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Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor + (The pursuit of circuits and metabolic path … 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.ng new sensors for other target compounds.)
Engineering Transcriptional Regulator Effector Specificity Through Rational Design and Rapid Prototyping + (The pursuit of circuits and metabolic path … 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.ng new sensors for other target compounds.)
Timing molecular motion and production with a synthetic transcriptional clock + (The realization of artificial biochemical … The realization of artificial biochemical reaction networks with unique functionality is one of the main challenges for the development of synthetic biology. Due to the reduced number of components, biochemical circuits constructed in vitro promise to be more amenable to systematic design and quantitative assessment than circuits embedded within living organisms. To make good on that promise, effective methods for composing subsystems into larger systems are needed. Here we used an artificial biochemical oscillator based on in vitro transcription and RNA degradation reactions to drive a variety of âloadâ processes such as the operation of a DNA-based nanomechanical device (âDNA tweezersâ) or the production of a functional RNA molecule (an aptamer for malachite green). We implemented several mechanisms for coupling the load processes to the oscillator circuit and compared them based on how much the load affected the frequency and amplitude of the core oscillator, and how much of the load was effectively driven. Based on heuristic insights and computational modeling, an âinsulator circuitâ was developed, which strongly reduced the detrimental influence of the load on the oscillator circuit. Understanding how to design effective insulation between biochemical subsystems will be critical for the synthesis of larger and more complex systems.thesis of larger and more complex systems.)
Quantitative Modeling of Integrase Dynamics Using a Novel Python Toolbox for Parameter Inference in Synthetic Biology + (The recent abundance of high-throughput da … The recent abundance of high-throughput data for biological circuits enables data-driven quantitative modeling and parameter estimation. Common modeling issues include long computational times during parameter estimation, and the need for many iterations of this cycle to match data. Here, we present BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation) - a Python package for fast and flexible modeling and simulation for biological circuits. The BioSCRAPE package can be used for deterministic or stochastic simulations and can incorporate delayed reactions, cell growth, and cell division. 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 for a model of integrase dynamics using experimental data. The BioSCRAPE package is publicly available online along with more detailed documentation and examples. more detailed documentation and examples.)
Identification of Decision Rules in a Human-controlled System: Vehicles at a Traffic Intersection + (The rules that govern decision making in s … The rules that govern decision making in systemscontrolled by humans are often simple to describe. However,deriving these rules from the actions of a group can be verydifficult, making human behavior hard to predict. We developan algorithm to determine the rules implemented by driversat a traffic intersection by observing the trajectories of theircars. We applied such algorithm to a traffic intersection scenarioreproduced in the Caltech multi-vehicle lab, with human subjectsremotely driving kinematic robots. The results obtained on thesedata suggest that this kind of human behavior is to some extentpredictable on our data set, and different subjects implementsimilar rules.ifferent subjects implement similar rules.)
Nonlinear Control of Rotating Stall and Surge with Axisymmetric Bleed and Air Injection on Axial Flow Compressors + (The study of compressor instabilities in g … The study of compressor instabilities in gas turbine engines has receivedmuch attention in recent years. In particular, rotating stall and surgeare major causes of problems ranging from component stress and lifespanreduction to engine explosion. In this thesis, modeling and control ofrotating stall and surge using bleed valve and air injection is studied andvalidated on a low speed, single stage, axial compressor at Caltech.Bleed valve control of stall is achieved only when the compressorcharacteristic is actuated, due to the fast growth rate of the stall cellcompared to the rate limit of the valve. Furthermore, experimental resultsshow that the actuator rate requirement for stall control is reduced by afactor of fourteen via compressor characteristic actuation. Analyticalexpressions based on low order models (2--3 states) and a high fidelitysimulation (37 states) tool are developed to estimate the minimum raterequirement of a bleed valve for control of stall. A comparison of thetools to experiments show a good qualitative agreement, with increasingquantitative accuracy as the complexity of the underlying model increases.Air injection control of stall and surge is also investigated.Simultaneous control of stall and surge is achieved using axisymmetric airinjection. Three cases with different injector back pressure are studied.Surge control via binary air injection is achieved in all three cases.Simultaneous stall and surge control is achieved for two of the cases, butis not achieved for the lowest authority case. This is consistent withprevious results for control of stall with axisymmetric air injectionwithout a plenum attached.Non--axisymmetric air injection control of stall and surge is also studied.Three existing control algorithms found in literature are modeled andanalyzed. A three--state model is obtained for each algorithm. For twocases, conditions for linear stability and bifurcation criticality oncontrol of rotating stall are derived and expressed in terms ofimplementation--oriented variables such as number of injectors. For thethird case, bifurcation criticality conditions are not obtained due tocomplexity, though linear stability property is derived. A theoreticalcomparison between the three algorithms is made, via the use of low--ordermodels, to investigate pros and cons of the algorithms in the context ofoperability.The effects of static distortion on the compressor facility at Caltech ischaracterized experimentally. Results consistent with literature areobtained. Simulations via a high fidelity model (34 states) are alsoperformed and show good qualitative as well as quantitative agreement toexperiments. A non--axisymmetric pulsed air injection controller for stallis shown to be robust to static distortion.n controller for stall is shown to be robust to static distortion.)
