-based TXTL reactions. We hope to establish in vitro testing as a rapid, easily accessible tool for engineering synthetic circuits in research and education.thetic circuits in research and education.)
• Development of cell-free transcription-translation systems in three soil Pseudomonads  + (In vitro transcription-translation (TX-TL) … In vitro transcription-translation (TX-TL) can enable faster engineering of biological systems. This speed-up can be significant, especially in difficult-to-transform chassis. This work shows the successful development of TX-TL systems using three soil-derived wild-type Pseudomonads known to promote plant growth: Pseudomonas synxantha, Pseudomonas chlororaphis, and Pseudomonas aureofaciens. One, P. synxantha, was further characterized. A lysate test of P. synxantha showed a maximum protein yield of 2.5 μM at 125 proteins per DNA template and a maximum protein synthesis rate of 20 nM/min. A set of different constitutive promoters driving mNeonGreen expression were tested in TX-TL and integrated into the genome, showing similar normalized strengths for in vivo and in vitro fluorescence. This correspondence between the TX-TL derived promoter strength and the in vivo promoter strength indicates these lysate-based cell-free systems can be used to characterize and engineer biological parts without genome integration, enabling a faster designbuild-test cycle. enabling a faster designbuild-test cycle.)
• Failure-Tolerant Contract-Based Design of an Automated Valet Parking System using a Directive-Response Architecture  + (Increased complexity in cyber-physical sys … Increased complexity in cyber-physical systems calls for modular system design methodologies that guarantee correct and reliable behavior, both in normal operations and in the presence of failures. This paper aims to extend the contract-based design approach using a directive-response architecture to enable reactivity to failure scenarios. The architecture is demonstrated on a modular automated valet parking (AVP) system. The contracts for the different components in the AVP system are explicitly defined, implemented, and validated against a Python implementation.validated against a Python implementation.)
• Bio-Inspired Visuomotor Convergence in Navigation and Flight Control Systems  + (Insects exhibit incredibly robust closed l … Insects exhibit incredibly robust closed loop flight dynamics in the face of uncertainties. </br>A fundamental principle contributing to this unparalleled behavior is rapid processing and </br>convergence of visual sensory information to flight motor commands via spatial wide-field </br>integration, accomplished by retinal motion pattern sensitive interneurons (LPTCs) in the </br>lobula plate portion of the visual ganglia. Within a control-theoretic framework, an inner </br>product model for wide-field integration of retinal image flow is developed, representing the </br>spatial decompositions performed by LPTCs in the insect visuomotor system. A rigorous </br>characterization of the information available from this visuomotor convergence technique </br>for motion within environments exhibiting non-omogeneous spatial distributions is performed, establishing the connection between retinal motion sensitivity shape and closed </br>loop behavior. The proposed output feedback methodology is shown to be sufficient to give </br>rise to experimentally observed insect navigational heuristics, including forward speed regulation, obstacle avoidance, hovering, and terrain following behaviors. Hence, extraction of </br>global retinal motion cues through computationally efficient wide-field integration process- </br>ing provides a novel and promising methodology for utilizing visual sensory information in </br>autonomous robotic navigation and flight control applications.avigation and flight control applications.)
• Sensorimotor Convergence in Visual Navigation and Flight Control Systems  + (Insects exhibit unparalleled and incredibl … Insects exhibit unparalleled and incredibly robust flight dynamics in</br>the face of uncertainties. A fundamental principle contributing to this amazing</br>behavior is rapid processing and convergence of visual sensory information to flight</br>motor commands via spatial wide-field integration. Within the control-theoretic</br>framework presented here, a model for wide-field integration of retinal image flow</br>is developed which explains how various image flow kernels correspond to feedback</br>terms that stabilize the different modes of planar fiight. It is also demonstrated that</br>the proposed output feedback methodology is su±cient to explain experimentally</br>observed navigational heuristics as the centering and forward speed regulation</br>responses exhibited by honeybees.gulation responses exhibited by honeybees.)
• A Control-Oriented Analysis of Bio-Inspired Visuomotor Convergence  + (Insects exhibit unparalleled and incredibl … Insects exhibit unparalleled and incredibly robust </br>flight dynamics in the face of uncertainties. A fundamental principle contributing to this amazing behavior is rapid processing </br>and convergence of visual sensory information to flight motor </br>commands via spatial wide-field integration, accomplished by </br>motion pattern sensitive interneurons in the lobula plate portion </br>of the visual ganglia. Within a control-theoretic framework, a </br>model for wide-field integration of retinal image flow is developed, establishing the connection between image flow kernels </br>(retinal motion pattern sensitivities) and the feedback terms </br>they represent. It is demonstrated that the proposed output </br>feedback methodology is sufficient to give rise to experimentally </br>observed navigational heuristics as the centering and forward </br>speed regulation responses exhibited by honeybees.gulation responses exhibited by honeybees.)
