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Stochastic gene expression poses an important challenge for engineering robust behaviors in a heterogeneous cell population. Cells address this challenge by operating on distributions of cellular responses generated by noisy processes. Similarly, a previously published temporal logic gate considers the distribution of responses across a cell population under chemical inducer pulsing events. The design uses a system of two integrases to engineer an E. coli strain with four DNA states that records the temporal order of two chemical signal events. The heterogeneous cell population response was used to infer the timing and duration of the two chemical signals for a small set of events. Here we use the temporal logic gate system to address the problem of extracting information about chemical signal events. We use the heterogeneous cell population response to infer whether any event has occurred or not and also to infer its properties such as timing and amplitude. Bayesian inference provides a natural framework to answer our questions about chemical signal occurrence, timing, and amplitude. We develop a probabilistic model that incorporates uncertainty in the how well our model captures the cell population and in how well a sample of measured cells represents the entire population. Using our probabilistic model and cell population measurements taken every five minutes on generated data, we ask how likely it was to observe the data for parameter values that describe square-shaped inducer pulses. We compare the likelihood functions associated with the probabilistic models for the event with the chemical signal pulses turned on versus turned off. Hence, we can determine whether an event of chemical induction of integrase expression has occurred or not. Using Markov Chain Monte Carlo, we sample the posterior distribution of chemical pulse parameters to identify likely pulses that produce the data measurements. We implement this method and obtain accurate results for detecting chemical inducer pulse timing, length, and amplitude. We can detect and identify chemical inducer pulses as short as half an hour, as well as all pulse amplitudes that fall under biologically relevant conditions.  
The acrobot is a simple mechanical system patterned after a gymnast performing on a single parallel bar. By swinging her legs, a gymnast is able to bring herself into an inverted position with her center of mass above the part and is able to perform manuevers about this configuration. This report studies the use of nonlinear control techniques for designing a controller to operate in a neighborhood of the manifold of inverted equilibrium points. The techniques described here are of particular interest because the dynamic model of the acrobot violates many of the necessary conditions required to apply current methods in linear and nonlinear control theory. <p> The approach used in this report is to approximate the system in such a way that the behavior of the system about the manifold of equilibrium points is correctly captured. In particular, we construct an approximating system which agrees with the linearization of the original system on the equilibrium manifold and is full state linearizable. For this class of approximations, controllers can be constructed using recent techniques from differential geometric control theory. We show that application of control laws derived in this manner results in approximate trajectory tracking for the system under certain restrictions on the class of desired trajectories. Simulation results based on a simplified model of the acrobot are included.  +
We introduce an algorithm for the optimal control of stochastic nonlinear systems subject to temporal logic constraints on their behavior. We compute directly on the state space of the system, avoiding the expensive pre-computation of a discrete abstraction. An automaton that corresponds to the temporal logic specification guides the computation of a control policy that maximizes the probability that the system satisfies the specification. This reduces controller synthesis to solving a sequence of stochastic constrained reachability problems. Each individual reachability problem is solved via the Hamilton-Jacobi-Bellman (HJB) partial differential equation of stochastic optimal control theory. To increase the efficiency of our approach, we exploit a class of systems where the HJB equation is linear due to structural assumptions on the noise. The linearity of the partial differential equation allows us to pre-compute control policy primitives and then compose them, at essentially zero cost, to conservatively satisfy a complex temporal logic specification.  +
We introduce an algorithm for the optimal con- trol of stochastic nonlinear systems subject to temporal logic constraints on their behavior. We directly compute on the state space of the system, avoiding the expensive pre-computation of a discrete abstraction. An automaton that corresponds to the temporal logic specification guides the computation of a control policy that maximizes the probability that the system satisfies the specification. This reduces controller synthesis to solving a sequence of stochastic constrained reachability problems. The solution to each reachability problem corresponds to the solution to a corresponding Hamilton-Jacobi-Bellman (HJB) partial differential equation. To increase the efficiency of our approach, we exploit a class of systems where the HJB equation is linear due to structural assumptions on the noise. The linearity of the PDE allows us to pre-compute control policy primitives and then compose them, at essentially zero cost, to satisfy a complex temporal logic specification.  +
A computational approach to generating aggressive trajectories in real-time for constrained mechanical systems is presented. The algorithm is based on a combination of nonlinear control theory, spline theory, and sequential quadratic programming. It is demonstrated that real-time trajectory generation for constrained mechanical systems is possible by mapping the problem to one of finding trajectory curves in a lower dimensional space. Performance of the algorithm is compared with existing optimal trajectory generation techniques. Numerical results are reported using the NTG software package.  +
This paper presents an optimization framework for broadcast power-control, specifically addressed at wireless networking issues arising in implementing information flows for multi-vehicle systems. We formulate an optimization problem for the minimization of an aggregate cost subject to a constraint on a quantity we call the geometric connection robustness, which is a locally computable numerical assessment of the robustness of the an information flow to perturbations in position. Our main result is a location-aided distributed power-control algorithm based on a gradient-like optimization scheme. We also use geometric connection robustness to develop a cheap distributed heuristic for the construction of sparse connected information flow.  +
In an aircraft electric power system, one or more supervisory control units actuate a set of electromechanical switches to dynamically distribute power from generators to loads, while satisfying safety, reliability, and real-time performance requirements. To reduce expensive redesign steps, this control problem is generally addressed by minor incremental changes on top of consolidated solutions. A more systematic approach is hindered by a lack of rigorous design methodologies that allow estimating the impact of earlier design decisions on the final implementation. To achieve an optimal implementation that satisfies a set of requirements, we propose a platform-based methodology for electric power system design, which enables independent implementation of system topology (i.e., interconnection among elements) and control protocol by using a compositional approach. In our flow, design space exploration is carried out as a sequence of refinement steps from the initial specification toward a final implementation by mapping higher level behavioral and performance models into a set of either existing or virtual library components at the lower level of abstraction. Specifications are first expressed using the formalisms of linear temporal logic, signal temporal logic, and arithmetic constraints on Boolean variables. To reason about different requirements, we use specialized analysis and synthesis frameworks and formulate assume guarantee contracts at the articulation points in the design flow. We show the effectiveness of our approach on a proof-of-concept electric power system design.  +
Insects exhibit unparalleled and incredibly robust flight dynamics in the face of uncertainties. A fundamental principle contributing to this amazing behavior is rapid processing and convergence of visual sensory information to flight motor commands via spatial wide-field integration, accomplished by motion pattern sensitive interneurons in the lobula plate portion of the visual ganglia. Within a control-theoretic framework, a model for wide-field integration of retinal image flow is developed, establishing the connection between image flow kernels (retinal motion pattern sensitivities) and the feedback terms they represent. It is demonstrated that the proposed output feedback methodology is sufficient to give rise to experimentally observed navigational heuristics as the centering and forward speed regulation responses exhibited by honeybees.  +
A reactor for the deposition of superconducting \ybcolong\;thin films is modeled and studied from a control perspective to determine the heat transfer dynamics of the reactor under active thermal control. A nonlinear wavelength-dependent heat transfer model is developed to predict reactor heat transfer throughout the film growth process, and preliminary component testing is conducted to validate the model. The model is linearized about a typical operating point and analyzed with linear feedback control methods to determine the performance of the reactor under observer-based feedback control with film growth disturbances. The controller and observer are selected through linear quadratic regulator and linear quadratic estimator methods. Rates of convergence of the controller and observer are determined through examination of the eigenvalues of the linearized system, and disturbance rejection is assessed with ${\mathcal H}_2$ and ${\mathcal H}_\infty$ norms. The eigenvalue and norm analysis is applied to varying reactor design parameters to quantify performance tradeoffs. The maximum errors associated with control and with estimation of a nominal design case are both 21 K, and the longest time scales are 45 seconds and 10 seconds for the controller and observer, respectively.  +
This paper describes the use of a domain-specific language, and an accompanying software tool, in constructing correct- by-construction control protocols for aircraft electric power systems. Given a base topology, the language consists of a set of primitives for standard specifications. The accompanying tool converts these primitives into formal specifica- tions, which are used to synthesize control protocols. We can then use TuLiP, a Python-based software toolbox, to synthesize centralized and distributed controllers. For sys- tems with no time involved in the specifications, this tool also provides an option to output specifications into a SAT-solver compatible format, thus reducing the synthesis problem to a satisfiability problem. We provide the results of our synthesis procedure on a range of topologies.  +
This paper explores the problem of finding a real--time optimal tra jectory for unmanned air vehicles (UAV) in order to minimize their probability of detection by opponent multiple radar detection systems. The problem is handled using the Nonlinear Tra jectory Generation (NTG) method developed by Milam et al. The paper presents a formulation of the trajectory generation task as an optimal control problem, where temporal constraints allow periods of high observability interspersed with periods of low observability. This feature can be used strategically to aid in avoiding detection by an opponent radar. The guidance is provided in the form of sampled tabular data. It is then shown that the success of NTG on the proposed low--observable tra jectory generation problem depends upon an accurate parameterization of the guidance data. In particular, such an approximator is desired to have a compact architecture, a minimum number of design parameters, and a smooth continuously--differentiable input-output mapping. Artificial Neural Networks (ANNs) as universal approximators are known to possess these features, and thus are considered here as appropriate candidates for this task. Comparison of ANNs against B-spline approximators is provided, as well. Numerical simulations on multiple radar scenarios illustrate UAV trajectories optimized for both detectability and time.  +
In this paper we present a dynamical systems representation for multi-agent rendezvous on the phase plane. We restrict our attention to two agents, each with scalar dynamics. The problem of rendezvous is cast as a stabilization problem, with a set of constraints on the trajectories of the agents, defined on the phase plane. We also describe a method to generate control Lyapunov functions that when used in conjunction with a stabilizing control law, such as Sontag's formula, make sure that the two-agent system attains rendezvous. The main result of this paper is a Lyapunov-like certificate theorem that describes a set of constraints, which when satisfied are su±cient to guarantee rendezvous.  +
In this paper analysis of interconnected dynamical systems is considered. A framework for the analysis of the stability of interconnection is given. The results from Fax and Murray that studies the SISO-case for a constant interconnection matrix are genralized to the MIMO-case where arbitrary interconnection is allowed. The analysis show existness of a separation principle that is very useful in the sense of the simplicity for stability analysis. Stability could be checked graphically using a Nyquist-like criterion. The problem with time-delays and interconnection variation and robustness appear to be natural special cases of the general framework, and hence, simple stability criteria are derived easly.  +
In this paper, we analyze the problem of bifurcation control from a geometric perspective. Our goal is to provide coordinate free, geometric conditions under which control can be used to alter the bifurcation properties of a nonlinear control system. These insights are expected to be useful in understanding the role that magnitude and rate limits play in bifurcation control, as well as giving deeper understanding of the types of control inputs that are required to alter the nonlinear dynamics of bifurcating systems. We also use a model from active control of rotating stall in axial compression systems to illustrate the geometric sufficient conditions of stabilizability.  +
In the geometric theory of nonlinear control systems, the notion of a distribution and the dual notion of codistribution play a central role. Many results in nonlinear control theory require certain distributions to be integrable. Distributions (and codistributions) are not generically integrable and, moreover, the integrability property is not likely to persist under small perturbations of the system. Therefore, it is natural to consider the problem of approximating a given codistribution by an integrable codistribution, and to determine to what extent such an approximation may be used for obtaining approximate solutions to various problems in control theory. In this note, we concentrate on the purely mathematical problem of approximating a given codistribution by an integrable codistribution. We present an algorithm for approximating an m-dimensional nonintegrable codistribution by an integrable one using a homotopy approach. The method yields an approximating codistribution that agrees with the original codistribution on an m-dimensional submanifold E_0 of R^n.  +
We introduce a MATLAB-based simulation toolbox, called txtlsim, for an Escherichia coli-based Transcription–Translation (TX–TL) system. This toolbox accounts for several cell-free-related phenomena, such as resource loading, consumption and degradation, and in doing so, models the dynamics of TX–TL reactions for the entire duration of solution phase batch-mode experiments. We use a Bayesian parameter inference approach to characterize the reaction rate parameters associated with the core transcription, translation and mRNA degradation mechanics of the toolbox, allowing it to reproduce constitutive mRNA and protein-expression trajectories. We demonstrate the use of this characterized toolbox in a circuit behavior prediction case study for an incoherent feed-forward loop.  +
The T7 bacteriophage RNA polymerase (T7 RNAP) serves as a model for understanding RNA synthesis, as a tool for protein expression, and as an actuator for synthetic gene circuit design in bacterial cells and cell-free extract. T7 RNAP is an attractive tool for orthogonal protein expression in bacteria owing to its compact single subunit structure and orthogonal promoter specificity. Understanding the mechanisms underlying T7 RNAP regulation is important to the design of engineered T7-based transcription factors, which can be used in gene circuit design. To explore regulatory mechanisms for T7 RNAP-driven expression, we developed a rapid and cost-effective method to characterize engineered T7-based transcription factors using cell-free protein synthesis and an acoustic liquid handler. Using this method, we investigated the effects of the tetracycline operator’s proximity to the T7 promoter on the regulation of T7 RNAP-driven expression. Our results reveal a mechanism for regulation that functions by interfering with the transition of T7 RNAP from initiation to elongation and validates the use of the method described here to engineer future T7-based transcription factors.  +
Due to the increasing complexity of space missions and distance to exploration targets, future robotic systems used for space exploration call for more resilience and autonomy. Instead of minimizing the failure risk, we are focusing on missions that will inevitably encounter significant failures and are developing an algorithm that will autonomously reconfigure the system controller to continue to make progress towards the mission goal despite being in a reduced capacity state - we call this extreme resilience. In this paper, we develop a model-free framework to autonomously react to locomotion failures of robotic systems. This is done by the use of a neural network for path planning using the neuroevolution of aug- menting topologies (NEAT) algorithm and a dynamic database of possible moves and their effect on the system’s position and orientation. Two modes of failure detection and resolution are being introduced: (a) relative position failure detection, which is triggered by large, unexpected moves and results in a complete update of the database before a retraining of the neural network, and (b) absolute position failure detection, which triggers from large build-ups of position error from small failures and will induce a retraining of the neural network without an explicit database reset. We implement and validate this framework on a high-fidelity planetary rover simulation using Unreal Engine and on a hardware setup of a TurtleBot2 with a PhantomX Pincher robot arm.  +
This paper considers the problem of motion planning for a car-like robot (i.e., a mobile robot with a nonholonomic constraint whose turning radius is lower-bounded). We present a fast and exact planner for our mobile robot model, based upon recursive subdivision of a collision-free path generated by a lower-level geometric planner that ignores the motion constraints. The resultant trajectory is optimized to give a path that is of near-minimal length in its homotopy class. Our claims of high speed are supported by experimental results for implementations that assume a robot moving amid polygonal obstacles. The completeness and the complexity of the algorithm are proven using an appropriate metric in the configuration space R2 x S1 of the robot. This metric is defined by using the length of the shortest paths in the absence of obstacles as the distance between two configurations. We prove that the new induced topology and the classical one are the same. Although we concentration upon the car-like robot, the generalization of these techniques leads to new theoretical issues involving sub-Riemannian geometry and to practical results for nonholonomic motion planning.  +
We present an identification framework for biochemical systems that allows multiple candidate models to be compared. This framework is designed to select a model that fits the data while maintaining model simplicity. The model identification task is divided into a parameter estimation stage and a model comparison stage. Model selection is based on calculating Akaike's Information Criterion, which is a systematic method for determining the model that best represents a set of experimental data. Two case studies are presented: a simulated transcriptional control circuit and a system of oscillators that has been built and characterized in vitro. In both examples the multi-model framework is able to discriminate between model candidates to select the one that best describes the data.  +
A computationally e±cient technique for the numerical solution of constrained optimal control problems governed by one-dimensional partial differential equations is considered in this paper. This technique utilizes inversion to map the optimal control problem to a lower dimensional space. Results are presented using the Nonlinear Trajectory Generation software package (NTG) showing that real-time implementation may be possible.  +
In this paper we discuss a resilient, risk-aware software architecture for onboard, real-time autonomous operations that is intended to robustly handle uncertainty in space- craft behavior within hazardous and unconstrained environ- ments, without unnecessarily increasing complexity. This architecture, the Resilient Spacecraft Executive (RSE), serves three main functions: (1) adapting to component failures to allow graceful degradation, (2) accommodating environments, science observations, and spacecraft capabilities that are not fully known in advance, and (3) making risk-aware decisions without waiting for slow ground-based reactions. This RSE is made up of four main parts: deliberative, habitual, and reflexive layers, and a state estimator that interfaces with all three. We use a risk-aware goal-directed executive within the deliberative layer to perform risk-informed planning, to satisfy the mission goals (specified by mission control) within the specified priorities and constraints. Other state-of-the-art algorithms to be integrated into the RSE include correct-by-construction control synthesis and model-based estimation and diagnosis. We demonstrate the feasibility of the architecture in a simple implementation of the RSE for a simulated Mars rover scenario.  +
Safety guarantees are built into a robust MPC (Model Predictive Control) algorithm for uncertain nonlinear systems. The algorithm is designed to obey all state and control constraints and blend two operational modes: (I) standard mode guarantees resolvability and asymptotic convergence to the origin in a robust receding-horizon manner; (II) safety mode, if activated, guarantees containment within an invariant set about a safety reference for all time. This research is motivated by physical vehicle control-algorithm design (e.g. spacecraft and hovercraft) in which operation mode changes must be considered. Incorporating safety mode provides robustness to unexpected state-constraint changes; e.g., other vehicles crossing/stopping in the feasible path, or unexpected ground proximity in landing scenarios. The safety-mode control is provided by an offline designed control policy that can be activated at any arbitrary time during standard mode. The standard-mode control consists of separate feedforward and feedback components; feedforward comes from online solution of a FHC (Finite-Horizon optimal Control problem), while feedback is designed offline to generate an invariant tube about the feedforward tra jectory. The tube provides robustness (to uncertainties and disturbances in the dynamics) and guarantees FHC resolvability. The algorithm design is demonstrated for a class of systems with uncertain nonlinear terms that have norm-bounded Jacobians.  +
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.  +
This paper proposes a set-based parameter identi- fication method for biochemical systems. The developed method identifies not a single parameter but a set of parameters that all explains time-series experimental data, enabling the systematic characterization of the uncertainty of identified parameters. Our key idea is to use a state-space realization that has the same input-output behavior as experimental data instead of the experimental data itself for the identification. This allows us to relax the originally nonlinear identification problem to an LMI feasibility problem validating the norm bound of an error system. We show that regions of parameters can be efficiently classified into consistent and inconsistent parameter sets by combining the LMI feasibility problems and a generalized bisection algorithm.  +
We study the synthesis problem of an LQR controller when the matrix describing the control law is constrained to lie in a particular vector space. Our motivation is the use of such control laws to stabilize networks of autonomous agents in a decentralized fashion; with the information flow being dictated by the constraints of a pre-specified topology. In this paper, we consider the finite-horizon version of the problem and provide both a computationally intensive optimal solution and a sub-optimal solution that is computationally more tractable. Then we apply the technique to the decentralized vehicle formation control problem and show that the loss in performance due to the use of the sub-optimal solution is not huge; however the topology can have a large effect on performance.  +
This paper considers the fundamental design and modeling of the Caltech ducted fan. The Caltech ducted fan is a scaled model of the longitudinal axis of a flight vehicle. The purpose of the ducted fan is the research and development of new nonlinear flight guidance and control techniques for Uninhabited Combat Aerial Vehicles. It is shown that critical design relations must be satisfied in order that the ducted fan's longitudinal dynamics behave similar to those of an flight vehicle. Preliminary flight test results illustrate the flying qualities of the ducted fan.  +
We consider the problem of attitude stabilization using exclusively visual sensory input, and we look for a solution which can satisfy the constraints of a ``bio-plausible'' computation. We obtain a PD controller which is a bilinear form of the goal image, and the current and delayed visual input. Moreover, this controller can be learned using classic neural networks algorithms. The structure of the resulting computation, derived from general principles by imposing a bilinear computation, has striking resemblances with existing models for visual information processing in insects (Reichardt Correlators and lobula plate tangential cells). We validate the algorithms using faithful simulations of the fruit fly visual input.  +
We consider the problem of purely visual pose stabilization (also known as servoing) of a second-order rigid- body system with six degrees of freedom: how to choose forces and torques, based on the current view and a memorized goal image, to steer the pose towards a desired one. Emphasis has been given to the bio-plausibility of the computation, in the sense that the control laws could be in principle implemented on the neural substrate of simple insects. We show that stabilizing laws can be realized by bilinear/quadratic operations on the visual input. This particular computational structure has several numerically favorable characteristics (sparse, local, and parallel), and thus permits an efficient engineering implementation. We show results of the control law tested on an indoor helicopter platform.  +