Temporal Logic Control of POMDPs via Label-based Stochastic Simulation Relations + (The synthesis of controllers guaranteeing … The synthesis of controllers guaranteeing linear temporal logic specifications on partially observable Markov decision processes (POMDP) via their belief models causes computational issues due to the continuous spaces. In this work, we construct a finite-state abstraction on which a control policy is synthesized and refined back to the original belief model. We introduce a new notion of label- based approximate stochastic simulation to quantify the deviation between belief models. We develop a robust synthesis methodology that yields a lower bound on the satisfaction probability, by compensating for deviations a priori, and that utilizes a less conservative control refinement.es a less conservative control refinement.)
Real-time trajectory generation for constrained nonlinear dynamical systems using non-uniform rational B-spline basis functions + (The thesis describes a new method for obta … The thesis describes a new method for obtaining minimizers for optimal control problems whose minima serve as control policies for guiding nonlinear dynamical systems to achieve prescribed goals under imposed trajectory and actuator constraints. One of the major contributions of the present work resides in the approximation of such minimizers by piecewise polynomial functions expressed in terms of a linear combination of non-uniform rational B-spline (NURBS) basis functions and the judicious exploitation of the properties of the resulting NURBS curves to improve the computational effort often associated with solving optimal control problems for constrained dynamical systems. In particular, by exploiting the two structures combined in a NURBS curve, NURBS basis functions and an associated union of overlapping polytopes constructed from the coefficients of the linear combination, we are able to separate an optimal control problem into two subproblemstimal control problem into two subproblems)
Counter-example Guided Learning of Bounds on Environment Behavior + (There is a growing interest in building au … 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.euver given real-world human driving data.)
Modeling and Control of Epitaxial Thin Film Growth + (Thin ﬁlm deposition is a manufacturing pro … Thin ﬁlm deposition is a manufacturing process in which tolerances may approachthe size of individual atoms. The ﬁnal film is highly sensitive to the processingconditions, which can be intentionally manipulated to control film properties. Alattice model of surface evolution during thin film growth captures many importantfeatures, including the nucleation and growth of clusters of atoms and thepropagation of atomic-height steps. The dimension of this probabilistic masterequation is too large to directly simulate for any physically realistic domain, andinstead stochastic realizations of the lattice model are obtained with kinetic MonteCarlo simulations.In this thesis simpler representations of the master equation are developed foruse in analysis and control. The static map between macroscopic process conditionsand microscopic transition rates is ﬁrst analyzed. In the limit of fast periodicprocess parameters, the surface responds only to the mean transition rates, and,since the map between process parameters and transition rates is nonlinear, neweffective combinations of transition rates may be generated. These effective ratesare the convex hull of the set of instantaneous rates.The map between transition rates and expected film properties is also studied.The dimension of a master equation can be reduced by eliminating or groupingconﬁgurations, yielding a reduced-order master equation that approximates theoriginal one. A linear method for identifying the coefficients in a master equationis then developed, using only simulation data. These concepts are extended togenerate low-order master equations that approximate the dynamic behavior seenin large Monte Carlo simulations. The models are then used to compute optimaltime-varying process parameters.The thesis concludes with an experimental and modeling study of germaniumfilm growth, using molecular beam epitaxy and reflection high-energy electrondiffraction. Growth under continuous and pulsed flux is compared in experiment,and physical parameters for the lattice model are extracted. The pulsing accessiblein the experiment does not trigger a change in growth mode, which is consistentwith the Monte Carlo simulations. The simulations are then used to suggest othergrowth strategies to produce rougher or smoother surfaces.ce rougher or smoother surfaces.)
Reduction Strategies for Kinetic Monte Carlo Models of Thin Film Growth + (Thin film deposition encompasses a variety … Thin film deposition encompasses a variety of physical processes,which occur over a wide range of length and time scales. A major challenge in modeling and simulating thin film deposition is this disparityin scales. In this study we focus on an atomic-scale lattice model ofsurface processes. Kinetic Monte Carlo simulations provide stochasticrealizations of the surface evolution, which may then inform a reacting flow or heat transfer model. Unfortunately, these simulations areextremely computationally intensive, particularly for design and optimization studies in which many cases are considered.We develop reduced-order models of thin film growth using two techniques: balanced truncation and eigensystem realization. After identifying the underlying structure of the lattice model as a linear differentialequation, we apply the reduction techniques to obtain reduced-ordermodels of root-mean-square roughness and step edge density. Threemodes are needed for a very small model system, while only five modescapture the evolution of a 200x200-site system over a range of growthmodes, from stochastic roughening to island nucleation and coalescence.roughening to island nucleation and coalescence.)