• Guidelines for Designing the Antithetic Feedback Motif  + (Integral control is commonly used in mecha … Integral control is commonly used in mechanical and electrical systems to ensure perfect adaptation. A proposed design of integral control for synthetic biological systems employs the sequestration of two biochemical controller species. The unbound amount of controller species captures the integral of the error between the current and the desired state of the system. However, implementing integral control inside bacterial cells using sequestration feedback has been challenging due to the controller molecules being degraded and diluted. Furthermore, integral control can only be achieved under stability conditions that not all sequestration feedback networks fulfill. In this work, we give guidelines for ensuring stability and good performance (small steady-state error) in sequestration feedback networks. Our guidelines provide simple tuning options to obtain a flexible and practical biological implementation of sequestration feedback control. Using tools and metrics from control theory, we pave the path for the systematic design of synthetic biological systems.ic design of synthetic biological systems.)
• A 65nm CMOS Living-Cell Dynamic Fluorescence Sensor with 1.05fA Sensitivity at 600/700nm Wavelengths  + (Integrated, low-cost and miniaturized devi … Integrated, low-cost and miniaturized devices that can detect clinically relevant biomarkers are crucial for the growing field of precision medicine as they can enable point-of-care diagnosis, continuous health monitoring and closed-loop drug delivery. Fluorescence (FL) sensing is known to be one of the most reliable, sensitive, and widely adopted sensing modality for many biomarkers. However, detecting the weak FL signal requires complex optical setups, especially narrowband optical filters to block the strong excitation (EX) light. Prior efforts to miniaturize and implement FL sensing in CMOS technologies have been limited to on-chip high-pass filters using dense vertical waveguide arrays. More importantly, the reported wavelength range of 800nm in prior work is not compatible with most of the commonly used fluorescent proteins that work with living cells. Luminescence is another mechanism for detecting biomarkers that does not require an EX source and optical filtering. However, there are limited number of luminescence proteins, and it is not feasible to use them in a closed-loop system since they can interfere with optogenetic control integration.fere with optogenetic control integration.)
• Systems Level Model of Dietary Effects on Cognition via the Microbiome-Gut-Brain Axis  + (Intercommunication of the microbiome-gut-b … Intercommunication of the microbiome-gut-brain axis occurs through various signaling pathways including the vagus nerve, immune system, endocrine/paracrine, and bacteria-derived metabolites. But how these pathways integrate to influence cognition remains undefined. In this paper, we create a systems level mathematical framework comprised of interconnected organ-level dynamical subsystems to increase conceptual understanding of how these subsystems contribute to cognitive performance. With this framework we propose that control of hippocampal long-term potentiation (hypothesized to correlate with cognitive performance) is influenced by inter- organ signaling with diet as the external control input. Specifically, diet can influence synaptic strength (LTP) homeostatic conditions necessary for learning. The proposed model provides new qualitative information about the functional relationship between diet and output cognitive performance. The results can give insight for optimization of cognitive performance via diet in experimental animal models.ce via diet in experimental animal models.)
• A Scalable Formulation for Engineering Combination Therapies for Evolutionary Dynamics of Disease  + (It has been shown that optimal controller … It has been shown that optimal controller synthesis for positive systems can be formulated as a linear program. Leveraging these results, we propose a scalable iterative algo- rithm for the systematic design of sparse, small gain feedback strategies that stabilize the evolutionary dynamics of a generic disease model. We achieve the desired feedback structure by augmenting the optimization problems with `1 and `2 regular- ization terms, and illustrate our method on an example inspired by an experimental study aimed at finding appropriate HIV neutralizing antibody therapy combinations in the presence of escape mutants.nations in the presence of escape mutants.)
• Stochastic Gene Expression in Single Gene Oscillator Variants  + (It is infeasible to understand all dynamic … It is infeasible to understand all dynamics in cell, but we can aim to understand the impact of design choices under our control. Here we consider a single gene oscillator as a case study to understand the influence of DNA copy number and repressor choice on the resulting dynamics. We first switch the repressor in the oscillator from the originally published lacI to treRL, a chimeric repressor with a lacI DNA binding domain that is inducible by trehalose. This slightly modified system produces faster and more regular oscillations than the original lacI oscillator. We then compare the treRL oscillator at three different DNA copy numbers. The period and amplitude of oscillations increases as the copy number is decreased. We cannot explain the change in period with differ- ential equation models without changing delays or degradation rates. The correlation and phase coherence between daughter cells after cell division also tend to fall off faster for the lower copy oscillator variants. These results suggest that lower copy number variants of our single gene oscillator produce more synchronized oscillations.or produce more synchronized oscillations.)