We consider the problem of purely visual pose stabilization of a second-order rigid-body system: how to choose forces and torques, based on the visual input alone, such that the view converges to a memorized goal image. Emphasis has been given to the bio-plausibility of the computation, in the sense that the control laws could be in principle implemented on the neural substrate of simple insects. We show that stabilizing laws can be realized by bilinear/quadratic operations on the visual input. Moreover, the control laws can be ``bootstrapped'' (learned unsupervisedly) from experience, which further substantiate the bio-plausibility of such computation.  +
Much of the progress in developing our ability to successfully design genetic circuits with predictable dynamics has followed the strategy of molding biological systems to fit into conceptual frameworks used in other disciplines, most notably the engineering sciences. Because biological systems have fundamental differences from systems in these other disciplines, this approach is challenging and the insights obtained from such analyses are often not framed in a biologically-intuitive way. Here, we present a new theoretical framework for analyzing the dynamics of genetic circuits that is tailored towards the unique properties associated with biological systems and experiments. Our framework approximates a complex circuit as a set of simpler circuits, which the system can transition between by saturating its various internal components. These approximations are connected to the intrinsic structure of the system, so this representation allows the analysis of dynamics which emerge solely from the system’s structure. Using our framework, we analyze the presence of structural bistability in a leaky autoactivation motif and the presence of structural oscillations in the Repressilator.  +
The bootstrapping problem consists in designing agents that laern a model of themsleves and the world, and utilize it to achieve useful tasks. It is different from other learning problems as the agent starts with uninterpreted observaions and commands, and with minimal prior information about the world. In this paper, we give a mathematical formalizatoin of this aspect of the problem. We argue that the vague constraint of having âno prior informationâ can be recast as a precise algebraic condition on the agent: that its behavior is invariant to particular classes of nuisances on the world, which we show can be well represented by actions of groups (diffeomorphisms, permutatations, linear transformations) on observations and commands. We then introduce the class of bilinear gradient dynamics sensors (DGDS) as a candidate for learning generic rootic sensorimotor cascades. We show how framing the problem as rejections of group nuisances allows a compact and modular analysis of typical preprocessing stages, such as learning the toplogy of sensors. We demonstrate learning and using such models on real-world range-finder and camera data from publicly available datasets.  +
In this paper we are concerned with the challenge of flight control of computationally-constrained micro-aerial vehicles that must rely primarily on vision to navigate confined spaces. We turn to insects for inspiration. We demonstrate that it is possible to control a robot with inertial, flight-like dynamics in the plane using insect-inspired visual autocorrelators or âelementary motion detectorsâ (EMDs) to detect patterns of visual optic flow. The controller, which requires minimal computation, receives visual information from a small omnidirectional array of visual sensors and computes thrust outputs for a fan pair to stabilize motion along the centerline of a corridor. To design the controller, we provide a frequency- domain analysis of the response of an array of correlators to a flat moving wall. The model incorporates the effects of motion parallax and perspective and provides a means for computing appropriate inter-sensor angular spacing and visual blurring. The controller estimates the state of robot motion by decomposing the correlator response into harmonics, an analogous operation to that performed by tangential cells in the fly. This work constitutes the first-known demonstration of control of non-kinematic inertial dynamics using purely correlators.  +
To contribute to efforts of bringing formal design-by-contract methods to hybrid systems, we introduce a variant of modal interface contract theory based on input/output automata with guarded transitions. We present an algebra of operators for interface composition, contract composition, contract conjunction, contract refinement and some theorems demonstrating that our contract object has reasonably universal semantics. As an application, we apply our framework to the design of a networked control systems of traffic.  +
Engineered bacterial sensors have potential applications in human health monitoring, environmental chemical detection, and materials biosynthesis. While such bacterial devices have long been engineered to differentiate between combinations of inputs, their potential to process signal timing and duration has been overlooked. In this work, we present a two-input temporal logic gate that can sense and record the order of the inputs, the timing between inputs, and the duration of input pulses. Our temporal logic gate design relies on unidirectional DNA recombination mediated by bacteriophage integrases to detect and encode sequences of input events. For an E. coli strain engineered to contain our temporal logic gate, we compare predictions of Markov model simulations with laboratory measurements of final population distributions for both step and pulse inputs. Although single cells were engineered to have digital outputs, stochastic noise created heterogeneous single-cell responses that translated into analog population responses. Furthermore, when single-cell genetic states were aggregated into population-level distributions, these distributions contained unique information not encoded in individual cells. Thus, final differentiated sub-populations could be used to deduce order, timing, and duration of transient chemical events.  +
A reactive safety mode is built into a robust model predictive control algorithm for uncertain nonlinear systems with bounded disturbances. The algorithm enforces state and control constraints and blends two modes: (I) standard, guarantees re-solvability and asymptotic convergence in a robust receding-horizon manner; (II) safety, if activated, guarantees containment within an invariant set about a reference. The reactive safety mode provides robustness to unexpected, but real-time anticipated, state-constraint changes during standard mode operation. The safety-mode control policy is designed offline and can be activated at any arbitrary time. The standard-mode control has feedforward and feedback components: feedforward is from online solution of a finite-horizon optimal control problem; feedback is designed offline to provide robustness to system uncertainty and disturbances and to establish an invariant âstate tubeâ that guarantees standard-mode re-solvability at any time. The algorithm design is shown for a class of systems with incrementally-conic uncertain/nonlinear terms and bounded disturbances.  +
Stochasticity plays an essential role in biochemical systems. Stochastic behaviors of bimodality, excitability, and fluctuations have been observed in biochemical reaction networks at low molecular numbers. Stochastic dynamics can be captured by modeling the system using a forward Kolmogorov equation known in the biochemical literature as the chemical master equation. The chemical master equation describes the time evolution of the probability distributions of the molecule species. We develop a stochastic framework for the design of these time evolving probability distributions that includes specifying their uni-/multi-modality, their first moments, and their rate of convergence to the stationary distribution. By solving the corresponding optimizations programs, we determine the reaction rates of the biochemical systems that satisfy our design specifications. We then apply the design framework to examples of biochemical reaction networks to illustrate its strengths and limitations.  +
We derive phenomenological models of gene expression from a mechanistic description of chemical reactions using an automated model reduction method. Using this method, we get analytical descriptions and computational performance guarantees to compare the reduced dynamics with the full models. We develop a new two-state model with the dynamics of the available free ribosomes in the system and the protein concentration. We show that this new two-state model captures the detailed mass-action kinetics of the chemical reaction network under various biologically plausible conditions on model parameters. On comparing the performance of this model with the commonly used mRNA transcript-protein dynamical model for gene expression, we analytically show that the free ribosome and protein model has superior error and robustness performance.  +
Substantial reductions in aircraft size are possible if shorter, more aggressive, serpentine inlet ducts are used for low-observability constrained propulsion installations. To obtain this benefit, both inlet separation and compressor stall dynamics must be controlled. In this paper the integrated control of this coupled inlet/compression system is considered. Initial results are shown using separation point actuation to control both separation and stall dynamics. Calculations show that separation can be substantially reduced with approximately 1.2% core flow, based on scaling previous results. Simulation results using a medium fidelity model show that proportional control of distortion has little effect on stall behavior.  +
This paper presents preliminary results on the use of low flow, high momentum, pulsed air injectors to control the onset of stall in a low-speed, axial flow compressor. By measuring the unsteady pressures in front of the rotor, the controller determines the magnitude and phase of a stall cell and controls the injection of air in front of the rotor face. Initial experimental results have verified that controller slightly extends the stall point of the compressor and virtually eliminates the hysteresis loop normally associated with stall. An explanation of this effect is proposed based on the quasi-steady effects of air injection on the compressor characteristic curve.  +
This paper presents the use of pulsed air injection to control the onset of rotating stall in a low-speed, axial flow compressor. By measuring the unsteady pressures near the rotor face, a control algorithm determines the magnitude and phase of the first mode of rotating stall and controls the injection of air in the front of the rotor face. Experimental results show that this technique slightly extends the stall point of the compressor and eliminates the hysteresis loop normally associated with rotating stall. A parametric study is used to determine the optimal control parameters for suppression of stall. Analytic results---using a low-dimensional model developed by Moore and Greitzer combined with an unsteady shift in the compressor characteristic to model the injectors---give further insights into the operation of the controller. Based on this model, we show that the behavior of the experiment can be explained as a change in the bifurcation behavior of the system under nonlinear feedback. A higher fidelity simulation model is then used to further verify some of the specific performance characteristics that are observed in experiments.  +
We develop a system for implementing “packet-based” intercellular communication in an engineered bacterial population via conjugation. Our system uses gRNA-based identification markers that allow messages to be addressed to specific strains via Cas9-mediated cleavage of messages sent to the wrong recipient, which we show reduces plasmid transfer by four orders of magnitude. Integrase-mediated editing of the address on the message plasmid allows cells to dynamically update the message’s recipients in vivo. As a proof-of-concept demonstration of our system, we propose a linear path scheme that would propagate a message sequentially through the strains of a population in a defined order.  +
In this paper, we provide tools for convergence and performance analysis of an agreement protocol for a network of integrator agents with directed information flow. We also analyze algorithmic robustness of this consensus protocol for networks with mobile nodes and switching topology. A connection is established between the Fiedler eigenvalue of the graph Laplacian and the performance of this agreement protocol. We demon- strate that a class of directed graphs, called balanced graphs, have a crucial role in solving average-consensus problems. Based on the properties of balanced graphs, a group disagreement function (i.e. Lyapunov function) is proposed for convergence analysis of this agreement protocol for networks with directed graphs and switching topology.  +
This paper describes the implementation and testing of Alice, the California Institute of Technology’s entry in the 2005 DARPA Grand Challenge. Alice utilizes a highly networked control system architecture to provide high performance, autonomous driving in unknown en- vironments. Innovations include a vehicle architecture designed for efficient testing in harsh environments, a highly sensory-driven approach to fuse sensor data into speed maps used by real-time trajectory optimization algorithms, health and contingency management algorithms to manage failures at the component and system level, and a software logging and display envi- ronment that enables rapid assessment of performance during testing. The system successfully completed several runs in the National Qualifying Event, but encountered a combination of sens- ing and control issues in the Grand Challenge Event that led to a critical failure after traversing approximately 8 miles.  +
Modern aircraft increasingly rely on electric power for sub- systems that have traditionally run on mechanical power. The complexity and safety-criticality of aircraft electric power systems have therefore increased, rendering the design of these systems more challenging. This work is mot vated by the potential that correct-by-construction reactive controller synthesis tools may have in increasing the effectiveness of the electric power system design cycle. In particular, we have built an experimental hardware platform that captures some key elements of aircraft electric power systems within a simplified setting. We intend to use this plat- form for validating the applicability of theoretical advances in correct-by-construction control synthesis and for study- ing implementation-related challenges. We demonstrate a simple design workflow from formal specifications to auto- generated code that can run on software models and be used in hardware implementation. We show some preliminary results with different control architectures on the developed hardware testbed.  +
A numerical algorithm for computing necessary conditions for performance specifications is developed for nonlinear uncertain systems. The algorithm is similar in nature and behavior to the power algorithm for the mu lower bound, and doesn't rely on a descent method. The algorithm is applied to a practical example.  +
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. In this case the controller sends a communication packet to the plant across a lossy network, but the controller does not receive any acknowledgement signal indicating the status of the control packet. Standard observer based estimators assume the estimator has knowledge of what control signal is applied to the plant. Under the UDP-like protocol the controller/estimator does not have explicit knowledge whether the control signals have been applied to the plant or not. We present a simple estimation algorithm that consists of a state and mode observer as well as a constraint on the control signal sent to the plant. For the class of systems considered, discrete time LTI plants where at least one of the states that is directly affected by the input is also part of the measurement vector, the estimator is able to recover the fate of the control packet from the measurement at the next timestep and exhibit better performance than other naive schemes. For single-input-single-output (SISO) systems we are able to show convergence properties of the estimation error and the state. Simulations are provided to demonstrate the algorithm and show it's effectiveness.  +
Experimental comparisons between four different control design methodologies are applied to a small vectored thrust engine. Each controller is applied to three trajectories of varying aggressiveness. The control strategies considered are LQR, H_infty, gain scheduling, and feedback linearization. The experiments show that gain scheduling is essential to achieving good performance. The strengths and weaknesses of each methodology are also examined.  +
Controllers developed for control of flexible-link robots in hybrid force-position control tasks by a new singular perturbation analysis of flexible manipulators are implemented on an experimental two-robot grasping setup. Various performance criteria are set up and experimental results are discussed within that setting to show tradeoffs in using flexible link robots for grasping. We conclude that large flexibility can be controlled without too much additional effort, has performance comparable to rigid robots and possesses enhancing properties which make it attractive for use in certain types of applications.  +
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.  +
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.  +
Biomolecular circuits with two distinct and stable steady states have been identified as essential components in a wide range of biological networks, with a variety of mechanisms and topologies giving rise to their important bistable property. Understanding the differences between circuit implementations is an important question, particularly for the synthetic biologist faced with determining which bistable circuit design out of many is best for their specific application. In this work we explore the applicability of Sturm's theorem—a tool from nineteenth-century real algebraic geometry—to comparing ‘functionally equivalent’ bistable circuits without the need for numerical simulation. We first consider two genetic toggle variants and two different positive feedback circuits, and show how specific topological properties present in each type of circuit can serve to increase the size of the regions of parameter space in which they function as switches. We then demonstrate that a single competitive monomeric activator added to a purely monomeric (and otherwise monostable) mutual repressor circuit is sufficient for bistability. Finally, we compare our approach with the Routh–Hurwitz method and derive consistent, yet more powerful, parametric conditions. The predictive power and ease of use of Sturm's theorem demonstrated in this work suggest that algebraic geometric techniques may be underused in biomolecular circuit analysis.  +
We present an automated model reduction algorithm that uses quasi-steady state approximation based reduction to minimize the error between the desired outputs. Additionally, the algorithm minimizes the sensitivity of the error with respect to parameters to ensure robust performance of the reduced model in the presence of parametric uncertainties. We develop the theory for this model reduction algorithm and present the implementation of the algorithm that can be used to perform model reduction of given SBML models. To demonstrate the utility of this algorithm, we consider the design of a synthetic biological circuit to control the population density and composition of a consortium consisting of two different cell strains. We show how the model reduction algorithm can be used to guide the design and analysis of this circuit.  +
This paper presents a mathematical model for a synthetic transcriptional regulatory network in vitro. This circuit design resembles one of the well-known network motifs, the inco- herent feed-forward loop, in which an activator regulates both a gene and a repressor of the gene. Through mathematical analysis, we show how the circuit can be controlled to demonstrate exact adaptation to input signals.  +
Designing genetic circuits to control the behaviors of microbial populations is an ongoing challenge in synthetic biology. Here we analyze circuits which implement dosage control by controlling levels of a global signal in a microbial population in face of varying cell density, growth rate, and environmental dilution. We utilize the Lux quorum sensing system to implement dosage control circuits, and we analyze the dynamics of circuits using both simplified analytical analysis and in silico simulations. We demonstrate that strong negative feedback through inhibiting LuxI synthase expression along with AiiA degradase activity results in circuits with fast response times and robustness to cell density and dilution rate. We find that degradase activity yields robustness to variations in population density for large population sizes, while negative feedback to synthase production decreases sensitivity to dilution rates.  +
This paper provides preliminary work in an aim to fundamentally understand the effects of temperature fluctuations in the dynamics of biological oscillators. Motivated by circadian rhythms, we are interested in understanding how time-varying temperatures might play a role in the properties of biochemical oscillators. This paper investigates time-dependent Arrhenius scaling of biochemical networks with delays. We assume these time-delays arise from a sequence of simpler reactions that can be modeled as an aggregate delay. We focus on a model system, the Goodwin oscillator, in which we use time-varying rate coefficients as a mechanism to understand the possible effects of temperature fluctuations. The emergence of delays from a sequence of reactions can be better understood through the Goodwin model. For a high order system and comparably high reaction rates, one can approximate the large sequence of reactions in the model with a delay, which can be interpreted as the time needed to go through the âqueueâ. Such types of delays can arise in the process of transcription for example. To study how these delays are affected by temperature fluctuations, we take the limit as the order of the system and the mean reaction rates approach infinity with a periodically time-varying rate coefficient. We show that the limit cycle of the Goodwin oscillator varies only in the limit when the oscillator frequency is much larger than the frequency of temperature oscillations. Otherwise, the instantaneous frequency of the oscillator is dominated by the mean value of the time-varying temperature.  +
We present a mathematical reconstruction of the kinematics and dynamics of flight initiation as observed in high-speed video recordings of the insect Drosophila melanogaster. The behavioral dichotomy observed in the fruit flies' flight initiation sequences, as a response to different stimuli, was reflected in two contrasting sets of dynamics once the flies had become airborne. By reconstructing the dynamics of unconstrained motion during flight initiations, we assess the fly's responses (generation of forces and moments) amidst these two dynamic patterns. Moreover, we introduce a 3D visual tracking algorithm as a tool to analyze the wing kinematics applied by the insect, and investigate their relation(s) to the production of these aerodynamic forces. Using this framework we formulate different hypotheses about the modulation of flight forces and moments during flight initiation as a way torefining our understanding of insect flight control.,  +
Gene expression is often controlled by natural genetic regulatory networks that govern the rates at which genes are transcribed. Recent work has shown that synthetic versions of genetic networks can be designed and built in living cells. Applications for these synthetic regulatory networks include intracellular decision-making and computation. In this study, we propose a new synthetic genetic network that behaves as a digital clock, producing square waveform oscillations. We analyze two models of the network, a deterministic model based on Michaelis-Menten kinetics, as well as a stochastic model based on the Gillespie algorithm. Both models predict regions of oscillatory behavior; the deterministic model provides insight into the conditions required to produce the oscillating clock-like behavior, while the stochastic model is truer to natural dynamics. Intracellular stochasticity is seen to contribute phase noise to the oscillator, and we propose improvements for the network and discuss the conceptual foundations of these improvements.  +
We study the dynamic and static input output behavior of several primitive genetic interactions and their e↵ect on the performance of a genetic signal di↵erentiator. In a simplified design, several requirements for the linearity and time-scales of processes like transcription, translation and competitive promoter binding were introduced. By ex- perimentally probing simple genetic constructs in a cell-free experimental environment and fitting semi-mechanistic models to these data, we show that some of these require- ments can be verified, while others are only met with reservations in certain operational regimes. Analyzing the linearized model of the resulting genetic network we conclude that it approximates a di↵erentiator with relative degree one. Taking also the discovered non-linearities into account and using a describing function approach, we further deter- mine the particular frequency and amplitude ranges where the genetic di↵erentiator can be expected to behave as such.  +
We have developed a new course as well as an undergraduate minor in Control and Dynamical Systems for teaching design and analysis of feedback systems to students from diverse fields such as biology, computer science, and economics as well as all traditional engineering %disciplines.  +
In this paper we discuss the application of correct-by-construction techniques to a resilient, risk-aware software architecture for onboard, real-time autonomous operations. We mean to combat complexity and the accidental introduction of bugs through the use of verifiable auto-coding software and correct-by-construction techniques, and discuss the use of a toolbox for correct-by-construction Temporal Logic Planning (TuLiP) for such a purpose. We describe some of TuLiPâs current functionality, specifically its ability to model symbolic discrete systems and synthesize software controllers and control policies that are correct-by-construction. We then move on to discuss the use of these techniques to define a deliberative goal-directed executive capability that performs risk-informed action-planning â to satisfy the mission goals (specified by mission control) within the specified priorities and constraints. Finally, we discuss an application of the TuLiP process to a simple rover resilience scenario.  +
The Goursat normal form theorem gives conditions under which an Pfaffian exterior differential system is equivalent to a certain normal form. This paper details how the Goursat normal form and its extensions provide a unified framework for understanding feedback linearization, chained form, and differential flatness. <p> Keywords: Exterior differential systems, nonholonomic constraints, chained form, feedback linearization, differentially flat.  +
We analyze the performance of an approximate distributed Kalman filter proposed in recent work on distributed coordination. This approach to distributed estimation is novel in that it admits a systematic analysis of its performance as various network quantities such as connection density, topology, and bandwidth are varied. Our main contribution is a frequency-domain characterization of the distributed estimator's steady-state performance; this is quantified in terms of a special matrix associated with the connection topology called the graph Laplacian, and also the rate of message exchange between immediate neighbors in the communication network.  +
