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The RoboFlag Competition + (RoboFlag is a robotic version of capture t … RoboFlag is a robotic version of capture the flag that can be played either with autonomous controllers or with up to two humans in the loop. The goal of the game is to capture the flag of the other team, which is located in their defense zone, and bring it back to your home zone. The other team defends their flag by tagging your robots on their side of the field, at the same time as trying to capture your flag. Some of the interesting features of RoboFlag are that the robots have limited sensing capability and distributed processing, requiring that information be communicated between robots across limited bandwidth links. This makes the game much more challenging since you have two determine your actions without a complete view of the playing field.This paper gives an overview of the RoboFlag competition and describes some of the research challenges that are represented in the game.rch challenges that are represented in the game.)
Situational Reasoning for Road Driving in an Urban Environment + (Robot navigation in urban environments req … Robot navigation in urban environments requires situational reasoning. Given the complexity of the environment and the behavior specified by traffic rules, it is necessary to recognize the current situation to impose the correct traffic rules. In an attempt to manage the complexity of the situational reasoning subsystem, this paper describes a finite state machine model to govern the situational reasoning process. The logic state machine and its interaction with the planning system are discussed. The approach was implemented on Alice, Team Caltech's entry into the 2007 DARPA Urban Challenge. Results from the qualifying rounds are discussed. The approach is validated and the shortcomings of the implementation are identified.ings of the implementation are identified.)
Geometric Phases and Robotic Locomotion + (Robotic locomotion is based in a variety o … Robotic locomotion is based in a variety of instances upon cyclic changes in the shapeof a robot mechanism. Certain variations in shape exploit the constrained nature of arobot's interaction with its environment to generate net motion. This is true for leggedrobots, snakelike robots, and wheeled mobile robots undertaking maneuvers such as parallelparking. In this paper we explore the use of tools from differential geometry to model andanalyze this class of locomotion mechanisms in a unified way. In particular, we describelocomotion in terms of the geometric phase associated with a connection on a principalbundle, and address issues such as controllability and choice of gait. We also provide anintroduction to the basic mathematical concepts which we require and apply the theory tonumerous example systems.ly the theory to numerous example systems.)
Robotic Manipulation with Flexible Link Fingers + (Robots with structural flexibility provide … Robots with structural flexibility provide an attractive alternativeto rigid robots for many of the new and evolving applications inrobotics. In certain applications their use is unavoidable. Theincreased complexity in modeling and control of such robots is offsetby desirable performance enhancements in some respects. In this thesiswe present a singular perturbation approach for modeling, analysis andcontrol of robots with flexibility. As our singular perturbationapproach does not treat the flexible manipulator as a perturbation ofthe rigid manipulator, it can treat significant flexibility, beyondthe linear range. Analysis based on this approach leads to someprovably stable control laws for the hybrid position and force controlof flexible-link manipulators. The analysis is done in the frameworkof a single robot manipulator in a constrained motiontask. Simulations and experimental results are presented for thiscase. To show applicability of the results to more general andcomplex systems with flexibilities we also present experimental datafrom a planar, two-fingered, reconfigurable grasping setup which allowsrigid and flexible configurations. The aim of the experimentation isto show the applicability of the control laws and analysis developed,and to determine the performance enhancements resulting from theintroduction of flexibility. Experimental data is analysed to show thetradeoffs between controller complexity and performance enhancement aswe deal with greater flexibility. Various performance criteria are setup and experimental results are discussed within their framework. Weconclude that large flexibility can be controlled without too muchadditional effort, has performance comparable to that of rigid robots,and possesses enhancing properties which make it appealing for use incertain types of applications. for use in certain types of applications.)
Assessment of Robustness to Temperature in a Negative Feedback Loop and a Feedforward Loop + (Robustness to temperature variation is an … 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.ature robustness in biomolecular circuits.)