• To Drop or Not to Drop: Design Principles for Kalman Filtering Over Wireless Fading Channels  + (It is the general assumption that in estim … It is the general assumption that in estimation and control over wireless links, the receiver should drop any erroneous packets. While this approach is appropriate for non real-time data-network applications, it can result in instability and loss of performance in networked control systems. In this technical note we consider estimation of a multiple-input multiple-output dynamical system over a mobile fading communication channel using a Kalman filter. We show that the communication protocols suitable for other already-existing applications like data networks may not be entirely applicable for estimation and control of a rapidly changing dynamical system. We then develop new design paradigms in terms of handling noisy packets for such delay-sensitive applications. We reformulate the estimation problem to include the impact of stochastic communication noise in the erroneous packets. We prove that, in the absence of a permanent cross-layer information path, packet drop should be designed to balance information loss and communication noise in order to optimize the performance.oise in order to optimize the performance.)
• The Effect of Compositional Context on Synthetic Gene Networks  + (It is well known that synthetic gene expre … It is well known that synthetic gene expression is highly sensitive to how genetic elements (promoter structure, spacing regions between promoter and coding sequences, ribosome binding sites, etc.) are spatially configured. An important topic that has received far less attention is how the compositional context, or spatial arrangement, of entire genes within a synthetic gene network affects their individual expression levels. In this paper we show, both quantitatively and qualitatively, that compositional context significantly alters transcription levels in synthetic gene networks. We demonstrate that key characteristics of gene induction, such as ultra-sensitivity and dynamic range, strongly depend on compositional context. We postulate that supercoiling can be used to explain this interference and validate this hypothesis through modeling and a series of in vitro supercoiling relaxation experiments. This compositional interference enables a novel form of feedback in synthetic gene networks. We illustrate the use of this feedback by redesigning the toggle switch to incorporate compositional context. We show the context-optimized toggle switch has improved threshold detection and memory properties.threshold detection and memory properties.)
• Configuration Flatness of Lagrangian Systems Underactuated by One Control  + (Lagrangian control systems that are differ … Lagrangian control systems that are differentially flat with flat outputs that only</br>depend on configuration variables are said to be configuration flat. We provide a complete</br>characterisation of configuration flatness for systems with $n$ degrees of freedom and</br>$n-1$ controls whose range of control forces only depends on configuration but not on</br>velocity and whose Lagrangian has the form of kinetic energy minus potential. The method</br>presented allows us to determine if such a system is configuration flat and, if so</br>provides a constructive method for finding all possible configuration flat outputs. Our</br>characterisation relates configuration flatness to Riemannian geometry. We illustrate the</br>method by two examples. We illustrate the method by two examples.)
• Layered Feedback Control Overcomes Performance Trade-Off in Synthetic Biomolecular Networks  + (Layered feedback is an optimization strate … Layered feedback is an optimization strategy in feedback control designs widely used in electrical and mechanical engineering. Layered control theory suggests that the performance of controllers is bound by the universal robustness-efficiency tradeoff limit, which could be overcome by layering two or more feedbacks together. In natural biological networks, genes are often regulated with redundancy and layering to adapt to environmental perturbations. Control theory hypothesizes that this layering architecture is also adopted by nature to overcome this performance trade-off. In this work, we validated this property of layered control with a synthetic network in living E. coli cells. We performed system analysis on a node-based design to confirm the tradeoff properties before proceeding to simulations with an effective mechanistic model, which guided us to the best performing design to engineer in cells. Finally, we interrogated its system dynamics experimentally with eight sets of perturbations on chemical signals, nutrient abundance, and growth temperature. For all cases, we consistently observed that the layered control overcomes the robustness-efficiency trade-off limit. This work experimentally confirmed that layered control could be adopted in synthetic biomolecular networks as a performance optimization strategy. It also provided insights in understanding genetic feedback control architectures in nature. feedback control architectures in nature.)