This paper describes algorithms to generate trajectories for differentially flat systems with zero dynamics. Zero dynamics in flat systems occur when the flat outputs are not the tracking outputs. This means that the output trajectories can be fully parametrized by the flat outputs, but that there is some additional freedom left. This freedom can be exploited to minimize a cost criterion. We parametrize the differentially flat outputs by basis functions, and solve for the parameters so as to track a prescribed trajectory approximately while minimizing a cost function. We focus on implementation issues and point out the computational cost involved in the various problems.  +
In this paper, we approximate models of interconnected systems that are to be used for decentralized control design. The suggested approach is based on approximation of so-called subnetwork models. A subnetwork model is a model of the interconnected system, as seen from one specific position in the network. The simplification is done by using weighted model reduction, and several approximation criteria are given. A new method for weighted model reduction is used. The method is based on a combination of known techniques that use semidefinite programming and frequency-data samples of transfer functions. The method is guaranteed to preserve stability and does not depend strongly on the order of the original model. This is particularly important for large interconnected systems. Two examples are given to illustrate the technique.  +
any interesting control systems are mechanical control systems. In spite of this, there has not been much effort to develop methods which use the special structure of mechanical systems to obtain analysis tools which are suitable for these systems. In this dissertation we take the first steps towards a methodical treatment of mechanical control systems. <p> First we develop a framework for analysis of certain classes of mechanical control systems. In the Lagrangian formulation we study ``simple mechanical control systems'' whose Lagrangian is ``kinetic energy minus potential energy.'' We propose a new and useful definition of controllability for these systems and obtain a computable set of conditions for this new version of controllability. We also obtain decompositions of simple mechanical systems in the case when they are not controllable. In the Hamiltonian formulation we study systems whose control vector fields are Hamiltonian. We obtain decompositions which describe the controllable and uncontrollable dynamics. In each case, the dynamics are shown to be Hamiltonian in a suitably general sense. <p> Next we develop intrinsic descriptions of Lagrangian and Hamiltonian mechanics in the presence of external inputs. This development is a first step towards a control theory for general Lagrangian and Hamiltonian control systems. Systems with constraints are also studied. We first give a thorough overview of variational methods including a comparison of the ``nonholonomic'' and ``vakonomic'' methods. We also give a generalised definition for a constraint and, with this more general definition, we are able to give some preliminary controllability results for constrained systems.  +
Robustness to temperature variation is an important specification in biomolecular circuit design. While the cancellation of parametric temperature dependencies has been shown to improve the temperature robustness of the period in a synthetic oscillator design, the performance of other biomolecular circuit designs in different temperature conditions is relatively unclear. Using a combination of experimental measurements and mathematical models, we assessed the temperature robustness of two biomolecular circuit motifs—a negative feedback loop and a feedforward loop. We found that the measured responses of both the circuits changed with temperature, both in the amplitude and in the transient response. We also found that, in addition to the cancellation of parametric temperature dependencies, certain parameter regimes could facilitate the temperature robustness of the negative feedback loop, although at a performance cost. We discuss these parameter regimes in the context of the measured data for the negative feedback loop. These results should help develop a framework for assessing and designing temperature robustness in biomolecular circuits.  +
Distributed algorithms for averaging have attracted interest in the control and sensing literature. However, previous works have not addressed some practical concerns that will arise in actual implementations on packet-switched communication networks.....  +
Fault tolerance and safety verification of control systems are essential for the success of autonomous robotic systems. A control architecture called Mission Data System (MDS), developed at the Jet Propulsion Laboratory, takes a goal-based control approach. In this paper, a software algorithm for converting goal network control programs into linear hybrid systems is described. The conversion process is a bisimulation; the resulting linear hybrid system can be verified for safety in the presence of failures using existing symbolic model checkers, and thus the original goal network is verified. A moderately complex goal network control program is converted to a linear hybrid system using the automatic conversion software and then verified.  +
We propose a methodology for automatic synthesis of embedded control software that accounts for exogenous disturbances. The resulting system is guaranteed, by construction, to satisfy a given specification expressed in linear temporal logic. The embedded control software consists of three components: a goal generator, a trajectory planner, and a continuous controller. We demonstrate the effectiveness of the proposed technique through an example of an autonomous vehicle navigating an urban environment. This example also illustrates that the system is not only robust with respect to exogenous disturbances but also capable of handling violation of the environment assumptions.  +
We develop a method for the control of discrete-time nonlinear systems subject to temporal logic specifications. Our approach uses a coarse abstraction of the system and an automaton representing the temporal logic specification to guide the search for a feasible trajectory. This decomposes the search for a feasible trajectory into a series of constrained reachability problems. Thus, one can create controllers for any system for which techniques exist to compute (approximate) solutions to constrained reachability problems. Representative techniques include sampling-based methods for motion planning, reachable set computations for linear systems, and graph search for finite discrete systems. Our approach avoids the expensive computation of a discrete abstraction, and its implementation is amenable to parallel computing. We demonstrate our approach with numerical experiments on temporal logic motion planning problems with high-dimensional (10+ states) continuous systems.  +
The development of autonomous vehicles for urban driving has seen rapid progress in the past 30 years. This paper provides a summary of the current state of the art in autonomous driving in urban environments, based primarily on the experiences of the authors in the 2007 DARPA Urban Challenge (DUC). The paper briefly summarizes the approaches that different teams used in the DUC, with the goal of describing some of the challenges that the teams faced in driving in urban environments. The paper also highlights the long term research challenges that must be overcome in order to enable autonomous driving and points to opportunities for new technologies to be applied in improving vehicle safety, exploiting intelligent road infrastructure and enabling robotic vehicles operating in human environments.  +
This report presents techniques for using discrete finite rotations to reorient a spacecraft from a given initial attitude to a final attitude which satisfies a specified aiming objective. The objective may be a fully specified final orientation or it may require that the spacecraft direct an instrument along a certain direction. Constraints are also imposed on the allowable intermediate orientations that the spacecraft may assume during the course of the maneuver, representing the operational requirements of onboard instrumentation. The algorithms presented consider solutions that will achieve the desired objective with only one or two slew maneuvers, although they may be easily extended to consider more complicated solutions requiring additional maneuvers.  +
This paper considers the problem of synthesizing correct-by-construction robotic controllers in environments with uncertain but fixed structure. âEnvironmentâ has two notions in this work: a map or âworldâ in which some controlled agent must operate and navigate (i.e. evolve in a configuration space with obstacles); and an adversarial player that selects con- tinuous and discrete variables to try to make the agent fail (as in a game). Both the robot and the environment are subjected to behavioral specifications expressed as an assume-guarantee linear temporal logic (LTL) formula. We then consider how to efficiently modify the synthesized controller when the robot encounters unexpected changes in its environment. The crucial insight is that a portion of this problem takes place in a metric space, which provides a notion of nearness. Thus if a nominal plan fails, we need not resynthesize it entirely, but instead can âpatchâ it locally. We present an algorithm for doing this, prove soundness, and demonstrate it on an example gridworld.  +
Wound healing is a complicated biological process consisting of many types of cellular dynamics and functions regulated by chemical and molecular signals. Recent advances in synthetic biology have made it possible to predictably design and build closed-loop controllers that can function appropriately alongside biological species. In this paper we develop a simple dynamical population model mimicking the sequential relay-like dynamics of cellular populations involved in the wound healing process. Our model consists of four nodes and five signals whose parameters we can tune to simulate various chronic healing conditions. We also develop a set of regulator functions based on type-1 incoherent feed forward loops (IFFL) that can sense the change from acute healing to incomplete chronic wounds, improving the system in a timely manner. Both the wound healing and type-1 IFFL controller architectures are compatible with available synthetic biology experimental tools for potential applications.  +
Nonlinear qualitative analysis is performed on the Moore-Greitzer model to evaluate the tradeoff of fluid noise, actuator magnitude saturation, bandwidth, rate limits, and the shape of compressor characteristics in active control of rotating stall in axial compressors with bleed valve actuators. Model order reduction is achieved by approximating the dynamics on the invariant manifold that captures the bifurcations and instabilities. Bifurcations and qualitative dynamics are obtained by analyzing the reduced system. The operability enhancement is defined as the extension of operating range for which fully developed rotating stall is avoided. Analytic formulas are derived for the operability enhancement as a function of noise level, actuator saturation limits, and the shape of the compressor characteristic, which is the major nonlinearity in the model. The shape of the compressor characteristic, especially the unstable part, is critical to the rate required for robust operability near the peak for the closed loop system. Experiments are carried out on a single-stage low-speed axial compressor using different level of steady air injections to generate different compressor characteristics. The theoretical formulas give good qualitative estimates to experimental data and simulations using a high fidelity model (37 states).  +
Insects exhibit incredibly robust closed loop flight dynamics in the face of uncertainties. A fundamental principle contributing to this unparalleled behavior is rapid processing and convergence of visual sensory information to flight motor commands via spatial wide-field integration, accomplished by retinal motion pattern sensitive interneurons (LPTCs) in the lobula plate portion of the visual ganglia. Within a control-theoretic framework, an inner product model for wide-field integration of retinal image flow is developed, representing the spatial decompositions performed by LPTCs in the insect visuomotor system. A rigorous characterization of the information available from this visuomotor convergence technique for motion within environments exhibiting non-omogeneous spatial distributions is performed, establishing the connection between retinal motion sensitivity shape and closed loop behavior. The proposed output feedback methodology is shown to be sufficient to give rise to experimentally observed insect navigational heuristics, including forward speed regulation, obstacle avoidance, hovering, and terrain following behaviors. Hence, extraction of global retinal motion cues through computationally efficient wide-field integration process- ing provides a novel and promising methodology for utilizing visual sensory information in autonomous robotic navigation and flight control applications.  +
Biochemical interactions in systems and synthetic biology are often modeled with chemical reaction networks (CRNs). CRNs provide a principled modeling environment capable of expressing a huge range of biochemical processes. In this paper, we present a software toolbox, written in Python, that compiles high-level design specifications represented using a modular library of biochemical parts, mechanisms, and contexts to CRN implementations. This compilation process offers four advantages. First, the building of the actual CRN representation is automatic and outputs Systems Biology Markup Language (SBML) models compatible with numerous simulators. Second, a library of modular biochemical components allows for different architectures and implementations of biochemical circuits to be represented succinctly with design choices propagated throughout the underlying CRN automatically. This prevents the often occurring mismatch between high-level designs and model dynamics. Third, high-level design specification can be embedded into diverse biomolecular environments, such as cell-free extracts and in vivo milieus. Finally, our software toolbox has a parameter database, which allows users to rapidly prototype large models using very few parameters which can be customized later. By using BioCRNpyler, users ranging from expert modelers to novice script-writers can easily build, manage, and explore sophisticated biochemical models using diverse biochemical implementations, environments, and modeling assumptions.  +
We present a detailed dynamical model of the behavior of transcription-translation circuits in vitro that makes explicit the roles played by essential molecular resources. A set of simple two-gene test circuits operating in a cell-free biochemical âbreadboardâ validate this model and highlight the consequences of limited resource availability. In particular, we are able to confirm the existence of biomolecular âcrosstalkâ and isolate its individual sources. The implications of crosstalk for biomolecular circuit design and function are discussed.  +
Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites). However, much less is known about the effects of intergenic compositional context (spatial arrangement and orientation of entire genes on DNA) on expression levels in synthetic gene networks. We compare expression of induced genes arranged in convergent, divergent, or tandem orientations. Induction of convergent genes yielded up to 400% higher expression, greater ultrasensitivity, and dynamic range than divergent- or tandem-oriented genes. Orientation affects gene expression whether one or both genes are induced. We postulate that transcriptional interference in divergent and tandem genes, mediated by supercoiling, can explain differences in expression and validate this hypothesis through modeling and in vitro supercoiling relaxation experiments. Treatment with gyrase abrogated intergenic context effects, bringing expression levels within 30% of each other. We rebuilt the toggle switch with convergent genes, taking advantage of supercoiling effects to improve threshold detection and switch stability.  +
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.  +
Molecular feedback control circuits can improve robustness of gene expression at the single cell-level. This achievement can be offset by requirements of rapid protein expression, that may induce cellular stress, known as burden, that reduces colony growth. To begin to address this challenge we take inspiration by ‘division-of-labor’ in heterogeneous cell populations: we propose to combine bistable switches and quorum sensing systems to coordinate gene expression at the population-level. We show that bistable switches in individual cells operating in parallel yield an ultrasensitive response, while cells maintain heterogeneous levels of gene expression to avoid burden across all cells. Within a feedback loop, these switches can achieve robust reference tracking and adaptation to disturbances at the population-level. We also demonstrate that molecular sequestration enables tunable hysteresis in individual switches, making it possible to obtain a wide range of stable population-level expressions.  +
We consider the bootstrapping problem, which consists in learning a model of the agent's sensors and actuators starting from zero prior informa- tion, and we take the problem of servoing as a cross-modal task to validate the learned models. We study the class of sensors with bilinear dynamics, for which the derivative of the observations is a bilinear form of the control commands and the observations themselves. This class of models is simple, yet general enough to represent the main phenomena of three representative sensors (field sampler, camera, and range-finder), apparently very different from one another. It also allows a bootstrapping algorithm based on Hebbian learning, and a simple bioplausible control strategy. The convergence proper- ties of learning and control are demonstrated with extensive simulations and by analytical arguments.  +
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.  +
A cascade discrete-continuous state estimator design is presented for a class of monotone systems with both continuous and discrete state evolution. The proposed estimator exploits the partial order preserved by the system dynamics in order to satisfy two properties. First, its computation complexity scales with the number of variables to be estimated instead of scaling with the size of the discrete state space. Second, a separation principle holds: the continuous state estimation error is bounded by a monotonically decreasing function of the discrete state estimation error, the latter one converging to zero. A multi-robot example is proposed.  +
The bottom up design of genetic circuits to control cellular behavior is one of the central objectives within Synthetic Biology. Performing design iterations on these circuits in vivo is often a time consuming process, which has led to E. coli cell extracts to be used as simplified circuit prototyping environments. Cell extracts, however, display large batch-to-batch variability in gene expression. In this paper, we develop the theoretical groundwork for a model based calibration methodology for correcting this variability. We also look at the interaction of this methodology with the phenomenon of parameter (structural) non-identifiability, which occurs when the parameter identification inverse problem has multiple solutions. In particular, we show that under certain consistency conditions on the sets of output- indistinguishable parameters, data variability reduction can still be performed, and when the parameter sets have a cer- tain structural feature called covariation, our methodology may be modified in a particular way to still achieve the desired variability reduction.  +
Synthetic biologists have turned towards quorum systems as a path for building sophisticated microbial consortia that exhibit group decision making. Currently, however, even the most complex consortium circuits rely on only one or two quorum sensing systems, greatly restricting the available design space. High-throughput characterization of available quorum sensing systems is useful for finding compatible sets of systems that are suitable for a defined circuit architecture. Recently, cell-free systems have gained popularity as a test-bed for rapid prototyping of genetic circuitry. We take advantage of the transcription-translation cell-free system to characterize three commonly used Lux-type quorum activators, Lux, Las, and Rpa. We then compare the cell-free characterization to results obtained in vivo. We find significant genetic crosstalk in both the Las and Rpa systems and substantial signal crosstalk in Lux activation. We show that cell-free characterization predicts crosstalk observed in vivo.  +
We present a full-stack modeling, analysis, and parameter identification pipeline to guide the modeling and design of biological systems starting from specifications to circuit implementations and parameterizations. We demonstrate this pipeline by characterizing the integrase and excisionase activity in cell-free protein expression system. We build on existing Python tools — BioCRNpyler, AutoReduce, and Bioscrape — to create this pipeline. For enzyme-mediated DNA recombination in cell-free system, we create detailed chemical reaction network models from simple high-level descriptions of the biological circuits and their context using BioCRNpyler. We use Bioscrape to show that the output of the detailed model is sensitive to many parameters. However, parameter identification is infeasible for this high-dimensional model, hence, we use AutoReduce to automatically obtain reduced models that have fewer parameters. This results in a hierarchy of reduced models under different assumptions to finally arrive at a minimal ODE model for each circuit. Then, we run sensitivity analysis-guided Bayesian inference using Bioscrape for each circuit to identify the model parameters. This process allows us to quantify integrase and excisionase activity in cell extracts enabling complex-circuit designs that depend on accurate control over protein expression levels through DNA recombination. The automated pipeline presented in this paper opens up a new approach to complex circuit design, modeling, reduction, and parameterization.  +
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.  +
A central goal of synthetic biology is to engineer cellular behavior by engineering synthetic gene networks for a variety of biotechnology and medical applications. The process of engineering gene networks often involves an iterative âdesign-build-testâ cycle, whereby the parts and connections that make up the network are built, characterized and varied until the desired network function is reached. Many advances have been made in the design and build portions of this cycle. However, the slow process of in vivo characterization of network function often limits the timescale of the testing step. Cell-free transcription-translation (TX-TL) systems offer a simple and fast alternative to performing these characterizations in cells. Here we provide an overview of a cell-free TX-TL system that utilizes the native Escherichia coli TX-TL machinery, thereby allowing a large repertoire of parts and networks to be characterized. As a way to demonstrate the utility of cell-free TX-TL, we illustrate the characterization of two genetic networks: an RNA transcriptional cascade and a protein regulated incoherent feed-forward loop. We also provide guidelines for designing TX-TL experiments to characterize new genetic networks. We end with a discussion of current and emerging applications of cell free systems.  +
Previous work at Caltech has developed an air injection controller for rotating stall based on the idea of a shifting compressor characteristic. To further understand the properties of this controllers, a series of open loop tests were performed to measure the performance characteristics of an axial flow compression system when air was injected upstream of the rotor face. The distance from the rotor face, the span-wise position, and the angle relative to the mean axial flow were varied. These tests show that the injection of air has drastic effects on the stalling mass flow rate and on the size of the hysteresis loop associated with rotating stall. The stalling mass flow rate was decreased by 10\% and the hysteresis loop was completely eliminated under some conditions.  +
We develop the study of primitives of human motion, which we refer to as movemes. The idea is to understand human motion by decomposing it into a sequence of elementary building blocks that belong to a known alphabet of dynamical systems. Where do these dynamic primitives come from in practice? How can we construct an alphabet of movemes from human data? In this paper we address these issues. We define conditions under which collections of signals are well-posed according to a dynamical model class M and thus can generate movemes. Using examples from human drawing data, we show that the definition of well-posedness can be applied in practice so to establish if sets of actions, reviewed as signals in time, can define movemes.  +
We describe a technique for the efficient computation of the dominant-scale dynamics of a fluid system when only a high-fidelity simulation is available. Such a technique is desirable when governing equations for the dominant scales are unavailable, when model reduction is impractical, or when the original high-fidelity computation is expensive. We adopt the coarse analysis framework proposed by I. G. Kevrekidis (Comm. Math. Sci. 2003), where a computational superstructure is designed to use short-time, high-fidelity simulations to extract the dominant features for a multi- scale system. We apply this technique to compute the dominant features of the compressible flow through a planar diffuser. We apply the proper orthogonal decomposition to classify the dominant and subdominant scales of diffuser flows. We derive a suitable coarse pro jective Adams-Bashforth time integration routine and apply it to compute averaged diffuser flows. The results include accu- rate tracking of the dominant-scale dynamics for a range of parameter values for the computational superstructure. These results demonstrate that coarse analysis methods are useful for solving fluid flow problems of a multiscale nature. <p> In order to elucidate the behavior of coarse analysis techniques, we make comparisons to averaging theory. To this end, we derive governing equations for the average motion of charged particles in a magnetic field in a number of different settings. First, we apply a novel procedure, inspired by WKB theory and Whitham averaging, to average the variational principle. The resulting equations are equivalent to the guiding center equations for charged particle motion; this marks an instance where averaging and variational principles commute. Secondly, we apply Lagrangian averaging techniques, previously applied in fluid mechanics, to derive averaged equations. Making comparisons to the WKB/Whitham-style derivation allows for the necessary closure of the Lagrangian averaging formulation. We also discuss the Hamiltonian setting and show that averaged Hamiltonian systems may be derivable using concepts from coarse analysis. Finally, we apply a prototypical coarse analysis procedure to the system of charged particles and generate tra jectories that resemble guiding center tra jectories. We make connections to perturbation theory to derive guidelines for the design of coarse analysis techniques and comment on the prototypical coarse analysis application.  