Nonlinear Control Design for Rotating Stall and Surge with Magnetic Bearing Actuators + (Rotating stall and surge are aerodynamic i … Rotating stall and surge are aerodynamic instabilities that limit the performance ofaeroengines. A set of magnetic bearings supporting the compressor rotor is a potentialactuator for active control of rotating stall and surge. Based on a first-principles modelwe show that using this type of actuation, the first harmonic mode of rotating stall islinearly controllable, but the second harmonic mode and the surge mode are linearlyuncontrollable. We then give an explicit procedure for designing feedback laws such thatthe first mode is linearly stabilized and the criticality of the Hopf bifurcations of thesecond mode and the surge mode are supercritical. We also investigate the effects ofmagnitude saturation on the regions of attraction. We demonstrate the theoretical resultsby numerical simulations of a model for a transonic compressor at the NASA Lewis ResearchCenter.pressor at the NASA Lewis Research Center.)
Towards Assume-Guarantee Profiles for Autonomous Vehicles + (Rules or specifications for autonomous veh … Rules or specifications for autonomous vehicles are currently formulated on a case-by-case basis, and put together in a rather ad-hoc fashion. As a step towards eliminating this practice, we propose a systematic procedure for generating a set of supervisory specifications for self-driving cars that are 1) associated with a distributed assume-guarantee structure and 2) characterizable by the notion of consistency and completeness. Besides helping autonomous vehicles make better decisions on the road, the assume-guarantee contract structure also helps address the notion of blame when undesirable events occur. We give several game-theoretic examples to demonstrate applic bility of our framework.emonstrate applic bility of our framework.)
Robust Model Predictive Control with a Safety Mode: Applied to Small-Body Proximity Operations + (Safe and robust G&C (Guidance and Cont … Safe and robust G&C (Guidance and Control) algorithms for onboard implementation are developed by augmenting a model predictive control technique with a safety mode. The application example herein is spacecraft small-body proximity operations where model and constraint uncertainty warrant G&C algorithms with a degree of autonomous, onboard decision capability. The algorithm enforces state and control constraints and merges two operational modes: (I) standard mode guides the spacecraft to the proximity of a target state in a robust and resolvable model-predictive manner; (II) safety mode, if activated, maintains the spacecraft near a safety reference for all time. The algorithm utilizes separate feedforward and feedback components. In standard mode, the feedforward guidance solutions come from a way-point generation algorithm that uses a discrete linear-time-varying dynamics model. This approach provides a convex formulation of the problem (solvable onboard as a second-order cone program) that includes control and state constraints; the safety-mode availability adds a constraint in this standard-mode formulation as well. The feedback guarantees standard-mode resolvability to update the guidance profile in a robust, model-predictive manner. In safety mode, an offline-designed feedforward policy with the added feedback maintains the spacecraft in a hovering state in the proximity of its position at safety-mode activation time; this provides robustness to unexpected state-constraint changes such as unexpected ground proximity during landing operations. A simulation demonstrating both the standard and safety modes is provided for a spacecraft autonomous-descent scenario toward a small asteroid with an uncertain gravity model and errors in the surface altitude constraint.del and errors in the surface altitude constraint.)
A Robust Nonlinear Model Predictive Control Algorithm with a Safety Mode + (Safety guarantees are built into a robust … 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.ar terms that have norm-bounded Jacobians.)
Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli + (Serine integrases are bacteriophage protei … Serine integrases are bacteriophage proteins responsible for integrating the phage genome into that of the host. Synthetic biologists have co-opted these proteins into useful tools for permanent DNA logic, utilizing their specific DNA recombination abilities to build synthetic cell differentiation and genetic memory systems. Each integrase has a specific pair of DNA sequences (attP/attB sites) that it recombines, but multiple identical sites can result in unpredictable recombination. We have developed a way to control integrase activity on identical attP/attB sites by using catalytically dead Cas9 (dCas9) as a programmable binding protein that can compete with integrase for binding to specific attachment sites. Utilizing a plasmid that contains two identical Bxb1 attP sites, integration can be repressed up to 8 fold at either one of the two attP sites when guide RNA and dCas9 are present. Guide RNA sequences that bind specifically to attB, or either of two attP sites, have been developed. Future goals are to utilize this technology to construct larger and more complex integrase logic circuits.and more complex integrase logic circuits.)