Effective Transition Rates for Epitaxial Growth Using Fast Modulation + (Thin film deposition is an industrially-im … Thin film deposition is an industrially-important process that is highly dependent on the processconditions. Most films are grown under constant conditions, but a few studies show that modifiedproperties may be obtained with periodic inputs. However, assessing the effects of modulationexperimentally becomes impractical with increasing material complexity. Here we consider periodicconditions in which the period is short relative to the time-scales of growth. We analyze a stochasticmodel of thin film growth, computing effective transition rates associated with rapid periodicprocess parameters. Combinations of effective rates may exist which are not attainable understeady conditions, potentially enabling new film properties. An algorithm is presented to constructthe periodic input for a desired set of effective transition rates. These ideas are first illustratedby two simple examples using kinetic Monte Carlo simulations and are then compared to existingdeposition techniques.ompared to existing deposition techniques.)
Modeling and Control of Thin Film Morphology Using Unsteady Processing Parameters: Problem Formulation and Initial Results + (Thin film deposition is an industrially-im … Thin film deposition is an industrially-important process to which control theory has not historically been applied. The need for control is growing as the size of integratedcircuits shrinks, requiring increasingly tighter tolerances in the manufacture of thin films. Our contributions in this study are two-fold: we formulate a model of thin filmgrowth as a control system and we examine the effects of fast periodic forcing.We choose a lattice formulation of crystal growth as our physical model, which captures atomic length scale effects at a time scale compatible with film growth. We focus on the control of film morphology, or surface height profile. Although the systemdimension is high, the structure is simple: the dynamics and the output are linear in the state. We consider the process conditions as inputs, which alter the transition ratefunctions. In the evolution equation, each of these nonlinear functions is multiplied by a linear vector field, yielding a system with a structure similar to a bilinear system.The process conditions in some deposition methods are inherently unsteady, whichproduces films with altered morphology. We use the model developed in this study to analyze the effects of fast periodic forcing on thin film evolution. With the method ofaveraging we develop new effective transition rates which may produce film propertiesunattainable with constant inputs. We show that these effective rates are the convexhull of the set of rates associated with constant inputs. We present conditions onthe convex hull for which the finite-time and infinite-time reachability sets cannot beexpanded with fast periodic forcing. An example in which this forcing increases thereachability set and produces more desirable morphology is also presented. produces more desirable morphology is also presented.)
Fault-Tolerant Controller Design with Applications in Power Systems and Synthetic Biology + (This paper deals with fault-tolerant contr … 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.ct all state-space matrices of the system.)
Control education for societal-scale challenges: A community roadmap + (This article focuses on extending, dissemi … This article focuses on extending, disseminating and interpreting the findings of an IEEE Control Systems Society working group looking at the role of control theory and engineering in solving some of the many current and future societal challenges. The findings are interpreted in a manner designed to give focus and direction to both future education and research work in the general control theory and engineering arena, interpreted in the broadest sense. The paper is intended to promote discussion in the community and also provide a useful starting point for colleagues wishing to re-imagine the design and delivery of control-related topics in our education systems, especially at the tertiary level and beyond.pecially at the tertiary level and beyond.)
Synthesis of Control Protocols for Autonomous Systems + (This article provides a review of control … This article provides a review of control protocol synthesis techniques that incorporate methodologies from formal methods and control theory to provide correctness guarantee for different types of autonomous systems, including those with discrete and continuous state space. The correctness of the system is defined with respect to a given specification expressed as a formula in linear temporal logic to precisely describe the desired properties of the system. The formalism presented in this article admits non-determinism, allowing uncertainties in the system to be captured. A particular emphasis is on alleviating some of the difficulties, e.g., heterogeneity in the underlying dynamics and computational complexity, that naturally arise in the construction of control protocols for autonomous systems. control protocols for autonomous systems.)