Standard schemes in system identification and adaptive control rely on persistence of excitation to guaran- tee parameter convergence. Inspired by networked systems, we extend parameter adaptation to the multi-agent setting by combining a gradient law with consensus dynamics. The gradient law introduces a learning signal, while consensus dynamics preferentially push each agentâs parameter estimates toward those of its neighbors. We show that the resulting online, decentralized parameter estimator combines local and neighboring information to identify the true parameters even if no single agent employs a persistently exciting input. We also elaborate upon collective persistence of excitation in networked adaptive algorithms.  +
Previous work at Caltech has developed a controller for rotating stall in axial flow compressors using pulsed air injection. In this work, theory is developed for the combination of this air injection controller with a bleed valve controller for the system's surge dynamics. The controller analysis is based on the surge dynamics acting on a slow time scale relative to the rotating stall dynamics. Experiments demonstrating this controller design on the Caltech rig are also presented.  +
In this paper we characterize the impact of imperfect communication on the performance of a decentralized mobile sensor network. We first examine and demonstrate the trade-offs between communication and sensing objectives, by determining the optimal sensor configurations when introducing imperfect communication. We further illustrate the performance degradation caused by non-ideal communication links in a decentralized mobile sensor network. To address this, we propose a decentralized motion-planning algorithm that considers communication effects. The algorithm is a cross-layer design based on the proper interface of physical and application layers. Simulation results will show the performance improvement attained by utilizing this algorithm.  +
In this paper we consider the impact of communication noise on distributed sensing and estimation in mobile networks. We characterize when a node should rely on getting information from others and when it should rely on self exploration. In doing so, we explore the trade-offs between sensing and communication by finding the optimum network configuration under communication constraints. We also show how to achieve the optimum configuration in a distributed manner. While our main results are presented in one dimension (1D), we provide insight into the two dimension (2D) setup and extend a number of key results to 2D.  +
We propose a compositional stability analysis methodology for verifying properties of systems that are interconnections of multiple subsystems. The proposed method assembles stability certificates for the interconnected system based on the certificates for the input-output properties of the subsystems. The hierarchy in the analysis is achieved by utilizing dual decomposition ideas in optimization. Decoupled subproblems establish subsystem level input-output properties whereas the ``master'' problem imposes and updates the conditions on the subproblems toward ensuring interconnected system level stability properties. Both global stabilityanalysis and region-of-attraction analysis are discussed.  +
This work is motivated by the problem of synthe- sizing mode sequences for continuous-time polynomial switched systems in order to guarantee that the trajectories of the system satisfy certain high-level specifications expressed in linear temporal logic. We use augmented finite transition systems as abstract models of continuous switched systems. Augmented finite transition systems are equipped with liveness properties that can be used to enforce progress in accordance with the underlying dynamics. We then introduce abstraction and refinement relations that induce a preorder on this class of finite transition systems. By construction, the resulting pre-order respects the feasibility (i.e., realizability) of the synthesis problem. Hence, existence of a discrete switching strategy for one of these abstract finite transition systems guarantees the existence of a mode sequence for the continuous system such that all of its trajectories satisfy the specification. We also present an algorithm, which can be implemented using sum-of-squares based relaxations, to compute such high fidelity abstract models in a computationally tractable way. Finally, these ideas are illustrated on an example.  +
In this paper we present a dynamical systems framework for analyzing multi-agent rendezvous problems and characterize the dynamical behavior of the collective system. Recently, the problem of rendezvous has been addressed considerably in the graph theoretic framework, which is strongly based on the communication aspects of the problem. The proposed approach is based on set invariance theory and focusses on how to generate feedback between the vehicles, a key part of the rendezvous problem. The rendezvous problem is defined on the positions of the agents and the dynamics is modeled as linear first order systems. The proposed framework however is not fundamentally limited to linear first order dynamics and can be extended to analyze rendezvous of higher order agents.  +
In this article is presented a dynamical systems framework for analysing multi-agent rendezvous problems and characterize the dynamical behaviour of the collective system. Recently, the problem of rendezvous has been addressed considerably in the graph theoretic framework, which is strongly based on the communication aspects of the problem. The proposed approach is based on the set invariance theory and focusses on how to generate feedback between the vehicles, a key part of the rendezvous problem. The rendezvous problem is defined on the positions of the agents and the dynamics is modelled as linear first-order systems. These algorithms have also been applied to non-linear first-order systems. The rendezvous problem in the framework of cooperative and competitive dynamical systems is analysed that has had some remarkable applications to biological sciences. Cooperative and competitive dynamical systems are shown to generate monotone flows by the classical Muller--Kamke theorem, which is analysed using the set invariance theory. In this article, equivalence between the rendezvous problem and invariance of an appropriately defined cone is established. The problem of rendezvous is cast as a stabilization problem, with a the set of constraints on the trajectories of the agents defined on the phase plane. The n-agent rendezvous problem is formulated as an ellipsoidal cone invariance problem in the n-dimensional phase space. Theoretical results based on set invariance theory and monotone dynamical systems are developed. The necessary and sufficient conditions for rendezvous of linear systems are presented in the form of linear matrix inequalities. These conditions are also interpreted in the Lyapunov framework using multiple Lyapunov functions. Numerical examples that demonstrate application are also presented.  +
In this paper we present a definition of "configuration controllability" for mechanical systems whose Lagrangian is kinetic energy with respect to a Riemannian metric minus potential energy. A computable test for this new version of controllability is also derived. This condition involves a new object which we call the symmetric product. Of particular interest is a definition of "equilibrium controllability" for which we are able to derive computable sufficient conditions. Examples illustrate the theory.  +
Lagrangian control systems that are differentially flat with flat outputs that only depend on configuration variables are said to be configuration flat. We provide a complete characterisation of configuration flatness for systems with $n$ degrees of freedom and $n-1$ controls whose range of control forces only depends on configuration but not on velocity and whose Lagrangian has the form of kinetic energy minus potential. The method presented allows us to determine if such a system is configuration flat and, if so provides a constructive method for finding all possible configuration flat outputs. Our characterisation relates configuration flatness to Riemannian geometry. We illustrate the method by two examples.  +
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.  +
In this paper, we introduce a consensus protocol for a network of dynamic agents that allows the agents to reach a decision in a distributed and cooperative fashion. We consider both linear and nonlinear protocols as well as the characteristic function of the communication links in the network. This includes links with delay and (possible) distortion/filtering effects. It turns out that for a number of protocols, the convergence properties and the decision-value obtained via this protocol is strongly related to connectivity and algebraic graph theoretic properties of the information flow in the network of decision-making agents. Standard tools from multivariable control and linear control theory such as Nyquist plots appear naturally for convergence analysis of the obtained linear protocols. For the analysis of the nonlinear protocols, certain disagreement costs are constructed that are minimized by the consensus protocols in a distributed way. Simulation results are provided for attitude alignment of a group of 20 dynamic agents.  +
We consider the problem of average consensus seeking in networked multi-agent systems. Based on local information and a simple distributed algorithm, states of all agents automatically converge to the average value of the initial conditions, where the convergence speed is determined by the algebraic connectivity of the underlying communication network. In order to achieve an average consensus quickly, we propose a new type of consensus protocol, multi-hop relay protocol, in which each agent expands its knowledge by employing multi-hop communication links. We explicitly show that multi-hop relay protocol increases the convergence speed without physically changing the network topology. Moreover, accumulated delays along communication links are discussed. We show that, for multi-hop relay protocol, the faster the protocol converges, the more sensitive it is to the delay. This tradeoff is identified when we investigate the stable delay margin using frequency sweep method.  +
This paper provides a theoretical framework for analysis of consensus algorithms for multi-agent networked systems with an emphasis on the role of directed information flow, robustness to changes in network topology due to link/node failures, time-delays, and performance guarantees. An overview of basic concepts of information consensus in networks and methods of convergence and performance analysis for the algorithms are provided. Our analysis framework is based on tools from matrix theory, algebraic graph theory, and control theory. We discuss the connections between consensus problems in networked dynamic systems and diverse applications including synchronization of coupled oscillators, flocking, formation control, fast consensus in small-world networks, Markov processes and gossip-based algorithms, load balancing in networks, rendezvous in space, distributed sensor fusion in sensor networks, and belief propagation. We establish direct connections between spectral and structural properties of complex networks and the speed of information diffusion of consensus algorithms. A brief introduction is provided on networked systems with nonlocal information flow that are considerably faster than distributed systems with lattice-type nearest neighbor interactions. Simulation results are presented that demonstrate the role of small-world effects on the speed of consensus algorithms and cooperative control of multivehicle formations.  +
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.  +
Station keeping and reorientation control of a cluster of fully-actuated low-thrust micro-satellites is considered in this paper. We address the control problem by taking advantage of the fully-actuated structure of the micro-satellite. We propose a very general open-loop solution by solving in real-time constrained trajectory generation problems for stationkeeping and reorientation. Performance of this methodology is reported for a typical micro-satellite format ion flying space mission using the Nonlinear Trajectory Generation software package.  +
We consider the problem of designing policies for Markov decision processes (MDPs) with dynamic coherent risk objectives and constraints. We begin by formulating the problem in a Lagrangian framework. Under the assumption that the risk objectives and constraints can be represented by a Markov risk transition mapping, we propose an optimization-based method to synthesize Markovian policies that lower-bound the constrained risk-averse problem. We demonstrate that the formulated optimization problems are in the form of difference convex programs (DCPs) and can be solved by the disciplined convex-concave programming (DCCP) framework. We show that these results generalize linear programs for constrained MDPs with total discounted expected costs and constraints. Finally, we illustrate the effectiveness of the proposed method with numerical experiments on a rover navigation problem involving conditional-value-at-risk (CVaR) and entropic-value-at-risk (EVaR) coherent risk measures.  +
Environmental applications of synthetic biology such as water remediation require engineered strains to function robustly in a fluctuating and potentially hostile environment. The construction of synthetic biofilm formation circuits could potentially alleviate this issue by promoting cell survival. Towards this end, we construct a xylose-inducible system for the expression of the functional amyloids CsgA and TasA in the soil bacterium Bacillus megaterium. We find that although both amyloids are expressed, only TasA is successfully exported from the cells. Furthermore, expression of CsgA results in a significant growth penalty for the cells while expression of TasA does not. Finally, we show that TasA expression conveys a small but detectable increase in cells’ adhesion to nickel beads. These results suggest that TasA is a promising candidate for future work on synthetic biofilm formation in B. megaterium.  +
We present a theory of contracts that is centered around reacting to failures and explore it from a general assume-guarantee perspective as well as from a concrete context of automated synthesis from linear temporal logic (LTL) specifications, all of which are compliant with a contract metatheory introduced by Benveniste et al. We also show how to obtain an automated procedure for synthesizing reactive assume-guarantee contracts and implementations that capture ideas like optimality and robustness based on assume-guarantee lattices computed from antitone Galois connection fixpoints. Lastly, we provide an example of a “reactive GR(1)” contract and a simulation of its implementation.  +
We consider a discrete time linear feedback control system with additive noise where the control signals are to be sent across a data link from the controller to the actuators. Due to network constraints it is desired to reduce the transmission frequency of the control signals. We show that by including a finite sequence of predicted control signals in each communication packet the frequency of transmission can be reduced by transmitting only when the previously sent sequence has run out. The price to pay is that the closed loop error will increase. We introduce a novel communication protocol, which we call Input Difference Transmission Scheme (IDTS), which transmits control packets when the difference between the newly computed control sequence and the predicted control sequence previously transmitted is larger than a certain thresh- old. This threshold is a design parameter and we show how the closed loop behavior varies with this threshold. Simulation results are provided to augment the theory and show how the protocol works.  +
In this paper, we consider a robust networked control problem. We consider linear unstable and uncertain discrete time plants with a network between the sensor and controller as well as between the controller and plant. We investigate the effect of data drop out in the form of packet losses and we focus on the tradeoff between packet arrival rate versus the uncertainties of the system dynamics. We show that the minimum packet arrival rate and the maximum uncertainty of the system dynamics have a positive correlation. Four distinct control schemes are explored and serve as examples to study this tradeoff. We derive sufficient condition for each scheme to ensure almost sure stability of the closed loop system. Simulation and examples are provided to assist the theory.  +
We present a set of primitive operations which forms the core of a robot system description and control language. The actions of the individual primitives are derived from the mathematical structure of the equations of motion for constrained mechanical systems. The recursive nature of the primitives allows composite robots to be constructed from more elementary daughter robots. We review a few pertinent results of classical mechanics, describe the functionality of our primitive operations, and present several different hierarchical strategies for the description and control of a two-fingered hand holding a box.  +
Fault tolerance and safety verification of control systems are essential for the success of autonomous robotic systems. A control architecture called Mission Data System (MDS), developed at the Jet Propulsion Laboratory, takes a goal-based control approach. A software algorithm for converting goal network control programs into linear hybrid systems exists and is a bisimulation; the resulting linear hybrid system can be verified for safety in the presence of failures using existing symbolic model checkers, and thus the original goal network is verified. A substantial example control program based on a proposed mission to Titan, a moon of Saturn, is converted using the procedures discussed.  +
Motivated by the desire to analyze high dimen- sional control systems without explicitly forming computation- ally expensive linear matrix inequality (LMI) constraints, we seek to exploit special structure in the dynamics matrix. By using Jordan algebraic techniques we show how to analyze continuous time linear dynamical systems whose dynamics are exponentially invariant with respect to a symmetric cone. This allows us to characterize the families of Lyapunov functions that suffice to verify the stability of such systems. We highlight, from a computational viewpoint, a class of systems for which stability verification can be cast as a second order cone program (SOCP), and show how the same framework reduces to linear programming (LP) when the system is internally positive, and to semidefinite programming (SDP) when the system has no special structure.  +
This survey aims to provide a general overview of relevant terms and resources for understanding the intersection of synthetic biology and control theory. A reader with a background in control theory should come away with a reasonable understanding of the current 24 state-of-the-art of biological system identification, controller design and implementation, and the open challenges facing the field. Additionally, this review updates and builds upon previous publications on this subject. As this particular work is limited to a selected number of topics, additional reviews are suggested throughout the text for deeper reading. In the following sections, each of the challenges is addressed within the typical workflow for control implementation of more traditionally engineered systems (Figure 1). Engineered biological systems present a number of challenges to all stages of this workflow for reasons such as limitations in real-time measurement, resource competition with the host organism, and incomplete knowledge of underlying biological processes. First, strategies for framing a biologi- cal organism as a system with defined inputs, outputs, sensors, actuators, and measurements are discussed (Figure 1a). Obtaining dynamic and reliable measurements within biological organisms is a daunting challenge, engineered or otherwise. An overview of the state-of-the-art tools for modeling and characterizing biological systems is presented, followed by system identification methods specifically designed for the types of data available from biological measurements. The difficulty in engineering complex genetic networks, combined with severe limitations in real- time measurement, means that the body of work for controller design (Figure 1b) is limited – as a result, we discuss the open problems and challenges awaiting the entrepreneurial reader, and also present a number of examples of feedback loop implementation in living cells (Figure 1c). Finally, the necessary challenges in synthetic biology and development of control theoretical frameworks that need to be addressed in order to advance the field are discussed.  
This tutorial describes TuLiP, the Temporal Logic Planning toolbox, a collection of tools for designing controllers for hybrid systems from specifications in temporal logic. The tools support a workflow that starts from a description of desired behavior, and of the system to be controlled. The system can have discrete state, or be a hybrid dynamical system with a mixed discrete and continuous state space. The desired behavior can be represented with temporal logic and discrete transition systems. The system description can include uncontrollable variables that take discrete or continuous values, and represent disturbances and other environmental factors that affect the dynamics, as well as communication signals that affect controller decisions. A control design problem is solved in phases that involve abstraction, discrete synthesis, and continuous feedback control. Abstraction yields a discrete description of system dynamics in logic. For piecewise affine dynamical systems, this abstraction is constructed automatically, guided by the geometry of the dynamics and under logical constraints from the specification. The resulting logic formulae describe admissible discrete behaviors that capture both controlled and environment variables. The discrete description resulting from abstraction is then conjoined with the desired logic specification. To find a controller, the toolbox solves a game of infinite duration. Existence of a discrete (winning) strategy for the controlled variables in this game is a proof certificate for the existence of a controller for the original problem, which guarantees satisfaction of the specification. This discrete strategy, concretized by using continuous controllers, yields a feedback controller for the original hybrid system. The toolbox frontend is written in Python, with backends in C, Python, and Cython. The tutorial starts with an overview of the theory behind TuLiP, and of its software architecture, organized into specifi- cation frontends and backends that implement algorithms for abstraction, solving games, and interfaces to other tools. Then, the main elements for writing a specification for input to TuLiP are introduced. These include logic formulae, discrete transition systems annotated with predicates, and hybrid dynamical systems, with linear or piecewise affine continuous dynamics. The working principles of the algorithms for predicate abstraction and discrete game solving using nested fixpoints are explained, by following the input specification through the various transformations that compile it to a symbolic representation that scales well to solving large games. The tutorial concludes with several design examples that demonstrate the toolbox’s capabilities.  