Use of population-level cell-state switching for recording transient inducer pulses + (Single-cell bacterial sensors have numerou … Single-cell bacterial sensors have numerous applications in human health monitoring, environmental chemical detection, and materials biosynthesis. Many previous efforts for synthetic bacteria strains seek to optimize homogenous single cell behavior. Rather than attempt to reduce noise in circuit behavior, we take advantage of heterogenous single cell responses to record sequences of chemical events within a population. Using an engineered E. coli strain with a 4-state temporal logic gate, we show, both in silico and in vivo, that stochastic digital switching within single cells results in an analog population fractionation that can be used to resolve inducer pulse duration within 30 minutes. Furthermore, these results are preserved in the genome and can be read out at a time that is much later than the time of the event. is much later than the time of the event.)
Layering assume-guarantee contracts for hierarchical system design + (Specifications for complex engineering sys … Specifications for complex engineering systems are typically decomposed into specifications for individual subsystems in a manner that ensures they are implementable and simpler to develop further. We describe a method to algorithmically construct component specifications that implement a given specification when assembled. By eliminating variables that are irrelevant to realizability of each component, we simplify the specifications and reduce the amount of information necessary for operation. We parametrize the information flow between components by introducing parameters that select whether each variable is visible to a component or not. The decomposition algorithm identifies which variables can be hidden while pre- serving realizability and ensuring correct composition, and these are eliminated from component specifications by quantification and conversion of binary decision diagrams to formulas. The resulting specifications describe component viewpoints with full information with respect to the remaining variables, which is essential for tractable algorithmic synthesis of implementations. The specifications are written in TLA+, with liveness properties restricted to an implication of conjoined recurrence properties, known as GR(1). We define an operator for forming open systems from closed systems, based on a variant of the “while-plus” operator. This operator simplifies the writing of specifications that are realizable without being vacuous. To convert the generated specifications from binary decision diagrams to readable formulas over integer variables, we symbolically solve a minimal covering problem. We show with examples how the method can be applied to obtain contracts that formalize the hierarchical structure of system design.e hierarchical structure of system design.)
Collaborative System Identification via Parameter Consensus + (Standard schemes in system identification … 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.citation in networked adaptive algorithms.)
Constrained Trajectory Generation for Microsatellite Formation Flying + (Station keeping and reorientation control … 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.ar Trajectory Generation software package.)
A Bayesian approach to inferring chemical signal timing and amplitude in a temporal logic gate using the cell population distributional response + (Stochastic gene expression poses an import … 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.ll under biologically relevant conditions.)
A stochastic framework for the design of transient and steady state behavior of biochemical reaction networks + (Stochasticity plays an essential role in b … 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. illustrate its strengths and limitations.)
Active Control of Integrated Inlet/Compression Systems: Initial Results + (Substantial reductions in aircraft size a … 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.tion has little effect on stall behavior.)
System architectures and environment modeling for high-speed autonomous navigation + (Successful high-speed autonomous navigatio … Successful high-speed autonomous navigation requires integration of tools from robotics, control theory, computer vision, and systems engineering. This thesis presents work that develops and combines these tools in the context of navigating desert terrain.A comparative analysis of reactive, behavior-based, and deliberative control architectures provides important guidelines for design of robotic systems. These guidelines depend on the particular task and environment of the vehicle. Two important factors are identified which guide an effective choice between these architectures: dynamic feasibility for the vehicle, and predictability of the environment. This is demonstrated by parallels to control theory, illustrative examples, simulations, and analysis of Bob and Alice---Caltech's full-scale autonomous ground vehicle entries in the 2004 and 2005 Grand Challenge races, respectively.Further, new model-based methods are developed for constructing and maintaining estimates of terrain elevation and road geometry. These are demonstrated in simulation and in fully autonomous operation of Alice, including accurate detection and tracking of the centerline of desert roads at speeds up to 5 m/s. Finally, Alice's navigation architecture is presented in full along with experimental results that demonstrate its capabilities.results that demonstrate its capabilities.)
Cell-free and in vivo characterization of Lux, Las, and Rpa quorum activation systems in E. coli + (Synthetic biologists have turned towards q … 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.ation predicts crosstalk observed in vivo.)
Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks + (Synthetic gene expression is highly sensit … 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. threshold detection and switch stability.)