Robotic Control and Nonholonomic Motion Planning + (This dissertation addresses the problem of … This dissertation addresses the problem of control and kinematicplanning for constrained robot systems. An example of a system ofthis type is a multifingered robot hand grasping an object. Theindividual fingers act as robot manipulators and are constrained bytheir contact with the object. If the contacts allow rolling betweenthe object and the fingertips, it is possible for the constraints tobe nonholonomic. That is, the constraints may not restrict thereachable configurations of the system, but rather, constrain only theallowable velocities of the system.Using the multifingered hand as a motivating example, thisdissertation presents a detailed analysis of the kinematics, dynamics,and control of robot systems with contact constraints. In particular,it presents a unified derivation of the dynamics of robot manipulatorswith Pfaffian velocity constraints, including the nonholonomic case.This derivation allows control laws to be specified which are provablystable for an entire class of systems, including unconstrained robots,robot hands, and other systems of multiple robots performing acoordinated task. A method for building complex controllers whichrespects this class of constraints is also developed using a set ofsimple primitives which allow hierarchical control structures to becreated in an organized fashion.Finally, the nonholonomic motion planning problem is introduced anddiscussed in detail. Using tools from differential geometric controltheory, it is possible to classify and analyze systems withnonholonomic constraints. A brief review of the necessary tools alongwith a review of the current literature is presented. A practicalmethod for steering nonholonomic systems using sinusoids is derivedand applied to several kinematic systems with contact constraints.to several kinematic systems with contact constraints.)
Exponential Stabilization of Driftless Nonlinear Control Systems + (This dissertation lays the foundation for … This dissertation lays the foundation for practical exponentialstabilization of driftless control systems. Driftless systems havethe 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 nonholonomicconstraints. In engineering applications it is often required tomaintain the mechanical system around a desired configuration. Thistask is treated as a stabilization problem where the desiredconfiguration is made an asymptotically stable equilibrium point. Thecontrol design is carried out on an approximate system. Theapproximation process yields a nilpotent set of input vector fieldswhich, in a special coordinate system, are homogeneous with respect toa non-standard dilation. Even though the approximation can be given acoordinate-free interpretation, the homogeneous structure is useful toexploit: the feedbacks are required to be homogeneous functions andthus 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 isexponentially attractive. This extended notion of exponentialstability is required since the feedback, and hence the closed-loopsystem, is not Lipschitz. However, it is shown that the convergencerate of a Lipschitz closed-loop driftless system cannot be bounded byan exponential envelope.The synthesis methods generate feedbacks which are smooth on\rminus. The solutions of the closed-loop system are proven to beunique in this case. In addition, the control inputs for manydriftless systems are velocities. For this class of systems it ismore appropriate for the control law to specify actuator forcesinstead of velocities. We have extended the kinematic velocitycontrollers to controllers which command forces and still$\rho$-exponentially stabilize the system.Perhaps the ultimate justification of the methods proposed in thisthesis are the experimental results. The experiments demonstrate thesuperior convergence performance of the $\rho$-exponential stabilizersversus traditional smooth feedbacks. The experiments also highlightthe importance of transformation conditioning in the feedbacks. Otherdesign issues, such as scaling the measured states to eliminatehunting, are discussed. The methods in this thesis bring thepractical control of strongly nonlinear systems one step closer.rol of strongly nonlinear systems one step closer. )
Model-Based Estimation of Off-Highway Road Geometry using Single-Axis LADAR and Inertial Sensing + (This paper applies some previously studied … This paper applies some previously studied extendedKalman filter techniques for planar road geometryestimation to the domain of autonomous navigation of offhighwayvehicles. In this work, a clothoid model of the roadgeometry is constructed and estimated recursively based onroad features extracted from single-axis LADAR range measurements.We present a method for feature extraction of theroad centerline in the image plane, and describe its applicationto recursive estimation of the road geometry. We analyzethe performance of our method against simulated motion ofvaried road geometries and against recorded data from previousautonomous navigation runs. Our method accomodates full 6DOF motion of the vehicle as it navigates, constructs consistentestimates of the road geometry with respect to a fixed globalreference frame, and requires an estimate of the sensor posefor each range measurement.he sensor pose for each range measurement.)
Receding Horizon Temporal Logic Planning for Dynamical Systems + (This paper bridges the advances in compute … This paper bridges the advances in computer science and control to allow automatic synthesis of complex dynamical systems which are guaranteed, by construction, to satisfy the desired properties even in the presence of adversary. The desired properties are expressed in the language of temporal logic. With its expressive power, a wider class of properties than safety and stability can be specified. The resulting system consists of a discrete planner which plans, in the abstracted discrete domain, a set of transitions of the system to ensure the correct behaviors and a continuous controller which continuously implements the plan. For a system with certain structure, we present an approach, based on a receding horizon scheme, to overcome computational difficulties in the synthesis of a discrete planner and allow more complex problems to be solved. allow more complex problems to be solved.)