Previous results in the use of pulsed air injection for active control of rotating stall have suggested that air injectors have the effect of shifting the steady state compressor characteristic. In this paper we analyze the effect of a compressor characteristic actuation scheme for the three state Moore Greitzer compression system model. It is shown that closed loop feedback based on the square magnitude of the first rotating stall mode can be used to decrease the hysteresis region associated with the transition from unstalled to stalled and back to unstalled operation. The compressor characteristic shifting idea is then applied to a higher fidelity distributed model in which the characteristic shifting has phase content in addition to the magnitude content captured by the three state model. The optimal phasing of the air injection relative to the sensed position of the stall cell is determined via simulation and the results found to agree with those obtained via an experimental parametric study on the Caltech low-speed axial flow compressor.}  +
As studies continue to demonstrate how our health is related to the status of our various commensal microbiomes, synthetic biologists are developing tools and approaches to control these microbiomes and stabilize healthy states or remediate unhealthy ones. Building on previous work to control bacterial communities, we have constructed a synthetic two-member bacterial consortium engineered to reach population density and composition steady states set by inducer inputs. We detail a screening strategy to search functional parameter space in this high-complexity genetic circuit as well as initial testing of a functional two-member circuit. We demonstrate non-independent changes in total population density and composition steady states with a limited set of varying inducer concentrations. After a dilution to perturb the system from its steady state, density and composition steady states are not regained. Modeling and simulation suggest a need for increased degradation of intercellular signals to improve circuit performance. Future experiments will implement increased signal degradation and investigate the robustness of control of each characteristic to perturbations from steady states.  +
This paper focuses on a new geometric approach to fully actuated control systems on the Riemannian manifold S^2. Our control laws exploit the basic and intuitive notions of geodesic direction and of distance between points, and generalize the classical proportional plus derivative feedback (PD) without the need of arbitrary local coordinate charts. Even for the stability analysis, the appropriate Lyapunov function relies upon the notion of distance and its properties. This methodology then applies to spin-axis stabilization of a spacecraft actuated by only two control torques: discarding the rotation about the unactuated axis, a reduced system is considered, whose state is in fact defined on the sphere. For this reduced attitude stabilization problem our approach allows us not only to deal optimally with the inevitable singularity, but also to achieve simplicity, versatility and (coordinate independent) adaptive capabilities.  +
Receding horizon control allows a blending of navigation and control functions at the inner and outer loop levels and significantly enhances the ability of the control system to react to complex dynamic and environmental constraints. In this paper, we explore some of the limits of receding horizon control, including the extent to which traditional control specifications can be cast as RHC problem specifications. Simulation results for a planar flight vehicle with representative flight dynamics illustrate the main features of the proposed approach.  +
This paper describes the use of time-delayed feedback to regulate the behavior of biological networks. The general ideas are demonstrated on specific transcriptional regulatory and neural networks. It is shown that robust yet tunable controllers can be constructed that provide the biological systems with model-engineered inputs. The results indicate that time delay modulation may serve as an efficient bio-compatible control tool.  +
Convergence properties of distributed consensus protocols on networks of dynamical agents have been analyzed by combinations of algebraic graph theory and control theory tools under certain assumptions, such as strong connectivity. Strong connectivity can be regarded as the requirement that the information of each agent propagates to all the others, possibly with intermediate steps and manipulations. However, because of network failures or malicious attacks, it is possible that this assumption no longer holds, so that some agents are only receiving or only transmitting information from other subsets of agents. In this case, strong connectivity is replaced by weak connectivity. We analyze the convergence properties of distributed consensus on directed graphs with weakly connected components. We show conditions for which the agreement is reached, and, for the cases in which such conditions do not hold, we provide bounds on the residual disagreement. in terms of the number of agents that must fail for the  +
Fault tolerance and safety verification of control systems are essential for the success of autonomous robotic systems. A control architecture called Mission Data System, developed at the Jet Propulsion Laboratory, takes a goal-based control approach. In this paper, a method for converting goal network control programs into linear hybrid systems is developed. The linear hybrid system can then be verified for safety in the presence of failures using existing symbolic model checkers. An example task is developed and successfully verified using HyTech, a symbolic model checking software for linear hybrid systems.  +
The main result of this paper is a theorem that allows smooth, time-varying controllers which asymptotically stabilize a driftless nonlinear system to be converted to homogeneous, time-varying controllers which provide {\em exponential} stability. The resulting controllers are smooth everywhere except the origin and are easily computed given the original asymptotic stabilizer. We illustrate the result with experimental results on a simple mobile robot.  +
Optimal uncertainty quantification (OUQ) is a framework for nu- merical extreme-case analysis of stochastic systems with imperfect knowl- edge of the underlying probability distribution and functions/events. This paper presents sufficient conditions (when underlying functions are known) under which an OUQ problem can be reformulated as a finite-dimensional convex optimization problem.  +
How does one evaluate the performance of a stochastic system in the absence of a perfect model (i.e. probability distribution)? We address this question under the framework of optimal uncertainty quantification (OUQ), which is an information-based approach for worst-case analysis of stochastic systems. We are able to generalize previous results and show that the OUQ problem can be solved using convex optimization when the function under evaluation can be expressed in a polytopic canonical form (PCF). We also propose iterative methods for scaling the convex formulation to larger systems. As an application, we study the problem of storage placement in power grids with renewable generation. Numerical simulation results for simple artificial examples as well as an example using the IEEE 14-bus test case with real wind generation data are presented to demonstrate the usage of OUQ analysis.  +
Designing synthetic microbial consortia is an emerging area in synthetic biology and a major goal is to realize stable and robust coexistence of multiple species. Cooperation and competition are fundamental intra/interspecies interactions that shape population level behaviors, yet it is not well-understood how these interactions affect the stability and robustness of coexistence. In this paper, we show that communities with cooperative interactions are more robust to population disturbance, e.g., depletion by antibiotics, by forming intermixed spatial patterns. Meanwhile, competition leads to population spatial heterogeneity and more fragile coexistence in communities. Using reaction-diffusion and nonlocal PDE models and simulations of a two-species E. coli consortium, we demonstrate that cooperation is more beneficial than competition in maintaining coexistence in spatially structured consortia, but not in well-mixed environments. This also suggests a trade-off between constructing heterogeneous communities with localized functions and maintaining robust coexistence. The results provide general strategies for engineering spatially structured consortia by designing interspecies interactions and suggest the importance of cooperation for biodiversity in microbial community.  +
We introduce a class of triangulated graphs for algebraic representation of formations that allows us to specify a mission cost for a group of vehicles. This representation plus the navigational information allows us to formally specify and solve tracking problems for groups of vehicles in formations using an optimization-based approach. The approach is illustrated using a collection of six underactuated vehicles that track a desired trajectory in formation.<br>  +
This paper discusses a design methodology of cooperative trajectory generation for multi-robot systems. The trajectory of achieving cooperative tasks, i.e., with temporal constraints, is constructed by a nonlinear trajectory generation (NTG) algorithm. Three scenarios of multi-robot tasking are proposed at the cooperative task planning framework. The NTG algorithm is, then, used to generate real-time trajectory for desired robot activities. Given robot dynamics and constraints, the NTG algorithm first finds trajectory curves in a lower dimensional space and, then, parameterizes the curves by a set of B-spline representations. The coe�cients of the B-splines are further solved by the sequential quadratic programming to satisfy the optimization objectives and constraints. The NTG algorithm has been implemented to generate real-time trajectories for a group of cooperative robots in the presence of spatial and temporal constraints. Finally, an illustrated example of cooperative task planning with temporal constraints is presented.  +
There is a growing interest in building autonomous systems that interact with complex environments. The difficulty associated with obtaining an accurate model for such environments poses a challenge to the task of assessing and guaranteeing the system’s performance. We present a data-driven solution that allows for a system to be evaluated for specification conformance without an accurate model of the environment. Our approach involves learning a conservative reactive bound of the environment’s behavior using data and specification of the system’s desired behavior. First, the approach begins by learning a conservative reactive bound on the environment’s actions that captures its possible behaviors with high probability. This bound is then used to assist verification, and if the verification fails under this bound, the algorithm returns counter-examples to show how failure occurs and then uses these to refine the bound. We demonstrate the applicability of the approach through two case-studies: i) verifying controllers for a toy multi-robot system, and ii) verifying an instance of human-robot interaction during a lane-change maneuver given real-world human driving data.  +
This paper presents a method for optimal trajectory generation for discrete-time nonlinear systems with linear temporal logic (LTL) task specifications. Our approach is based on recent advances in stochastic optimization algorithms for optimal trajectory generation. These methods rely on estimation of the rare event of sampling optimal trajectories, which is achieved by incrementally improving a sampling distribution so as to minimize the cross-entropy. A key component of these stochastic optimization algorithms is determining whether or not a trajectory is collision-free. We generalize this collision checking to e�ciently verify whether or not a trajectory satisfies a LTL formula. Interestingly, this verification can be done in time polynomial in the length of the LTL formula and the trajectory. We also propose a method for e�ciently re-using parts of trajectories that only partially satisfy the specification, instead of simply discarding the entire sample. Our approach is demonstrated through numerical experiments involving Dubins car and a generic point-mass model subject to complex temporal logic task specifications.  +
In this paper, we consider the following problem. Suppose a sensor is taking measurements of a dynamic process. It needs to communicate the information over a network of communication links that can drop packets stochastically. What is the optimal processing at each node in the network? We provide a strategy that yields the optimal performance at the cost of constant memory and processing at each node. We also provide conditions on the network for the estimate error covariance to be stable under this algorithm.  +
We consider the problem of controlling a linear time invariant process when the controller is located at a location remote from where the sensor measurements are being generated. The communication from the sensor to the controller is supported by a communication network with arbitrary topology composed of analog erasure channels. Using a separation principle, we prove that the optimal LQG controller consists of an LQ optimal regulator along with an estimator that estimates the state of the process across the communication network mentioned above. We then determine the optimal information processing strategy that should be followed by each node in the network so that the estimator is able to compute the best possible estimate in the minimum mean squared error sense. The algorithm is optimal for any packet-dropping process and at every time step, even though it is recursive and hence requires a constant amount of memory, processing and transmission at every node in the network per time step. For the case when the packet drop processes are memoryless and independent across links, we analyze the stability properties and the performance of the closed loop system. The algorithm is an attempt to escape the more commonly used viewpoint of treating a network of communication links as a single end-to-end link with the probability of successful transmission determined by some measure of the reliability of the network.  +
Synthetic gene networks are frequently conceptualized and visualized as static graphs. This view of biological programming stands in stark contrast to the transient nature of biomolecular interaction, which is frequently enacted by labile molecules that are often unmeasured. Thus, the network topology and dynamics of synthetic gene networks can be difficult to verify in vivo or in vitro, due to the presence of unmeasured biological states. Here we introduce the dynamical structure function as a new mesoscopic, data-driven class of models to describe gene networks with incomplete measurements. We introduce a network reconstruction algorithm and a code base for reconstructing the dynamical structure function from data, to enable discovery and visualization of graphical relationships in a genetic circuit diagram as time-dependent functions rather than static, unknown weights. We prove a theorem, showing that dynamical structure functions can provide a data-driven estimate of the size of crosstalk fluctuations from an idealized model. We illustrate this idea with numerical examples. Finally, we show how data-driven estimation of dynamical structure functions can explain failure modes in two experimentally implemented genetic circuits, a historical genetic circuit and a new E. coli based transcriptional event detector.  +
This paper considers a group of agents that aim to reach an agreement on individually measured time-varying signals by local communication. In contrast to static network averaging problem, the consensus we mean in this paper is reached in a dynamic sense. A discrete-time dynamic average consensus protocol can be designed to allow all the agents tracking the average of their reference inputs asymptotically. We propose a minimal-time dynamic consensus algorithm, which only utilises minimal number of local observations of randomly picked node in a network to compute the final consensus signal. Our results illustrate that with memory and computational ability, the running time of distributed averaging algorithms can be indeed improved dramatically using local information as suggested by Olshevsky and Tsitsiklis.  +
We study a distributed multi-agent optimization problem of minimizing the sum of convex objective functions. A new decentralized optimization algorithm is introduced, based on dual decomposition, together with the subgradient method for finding the optimal solution. The iterative algorithm is implemented on a multi-hop network and is designed to handle communication delays. The convergence of the algorithm is proved for communication networks with bounded delays. An explicit bound, which depends on the communication delays, on the convergence rate is given. A numerical comparison with a decentralized primal algorithm shows that the dual algorithm converges faster, with less communication.  +
Temporal logic based synthesis approaches are often used to find trajectories that are correct-by-construction in systems–eg. synchronization for multi-agent hybrid systems, reactive motion planning for robots. However, the scalability of such approaches is of concern and at times a bottleneck when transitioning from theory to practice. In this paper, we identify a class of problems in the GR(1) fragment of linear-time temporal logic (LTL) where the synthesis problem allows for a decomposition that enables easy parallelization. This decomposition also reduces the alternation depth, resulting in more efficient synthesis. A multi-agent robot gridworld example with coordination tasks is presented to demonstrate the application of the developed ideas and also to perform empirical analysis for benchmarking the decomposition-based synthesis approach.  +
Using tools from dynamical systems and systems identification we develop a framework for the study of primitives for human motion, which we refer to as movemes. The objective is understanding human motion by decomposing it into a sequence of elementary building blocks that belong to a known alphabet of dynamical systems. In this work we address the problem of defining conditions under which collections of signals are well-posed according to a dynamical model class M and then can generate movemes. Based on the assumption of well-posedness, we develop segmentation and classification algorithms in order to reduce a complex activity into the sequence of movemes that have generated it. Using examples we show that the definition of well-posedness can be applied in practice and show analytically that the proposed algorithms are robust with respect to noise and model uncertainty. We test our ideas on data sampled from five human subjects who were drawing figures using a computer mouse. Our experiments show that we are able to distinguish between movemes and recognize them even when they take place in activities containing more than one moveme at a time.  +
In this letter we present a decomposition for control systems whose drift vector field is the geodesic spray associated with an affine connection. With the geometric insight gained with this decomposition, we are able to easily prove some special results for this class of control systems. Examples illustrate the theory.  +
In this paper we explore the use of time-delayed differential equation as a means of obtaining a simplified description of very high order dynamics.This paper finds results for a particular type of system, a single-input single-output (SISO) linear system with a nonlinear feedback. We begin with a high dimensional system in state space and reduce the dimension by finding a delay based approximation which could be a smaller set of integro-differential equations or DDEs. We argue that approximations of high order linear subsystems whose distribution functions have relatively smaller variance such as delta functions, give a conservative approximation of a system's stable parameter space. Through examples inspired by biology, we show how these approximations can be used to verify stability. We analyze the system's stability and robustness dependence on statistical properties, mainly relative variance and expectation for a symmetric distribution function.  +
Motivated by the availability of different types of delays in embedded systems and biological circuits, the objective of this work is to study the benefits that delay can provide in simplifying the implementation of controllers for continuous-time systems. Given a continuous-time linear time-invariant (LTI) controller, we propose three methods to approximate this controller arbitrarily precisely by a simple controller composed of delay blocks, a few integrators and possibly a unity feedback. Different problems associated with the approximation procedures, such as finding the optimal number of delay blocks or studying the robustness of the designed controller with respect to delay values, are then investigated. We also study the design of an LTI continuous-time controller satisfying given control objectives whose delay-based implementation needs the least number of delay blocks. A direct application of this work is in the sampled-data control of a real-time embedded system, where the sampling frequency is relatively high and/or the output of the system is sampled irregularly. Based on our results on delay-based controller design, we propose a digital-control scheme that can implement every continuous-time stabilizing (LTI) controller. Unlike a typical sampled-data controller, the hybrid controller introduced here---consisting of an ideal sampler, a digital controller, a number of modified second-order holds and possibly a unity feedback---is robust to sampling jitter and can operate at arbitrarily high sampling frequencies without requiring expensive, high-precision computation.  +
Genetic regulatory networks are biochemical reaction systems, consisting of a network of interacting genes and associated proteins. The dynamics of genetic regulatory networks contain many complex facets that require careful consideration during the modeling process. The classical modeling approach involves studying systems of ordinary differential equations (ODEs) that model biochemical reactions in a deterministic, continuous, and instantaneous fashion. In reality, the dynamics of these systems are stochastic, discrete, and widely delayed. The first two complications are often successfully addressed by modeling regulatory networks using the Gillespie stochastic simulation algorithm (SSA), while the delayed behavior of biochemical events such as transcription and translation are often ignored due to their mathematically difficult nature. We develop techniques based on delay-differential equations (DDEs) and the delayed Gillespie SSA to study the effects of delays, in both continuous deterministic and discrete stochastic settings. Our analysis applies techniques from Floquet theory and advanced numerical analysis within the context of delay-differential equations, and we are able to derive stability sensitivities for biochemical switches and oscillators across the constituent pathways, showing which pathways in the regulatory networks improve or worsen the stability of the system attractors. These delay sensitivities can be far from trivial, and we offer a computational framework validated across multiple levels of modeling fidelity. This work suggests that delays may play an important and previously overlooked role in providing robust dynamical behavior for certain genetic regulatory networks, and perhaps more importantly, may offer an accessible tuning parameter for robust bioengineering.  +
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.  +
This paper describes the design, modeling, synthesis and preliminary validation of a protein concentration regulator circuit. The circuit is designed to maintain the level of a target protein to a reference level, specified by the amount of another protein. This is implemented using a single negative feedback loop that inhibited the production of the target protein once its concentration was equal to the reference amount. A mathematical model consisting of a set of ODEs is derived from mass action laws and Hill function approximations of protein production. Steady-state analysis of the model is used to predict parameter sensitivity and experimental behavior. We implemented this circuit in ''E. coli'' using scaffold-based sequestration and transcriptional activation. Preliminary experimental results show the system matching predictions from our model and performing the expected task.  +
Current bacterial synthetic circuits rely on the fast dilution and high protein expression that occurs during exponential phase. However, constant exponential phase is both difficult to ensure in a lab environment and almost certainly impractical in any natural setting. Here, we characterize the performance of 13 E. coli native 38 promoters, as well as a previously identified 38 consensus promoter. We then make tetO combinatorial versions of the three strongest promoters to allow for inducible delayed expression. The design of these combinatorial promoters allows for design of circuits with inducible stationary phase activity that can be used for phase-dependent delays in dynamic circuits or spatial partitioning of biofilms.  +
As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we use synthetic protein scaffolds as a modular and tunable mechanism for concentration tracking through negative feedback. Input to the circuit initiates scaffold production, leading to colocalization of a two-component system and resulting in the production of an inhibitory antiscaffold protein. Using a combination of modeling and experimental work, we show that the biomolecular concentration tracker circuit achieves dynamic protein concentration tracking in ''Escherichia coli'' and that steady state outputs can be tuned.  +
This paper proposes a new synthetic in vitro circuit that aims at regulating the rate of RNA transcription through positive feedback interactions. This design is dual to a previously synthesized transcriptional rate regulator based on self-repression. Two DNA templates are designed to interact through their transcripts, creating cross activating feedback loops that will equate their transcription rates at steady state. A mathematical model is developed for this circuit, consisting of a set of ODEs derived from the mass action laws and Michaelis--Menten kinetics involving all the present chemical species. This circuit is then compared to its regulatory counterpart based on negative feedback. A global sensitivity analysis reveals the fundamental features of the two designs, by evaluating their equilibrium response to changes in the most crucial parameters of the system.  +
RNA thermometers mediate responses to temperature changes in various natural circuits, and have been developed in a synthetic context as well. However, a toolbox of RNA thermometers with diâµerent sensitivities to temperature is lacking. Here, we address this issue using a combination of computational and experimental methodologies. We analysed a set of available synthetic RNA thermometers through a quantification of their activity as a function of temperatures in a cell- free expression molecular breadboard system as well as through computation of their melt profiles. Based on this, we computed melt profiles of a library of RNA thermometers and found that the library contained RNA thermometers with a range of sensitivities and thresholds in their response to temperature. We constructed this library and found, through preliminary measurements, a wide range of responses to temperature, which in some cases matched the computational predictions. The constructed library represents a toolbox of RNA thermometers with different sensitivities and is foun- dational work towards synthetic biology applications such as efficient control of large volume chemical reactors, precise spatiotemporal control of gene expression as well as tools to engineer robustness to temperature in biomolecular circuits.  +
Feedback control is the key to achieve robust performances for many engineered systems. However, its application in biological contexts is still largely unexplored. In this work, we designed, analyzed and simulated a layered controller functioning at both molecular and populational levels. First, we used a minimal model of three states to represent a system where state A activates state B; state R is a by-product of state B that acts as a negative feedback regulating both state A, B, and sequentially R. We call the feedback applied to state B a cis feedback and the one applied to state A a trans feedback. Through stability analysis via linearization at equilibrium and sensitivity analysis at transient state, we found that the cis feedback attenuates disturbances better but recovers slower; the trans feedback recovers faster but has more dramatic responses to fluctuations; the layered feedback demonstrates both advantageous traits of the two single layers. Then we designed two versions of synthetic genetic circuits to implement the layered controller in living cells. One version with an sRNA as regulator R, the other with a transcription factor protein as the regulator R. The analysis and dynamical simulation of the models confirmed the analytical results from the minimal model. At the same time, we found that the protein regulated feedback controls have faster recovery speed but the RNA version has a stronger disturbance attenuation effect.  +
This paper describes a synthetic in vitro genetic circuit programmed to work as an insulating device. This circuit is composed of nucleic acids, which can be designed to interact according to user defined rules, and of few proteins that perform catalytic functions. A model of the circuit is derived from first principle biochemical laws. This model is shown to exhibit time-scale separation that makes its output insensitive to downstream time varying loads. Simulation results show the circuit effectiveness and represent the starting point for future experimental testing of the device.  +
âIncoherent feedforward loopsâ represent important biomolecular circuit elements capable of a rich set of dynamic behavior including adaptation and pulsed responses. Temperature can modulate some of these properties through its effect on the underlying reaction rate parameters. It is generally unclear how to design a circuit where these properties are robust to variations in temperature. Here, we address this issue using a combination of tools from control and dynamical systems theory as well as preliminary experimental measurements towards such a design. Using a structured uncertainty representation, we analyze a standard incoherent feedforward loop circuit, noting mechanisms that intrinsically confer temperature robustness to some of its properties. Further, we study design variants that can enhance this robustness to temperature, including different negative feedback configurations as well as conditions for perfect temperature compensation. Finally, we find that the response of an incoherent feedforward loop circuit in cells can change with temperature. These results present groundwork for the design of a temperature-robust incoherent feedforward loop circuit.  +
In this paper we give a formulation of differential flatness---a concept originally introduced by Fleiss, Levine, Martin, and Rouchon---in terms of absolute equivalence between exterior differential systems. Systems which are differentially flat have several useful properties which can be exploited to generate effective control strategies for nonlinear systems. The original definition of flatness was given in the context of differentiable algebra, and required that all mappings be meromorphic functions. Our formulation of flatness does not require any algebraic structure and allows one to use tools from exterior differential systems to help characterize differentially flat systems. In particular, we shown that in the case of single input control systems (i.e., codimension 2 Pfaffian systems), a system is differentially flat if and only if it is feedback linearizable via static state feedback. However, in higher codimensions feedback linearizability and flatness are *not* equivalent: one must be careful with the role of time as well the use of prolongations which may not be realizable as dynamic feedbacks in a control setting. Applications of differential flatness to nonlinear control systems and open questions will be discussed.  +
This paper describes the application of differential flatness techniques from nonlinear control theory to mechanical (Lagrangian) systems. Systems which are differentially flat have several useful properties which can be exploited to generate effective control strategies for nonlinear systems. For the special case of mechanical control systems, much more geometric information is present and the purpose of this paper is to explore the implications and features of that class of systems. We concentrate on several worked examples which illustrate the general theory and present a detailed catalog of known examples of differentially flat mechanical systems.  +
Given a differentially flat system of ODEs, flat outputs that depend only on original variables but not on their derivatives are called zero-flat outputs and systems possessing such outputs are called zero-flat. In this paper we present a theory of zero-flatness for a system of two one-forms in arbitrary number of variables $(t,x^1,\dots,x^N)$. Our approach splits the task of finding zero-flat outputs into two parts. First part involves solving for distributions that satisfy a set of algebraic conditions. If the first part has no solution then the system is not zero-flat. The second part involves finding an integrable distribution from the solution set of the first part. Typically this part involves solving PDEs. Our results are also applicable in determining if a control affine system in $n$ states and $n-2$ controls has flat outputs that depend only on states. We illustrate our method by examples.  +
Differentially flat systems are underdetermined systems of (nonlinear) ordinary differential equations (ODEs) whose solution curves are in smooth one-one correspondence with arbitrary curves in a space whose dimension equals the number of equations by which the system is underdetermined. For control systems this is the same as the number of inputs. The components of the map from the system space to the smaller dimensional space are referred to as the flat outputs. Flatness allows one to systematically generate feasible trajectories in a relatively simple way. Typically the flat outputs may depend on the original independent and dependent variables in terms of which the ODEs are written as well as finitely many derivatives of the dependent variables. Flatness of systems underdetermined by one equation is completely characterised by Elie Cartan's work. But for general underdetermined systems no complete characterisation of flatness exists. <p> In this dissertation we describe two different geometric frameworks for studying flatness and provide constructive methods for deciding the flatness of certain classes of nonlinear systems and for finding these flat outputs if they exist. We first introduce the concept of ``absolute equivalence'' due to Cartan and define flatness in this frame work. We provide a method of testing for the flatness of systems, which involves making a guess for all but one of the flat outputs after which the problem is reduced to the case solved by Cartan. Secondly we present an alternative geometric approach to flatness which uses ``jet bundles'' and present a theorem which partially characterises flat outputs that depend only on the original variables but not on their derivatives, for the case of systems described by two independent one-forms in arbitrary number of variables. Finally, for the class of Lagrangian mechanical systems whose number of control inputs is one less than the number of degrees of freedom, we provide a characterisation of flat outputs that depend only on the configuration variables, but not on their derivatives. This characterisation makes use of the Riemannian metric provided by the kinetic energy of the system.  