Data-driven network models for genetic circuits from time-series data with incomplete measurements + (Synthetic gene networks are frequently con … 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.coli based transcriptional event detector.)
Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking + (Synthetic transcriptional networks built f … Synthetic transcriptional networks built from CRISPR-based repressors (CRISPRi) rely on shared use of a core dCas9 protein. In E. coli, CRISPRi cannot support more than about a dozen simultaneous gRNAs before the fold repression of any individual gRNA drops below 10x. We show with a simple model based on previous characterization of competition in CRISPRi that activation by CRISPR-based activators (CRISPRa) is much less sensitive to dCas9 bottle-necking than CRISPRi. We predict that E. coli should be able to support dozens to hundreds of CRISPRa gRNAs at >10-fold activation.s of CRISPRa gRNAs at >10-fold activation.)
Modeling Dynamic Transcriptional Circuits with CRISPRi + (Targeted transcriptional repression with c … Targeted transcriptional repression with catalytically inactive Cas9 (CRISPRi) can be used to build gene regulatory nets similar in principle to those made with traditional transcription factors, and promises to do so with better orthogonality, programmability, and extensibility. We use a simple dynamical model of CRISPRi to understand its behavior and requirements, and to show that CRISPRi can recapitulate several classic gene regulatory circuits, including the repressilator, a toggle switch, and an incoherent feed-forward loop pulse generator. Our model also predicts that these circuits are highly sensitive to promoter leak, but that promoter leak can be offset with active degradation of dCas. We provide specifications for required fold-repression and dCas degradation rates for several dynamic circuits. Our modeling reveals key engineering requirements and considerations for the construction of dynamic CRISPRi circuits, and provides a roadmap for building those circuits.des a roadmap for building those circuits.)
Negative Feedback Facilitates Temperature Robustness in Biomolecular Circuit Dynamics + (Temporal dynamics in many biomolecular cir … Temporal dynamics in many biomolecular circuits can change with temperature because of the temperature dependence of underlying reaction rate parameters. It is generally unclear what circuit mechanisms can inherently facilitate robustness in the dynamics to variations in temperature. Here, we address this issue using a combination of mathematical models and experimental measure- ments in a cell-free transcription-translation system. We find that negative transcriptional feedback can reduce the eâµect of temperature variation on circuit dynamics. Further, we find that effective negative feedback due to first-order degradation mechanisms can also enable such a temperature robustness effect. Finally, we estimate temperature dependence of key parameters mediating such negative feedback mechanisms. These results should be useful in the design of temperature robust circuit dynamics.gn of temperature robust circuit dynamics.)
Decomposing GR(1) Games with Singleton Liveness Guarantees for Efficient Synthesis + (Temporal logic based synthesis approaches … 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.he decomposition-based synthesis approach.)

(Temporal logic based synthesis approaches are often used to find traject)

Online Horizon Selection in Receding Horizon Temporal Logic Planning + (Temporal logics have proven effective for … Temporal logics have proven effective for correct-by-constructionsynthesis of controllers for a wide range ofapplications. Receding horizon frameworks mitigate thecomputational intractability of reactive synthesis for temporallogic, but have thus far been limited by pursuing a singlesequence of short horizon problems to the current goal. Wepropose a receding horizon algorithm for reactive synthesis thatautomatically determines a path to the currently pursued goal atruntime, in response to a nondeterministic environment. This isachieved by allowing each short horizon to have multiple localgoals, and determining which local goal to pursue based on thecurrent global goal, currently perceived environment and apre-computed invariant dependent on each global goal. Wedemonstrate the utility of this additional flexibility ingrant-response tasks, using a search-and-rescueexample. Moreover, we show that these goal-dependent invariantsmitigate the conservativeness of the receding horizon approach.tiveness of the receding horizon approach.)