Exponential Stabilization of Driftless Nonlinear Control Systems via Time-varying, Homogeneous Feedback + (This paper brings together results from a … This paper brings together results from a number of different areas incontrol theory to provide an algorithm for the synthesis of locallyexponentially stabilizing control laws for a large class of driftlessnonlinear control systems. The exponential stabilization relies on theuse of feedbacks which render the closed loop vector field homogeneouswith respect to a dilation. These feedbacks are generated from amodification of Pomet's algorithm for smooth feedbacks. ConverseLiapunov theorems for time-periodic homogeneous vector fieldsguarantee that local exponential stability is maintained in thepresence of higher order (with respect to the dilation) perturbingterms.ect to the dilation) perturbing terms. )
Real-valued average consensus over noisy quantized channels + (This paper concerns the average consensus … This paper concerns the average consensus problem with the constraint of quantized communication between nodes. A broad class of algorithms is analyzed, in which the transmission strategy, which decides what value to communicate to the neighbors, can include various kinds of rounding, probabilistic quantization, and bounded noise. The arbitrariness of the transmission strategy is compensated by a feedback mechanism which can be interpreted as a self-inhibitory action. The result is that the average of the nodes state is not conserved across iterations, and the nodes do not converge to a consensus; however, we show that both errors can be made as small as desired. Bounds on these quantities involve the spectral properties of the graph and can be proved by employing elementary techniques of LTI systems analysis.entary techniques of LTI systems analysis.)
Decentralised minimal-time dynamic consensus + (This paper considers a group of agents tha … 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. as suggested by Olshevsky and Tsitsiklis.)
Stability and Performance of Non-Homogeneous Multi-Agent Systems on a Graph + (This paper considers distributed control o … This paper considers distributed control of interconnected multi-agent systems. The dynamics of the individual agents are not required to be homogeneous and the interaction topology is described by an arbitrary directed graph. We derive the sensitivity transfer functions between every pair of agents and we analyze stability and performance of non-homogeneous systems, showing that the low frequency behavior is influenced not only by topology, but also by static gain and poles of the agents.so by static gain and poles of the agents.)
On Decentralized Classification using a Network of Mobile Sensors + (This paper considers how a team of mobile … This paper considers how a team of mobile sensorsshould cooperatively move so as to optimally categorize asingle moving target from their noisy sensor readings. Thecooperative control procedure is based on the development ofa cost function that quantifies the teamâs classification error.The robotsâ motions are then chosen to minimize this function.We particularly investigate the case where the sensor noise andclass distributions are Gaussian. In this case, we can derive aduality principle which states that optimal classification will berealized when the covariance of the target estimate is minimized.That is, in this case, optimal estimation leads naturally tooptimal classification. We extend previous work to develop adistributed discrete-gradient search algorithm that guides theteamâs location motions for purposes of optimal estimation andclassification. The concepts developed are validated throughnumerical studies.d are validated through numerical studies.)

(This paper considers how a team of mobile sensors should cooperatively m)

Nonlinear Control Methods for Planar Carangiform Robot Fish + (This paper considers the design of motion … This paper considers the design of motion control algorithms for robot fish. We present modeling, control design, and experimental trajectory tracking results for a planar robotic fish that is propelled using the carangiform style of locomotion. Our experimental apparatus consists of a freely translating and rotating flat plate and a two-link actuated tail. We develop a model for the fish's propulsion that is based on quasi-steady fluid flow. Using this model, we predict system response to sinusoidal motions of the tail joints andcompare these predictions to the experimental results. We then propose gaits for forward and turning trajectories and analyze system response under such control strategies. Our models and predictions are verified by experiment.nd predictions are verified by experiment.)
A Testbed for Nonlinear Flight Control Techniques: The Caltech Ducted Fan + (This paper considers the fundamental desig … 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. Thepurpose of the ducted fan is the research and development of new nonlinear flight guidanceand control techniques for Uninhabited Combat Aerial Vehicles. It is shown that criticaldesign relations must be satisfied in order that the ducted fan's longitudinal dynamicsbehave similar to those of an flight vehicle. Preliminary flight test results illustratethe flying qualities of the ducted fan.te the flying qualities of the ducted fan.)
Estimation over Communication Networks: Performance Bounds and Achievability Results + (This paper considers the problem of estima … This paper considers the problem of estimation overcommunication networks. Suppose a sensor is takingmeasurements of a dynamic process. However the process needs to be estimated at aremotelocation connected to the sensor through a network ofcommunication links that droppackets stochastically. We provide a framework forcomputing theoptimal performance in the sense of expected errorcovariance. Usingthis framework we characterize the dependency of theperformance onthe topology of the network and the packet droppingprocess. Forindependent and memoryless packet dropping processes wefind thesteady-state error for some classes of networks and obtainlower andupper bounds for the performance of a general network. Wealsoillustrate how this framework can be used in the synthesisofnetworks for the purpose of estimation. Finally we find anecessaryand sufficient condition for the stability of the estimateerrorcovariance for general networks with spatially correlatedand Markovtype dropping process. This interesting condition has amax-cutinterpretation.ng condition has a max-cut interpretation.)