This paper proposes a real-time planning scheme and its implementation for a class of dynamic systems. The planner is aimed to satisfy the state equations, the path and actuator constriants, and the given initial and terminal constraints. In order to generate trajectories in real-time, three broad steps are performed: (1) the structure of differentially flat systems is used to explicitly encapsulate the state equations into linear differential constraints in a flat space, and appropriately transform the boundary conditions; (ii) using semi-infinite optimization theory, an inner approximation of nonlinear constraints is made to replace these by a set of linear inequalities in the flat space, i.e., by a polytope; (iii) this polytopic representation of the system that satisfies the state equations and the constraints is then parameterized using basis functions and the planning problem is turned around into solution of a set of linear inequalities in the coefficient space of the basis functions. It is then demonstrated that numerically efficient algorithms can be built to solve the planning problem in real-time. The essence of the approach is demonstrated by two examples: (1) an implementation is performed on a spring-mass-damper system to demonstrate the real-time capability of evasion-pursuit; (ii) a VTOL aircraft is used to illustrate the application of this approach in simulation to nonlinear problems.  +
We describe a method for discrete representation of continuous functions and show how this may be used for typical computations in nonlinear control desi gn. The method involves representing functions by their values and finitely many derivatives at discrete set of points on the domain. We propose a grid structure based on a hierarchy of rectangular boxes that provides flexibility in placing grid points densely in some regions and sparsely in the other. The grids possess enough structure to facilitate easy interpolation schemes based on piecewise polynomials. We illustrate the method using a simple example where we compute the feedback linearizing output of a system.  +
We address the problem of estimating discrete variables in a class of deterministic transition systems where the continuous variables are available for measurement. This simplified scenario has practical interest, for example, in the case of decentralized multi-robot systems. In these systems, the continuous variables represent physical quantities such as the position and velocity of a robot, while discrete variables may represent the state of the logical system that is used for control and coordination. We propose a novel approach to the estimation of discrete variables using basic lattice theory that overcomes some of the severe complexity issues encountered in previous work. We show how to construct the proposed estimator for a multi-robot system performing a cooperative assignment task.  +
The problem of estimating the discrete variables in nondeterministic hybrid systems where the continuous variables are available for measurement is considered. Using partial order and lattice theory, we construct a discrete state estimator, the LU estimator, which updates two variables at each step. Namely, it updates the lower (L) and upper (U) bounds of the set of all possible discrete variables values compatible with the output sequence and with the systems' dynamics. If the system is weakly observable, we show that there always exist a lattice on which to construct the LU estimator. For computational issues, some partial orders are to be preferred to others.We thus show that nondeterminism may be added to a system so as to obtain a new system that satisfies the requirements for the construction of the LU estimator on a chosen lattice. These ideas are applied to a nondeterministic multi-robot system.  +
Distributed algorithms for averaging have at- tracted interest in the control and sensing literature. However, previous works have not addressed some practical concerns that will arise in actual implementations on packet-switched communication networks such as the Internet. In this paper, we present several implementable algorithms that are robust to asynchronism and dynamic topology changes. The algorithms do not require global coordination and can be proven to converge under very general asynchronous timing assumptions. Our results are verified by both simulation and experiments on a real-world TCP/IP network.  +
A cooperative control system consists of multiple, autonomous components interacting to<br> control their environment. Examples include air tra±c control systems, automated factories,<br> robot soccer teams and sensor/actuator networks. Designing such systems requires a combination of tools from control theory and distributed systems. In this article, we review some of these tools and then focus on the Computation and Control Language, CCL, which we have developed as a modeling tool and a programming language for cooperative control systems.  +
In this paper, we propose a framework for formation stabilization of multiple autonomous vehicles in a distributed fashion. Each vehicle is assumed to have simple dynamics, i.e. a double-integrator, with a directed (or an undirected) information ow over the formation graph of the vehicles. Our goal is to find a distributed control law (with an efficient computational cost) for each vehicle that makes use of limited information regarding the state of other vehicles. Here, the key idea in formation stabilization is the use of natural potential functions obtained from structural constraints of a desired formation in a way that leads to a collision-free, distributed, and bounded state feedback law for each vehicle.  +
Many systems comprised of interconnected sub-units exhibit coordinated behaviors; social groups, networked computers, financial markets, and numerous biological systems come to mind. There has been long-standing interest in developing a scientific understanding of coordination, both for ex- planatory power in the natural and economic sciences, and also for constructive power in engineering and applied sciences. This thesis is an abstract study of coordination, focused on developing a sys- tematic âdesign theoryâ for producing interconnected systems with specifiable coordinated behavior; this is in contrast to the bulk of previous work on this sub ject, in which any design component has been primarily ad-hoc. <p>The main theoretical contribution of this work is a geometric formalism in which to cast dis- tributed systems. This has numerous advantages and ânaturallyâ parametrizes a wide class of distributed interaction mechanisms in a uniform way. We make use of this framework to present a model for distributed optimization, and we introduce the distributed gradient as a general design tool for synthesizing dynamics for distributed systems. The distributed optimization model is a useful abstraction in its own right and motivates a definition for a distributed extremum. As one might expect, the distributed gradient is zero at a distributed extremum, and the dynamics of a distributed gradient flow must converge to a distributed extremum. This forms the basis for a wide variety of designs, and we are in fact able to recover a widely studied distributed averaging algorithm as a very special case. <p>We also make use of our geometric model to introduce the notion of coordination capacity; intuitively, this is an upper bound on the âcomplexityâ of coordination that is feasible given a particular distributed interaction structure. This gives intuitive results for local, distributed, and global control architectures, and allows formal statements to be made regarding the possibility of âsolvingâ certain optimization problems under a particular distributed interaction model. <p>Finally, we present a number of applications to illustrate the theoretical approach presented; these range from âstandardâ distributed systems tasks (leader election and clock synchronization) to more exotic tasks like graph coloring, distributed account balancing, and distributed statistical computations.  
We present an approach that allows mission and contingency management to be achieved in a distributed and dynamic manner without any central control over multiple software modules. This approach comprises two key elements---a mission management subsystem and a Canonical Software Architecture (CSA) for a planning subsystem. The mission management subsystem works in conjunction with the planning subsystem to dynamically replan in reaction to contingencies. The CSA ensures the consistency of the states of all the software modules in the planning subsystem. System faults are identified and replanning strategies are performed distributedly in the planning and the mission management subsystems through the CSA. The approach has been implemented and tested on Alice, an autonomous vehicle developed by the California Institute of Technology for the 2007 DARPA Urban Challenge.  +
We consider the problem of designing distributed control protocols -for aircraft vehicle management systems- that cooperatively allocate electric power while meeting certain higher level goals and requirements, and dynamically reacting to the changes in the internal system state and external environment. A decentralized control problem is posed where each power distribution unit is equipped with a controller that implements a local protocol to allocate power to a certain subset of loads. We use linear temporal logic as the specification language for describing correct behaviors of the system (e.g., safe operating conditions) as well as the admissible dynamic behavior of the environment due to, for example, wind gusts and changes in system health. We start with a global specification and decompose it into local ones. These decompositions allow the protocols for each local controller to be separately synthe- sized and locally implemented while guaranteeing the global specifications to hold. Through a design example, we show that by refining the interface rules between power distribution units, it is possible to reduce the total power requirement.  +
We consider the control of interacting subsystems whose dynamics and constraints are uncoupled, but whose state vectors are coupled non-separably in a single centralized cost function of a finite horizon optimal control problem. For a given centralized cost structure, we generate distributed optimal control problems for each subsystem and establish that the distributed receding horizon implementation is asymptotically stabilizing. The communication requirements between subsystems with coupling in the cost function are that each subsystem obtain the previous optimal control trajectory of those subsystems at each receding horizon update. The key requirements for stability are that each distributed optimal control not deviate too far from the previous optimal control, and that the receding horizon updates happen sufficiently fast. The theory is applied in simulation for stabilization of a formation of vehicles.  +
This work is an extension to a companion paper describing consensus-tracking for networked agents, and shows how those results can be applied to obtain least-squares fused estimates based on spatially distributed measurements. This mechanism is very robust to changes in the underlying network topology and performance, making it an interesting candidate for sensor fusion on autonomous mobile networks. We conclude with an example of a preliminary application to distributed Kalman Filtering using the proposed technique, illustrating the dependence of the performance on the structure of the underlying network.  +
In this paper, we provide a theoretical framework that consists of graph theoretical and Lyapunov-based approaches to stability analysis and distributed control of multi-agent formations. This framework relays on the notion of graph rigidity as a means of identifying the shape variables of a formation. Using this approach, we can formally define formations of multiple vehicles and three types of stabilization/tracking problems for dynamic multi-agent systems. We show how these three problems can be addressed mutually independent of each other for a formation of two agents. Then, we introduce a procedure called dynamic node augmentation that allows construction of a larger formation with more agents that can be rendered structurally stable in a distributed manner from some initial formation that is structurally stable. We provide two examples of formations that can be controlled using this approach, namely, the V-formation and the diamond formation.  +
We consider the problem of synthesizing control protocols for smart camera networks where the goal is to guarantee that certain linear temporal logic (LTL) specifications related to a given surveillance task are met. We first present a centralized control architecture for assigning pan-tilt-zoom (PTZ) cameras to targets so that the specification is met for any admissible behavior of the targets. Then, in order to alleviate the computational complexity associated with LTL synthesis and to enable implementation of local control protocols on individual PTZ cameras, we propose a distributed synthe- sis methodology. The main idea is to decompose the global specification into local specifications for each PTZ camera. A thorough design example is presented to illustrate the steps of the proposed procedure.  +
This work examines several dynamical aspects of average consensus in mobile networks. The results herein allow consensus on general time-varying signals, and allow tracking analysis using standard frequency-domain techniques. Further, the frequency-domain analysis naturally inspires a robust small-gain version of the algorithm, which tolerates arbitrary non-uniform time delays. Finally, we show how to exploit a dynamical conservation property in order to ensure consensus tracking despite splitting and merging of the underlying mobile network.  +
This paper presents an experimental investigation into the effect of a varying downstream boundary condition on dynamic separation control in a twodimensional low-speed asymmetric diffuser. The potential for coupling between the downstream boundary condition and the separation dynamics is relevant, for example, in using separation control to enable more aggressive serpentine aircraft inlets, where the compressor may be close to the separation point. Separation control in the experiment is obtained using spanwise unsteady forcing from a single tangential actuator located directly upstream of the separation point. The downstream boundary condition simulates the dominant quasi-steady and reflection characteristics of a compressor. Although the boundary condition affects the uncontrolled pressure recovery, the optimal forcing frequency is shown to depend only on the mass flow rate and not on either the presence, impedance, or location of the downstream boundary condition. At the conditions tested herein, we therefore conclude that the mechanism underlying dynamic separation control is local in nature, and is not influenced by global system dynamics.  +
We consider the problem of estimating the discrete state of an aircraft electric system under a distributed control architecture through active sensing. The main idea is to use a set of controllable switches to reconfigure the system in order to gather more information about the unknown state. By adaptively making a sequence of reconfiguration decisions with uncertain outcome and by correlating the measurements and prior information to make the next decision, we aim to reduce the uncertainty. A greedy strategy is developed that maximizes the one-step expected uncertainty reduction. By exploiting recent results on adaptive submodularity, we give theoretical guarantees on the worst-case performance of the greedy strategy. We apply the proposed method in a fault de- tection scenario where the discrete state captures possible faults in various circuit components. In addition, simple abstraction rules are proposed to alleviate state space explosion and to scale up the strategy. Finally, the efficiency of the proposed method is demonstrated empirically on different circuits.  +
We investigate nonlinear dynamical models for self- sustained oscillations in the flow past a rectangular cavity. The models are based on the method of Proper Orthogonal Decomposition (POD) and Galerkin projection, and we introduce an inner product and formulation of the equations of motion which enables one to use vector-valued POD modes for compressible flows. We obtain models between 3 and 20 states, which accurately describe both the short-time and long-time dynamics. This is a substantial improvement over previous models based on scalar-valued POD modes,which capture the dynamics for short time, but deviate for long time.  +
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.  +
We study the dynamic stability of low Reynolds number swimming near a plane wall from a control-theoretic viewpoint. We consider a special class of swimmers having a constant shape, focus on steady motion parallel to the wall, and derive conditions under which it is passively stable without sensing or feedback. We study the geometric structure of the swimming equation and highlight the relation between stability and reversing symmetry of the dynamical system. Finally, our numerical simulations reveal the existence of stable periodic motion. The results have implications for design of miniature robotic swimmers, as well as for explaining the attraction of micro-organisms to surfaces.  +
In mobile sensor networks, sensor measurements as well as control commands are transmitted over wireless time-varying links. It then becomes considerably important to address the impact of imperfect communication on the overall performance. In this paper, we study the effect of time-varying communication links on the control performance of a mobile sensor node. In particular, we investigate the impact of fading. We derive key performance measure parameters to evaluate the overall feedback control performance over narrowband channels. We show that fading can result in considerable delay and/or poor performance of the mobile sensor depending on the system requirements. To improve the performance, we then show how the application layer can use the channel status information of the physical layer to adapt control commands accordingly. We show that sharing information across layers can improve the overall performance considerably. We verify our analytical results by simulating a wireless speed control problem.  +
AbstractâIn this paper, we consider a state estimation problem over a bandwidth limited network. A sensor network consisting of N sensors is used to observe the states of M plants, but only p · N sensors can transmit their measurements to a centralized estimator at each time. Therefore a suitable scheme that schedules the proper sensors to access the network at each time so that the total estimation error is minimized is required. We propose four different sensor scheduling schemes. The static and stochastic schemes assume no feedback from the estimator to the scheduler, while the two dynamic schemes, Maximum Error First (MEF) and Maximum Deduction First (MDF) assume such feedback is available. We compare the four schemes via some examples and show MEF and MDF schemes are better than the static and stochastic schemes, which demonstrates that feedback can play an important role in this remote state estimation problem. We also show that MDF is better than MEF as MDF considers the total estimation error while MEF considers the individual estimation error.  +
In this paper, we consider a state estimation problem over a bandwidth limited network. A sensor network consisting of N sensors is used to observe the states of M plants, but only p les N sensors can transmit their measurements to a centralized esti.....  +
Thin film deposition is an industrially-important process that is highly dependent on the process conditions. Most films are grown under constant conditions, but a few studies show that modified properties may be obtained with periodic inputs. However, assessing the effects of modulation experimentally becomes impractical with increasing material complexity. Here we consider periodic conditions in which the period is short relative to the time-scales of growth. We analyze a stochastic model of thin film growth, computing effective transition rates associated with rapid periodic process parameters. Combinations of effective rates may exist which are not attainable under steady conditions, potentially enabling new film properties. An algorithm is presented to construct the periodic input for a desired set of effective transition rates. These ideas are first illustrated by two simple examples using kinetic Monte Carlo simulations and are then compared to existing deposition techniques.  +
Bifurcations are ubiquitous in engineering applications. Subcritical bifurcations are typically associated with hysteresis and catastrophic instability inception, while supercritical bifurcations are usually associated with gradual and more benign instability inception. With the assumption that the bifurcating modes are linearly unstabilizable, we give a constructive procedure of designing feedback laws to change the criticality of bifurcations from subcritical to supercritical. Algebraic necessary and sufficient conditions are obtained under which the criticality of a simple steady-state or Hopf bifurcation can be changed to supercritical by a smooth feedback. The effects of magnitude saturation, bandwidth, and rate limits are important issues in control engineering. We give qualitative estimates of the region of attraction to the stabilized bifurcating equilibrium/periodic orbits under these constraints. <p> We apply the above theoretical results to the Moore-Greitzer model in active control of rotating stall and surge in gas turbine engines. Though linear stabilizability can be achieved using distributed actuation, it limits the practical usefulness due to considerations of affordability and reliability. On the other hand, simple but practically promising actuation schemes such as outlet bleed valves, a couple of air injectors, and magnetic bearings will make the system loss of linear stabilizability, thus the control design becomes a challenging task. The above mentioned theory in bifurcation stabilization can be applied to these cases. We analyze the effects of magnitude and rate saturations in active control of rotating stall using bleed valves. Analytic formulas are obtained for the operability enhancement as a function of system parameters, noise level, and actuator magnitude and rate limits. The formulas give good qualitative predictions when compared with experiments. Our conclusion is that actuator magnitude and rate limits are serious limiting factors in stall control and must be addressed in practical implementation to the aircraft engines. <p>  
Motivated by problems such as active control of rotating stall in compression systems, an analysis of the effects of controller magnitude saturation in feedback stabilization of steady-state bifurcations is performed. In particular the region of attraction to the stabilized bifurcated equilibria is solved for feedback controllers with magnitude saturation limits using the technique of center manifold reduction and bifurcation analysis. It has been shown that the stability boundary is the saturation envelope formed by the unstable (or stable) equilibria for the closed loop system when the controllers saturate. The framework allows the design of feedback control laws to achieve desirable size of region of attraction when the noise is modeled as a closed set of initial conditions in the phase space. It is also possible to extend the techniques and results to Hopf bifurcations.  +
Operability enhancement is one of the major goals for active control of rotating stall and surge in aeroengines. The model developed by Moore and Greitzer exhibits the qualitative behavior of rotating stall and surge dynamics and thus can be used for controller designs. Based on this model, we derive a normal form from which explicit relations between the stall and surge inception process and the shape of compressor characteristics are obtained via bifurcation analysis. Analysis for the normal form with bleed valve actuator dynamics shows that under certain circumstances the optimal control is the "bang-on" control law that drives the bleed valve to open against its rate limit once the disturbances grow out of the noise level.  +
In this paper we analyze the effects of fluid noise, actuator bandwidth, magnitude saturation and rate limits on rotating stall control by studying a two dimensional system which is the approximation of the dynamics on the attracting saddle-sink connections of the three state low $B$ parameter Moore Greitzer model together with the dynamics of the bleed valve controller. We show that the region of attraction to the stabilized rotating stall equilibria is seriously restrained by the fluid noise level, the actuator bandwidth, magnitude saturation and rate limits. The bandwidth and rate requirement for a fixed extension of stable region is estimated by calculating the stable manifold of the saddle fixed point of the two dimensional system.  +
ugmented finite transition systems generalize nondeterministic transition systems with additional liveness conditions. We propose efficient algorithms for synthesizing control protocols for augmented finite transition systems to satisfy high-level specifications expressed in a fragment of linear temporal logic (LTL). We then use these algorithms within a framework for switching protocol synthesis for discrete-time dynamical systems, where augmented finite transition systems are used for abstracting the underlying dynamics. We introduce a notion of minimality for abstractions of certain fidelity and show that such minimal abstractions can be exactly computed for switched affine systems. Additionally, based on this framework, we present a procedure for computing digitally implementable switching protocols for continuous-time systems. The effectiveness of the proposed framework is illustrated through two examples of temperature control for buildings.  +