Nonlinear Trajectory Generation for the Caltech Multi-Vehicle Wireless Testbed + (The Caltech Multi Vehicles Wireless Testbe … The Caltech Multi Vehicles Wireless Testbed (MVWT)is a platform designed to explore theoritical advancesin multi-vehicle coordination and control, networkedcontrol systems and high con�dence distributedcomputation. The contribution of this report is topresent simulation and experimental results on thegeneration and implementation of optimal trajectoriesfor the MVWT vehicles. The vehicles are nonlinearand spatially contrained with bounded input control.The trajectories are generated using the NTG softwarepackage developed at Caltech. Minimum time trajectoriesand the application of Model Predictive Control (MPC)are investigated.can actually follow i.e. trajectories that satisfy everyconstraint of the testbed. Those constraints can eitherbe linear, like the boundaries of the testbed or nonlinearlike the constraints on the input. The main di�erence andalso di�culty in our case is that the system is not linearlycontrollable around its equilibrium.In Section 2 we will give a quick description of the systemsproperties and in Section 3 and 4 we will describe theprogression which led us from the optimization problemto the implementation on the real vehicles. In Section5 other optimization problems such as minimum timetrajectory generation and model predictive control areinvestigated.model predictive control are investigated.)
MVWT-II: The Second Generation Caltech Multi-Vehicle Wireless Testbed + (The Caltech Multi-Vehicle Wireless Testbed … The Caltech Multi-Vehicle Wireless Testbed isan experimental platform for validating theoretical advancesin multiple-vehicle coordination and cooperation, real-timenetworked control system, and distributed computation. Thispaper describes the design and development of an additionalfleet of 12 second-generation vehicles. These vehicles arehovercrafts and designed to have lower mass and friction aswell as smaller size than the first generation vehicles. Thesehovercrafts combined with the outdoor wireless testbed providea perfect hardware platform for RoboFlag competition.ardware platform for RoboFlag competition.)
Robustness Analysis of Accelerometry Using an Electrostatically Suspended Gyroscope + (The Electrostatically Suspended Gyroscope … The Electrostatically Suspended Gyroscope (ESG) is a two-axis inertial orientati onsensor manufactured by Boeing and currently in use on U.S. Navy submarines. The additional ability of the ESG to act as an accelerometer is well known, but extraction ofprecision acceleration measuremen ts from an ESG has not been achieved. The majorobstacles to precision accelerometry are the nonlinear dynamics of the ESG rotor and parametric variation of the ESG electronics. In this paper, we derive a model for the ESGdynamics with an eye toward efficient representation of the uncertainties in the model. Werepresent the model uncert ainties and nonlinearities in a framework amenable tomu-analysis and analyze ESG accelerometer precision using $\mu$-analysis tools. Finally,we discuss the implementation of a digital ESG control architecture for use in ESG systemidentification and testing of suspension control and acce lerometer algorithms.ion control and acce lerometer algorithms.)
Applications and Extensions of Goursat Normal Form to Control of Nonlinear Systems + (The Goursat normal form theorem gives cond … The Goursat normal form theorem gives conditions under which anPfaffian exterior differential system is equivalent to a certainnormal form. This paper details how the Goursat normal form and itsextensions provide a unified framework for understanding feedbacklinearization, chained form, and differential flatness. Keywords: Exterior differential systems, nonholonomic constraints,chained form, feedback linearization, differentially flat.rm, feedback linearization, differentially flat.)
Optimizing protein expression in the One-Pot PURE system: Insights into reaction composition and translation efficiency + (The One-Pot PURE system for in vitro prote … The One-Pot PURE system for in vitro protein expression, which results from a co-culture and one-step purification of 36 essential proteins to support gene transcription and translation, can significantly improve the accessibility and affordability of PURE systems. However, replicating this protocol to match the productivity of the traditional PURE system can take considerable time and effort due to variability in the expression level of individual proteins. In this work, we observed unstable PURE protein expression in two E. coli protein expression strains, M15/pREP4 and BL21(DE3), and addressed this instability using catabolite repression. We identified key proteins whose concentration in the One-Pot PURE mixture significantly impacted the reaction’s protein expression capacity. Compared to the original method using two E. coli protein expression strains, we found that consolidating all expression vectors onto one BL21 (DE3) strain led to more uniform cell growth at the time of protein induction, thereby improving the composition of critical translation initiation factors in the purified mixture for efficient translation. We also found that variations in commercial energy solution formulations could compensate for deficiencies in the One-Pot PURE protein composition. Additionally, our study revealed significant differences in the translation capacity of commercially available E. coli tRNAs, suggesting the potential of optimizing tRNA composition to improve protein translation. Taken together, this work highlights the intricate biochemical interplay influencing protein expression capacity in the One-Pot PURE system and presents strategies to improve its robustness and productivity.o improve its robustness and productivity.)