A Motion Planner for Nonholonomic Robots + (This paper considers the problem of motion … This paper considers the problem of motion planning for a car-like robot (i.e., amobile robot with a nonholonomic constraint whose turning radius is lower-bounded). Wepresent a fast and exact planner for our mobile robot model, based upon recursivesubdivision of a collision-free path generated by a lower-level geometric planner thatignores the motion constraints. The resultant trajectory is optimized to give a path thatis of near-minimal length in its homotopy class. Our claims of high speed are supported byexperimental results for implementations that assume a robot moving amid polygonalobstacles. The completeness and the complexity of the algorithm are proven using anappropriate metric in the configuration space R2 x S1 of the robot. This metric is definedby using the length of the shortest paths in the absence of obstacles as the distancebetween two configurations. We prove that the new induced topology and the classical oneare the same. Although we concentration upon the car-like robot, the generalization ofthese techniques leads to new theoretical issues involving sub-Riemannian geometry and topractical results for nonholonomic motion planning. results for nonholonomic motion planning.)
Real Time Trajectory Generation for Differentially Flat Systems + (This paper considers the problem of real t … This paper considers the problem of real time trajectory generation and tracking fornonlinear control systems. We employ a two degree of freedom approach that separates thenonlinear tracking problem into real time trajectory generation followed by local(gain-scheduled) stabilization. The central problem which we consider is how to generate,possibly with some delay, a feasible state space and input trajectory in real time from anoutput trajectory that is given online. We propose two algorithms that solve the real timetrajectory generation problem for differentially flat systems with (possibly non-minimumphase) zero dynamics. One is based on receding horizon point to point steering, the otherallows additional minimization of a cost function. Both algorithms explicitly address thetradeoff between stability and performance and we prove convergence of the algorithms fora reasonable class of output trajectories. To illustrate the application of thesetechniques to physical systems, we present experimental results using a vectored thrustflight control experiment built at Caltech. A brief introduction to differentially flatsystems and its relationship with feedback linearization is also included.h feedback linearization is also included.)
Synthesis of Correct-by-construction Control Protocols for Hybrid Systems Using Partial State Information + (This paper considers the problem of synthe … This paper considers the problem of synthesizing output-feedback control laws for a class of discrete-time hybrid systems in order for the trajectories of the system to satisfy certain high-level specifications expressed in linear temporal logic. By leveraging ideas from robust interpretation of temporal logic formulas and bounded-error estimation, we identify a subclass of systems for which it is possible to reduce the problem to a state-feedback form. In particular, we use locally superstable hybrid observers to resolve the partial information at the continuous level. This allows us to use recent results in temporal logic planning to synthesize the desired controllers based on two-player perfect- information games. The overall control architecture consists of a hybrid observer, a high-level switching protocol and a low-level continuous controller. We demonstrate the proposed framework in a case study on designing control protocols for an aircraft air management system.ols for an aircraft air management system.)
Backtracking temporal logic synthesis for uncertain environments + (This paper considers the problem of synthe … 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.nd demonstrate it on an example gridworld.)
On Quantized Consensus by Means of Gossip Algorithm -- Part II: Convergence Time + (This paper deals with the distributed aver … This paper deals with the distributed averaging problem over a connected network of agents, subject to a quantization constraint. It is assumed that at each time update, only a pair of agents can update their own numbers in terms of the quantized data being exchanged. The agents are also required to communicate with one another in a stochastic fashion. In the first part of the paper, it was shown that the quantized consensus is reached by means of a stochastic gossip algorithm proposed in a recent paper, for any arbitrary quantization. The current part of the paper considers the expected value of the time at which the quantized consensus is reached. This quantity (corresponding to the worst case) is upper and lower bounded in terms of the topology of the graph, for uniform quantization. In particular, it is shown that these bounds are related to the principal minors of the weighted Laplacian matrix. A convex optimization is also proposed to determine the set of probabilities (used to pick a pair of agents) which leads to the fast convergence of the gossip algorithm. fast convergence of the gossip algorithm.)
Tuning a synthetic in vitro oscillator using control-theoretic tools + (This paper demonstrates the effectiveness … This paper demonstrates the effectiveness of sim- ple control-theoretic tools in generating simulation-guided ex- periments on a synthetic in vitro oscillator. A theoretical analysis of the behavior of such system is motivated by high cost, time consuming experiments, together with the excessive number of tuning parameters. A simplified model of the synthetic oscillator is chosen to capture only its essential features. The model is analyzed using the small gain theorem and the theory of describing functions. Such analysis reveals what are the parameters that primarily determine when the system can admit stable oscillations. Experimental verification of the theoretical and numerical findings is carried out and confirms the predicted results regarding the role of production and degradation rates. role of production and degradation rates.)