Motivated by robotic motion planning, we develop a framework for control policy synthesis for both non-deterministic transition systems and Markov decision processes that are subject to temporal logic task specifications. We introduce a fragment of linear temporal logic that can be used to specify common motion planning tasks such as safe navigation, response to the environment, surveillance, and persistent coverage. This fragment is computationally efficient; the complexity of control policy synthesis is a doubly-exponential improvement over standard linear temporal logic for both non-deterministic transition systems and Markov decision processes. This improvement is possible since we compute directly on the original system, as opposed to the automata-based approach commonly used for linear temporal logic. We give simulation results for representative motion planning tasks and compare to generalized reactivity(1).  +
In this paper we use ellipsoidal cones to achieve rendezvous of multiple agents. Rendezvous of multiple agents is shown to be equivalent to ellipsoidal cone invariance and a controller synthesis framework is presented. We first demonstrate the methodology on first order LTI systems and then extend it to rendezvous of mechanical systems, that is systems that are force driven.  +
Reinforcement Learning (RL) algorithms have found limited success beyond simulated applications, and one main reason is the absence of safety guarantees during the learning process. Real world systems would realistically fail or break be- fore an optimal controller can be learned. To address this issue, we propose a controller architecture that combines (1) a model-free RL-based controller with (2) model-based controllers utilizing control barrier functions (CBFs) and (3) on- line learning of the unknown system dynamics, in order to ensure safety during learning. Our general framework lever- ages the success of RL algorithms to learn high-performance controllers, while the CBF-based controllers both guarantee safety and guide the learning process by constraining the set of explorable polices. We utilize Gaussian Processes (GPs) to model the system dynamics and its uncertainties. Our novel controller synthesis algorithm, RL-CBF, guaran- tees safety with high probability during the learning process, regardless of the RL algorithm used, and demonstrates greater policy exploration efficiency. We test our algorithm on (1) control of an inverted pendulum and (2) autonomous car-following with wireless vehicle-to-vehicle communication, and show that our algorithm attains much greater sample efficiency in learning than other state-of-the-art algorithms and maintains safety during the entire learning process.  +
The mammalian gut contains trillions of microbes that interact with host cells and monitor changes in the environment. Opportunistic pathogens exploit environmental conditions to stimulate their growth and virulence, leading to a resurgence of chronic disorders such as inflammatory bowel disease (IBD). Current therapies are effective in less than 30% of patients due to the lack of adherence to prescription schedules and overall, off-target effects. Smart microbial therapeutics can be engineered to colonize the gut, providing in situ surveillance and conditional disease modulation. However, many current engineered microbes can only respond to single gut environmental factors, limiting their effectiveness. In this work, we implement the previously characterized split activator AND logic gate in the probiotic E. coli strain Nissle 1917. Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, IPTG. We report 4-6 fold induction with minimal leak when both signals are present. We model the dynamics of the AND gate using chemical reaction networks, and by tuning parameters in silico, we identified perturbations that affect our circuit's selectivity. We anticipate that our results will prove useful for designing living therapeutics for spatial targeting and signal processing in complex environments.  +
In this paper, we analyze the oscillatory dynamics of a class of cyclic gene regulatory networks and provide engineering principles for the robust synthesis of biochemical oscillators. We first review the first authorâs previous result that the oscillatory parameter regime of the gene regulatory circuits can be rigorously explored by the local stability analysis of a unique equilibrium. The local stability analysis then leads to the first engineering principle that the circuit components, or genes, should be chosen so that the kinetic profiles of the circuit components are similar to each other. Using a homogeneous oscillator model, we further discuss how to reduce the cell-to-cell variability of the oscillators that is caused by intrinsic noise.  +
The pursuit of circuits and metabolic pathways of increasing complexity and robustness in synthetic biology will require engineering new regulatory tools. Feedback control based on relevant molecules, including toxic intermediates and environmental signals, would enable genetic circuits to react appropriately to changing conditions. In this work, computational protein design was used to create functional variants of qacR, a tetR family repressor, responsive to a new targeted effector. The modified repressors target vanillin, a growth-inhibiting small molecule found in lignocellulosic hydrolysates and other industrial processes. A computatio ally designed library was screened using an in vitro transcription-translation (TX-TL) system. Leads from the in vitro screen were characterized in vivo. Preliminary results demonstrate dose-dependent regulation of a downstream fluorescent reporter by vanillin. These repressor designs provide a starting point for the evolution of improved variants. We believe this process can serve as a framework for designing new sensors for other target compounds.  +
The pursuit of circuits and metabolic pathways of increasing complexity and robustness in synthetic biology will require engineering new regulatory tools. Feedback control based on relevant molecules, including toxic intermediates and environmental signals, would enable genetic circuits to react appropriately to changing conditions. In this work, variants of qacR, a tetR family repressor, were generated by computational protein design and screened in a cell-free transcription-translation (TX-TL) system for responsiveness to a new targeted effector. The modified repressors target vanillin, a growth-inhibiting small molecule found in lignocellulosic hydrolysates and other industrial processes. Promising candidates from the in vitro screen were further characterized in vitro and in vivo in a gene circuit. The screen yielded two qacR mutants that respond to vanillin both in vitro and in vivo. While the mutants exhibit some toxicity to cells, presumably due to off-target effects, they are prime starting points for directed evolution toward vanillin sensors with the specifications required for use in a dynamic control loop. We believe this process, a combination of the generation of variants coupled with in vitro screening, can serve as a framework for designing new sensors for other target compounds.  +
The pursuit of circuits and metabolic pathways of increasing complexity and robustness in synthetic biology will require engineering new regulatory tools. Feedback control based on relevant molecules, including toxic intermediates and environmental signals, would enable genetic circuits to react appropriately to changing conditions. In this work, variants of qacR, a tetR family repressor, were generated by compu- tational protein design and screened in a cell-free transcription-translation (TX-TL) system for responsiveness to a new targeted effector. The modified repressors target vanillin, a growth-inhibiting small molecule found in lignocellulosic hydrolysates and other industrial processes. Promising candidates from the in vitro screen were further characterized in vitro and in vivo in a gene circuit. The screen yielded two qacR mutants that respond to vanillin both in vitro and in vivo. We believe this process, a combination of the generation of variants coupled with in vitro screening, can serve as a framework for designing new sensors for other target compounds.  +
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.  +
When used as part of a hybrid controller, finite-memory strategies synthesized from linear-time temporal logic (LTL) specifications rely on an accurate dynamics model in order to ensure correctness of trajectories. In the presence of uncertainty about the underlying model, there may exist unexpected trajectories that manifest as unexpected transitions under control of the strategy. While some disturbances can be captured by augment- ing the dynamics model, such approaches may be con- servative in that bisimulations may fail to exist for which strategies can be synthesized. In this paper, we consider games of the GR(1) fragment of LTL, and we character- ize the tolerance of hybrid controllers to perturbations that appear as unexpected jumps (transitions) to states in the discrete strategy part of the controller. As a first step, we show robustness to certain unexpected transi- tions that occur in a finite manner, i.e., despite a certain number of unexpected jumps, the sequence of states ob- tained will still meet a stricter specification and hence the original specification. Additionally, we propose al- gorithms to improve robustness by increasing tolerance to additional disturbances. A robot gridworld example is presented to demonstrate the application of the de- veloped ideas and also to perform empirical analysis.  +
We define a notion of controllability for mechanical systems which determines the configurations which are accessible from a given configuration. We derive sufficient conditions for this notion of controllability in terms of the given inputs, their Lie brackets, and their covariant derivatives.  +
In this paper we consider a state estimation problem over a wireless sensor network. A fusion center dynamically forms a local multi-hop tree of sensors and fuses the data into a state estimate. It is shown that the optimal estimator over a sensor tree is given by a Kalman filter of certain structure. Using estimation quality as a metric, two communication schemes are studied and compared. In scheme one, sensor nodes communicate measurement data to their parent nodes, while in scheme two, sensor nodes communicate their local state estimates to their parent nodes. We show that under perfect communication links, the two schemes produce the same estimate at the fusion center with unlimited computation at each sensor node; scheme one is always better than scheme two with limited computation. When data packet drops occur on the communication links, we show that scheme two always outperforms scheme one with unlimited computation; with limited computation, we show that there exists a critical packet arrival rate, above which, scheme one outperforms scheme two. Simulations are provided to demonstrate the two schemes under various circumstances.  +
This paper considers the problem of estimation over communication networks. Suppose a sensor is taking measurements of a dynamic process. However the process needs to be estimated at a remote location connected to the sensor through a network of communication links that drop packets stochastically. We provide a framework for computing the optimal performance in the sense of expected error covariance. Using this framework we characterize the dependency of the performance on the topology of the network and the packet dropping process. For independent and memoryless packet dropping processes we find the steady-state error for some classes of networks and obtain lower and upper bounds for the performance of a general network. We also illustrate how this framework can be used in the synthesis of networks for the purpose of estimation. Finally we find a necessary and sufficient condition for the stability of the estimate error covariance for general networks with spatially correlated and Markov type dropping process. This interesting condition has a max-cut interpretation.  +
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.....  +
In this paper, we consider a discrete time state estimation problem over a packet-based network. In each discrete time step, the measurement is sent to a Kalman filter with some probability that it is received or dropped. Previous pioneering work on Kalman filtering with intermittent observation losses shows that there exists a certain threshold of the packet dropping rate below which the estimator is stable in the expected sense. In their analysis, they assume that packets are dropped independently between all time steps. However we give a completely different point of view. On the one hand, it is not required that the packets are dropped independently but just that the information gain pi_g, defined to be the limit of the ratio of the number of received packets n during N time steps as N goes to infinity, exists. On the other hand, we show that for any given pi_g, as long as pi_g > 0, the estimator is stable almost surely, i.e. for any given epsilon > 0 the error covariance matrix P{k is bounded by a finite matrix M, with probability 1 â epsilon. Given an error tolerance M, pi_g can in turn be found. We also give explicit formula for the relationship between M and epsilon.  +
This paper studies the evaluation of learning- based object detection models in conjunction with model-checking of formal specifications defined on an abstract model of an autonomous system and its environment. In particular, we define two metrics – proposition-labeled and class-labeled confusion matrices – for evaluating object detection, and we incorporate these metrics to compute the satisfaction probability of system-level safety requirements. While confusion matrices have been effective for comparative evaluation of classification and object detection models, our framework fills two key gaps. First, we relate the performance of object detection to formal requirements defined over downstream high-level planning tasks. In particular, we provide empirical results that show that the choice of a good object detection algorithm, with respect to formal requirements on the overall system, significantly depends on the downstream planning and control design. Secondly, unlike the traditional confusion matrix, our metrics account for variations in performance with respect to the distance between the ego and the object being detected. We demonstrate this framework on a car-pedestrian example by computing the satisfaction probabilities for safety requirements formalized in Linear Temporal Logic (LTL).  +
In this paper we evaluate the actuator rate requirements for control of rotating stall using a bleed valve and provide tools for predicting these requirements. Modification of both the stable and unstable parts of the compressor characteristic via addition of continuous air injection serves to reduce the requirement of a bleed valve used for the purpose of rotating stall stabilization. Analytical tools based on low order models (2-3 states) and simulation tools based on a reduced order model (37 states) are described. A bleed actuator rate limit study is presented to compare the actuator requirements predicted by theory, simulation, and experiment. The comparisons show that the predictions obtained from theory and simulations share the same trend as the experiments, with increasing accuracy as the complexity of the underlying model increases. Some insights on the design of a bleed-compressor pair are given.  +
This paper provides analytical results regarding the stability of linear discrete-time systems with stochastic delays. Necessary and sufficient stability conditions are derived by using the second moment dynamics which can be used to draw stability charts. The results are applied to a simple connected vehicle system where the stability regions are com- pared to those given by the mean dynamics. Our results reveal some fundamental limitations of connected cruise control which becomes more significant as the packet drop ratio increases.  +
In this paper, a cascade discrete-continuous state estimator on a partial order is proposed and its existence investigated. The continuous state estimation error is bounded by a monotonically nonincreasing function of the discrete state estimation error, with both the estimation errors converging to zero. This work shows that the lattice approach to estimation is general as the proposed estimator can be constructed for any observable and discrete state observable system. The main advantage of using the lattice approach for estimation becomes clear when the system has monotone properties that can be exploited in the estimator design. In such a case, the computational complexity of the estimator can be drastically reduced and tractability can be achieved. Some examples are proposed to illustrate these ideas.  +
In this paper various design techniques are applied to the trajectory tracking problem for a mobile robot with trailers. Using simulations and experiments, we evaluate linear and nonlinear designs on the basis of implementation issues, stability and performance. After a careful design of their gains, the various feedback controllers have very close performance measures. In both the simulations and the experiments, all the controllers show a strong dependence on the knowledge of the reference trajectory. The flatness of the system is exploited in precomputing this quantity.  +
The motion of microorganisms as well as of tiny robotic swimmers for biomedical applications is governed by low Reynolds number (Re) hydrodynamics, where viscous effects dominate and inertial effects are negligible. This paper presents experimental results that verify theoretical predictions of our recent work which analyzed the dynamics and stability of a low-Re swimmer near a plane wall. The experimental setup uses macro-scale swimmer prototypes which are propelled by rotating cylinders in highly viscous silicone oil. The motion was recorded by a video camera and position measurements were taken by an optical tracking system. The results show good qualitative agreement with our recent theoretical predictions.  +
This paper presents an experimental investigation of the effects of air injection on the rotating stall instability in a low speed axial compressor. Two experiments concerning air injection were tried. The first experiment used a continuous forcing perpendicular to the flow in the same or opposite direction of the tip velocity. The results show a dramatic difference between the two directions, with opposite direction forcing causing a significant increase in performance, and same direction forcing causing a significant decrease in performance. This result contradicts the Emmons stall propagation model. The second experiment investigated the differences with respect to different frequencies of air injection, with the injector pointed at the fan, parallel to the flow. We found that the change in the compressor characteristic in the unstalled region was highly dependent upon the forcing frequency with the maximum change occurring near the frequency of stall.  +
In this paper we apply some recently developed control laws for stabilization of mechanical systems with nonholonomic constraints to an experimental system consisting of a mobile robot towing a trailer. We verify the applicability of various control laws which have appeared in the recent literature, and compare the performance of these controllers in an experimental setting. In particular, we show that time-periodic, non-smooth controllers can be used to achieve exponential stability of a desired equilibrium configuration, and that these controllers outperform smooth, time-varying control laws. We also point out several practical considerations which must be taken into account when implementing these controllers.  +
Many algorithms have been proposed in the literature for control of multi-fingered robot hands. This paper compares the performance of several of these algorithms, as well as some extensions of more conventional manipulator control laws, in the case of planar grasping. A brief introduction to the subject of robot hands and the notation used in this paper is included.  +
This dissertation lays the foundation for practical exponential stabilization of driftless control systems. Driftless systems have the form $$\dot x = X_1(x)u_1+\cdots +X_m(x)u_m, \quad x\in\real^n$$. Such systems arise when modeling mechanical systems with nonholonomic constraints. In engineering applications it is often required to maintain the mechanical system around a desired configuration. This task is treated as a stabilization problem where the desired configuration is made an asymptotically stable equilibrium point. The control design is carried out on an approximate system. The approximation process yields a nilpotent set of input vector fields which, in a special coordinate system, are homogeneous with respect to a non-standard dilation. Even though the approximation can be given a coordinate-free interpretation, the homogeneous structure is useful to exploit: the feedbacks are required to be homogeneous functions and thus preserve the homogeneous structure in the closed-loop system. The stability achieved is called {\em $\rho$-exponential stability}. The closed-loop system is stable and the equilibrium point is exponentially attractive. This extended notion of exponential stability is required since the feedback, and hence the closed-loop system, is not Lipschitz. However, it is shown that the convergence rate of a Lipschitz closed-loop driftless system cannot be bounded by an exponential envelope. <p> The synthesis methods generate feedbacks which are smooth on \rminus. The solutions of the closed-loop system are proven to be unique in this case. In addition, the control inputs for many driftless systems are velocities. For this class of systems it is more appropriate for the control law to specify actuator forces instead of velocities. We have extended the kinematic velocity controllers to controllers which command forces and still $\rho$-exponentially stabilize the system. <p> Perhaps the ultimate justification of the methods proposed in this thesis are the experimental results. The experiments demonstrate the superior convergence performance of the $\rho$-exponential stabilizers versus traditional smooth feedbacks. The experiments also highlight the importance of transformation conditioning in the feedbacks. Other design issues, such as scaling the measured states to eliminate hunting, are discussed. The methods in this thesis bring the practical control of strongly nonlinear systems one step closer. <p>  
This paper brings together results from a number of different areas in control theory to provide an algorithm for the synthesis of locally exponentially stabilizing control laws for a large class of driftless nonlinear control systems. The exponential stabilization relies on the use of feedbacks which render the closed loop vector field homogeneous with respect to a dilation. These feedbacks are generated from a modification of Pomet's algorithm for smooth feedbacks. Converse Liapunov theorems for time-periodic homogeneous vector fields guarantee that local exponential stability is maintained in the presence of higher order (with respect to the dilation) perturbing terms. <p>  +
This paper describes an approach for extending (time-varying) exponential stabilizers for nonholonomic systems from controllers which command input velocity to controllers which command input torques. Due to the nondifferentiable nature of exponential stablizers, additional structure is required in order to ensure that the extended controllers generate continuous control actions. In this paper we show how to extend homogeneous controllers which use a nonstandard dilation adapted to the problem.  +
We describe the structure of connected graphs with the minimum and maximum average distance, radius, diameter, betweenness centrality, efficiency and resistance distance, given their order and size. We find tight bounds on these graph qualities for any arbitrary number of nodes and edges and analytically derive the form and properties of such networks.  +
Fault tolerance and safety verification of control systems that have state estimation uncertainty are essential for the success of autonomous robotic systems. A software control architecture called Mission Data System, developed at the Jet Propulsion Laboratory, uses goal networks as the control program for autonomous systems. Certain types of goal networks can be converted into linear hybrid systems and verified for safety using existing symbolic model checking software. A process for calculating the probability of failure of some verifiable goal networks due to state estimation uncertainty is presented. Extensions of this procedure to include other types of uncertainties are discussed, and example problems are presented to illustrate these procedures.  +
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.  +
Modern safety-critical systems are difficult to formally verify, largely due to their large scale. In particular, the widespread use of lookup tables in embedded systems across diverse industries, such as aeronautics and automotive systems, create a critical obstacle to the scala- bility of formal verification. This paper presents a novel approach for the formal verification of large-scale systems with lookup tables. We use a learning-based technique to automatically learn abstractions of the lookup tables and use the abstractions to then prove the desired property. If the verification fails, we propose a falsification heuristic to search for a violation of the specification. In contrast with previous work on lookup table verification, our technique is completely automatic, making it ideal for deployment in a production environment. To our knowledge, our approach is the only technique that can automatically verify large-scale systems lookup with tables. We illustrate the effectiveness of our technique on a benchmark which cannot be handled by the commer- cial tool SLDV, and we demonstrate the performance improvement provided by our technique.  +
Aircraft operate in different modes during flight, corresponding to different flight conditions and control schemes. We use differential flatness of an approximate model of the pitch dynamics of a thrust vectored aircraft to achieve fast switching between those modes. We investigate some methods to compensate for the perturbations to flatness. Simulations and experimental data are provided to validate the approach.  +