• Bootstrapping bilinear models of simple vehicles  + (Learning and adaptivity will play a large … Learning and adaptivity will play a large role in robotics in the future, as robots move from structured to unstructured environments that cannot be fully predicted or understood by the designer. Two questions that are open: 1) in principle, how much it is possible to learn; and, 2) in practice, how much we should learn. The bootstrapping scenario describes the extremum case where agents need to learn âeverythingâ from scratch, including a torque-to-pixels models for its robotic body. Systems with such capabilities will be advantaged in terms of being resilient to unforeseen changes and deviations from prior assumptions. This paper considers the bootstrapping problem for a subset of the set of all robots: the Vehicles, inspired by Braitenbergâs work, are idealization of mobile robots equipped with a set of âcanonicalâ exteroceptive sensors (camera; range- finder; field-sampler). Their sensel-level dynamics are derived and shown to be surprising close. We define the class of BDS models, which assume an instantaneous bilinear dynamics between observations and commands, and derive streaming-based bilinear strategies for them. We show in what sense the BDS dynamics approximates the set of Vehicles to guarantee success in the task of generalized servoing: driving the observations to a given goal snapshot. Simulations and experiments substantiate the theoretical results. This is the first instance of a bootstrapping agent that can learn the dynamics of a relatively large universe of systems, and use the models to solve well-defined tasks, with no parameter tuning or hand-designed features.arameter tuning or hand-designed features.)
• Dynamics and Stability of Low Reynolds Number Swimming Near a Wall  + (Locomotion of microorganisms and tiny arti … Locomotion of microorganisms and tiny artificial swimmers is governed by low- Reynolds-number hydrodynamics, where viscous effects dominate and inertial effects are negligible. While the theory of low-Reynolds-number locomotion is well studied for unbounded fluid domains, the presence of a boundary has a significant influence on the swimmer's trajectories, and poses problems of dynamic stability of its motion. In this paper we consider a simple theoretical model of a micro-swimmer near a wall, study its dynamics, and analyze the stability of its motion. We highlight the underlying geometric structure of the dynamics, and establish a relation between the reversing symmetry of the system and existence and stability of periodic and steady solutions of motion near the wall. The results are demonstrated by numerical simulations and validated by motion experiments with robotic swimmer prototypes.periments with robotic swimmer prototypes.)
• Engineering pulsatile communication in bacterial consortia  + (Lux-type quorum sensing systems enable com … Lux-type quorum sensing systems enable communication in bacteria with only two protein components: a signal synthase and an inducible transcription activator. The simplicity of these systems makes them a popular choice for engineering collaborative behaviors in synthetic bacterial consortia, such as photographic edge detection and synchronized oscillation. To add to this body of work, we propose a pulsatile communication circuit that enables dynamic patterning and long-distance communication analogous to action potentials traveling through nerve tissue. We employed a model-driven design paradigm involving incremental characterization of in vivo design candidates with increasing circuit complexity. Beginning with a simple inducible reporter system, we screened a small number of circuits varying in their promoter and ribosomal binding site strengths. From this candidate pool, we selected a candidate to be the seed network for the subsequent round of more complex circuit variants, likewise variable in promoter and RBS strengths. The selection criteria at each level of complexity is tailored to optimize a different desirable performance characteristic. By this approach we individually optimized reporter signal-to-background ratio, pulsatile response to induction, and quiescent basal transcription, avoiding large library screens while ensuring robust performance of the composite circuit.bust performance of the composite circuit.)
• Geometric Control of Particle Manipulation in a Two-Dimensional Fluid  + (Manipulation of particles suspended in flu … Manipulation of particles suspended in fluids is crucial for many applications, such as precision machining, chemical processes, bio-engineering, and self-feeding of microorganisms. In this paper, we study the problem of particle manipulation by cyclic fluid boundary excitations from a geometric-control viewpoint. We focus on the simplified problem of manipulating a single particle by generating controlled cyclic motion of a circular rigid body in a two-dimensional perfect fluid. We show that the drift in the particle location after one cyclic motion of the body can be interpreted as the geometric phase of a connection induced by the system's hydrodynamics. We then formulate the problem as a control system, and derive a geometric criterion for its nonlinear controllability. Moreover, by exploiting the geometric structure of the system, we explicitly construct a feedback-based gait that results in attraction of the particle towards the rigid body. We argue that our gait is robust and model-independent, and demonstrate it in both perfect fluid and Stokes fluid.it in both perfect fluid and Stokes fluid.)