TuLiP: A Software Toolbox for Receding Horizon Temporal Logic Planning + (This paper describes TuLiP, a Python-based … This paper describes TuLiP, a Python-based software tool- box for the synthesis of embedded control software that is provably correct with respect to an expressive subset of lin- ear temporal logic (LTL) specifications. TuLiP combines routines for (1) finite state abstraction of control systems, (2) digital design synthesis from LTL specifications, and (3) receding horizon planning. The underlying digital de- sign synthesis routine treats the environment as adversary; hence, the resulting controller is guaranteed to be correct for any admissible environment profile. TuLiP applies the re- ceding horizon framework, allowing the synthesis problem to be broken into a set of smaller problems, and consequently alleviating the computational complexity of the synthesis procedure, while preserving the correctness guarantee.hile preserving the correctness guarantee.)
Design of insulating devices for in vitro synthetic circuits + (This paper describes a synthetic in vitro … 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.future experimental testing of the device.)
Reduction of Bleed Valve Bandwidth Requirements for Control of Rotating Stall using Continuous Air Injection + (This paper describes a technique for reduc … This paper describes a technique for reducing the actuator raterequirement in active control of rotating stall and surge oncompressors. Actuation of the compressor characteristic, via the useof continuous air injection at the rotor face in a single-stage, lowspeed axial compressor, has been experimentally verified to provide amethod of reducing the actuator rate requirement of bleed valvecontrol of rotating stall. With a compressor rotor frequency of 100Hz, active control of stall with a high speed bleed valve is achievedonly when the compressor characteristic is actuated. Furthermore, theexperiments show that the bleed valve rate requirement is reduced fromapproximately 145 Hz to below 10 Hz when the amount of compressorcharacteristic actuation is increased. Theoretical tools based on alow order model (1-3 states) and simulations based on a reduced orderdistributed model (37 states) have been developed to estimate the gainand rate requirements of the bleed controller. All of the analyticalformulas and simulations share the same qualitative trends withrespect to the second and third derivatives of the compressorcharacteristic function evaluated at the peak, and the experiments.The agreement implies that bleed valve control of rotating stalldepends crucially on the rate limit of the bleed valve which in turndepends on both the stable and the unstable part of the compressorcharacteristic. Actuation of the compressor characteristic isconcluded to be a valuable tool in circumventing the rate limitationof bleed valves for control of stall. By combining the compressorcharacteristic identification tools and the analytic relations,insights for designing a compressor-bleed pair are provided.ning a compressor-bleed pair are provided.)
Approximate Trajectory Generation for Differentially Flat Systems with Zero Dynamics + (This paper describes algorithms to generat … 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.al cost involved in the various problems.)
Extending Exponential Stabilizers for Nonholonomic Systems from Kinematic Controllers to Dynamic Controllers + (This paper describes an approach for exten … This paper describes an approach for extending (time-varying)exponential stabilizers for nonholonomic systems from controllers whichcommand input velocity to controllers which command input torques. Dueto the nondifferentiable nature of exponential stablizers, additionalstructure is required in order to ensure that the extended controllersgenerate continuous control actions. In this paper we show how toextend homogeneous controllers which use a nonstandard dilation adaptedto the problem.nstandard dilation adapted to the problem.)
Differential Flatness of Mechanical Control Systems: A Catalog of Prototype Systems + (This paper describes the application of di … This paper describes the application of differential flatnesstechniques from nonlinear control theory to mechanical (Lagrangian)systems. Systems which are differentially flat have several usefulproperties which can be exploited to generate effective controlstrategies for nonlinear systems. For the special case of mechanicalcontrol systems, much more geometric information is present and thepurpose of this paper is to explore the implications and features ofthat class of systems. We concentrate on several worked exampleswhich illustrate the general theory and present a detailed catalog ofknown examples of differentially flat mechanical systems.of differentially flat mechanical systems.)
Design and Implementation of a Biomolecular Circuit for Tracking Protein Concentration + (This paper describes the design, modeling, … 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.ur model and performing the expected task.)
Interfacing TuLiP with the JPL Statechart Autocoder: Initial progress toward synthesis of flight software from formal specifications + (This paper describes the implementation of … This paper describes the implementation of an in- terface connecting the two tools : the JPL SCA (Statechart Autocoder) and TuLiP (Temporal Logic Planning Toolbox) to enable the automatic synthesis of low level implementation code directly from formal specifications. With system dynamics, bounds on uncertainty and formal specifications as inputs, TuLiP synthesizes Mealy machines that are correct-by-construction. An interface is built that automatically translates these Mealy machines into UML statecharts. The SCA accepts the UML statecharts (as XML files) to synthesize flight-certified2 implementation code. The functionality of the interface is demonstrated through three example systems of varying com- plexity a) a simple thermostat b) a simple speed controller for an autonomous vehicle and c) a more complex speed controller for an autonomous vehicle with a map-element. In the thermostat controller, there is a specification regarding the desired temperature range that has to be met despite disturbance from the environment. Similarly, in the speed-controllers there are specifications about safe driving speeds depending on sensor health (sensors fail unpredictably) and the map-location. The significance of these demonstrations is the potential circumventing of some of the manual design of statecharts for flight software/controllers. As a result, we expect that less testing and validation will be necessary. In applications where the products of synthesis are used alongside manually designed components, extensive testing or new certificates of correctness of the composition may still be required. of the composition may still be required.)