In systems and synthetic biology, it is common to build chemical reaction network (CRN) models of biochemical circuits and networks. Although automation and other high-throughput techniques have led to an abundance of data enabling data-driven quantitative modeling and parameter estimation, the intense amount of simulation needed for these methods still frequently results in a computational bottleneck. Here we present bioscrape (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation) - a Python package for fast and flexible modeling and simulation of highly customizable chemical reaction networks. Specifically, bioscrape supports deterministic and stochastic simulations, which can incorporate delay, cell growth, and cell division. All functionalities - reaction models, simulation algorithms, cell growth models, and partioning models - are implemented as interfaces in an easily extensible and modular object-oriented framework. Models can be constructed via Systems Biology Markup Language (SBML), a simple internal XML language, or specified programmatically via a Python API. Simulation run times obtained with the package are comparable to those obtained using C code - this is particularly advantageous for computationally expensive applications such as Bayesian inference or simulation of cell lineages. We first show the package’s simulation capabilities on a variety of example simulations of stochastic gene expression. We then further demonstrate the package by using it to do parameter inference on a model of integrase enzyme-mediated DNA recombination dynamics with experimental data. The bioscrape package is publicly available online ( along with more detailed documentation and examples.  +
One of the challenges in designing the next genera- tion of robots operating in non-engineered environments is that there seems to be an infinite amount of causes that make the sensor data unreliable or actuators ineffective. In this paper, we discuss what faults are possible to detect using zero modeling effort: we start from uninterpreted streams of observations and commands, and without a prior knowledge of a model of the world. We show that in sensorimotor cascades it is possible to define static faults independently of a nominal model. We define an information-theoretic usefulness of a sensor reading and we show that it captures several kind of sensorimotor faults frequently encountered in practice. We particularize these ideas to the case of BDS/BGDS models, proposed in previous work as suitable candidates for describing generic sensorimotor cascades. We show several examples with camera and range-finder data, and we discuss a possible way to integrate these techniques in an existing robot software architecture.  +
This paper deals with fault-tolerant controller design for linear time-invariant (LTI) systems with multiple actuators. Given some critical subsets of the actuators, it is assumed that every combination of actuators can fail as long as the set of the remaining actuators includes one of these subsets. Motivated by electric power systems and biological systems, the goal is to design a controller so that the closed-loop system satisfies two properties: (i) stability under all permissible sets of faults and (ii) better performance after clearing every subset of the existing faults in the system. It is shown that a state-feedback controller satisfying these properties exists if and only if a linear matrix inequality (LMI) problem is feasible. This LMI condition is then transformed into an optimal-control condition, which has a useful interpretation. The results are also generalized to output-feedback and decentralized control cases. The efficacy of this work is demonstrated by designing fault-tolerant speed governors for a power system. The results developed here can be extended to more general types of faults, where each fault can possibly affect all state-space matrices of the system.  +
This paper proposes a method to determine trajectories of dynamic systems that steer between two end points while satisfying linear inequality constraints arising from limits on states and inputs. The method exploits the structure of the dynamic system written in a higher-order form to explicitly eliminate the state equations. The feasible trajectories of the dynamic system are sought within a characterization with a finite sum of mode functions. In this paper, the linear inequalities on inputs and states are replaced by a finite set of linear inequalities on the mode coefficients. This step changes the problem of trajectory generation into finding a convex polytope enclosed by the linear inequalities on the mode coefficients. A procedure is then developed to efficiently find the vertices of this bounding polytope. It is demonstrated in this paper that this method can generate feasible trajectories of the system in real-time and can quickly update the trajectories as the terminal conditions are changed. The procedure is demonstrated numerically by two examples. The results of one of the examples is implemented in hardware to explore the issues of real-time planning and control.  +
In this paper we consider nonlinear systems with steady-state or Hopf bifurcations for which the bifurcated modes are linearly uncontrollable. The goal is to find state feedbacks such that the bifurcation for the closed loop system is supercritical, and at the same time, the linearly controllable subsystem is asymptotically stable. Necessary and sufficient conditions for the non-existence of sufficiently smooth state feedbacks have been obtained under certain nondegeneracy conditions. For the cases when those conditions are not satisfied, we give explicit constructions of the feedbacks. The construction has the following separation property: for any linear state feedback such that the controllable subsystem is asymptotically stable, we could construct gains in the nonlinear state feedbacks such that the closed loop system is asymptotically stable at the bifurcation point.  +
Classification of stabilizability is obtained for multi-input nonlinear systems possessing a simple steady-state or Hopf bifurcation with the critical mode being linearly uncontrollable. Stabilizability is defined as the existence of a sufficiently smooth state feedback such that the bifurcation for the closed loop system is supercritical, and in the meantime, the linearly controllable modes are locally asymptotically stable. Necessary and sufficient conditions of stabilizability are derived under certain nondegeneracy conditions. Explicit construction of stabilizing feedbacks is obtained for the cases when the system is stabilizable.  +
This paper focuses on RNA flux regulation for in vitro synthetic gene networks and considers architectures that can be scaled to an arbitrary number of species. Feedback loops are designed based on negative autoâregulation (which can minimize the potentially harmful amount of molecules not used to form useful products) and crossâactivation (which can maximize the overall output flux): transcription rate matching can be achieved through proper feedback constants; negative feedback is faster and maintains stability. A possible experimen- tal implementation of a three and four genes negative feedback architecture is also numerically studied.  +
Noise is indispensible to key cellular activities, including gene expression coordination and probabilistic differentiation. Stochastic models, such as the chemical master equation (CME), are essential to model noise in the levels of cellular components. In the CME framework, each state is associated with the molecular counts of all component species, and specifies the probability for the system to have that set of molecular counts. Analytic solutions to the CME are rarely known but can bring exciting benefits. For instance, simulations of biochemical reaction networks that are multiscale in time can be sped up tremendously by incorporating analytic solutions of the slow time-scale dynamics. Ana- lytic solutions also enable the design of stationary distributions with properties such as the modality of the distribution, the mean expression level, and the level of noise. One way to derive the analytic steady state response of a biochemical reaction network was re- cently proposed by (Mélykúti et al. 2014). The paper recursively glues simple state spaces together, for which we have analytic solutions, at one or two states. <p> In this work, we explore the benefits and limitations of the gluing technique proposed by Mélykúti et al., and introduce recursive algorithms that use the technique to solve for the analytic steady state response of stochastic biochemical reaction networks. We give formal characterizations of the set of reaction networks whose state spaces can be obtained by carrying out single-point gluing of paths, cycles or both sequentially. We find that the dimension of the state space of a reaction network equals the maximum number of linearly independent reactions in the system. We then characterize the complete set of stochastic biochemical reaction networks that have elementary reactions and two-dimensional state spaces. As an example, we propose a recursive algorithm that uses the gluing technique to solve for the steady state response of a mass-conserving system with two connected monomolecular reversible reactions. Even though the gluing technique can only construct finite state spaces, we find that, by taking the size of a finite state space to infinity, the steady state response can converge to the analytic solution on the resulting infinite state space. Finally, we illustrate the aforementioned ideas with the example of two interconnected transcriptional components, which was first studied by (Ghaemi and Del Vecchio 2012).  
In this paper, we consider the optimal control of time-scalable systems. The time-scaling property is shown to convert the PDE associated with the Hamilton-Jacobi-Bellman (HJB) equation to a purely spatial PDE. Solution of this PDE yields the value function at a fixed time, and that solutio n can be scaled to find the value function at any point in time. Furthermore, in certain cases the unscaled control law stabilizes the system, and the unscaled value function acts as a Lyapunov function for that system. For the example of the nonholonomic integrator, this PDE is solved, and the resulting optimal trajectories coincide with the known solution to that problem.  +
Flat systems, an important subclass of nonlinear control systems introduced via differential-algebraic methods, are defined in a differential geometric framework. We utilize the infinite dimensional geometry developed by Vinogradov and coworkers: a control system is a diffiety, or more precisely, an ordinary diffiety, i.e. a smooth infinite-dimensional manifold equipped with a privileged vector field. After recalling the definition of a Lie-Backlund mapping, we say that two systems are equivalent if they are related by a Lie-Backlund isomorphism. Flat systems are those systems which are equivalent to a controllable linear one. The interest of such an abstract setting relies mainly on the fact that the above system equivalence is interpreted in terms of endogenous dynamic feedback. The presentation is as elementary as possible and illustrated by the VTOL aircraft.  +
A feedback controller closes the loop from vision to wing motion to stabilize forward flight in a simulation of Drosophila Melanogaster.  +
We have approached the problem of reverse engineering the flight control mechanism of the fruit fly by studying the dynamics of the responses to a visual stimulus during takeoff. Building upon a prior framework we seek to understand the strategies employed by the animal to stabilize attitude and orientation during these evasive, highly dynamical maneuvers. As a first step, we consider the dynamics from a gray-box perspective: examining lumped forces produced by the insect's legs and wings. The reconstruction of the flight initiation dynamics, based on the unconstrained motion formulation for a rigid body, allows us to assess the fly's responses to a variety of initial conditions induced by its jump. Such assessment permits refinement by using a visual tracking algorithm to extract the kinematic envelope of the wings in order to estimate lift and drag forces, and recording actual leg-joint kinematics and using them to estimate jump forces. In this paper we present the details of our approach in a comprehensive manner including the salient results.  +
The prolific rise in autonomous systems has led to questions regarding their safe instantiation in real-world scenarios. Failures in safety-critical contexts such as human-robot interactions or even autonomous driving can ultimately lead to loss of life. In this context, this paper aims to provide a method by which one can algorithmically test and evaluate an autonomous system. Given a black-box autonomous system with some operational specifications, we construct a minimax problem based on control barrier functions to generate a family of test parameters designed to optimally evaluate whether the system can satisfy the specifications. To illustrate our results, we utilize the Robotarium as a case study for an autonomous system that claims to satisfy waypoint navigation and obstacle avoidance simultaneously. We demonstrate that the proposed test synthesis framework systematically finds those sequences of events (tests) that identify points of system failure.  +
Model checking is a widely used technique for formal verification of distributed systems. It works by effectively examining the complete reachable state space of a model in order to determine whether the system satisfies its requirements or desired properties. The complexity of an autonomous vehicle system, however, renders model checking of the entire system infeasible due to the state explosion problem. In this paper, we illustrate how to exploit the structure of the system to systematically decompose the overall system-level requirements into a set of component-level requirements. Each of the components can then be model checked separately. A case study is presented where we formally verify the state consistency between different software modules of Alice, an autonomous vehicle developed by the California Institute of Technology for the 2007 DARPA Urban Challenge.  +
In this paper, we generalize a recently proposed method for model reduction of linear systems to the frequencyweighted case. The method uses convex optimization and can be used both with sample data and exact models. We also derive simple a priori bounds on the frequency-weighted error. We combine the method with a rank-minimization heuristic, to approximate multi-inputÂmulti-output systems. We also present two applications  environment compensation and simpli�cation of interconnected models  where we argue the proposed methods are useful.  +
We provide a new perspective on using formal methods to model specifications and synthesize implementations for the design of biological circuits. In synthetic biology, design objectives are rarely described formally. We present an assume-guarantee contract framework to describe biological circuit design objectives as formal specifications. In our approach, these formal specifications are implemented by circuits modeled by ordinary differential equations, yielding a design framework that can be used to design complex synthetic biological circuits at scale. We describe our approach using the design of a biological AND gate as a motivating, running example.  +
The field of control provides the principles and methods used to design physical and information systems that maintain desirable performance by sensing and automatically adapting to changes in the environment. As we begin the 21st Century, the opportunities to apply control principles and methods are exploding. New developments in this increasingly information rich world will require a significant expansion of the basic tool sets of control. This article summarizes the main findings and recommendations of the Panel on Future Directions in Control, Dynamics, and Systems, which has recently released its report. The report spells out some of the prospects for control in the current and future technological environment, describes the role the field will play in military, commercial, and scientific applications over the next decade, and recommends actions required to enable new breakthroughs in engineering and technology through application of control research.  +
This paper summarizes the findings and recommendations of a recent panel on Future Directions in Control, Dynamics, and Systems, sponsored by the US Air Force Office of Scientific Research. A set of grand challenges that illustrate some of the recommendations and opportunities are provided. Finally, the paper describes two new courses being developed at Caltech that are aligned with the recommendations of the report.  +
This paper gives a survey of some recent results on control of systems with magnitude and rate limits, motivated by problems in real-time trajectory generation and tracking for unmanned aerial vehicles. Two problems are considered: stabilization using ``nonlinear wrappers'' to rescale a given control law and real-time trajectory generation using differential flatness. For both problems, simplified versions of the general problem are studied using tools from differential geometry and nonlinear control to give insights into the limitations imposed by magnitude and rate limits and provide insights into constructive solutions to the trajectory generation and tracking problems.  +
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.  +
Robotic locomotion is based in a variety of instances upon cyclic changes in the shape of a robot mechanism. Certain variations in shape exploit the constrained nature of a robot's interaction with its environment to generate net motion. This is true for legged robots, snakelike robots, and wheeled mobile robots undertaking maneuvers such as parallel parking. In this paper we explore the use of tools from differential geometry to model and analyze this class of locomotion mechanisms in a unified way. In particular, we describe locomotion in terms of the geometric phase associated with a connection on a principal bundle, and address issues such as controllability and choice of gait. We also provide an introduction to the basic mathematical concepts which we require and apply the theory to numerous example systems.  +
Differential geometry and nonlinear control theory provide essential tools for studying motion generation in robot systems. Two areas where progress is being made are motion planning for mobile robots on the factory floor (or on the surface of Mars), and control of highly articulated robots---such as multifingered robot hands and robot ``snakes''---for medical inspection and manipulation inside the gastrointestinal tract. A common feature of these systems is the role of constraints on the behavior of the system. Typically, these constraints force the instantaneous velocities of the system to lie in a restricted set of directions, but do not actually restrict the reachable configurations of the system. A familiar example in which this geometric structure can be exploited is parallel parking of an automobile, where periodic motion in the driving speed and steering angle can be used to achieve a net sideways motion. By studying the geometric nature of velocity constraints in a more general setting, it is possible to synthesize gaits for snake-like robots, generate parking and docking maneuvers for automated vehicles, and study the effects of rolling contacts on multifingered robot hands. As in parallel parking, rectification of periodic motions in the control variables plays a central role in the techniques which are used to generation motion in this broad class of robot systems.  +
The paper studies the problem which we refer to as geometric trajectory filtering, where only trajectories that satisfy the local safety constraints are selected from a library of trajectories. The goal is to speed up primitive-based motion planning while still maintaining a relatively a large collection of motion primitives. One way to solve this problem is to obtain a proper (preferably smooth) function, referred to as the containment indicator function, that describes the shape of the free space. To construct the containment indicator function for an arbitrary shape, the paper uses conformal mapping to transform the original shape of interest to a simpler target shape (e.g. disk, rectangle), which can then be characterized by elementary functions. Computational methods for finding the desired conformal maps are studied. It is shown that they can be formulated as convex optimization problems, whose solution can be obtained efficiently.  +
In this paper we consider the problem of network reconstruction, with applications to biochemical reaction networks. In particular, we consider the problem of global network reconstruction when there are a limited number of sensors that can be used to simultaneously measure state information. We introduce dynamical structure functions as a way to formulate the network reconstruction problem and motivate their usage with an example physical system from synthetic biology. In particular, we argue that in synthetic biology research, network verification is paramount to robust circuit operation and thus, network reconstruction is an invaluable tool. Nonetheless, we argue that existing approaches for reconstruction are hampered by limited numbers of biological sensors with high temporal resolution. In this way, we motivate the global network reconstruction problem using partial network information and prove that by performing a series of reconstruction experiments, where each experiment reconstructs a subnetwork dynamical structure function, the global dynamical structure function can be recovered in most cases. We illustrate these reconstruction techniques on a recently developed four gene biocircuit, an event detector, and show that it is capable of differentiating the temporal order of input events.  +
Control of vehicle formations has emerged as a topic of significant interest to the controls community. In this paper, we merge tools from graph theory and control theory to derive stability criteria for formation stabilization. The interconnection between vehicles (i.e., which vehicles are sensed by other vehicles) is modeled as a graph, and the eigenvalues of the Laplacian matrix of the graph are used in stating a Nyquist-like stability criterion for vehicle formations. The location of the Laplacian eigenvalues can be correlated to the graph structure, and therefore used to identify desirable and undesirable formation interconnection topologies.  +
Grasping with flexible fingers presents an attractive approach for certain robotic tasks. Its implementation requires simultaneous position and force control of flexible manipulators, an area about which there is little information in the literature. This paper presents an initial effort at designing controllers for flexible link robots to control both position and force. The analysis is done on a two degree-of-freedom two-link manipulator with the last link flexible. A control strategy is proposed and asymptotic stability is proved. Results from using this control law in simulations and on an experimental setup are presented.  +
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.  +
Feedback regulation is pervasive in biology at both the organismal and cellular level. In this article, we explore the properties of a particular biomolecular feedback mechanism implemented using the sequestration binding of two molecules. Our work develops an analytic framework for understanding the hard limits, performance tradeoffs, and architectural properties of this simple model of biological feedback control. Using tools from control theory, we show that there are simple parametric relationships that determine both the stability and the performance of these systems in terms of speed, robustness, steady-state error, and leakiness. These findings yield a holistic understanding of the behavior of sequestration feedback and contribute to a more general theory of biological control systems.  +
We propose a method for eliminating variables from component specifications during the decomposition of GR(1) properties into contracts. The variables that can be eliminated are identified by parameterizing the communication architecture to investigate the dependence of realizability on the availability of information. We prove that the selected variables can be hidden from other components, while still expressing the resulting specification as a game with full information with respect to the remaining variables. The values of other variables need not be known all the time, so we hide them for part of the time, thus reducing the amount of information that needs to be communicated between components. We improve on our previous results on algorithmic decomposition of GR(1) properties, and prove existence of decompositions in the full information case. We use semantic methods of computation based on binary decision diagrams. To recover the constructed specifications so that humans can read them, we implement exact symbolic minimal covering over the lattice of integer orthotopes, thus deriving minimal formulae in disjunctive normal form over integer variable intervals.  +
We consider the problem of synthesizing robot controllers to realize a task that unpredictably changes with time. Tasks are formally expressed in the GR(1) fragment of temporal logic, in which some of the variables are set by an adversary. The task changes by the addition or removal of goals, which occurs online (i.e., at run-time). We present an algorithm for mending control strategies to realize tasks after the addition of goals, while avoiding global re-synthesis of the strategy. Experiments are presented for a planar surveillance task in which new regions of interest are incrementally added. Run-times are empirically shown to be extremely favorable compared to re-synthesizing from scratch. We also present an algorithm for mending control strategies for the removal of goals. While in this setting the original strategy is still feasible (as we prove), our algorithm provides a more satisfying solution by âtightening loose ends.â Both algorithms are shown to yield so-called reach annotations, and thus the control strategies are easily amenable to other algorithms concerning incremental synthesis, e.g., as in previous work by the authors for robot navigation in uncertain environments.  +
Biocircuit modeling sometimes requires explicit tracking of a self-replicating DNA species. The most obvious, straightforward way to model a replicating DNA is structurally unstable and leads to pathological model behavior. We describe a simple, stable replication mechanism with good model behavior and show how to derive it from a mechanistic model of ColE1 replication.  +