The Python Control Systems Library (python-control) + (The Python Control Systems Library (python … The Python Control Systems Library (python-control) is an open source set of Python classes and functions that implement common operations for the analysis and design of feedback control systems. In addition to support for standard LTI control systems (including time and frequency response, block diagram algebra, stability and robustness analysis, and control system synthesis), the package provides support for nonlinear input/output systems, including system interconnection, simulation, and describing function analysis. A MATLAB compatibility layer provides an many of the common functions corresponding to commands available in the MATLAB Control Systems Toolbox. The library takes advantage of the Python “scientific stack” of Numpy, Matplotlib, and Jupyter Notebooks and offers easy interoperation with other category-leading software systems in data science, machine learning, and robotics that have largely been built on Python.cs that have largely been built on Python.)
A Method for Cost-Effective and Rapid Characterization of Engineered T7-based Transcription Factors by Cell-Free Protein Synthesis Reveals Insights into the Regulation of T7 RNA Polymerase-Driven Expression + (The T7 bacteriophage RNA polymerase (T7 RN … 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.eer future T7-based transcription factors.)
Rules of the Road: Safety and Liveness Guarantees for Autonomous Vehicles + (The ability to guarantee safety and progre … The ability to guarantee safety and progress for all vehicles is vital to the success of the autonomous vehicle industry. We present a framework for designing autonomous vehicle behavior in a way that is safe and guarantees progress for all agents. In this paper, we first introduce a new game paradigm which we term the quasi-simultaneous game. We then define an agent protocol that all agents must use to make decisions in this quasi-simultaneous game setting. According to the protocol, agents first select an intended action using a behavioral profile. Then, the protocol defines whether an agent has precedence to take its intended action or must take a sub-optimal action. The protocol ensures safety under all traffic conditions and liveness for all agents under `sparse' traffic conditions. We provide proofs of correctness of the protocol and validate our results in simulation.ol and validate our results in simulation.)
Single day construction of multi-gene circuits with 3G assembly + (The ability to rapidly design, build, and … The ability to rapidly design, build, and test prototypes is of key importance to every engineering discipline. DNA assembly often serves as a rate limiting step of the prototyping cycle for synthetic biology. Recently developed DNA assembly methods such as isothermal assembly and type IIS restriction enzyme systems take different approaches to accelerate DNA construction. We introduce a hybrid method, Golden Gate-Gibson (3G), that takes advantage of modular part libraries introduced by type IIS restriction enzyme systems and isothermal assembly's ability to build large DNA constructs in single pot reactions. Our method is highly efficient and rapid, facilitating construction of entire multi-gene circuits in a single day. Additionally, 3G allows generation of variant libraries enabling efficient screening of different possible circuit constructions. We characterize the efficiency and accuracy of 3G assembly for various construct sizes, and demonstrate 3G by characterizing variants of an inducible cell-lysis circuit.riants of an inducible cell-lysis circuit.)
A Case Study in Approximate Linearization: The Acrobot Example + (The acrobot is a simple mechanical system … The acrobot is a simple mechanical system patterned after a gymnastperforming on a single parallel bar. By swinging her legs, a gymnastis able to bring herself into an inverted position with her center ofmass above the part and is able to perform manuevers about thisconfiguration. This report studies the use of nonlinear controltechniques for designing a controller to operate in a neighborhood ofthe manifold of inverted equilibrium points. The techniques describedhere are of particular interest because the dynamic model of theacrobot violates many of the necessary conditions required to applycurrent methods in linear and nonlinear control theory.The approach used in this report is to approximate the system in sucha way that the behavior of the system about the manifold ofequilibrium points is correctly captured. In particular, we constructan approximating system which agrees with the linearization of theoriginal system on the equilibrium manifold and is full statelinearizable. For this class of approximations, controllers can beconstructed using recent techniques from differential geometric control theory. We show that application of control laws derived in thismanner results in approximate trajectory tracking for the system undercertain restrictions on the class of desired trajectories. Simulationresults based on a simplified model of the acrobot are included. a simplified model of the acrobot are included.)