Alice: An information-rich autonomous vehicle for high-speed desert navigation + (This paper describes the implementation an … 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.re after traversing approximately 8 miles.)
A Domain-Specific Language for Reactive Control Protocols for Aircraft Electric Power Systems + (This paper describes the use of a domain-s … 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.thesis procedure on a range of topologies.)
Controlling biological networks by time-delayed signals + (This paper describes the use of time-delay … 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. an efficient bio-compatible control tool.)
Receding Horizon Control of a Vectored Thrust Flight Experiment + (This paper details the application of a co … This paper details the application of a constrained receding horizon control techniques tostabilize an indoor vectored-thrust flight experiment, known as the Caltech Ducted Fan, subjected to step commands. The result of the experiment sheds light on the theoretical stabilityof the receding horizon control strategy as well as validates some efficient computation techniques for solving nonlinear optimal control problems with constraints. The receding horizoncontrol problem is formulated as a constrained optimal control problem, which was solved withan e±cient computational method developed and implemented by Milam et al., that combinesnonlinear control theory, B-spline basis functions, and nonlinear programming. Characteristicissues including non-zero computational times, convergence property, choice of horizon lengthand terminal cost are discussed. The study confirms the applicability of real-time recedinghorizon control for constrained systems with fast dynamics.or constrained systems with fast dynamics.)
Real-Time Trajectory Generation for the Cooperative Path Planning of Multi-Vehicle Systems + (This paper discusses a Cooperative Path Pl … This paper discusses a Cooperative Path Planning (CPP) designmethodology for multi-vehicle systems and a NonlinearTrajectory Generation (NTG) algorithm. Three scenariosof multi-vehicle tasking are proposed at the CPP framework.The NTG algorithm is, then, used to generate realtimetrajectory for desired vehicle activities. Given systemdynamics and constraints, the NTG algorithm first finds trajectorycurves in a lower dimensional space and, then, parameterizesthe curves by the B-spline basis. The coefficients of the B-splines are further solved by the sequentialquadratic programming to satisfy the optimization objectivesand constraints. The NTG algorithm has been implementedto generate real-time trajectories for a group ofcooperative vehicles in the presence of changing missionsand constraints.ence of changing missions and constraints.)
Cooperative Task Planning of Multi-Robot Systems with Temporal Constraints + (This paper discusses a design methodology … This paper discusses a design methodology of cooperativetrajectory generation for multi-robot systems.The trajectory of achieving cooperative tasks, i.e., withtemporal constraints, is constructed by a nonlinear trajectorygeneration (NTG) algorithm. Three scenariosof multi-robot tasking are proposed at the cooperativetask planning framework. The NTG algorithm is, then,used to generate real-time trajectory for desired robotactivities. Given robot dynamics and constraints, theNTG algorithm first finds trajectory curves in a lowerdimensional space and, then, parameterizes the curvesby a set of B-spline representations. The coe�cientsof the B-splines are further solved by the sequentialquadratic programming to satisfy the optimization objectivesand constraints. The NTG algorithm has beenimplemented to generate real-time trajectories for agroup of cooperative robots in the presence of spatialand temporal constraints. Finally, an illustrated exampleof cooperative task planning with temporal constraintsis presented.ng with temporal constraints is presented.)
Low-Observable Nonlinear Trajectory Generation for Unmanned Air Vehicles + (This paper explores low observability flig … This paper explores low observability flight path planning of unmanned air vehicles (UAVs)in the presence of radar detection systems. The probability of detection model of an aircraftnear an enemy radar depends on aircraft attitude, range, and configuration. A detection modelis coupled with a simplified aircraft dynamics model. The Nonlinear Trajectory Generation(NTG) software package developed at Caltech is used. The NTG algorithm is a gradient descentoptimization method that combines three technologies: Bsplines, output space collocation andnonlinear optimization tools. Implementations are formulated with temporal constraints thatallow periods of high observability interspersed with periods of low observability. Illustrativeexamples of optimized routes for low observability are presented.outes for low observability are presented.)
A Framework for Low--Observable Tra jectory Generation in the Presence of Multiple Radars + (This paper explores the problem of finding … 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.optimized for both detectability and time.)

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