• Experiments in Planar Manipulation and Grasping  + (Many algorithms have been proposed in the … Many algorithms have been proposed in the literature for control of</br>multi-fingered robot hands. This paper compares the performance of</br>several of these algorithms, as well as some extensions of more</br>conventional manipulator control laws, in the case of planar grasping.</br>A brief introduction to the subject of robot hands and the notation</br>used in this paper is included.e notation used in this paper is included.)
• On Measures of Non-Integrability of Pfaffian Systems  + (Many problems in nonlinear control theory … Many problems in nonlinear control theory (like, for instance, feedback</br>linearization problem) lead to examination of integrability of a Pfaffian</br>system. In a generic case a Pfaffian system is not integrable. Therefore,</br>how to approximate nonintegrable Pfaffian systems by integrable ones and how</br>this approximation can be applied in practice appears to be a natural and</br>important problem. In the present paper we establish some measures of</br>non-integrability of Pfaffian system of arbitrary dimension and discuss</br>their relation to approxiations of non-integrable Pfaffian systems by</br>integrable ones. Our work is motivated by expected applications to</br>approximate feedback linearization of multi-input nonlinear systems.rization of multi-input nonlinear systems.)
• Distributed Gradient Systems and Dynamic Coordination  + (Many systems comprised of interconnected s … Many systems comprised of interconnected sub-units exhibit coordinated behaviors; social groups, </br>networked computers, financial markets, and numerous biological systems come to mind. There </br>has been long-standing interest in developing a scientific understanding of coordination, both for ex- </br>planatory power in the natural and economic sciences, and also for constructive power in engineering </br>and applied sciences. This thesis is an abstract study of coordination, focused on developing a sys- </br>tematic âdesign theoryâ for producing interconnected systems with specifiable coordinated behavior; </br>this is in contrast to the bulk of previous work on this sub ject, in which any design component has </br>been primarily ad-hoc. </br></br><p>The main theoretical contribution of this work is a geometric formalism in which to cast dis- </br>tributed systems. This has numerous advantages and ânaturallyâ parametrizes a wide class of </br>distributed interaction mechanisms in a uniform way. We make use of this framework to present </br>a model for distributed optimization, and we introduce the distributed gradient as a general design </br>tool for synthesizing dynamics for distributed systems. The distributed optimization model is a </br>useful abstraction in its own right and motivates a definition for a distributed extremum. As one </br>might expect, the distributed gradient is zero at a distributed extremum, and the dynamics of a </br>distributed gradient flow must converge to a distributed extremum. This forms the basis for a wide </br>variety of designs, and we are in fact able to recover a widely studied distributed averaging algorithm </br>as a very special case. </br></br><p>We also make use of our geometric model to introduce the notion of coordination capacity; </br>intuitively, this is an upper bound on the âcomplexityâ of coordination that is feasible given a </br>particular distributed interaction structure. This gives intuitive results for local, distributed, and </br>global control architectures, and allows formal statements to be made regarding the possibility of </br>âsolvingâ certain optimization problems under a particular distributed interaction model. </br></br><p>Finally, we present a number of applications to illustrate the theoretical approach presented; </br>these range from âstandardâ distributed systems tasks (leader election and clock synchronization) </br>to more exotic tasks like graph coloring, distributed account balancing, and distributed statistical </br>computations.ccount balancing, and distributed statistical computations.)
• Engineering the soil bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation  + (Microbial bioreporters hold promise for ad … Microbial bioreporters hold promise for addressing challenges in medical and environmental applications. However, the difficulty of ensuring their stable persistence and function within the target environment remains a challenge. One strategy is to integrate information about the host strain and target environment into the design-build-test cycle of the bioreporter itself. Here, we present a case study for such an environmentally-motivated design process by engineering the wheat commensal bacterium Pseudomonas synxantha 2-79 into a ratiometric bioreporter for phosphorus limitation. Comparative analysis showed that an exogenous P-responsive promoter outperformed its native counterparts. This reporter can selectively sense and report phosphorus limitation at plant-relevant concentrations of 25-100 µM without cross-activation from carbon or nitrogen limitation or high cell densities. Its performance is robust over a field-relevant pH range (5.8-8), and it responds only to inorganic phosphorus, even in the presence of common soil organic P. Finally, we used fluorescein-calibrated flow cytometry to assess whether the reporter’s performance in shaken liquid culture predict its performance in soil, finding that although the reporter is still functional at the bulk level, its variability in performance increases when grown in a soil slurry as compared to planktonic culture, with a fraction of the population not expressing the reporter proteins. Together, our environmentally-aware design process provides an example of how laboratory bioengineering efforts can generate microbes with greater promise to function reliably in their applied contexts.nction reliably in their applied contexts.)