A group-theoretic approach to formalizing bootstrapping problems + (The bootstrapping problem consists in desi … 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.era data from publicly available datasets.)
Cell-Free Extract Data Variability Reduction in the Presence of Structural Non-Identifiability + (The bottom up design of genetic circuits t … 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.achieve the desired variability reduction.)
Probabilistic Safety Analysis of Sensor-Driven Hybrid Automata + (The control programs of complex autonomous … The control programs of complex autonomous systems that have conditional branching can be modeled as linear hybrid systems. When the state knowledge is perfect, linear hybrid systems with state-based transition conditions can be verified against a specified unsafe set using existing model checking software. This paper introduces a formal method for calculating the failure probability due to state estimation uncertainty of these sensor-driven hybrid systems. Problem complexity is described and some reduction techniques for the failure probability calculation are given. An example goal-based control program is given and the failure probability for that system is calculated.probability for that system is calculated.)
Just-in-time synthesis for motion planning with temporal logic + (The cost of the great expressivity of moti … The cost of the great expressivity of motion planning subject to temporal logic formulae is intractability. Recent advances in sampling-based methods seem to be only applicable to âlow-levelâ control. The problem of realizing âhigh-levelâ controllers that satisfy a temporal logic specification does not readily admit approximations, unless the notion of correctness is relaxed as might be achieved with probabilistic variants of temporal logics. In this paper, we argue that not all possible environment (uncontrolled) behaviors need to be explicitly planned for, but rather short-time strategies can be generated online while maintaining global correctness. We achieve this by separating feasibility from controller synthesis, using a metric from the underlying continuous state space to ensure short-time strategies chained together provide globally correct behavior.ogether provide globally correct behavior.)
Autonomous Driving in Urban Environments: Approaches, Lessons and Challenges + (The development of autonomous vehicles for … 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. vehicles operating in human environments.)
Optimal Experiment Design and Leveraging Competition for Shared Resources in Cell-free Extracts + (The fact that genes compete for shared cel … The fact that genes compete for shared cellular resources poses a fundamental challenge when identifying pa- rameters of synthetic gene circuits. A recently developed model of gene expression tackles this problem by explicitly accounting for resource competition. In addition to accurately describing experimental data, this model only depends on a handful of easily identifiable parameters with clear physical interpretation. Based on this model, we outline a procedure how to select the optimal set of experiments to characterize biomolecular parts in synthetic biology. Additionally, we reveal the role competition for shared resources plays, provide guidelines how to minimize its detrimental effects, and how to leverage this phenomenon to extract the most information about unknown parameters. To illustrate the results, we consider the case of part characterization in cell-free extracts, treat plasmid DNA concentrations as decision variables, and demonstrate the significant performance difference between na ̈ıve and optimal experiment design.een na ̈ıve and optimal experiment design.)
Future Directions in Control in an Information-Rich World + (The field of control provides the principl … 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.y through application of control research.)
Model Predictive Control for an Uncertain Smart Thermal Grid + (The focus of this paper is on modeling and … The focus of this paper is on modeling and control of Smart Thermal Grids (STGs) in which the uncertainties in the demand and/or supply are included. We solve the corre- sponding robust model predictive control (MPC) optimization problem using mixed-integer-linear programming techniques to provide a day-ahead prediction for the heat production in the grid. In an example, we compare the robust MPC approach with the robust optimal control approach, in which the day-ahead production plan is obtained by optimizing the objective function for entire day at once. There, we show that the robust MPC approach successfully keeps the supply-demand balance in the STG while satisfying the constraints of the production units in the presence of uncertainties in the heat demand. Moreover, we see that despite the longer computation time, the performance of the robust MPC controller is considerably better than the one of the robust optimal controller. the one of the robust optimal controller.)
POD Based Models of Self-Sustained Oscillations in the Flow Past an Open Cavity + (The goal of this work is to provide accura … The goal of this work is to provide accurate dynamical models of oscillations in the flow past a rectangular cavity, for the purpose of bifurcation analysis and control. We have performed an extensive set of direct numerical simulations which provide the data used to derive and evaluate the models. Based on the method of Proper Orthogonal Decomposition (POD) and Galerkin projection, we obtain low-order models (from 6 to 60 states) which capture the dynamics very accurately over a few periods of oscillations, but deviate for long time.f oscillations, but deviate for long time.)
Reactive Protocols for Aircraft Electric Power Distribution + (The increasing complexity of electric powe … The increasing complexity of electric power sys- tems leads to integration and verification challenges. We consider the problem of designing a control protocol for the aircraft electric power system that meets these system requirements and reacts dynamically to changes in internal system states. We formalize these requirements by translating them into a temporal logic specification language describing the correct behaviors of the system, and apply formal methods to automatically synthesize a controller protocol that satisfies these overall properties and requirements. Through an example, we perform a design exploration to show the benefits and tradeoffs between centralized and distributed control architectures.zed and distributed control architectures.)
Converting Smooth, Time-Varying, Asymptotic Stabilizers for Driftless Systems to Homogeneous, Exponential Stabilizers + (The main result of this paper is a theorem … The main result of this paper is a theorem that allows smooth,time-varying controllers which asymptotically stabilize a driftlessnonlinear system to be converted to homogeneous, time-varyingcontrollers which provide {\em exponential} stability. The resultingcontrollers are smooth everywhere except the origin and are easilycomputed given the original asymptotic stabilizer. We illustrate theresult with experimental results on a simple mobile robot.rimental results on a simple mobile robot.)
Impact of Chemical Dynamics of Commercial PURE Systems on Malachite Green Aptamer Fluorescence + (The malachite green aptamer (MGapt) is kno … The malachite green aptamer (MGapt) is known for its utility in RNA measurement in vivo and lysate-based cell-free protein systems. However, MGapt fluorescence dynamics do not accurately reflect mRNA concentration. Our study finds that MGapt fluorescence is unstable in commercial PURE systems. We discovered that the chemical composition of the cell-free reaction strongly influences MGapt fluorescence, which leads to inaccurate RNA calculations. Specific to the commercial system, we posit that MGapt fluorescence is significantly affected by the system’s chemical properties, governed notably by the presence of dithiothreitol (DTT). We propose a model that, on average, accurately predicts MGapt measurement within a 10% margin, leveraging DTT concentration as a critical factor. This model sheds light on the complex dynamics of MGapt in cell-free systems and underscores the importance of considering environmental factors in RNA measurements using aptamers.actors in RNA measurements using aptamers.)
Engineering Logical Inflammation Sensing Circuit for Modulating Gut Conditions + (The mammalian gut contains trillions of mi … 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.signal processing in complex environments.)
Resource usage and gene circuit performance characterization in a cell-free âbreadboardâ + (The many successes of synthetic biology ha … The many successes of synthetic biology have come in a manner largely different from those in other en- gineering disciplines; in particular, without well-characterized and simplified prototyping environments to play a role analogous to wind-tunnels in aerodynamics and breadboards in electrical engineering. However, as the complexity of synthetic circuits increases, the benefitsÂin cost savings and design cycle timeÂ of a more traditional engineering approach can be significant. We have recently developed an in vitro ÂbreadboardÂ prototyping platform based on E. coli cell extract that allows biocircuits to operate in an environment considerably simpler than but functionally similar to in vivo. The simplicity of the cell-free transcription-translation breadboard makes it a promising tool for rapid biocircuit design and testing, as well as for probing the fundamentals of gene circuit functions that are normally masked by cellular complex- ity. In this work we characterize the cell-free breadboard using real-time and simultaneous measurements of transcriptional and translational activities of a small set of reporter genes and a transcriptional activation cascade. We determine the effects of promoter strength, gene and nucleoside triphosphate concentrations on biocircuits properties, and we isolate contributions of the essential componentsÂcore RNA polymerase, housekeeping sigma factor, and ribosomesÂto overall performance. Importantly, we show how limits on essential resources, particularly those involved in translation steps, manifest themselves in the form of reduced expression in the presence of orthogonal genes as load processes.nce of orthogonal genes as load processes.)

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