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• 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 </br>size are possible if shorter, more aggressive, serpentine inlet ducts are used </br>for low-observability constrained propulsion installations. To obtain this benefit, </br>both inlet separation and compressor stall dynamics must be controlled. In this </br>paper the integrated control of this coupled inlet/compression system is considered. </br>Initial results are shown using separation point actuation to control both separation </br>and stall dynamics. Calculations show that separation can be substantially reduced </br>with approximately 1.2% core flow, based on scaling previous results. Simulation </br>results using a medium fidelity model show that proportional control of distortion </br>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.</br>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.</br></br>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.)
• Online Horizon Selection in Receding Horizon Temporal Logic Planning  + (Temporal logics have proven effective for … Temporal logics have proven effective for correct-by-construction</br>synthesis of controllers for a wide range of</br>applications. Receding horizon frameworks mitigate the</br>computational intractability of reactive synthesis for temporal</br>logic, but have thus far been limited by pursuing a single</br>sequence of short horizon problems to the current goal. We</br>propose a receding horizon algorithm for reactive synthesis that</br>automatically determines a path to the currently pursued goal at</br>runtime, in response to a nondeterministic environment. This is</br>achieved by allowing each short horizon to have multiple local</br>goals, and determining which local goal to pursue based on the</br>current global goal, currently perceived environment and a</br>pre-computed invariant dependent on each global goal. We</br>demonstrate the utility of this additional flexibility in</br>grant-response tasks, using a search-and-rescue</br>example. Moreover, we show that these goal-dependent invariants</br>mitigate 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)</br>is a platform designed to explore theoritical advances</br>in multi-vehicle coordination and control, networked</br>control systems and high con�dence distributed</br>computation. The contribution of this report is to</br>present simulation and experimental results on the</br>generation and implementation of optimal trajectories</br>for the MVWT vehicles. The vehicles are nonlinear</br>and spatially contrained with bounded input control.</br>The trajectories are generated using the NTG software</br>package developed at Caltech. Minimum time trajectories</br>and the application of Model Predictive Control (MPC)</br>are investigated.</br>can actually follow i.e. trajectories that satisfy every</br>constraint of the testbed. Those constraints can either</br>be linear, like the boundaries of the testbed or nonlinear</br>like the constraints on the input. The main di�erence and</br>also di�culty in our case is that the system is not linearly</br>controllable around its equilibrium.</br>In Section 2 we will give a quick description of the systems</br>properties and in Section 3 and 4 we will describe the</br>progression which led us from the optimization problem</br>to the implementation on the real vehicles. In Section</br>5 other optimization problems such as minimum time</br>trajectory generation and model predictive control are</br>investigated.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 is</br>an experimental platform for validating theoretical advances</br>in multiple-vehicle coordination and cooperation, real-time</br>networked control system, and distributed computation. This</br>paper describes the design and development of an additional</br>fleet of 12 second-generation vehicles. These vehicles are</br>hovercrafts and designed to have lower mass and friction as</br>well as smaller size than the first generation vehicles. These</br>hovercrafts combined with the outdoor wireless testbed provide</br>a 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 on</br>sensor manufactured by Boeing and currently in use on U.S. Navy submarines. The additi</br>onal ability of the ESG to act as an accelerometer is well known, but extraction of</br>precision acceleration measuremen ts from an ESG has not been achieved. The major</br>obstacles to precision accelerometry are the nonlinear dynamics of the ESG rotor and param</br>etric variation of the ESG electronics. In this paper, we derive a model for the ESG</br>dynamics with an eye toward efficient representation of the uncertainties in the model. We</br>represent the model uncert ainties and nonlinearities in a framework amenable to</br>mu-analysis and analyze ESG accelerometer precision using $\mu$-analysis tools. Finally,</br>we discuss the implementation of a digital ESG control architecture for use in ESG system</br>identification 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 an</br>Pfaffian exterior differential system is equivalent to a certain</br>normal form. This paper details how the Goursat normal form and its</br>extensions provide a unified framework for understanding feedback</br>linearization, chained form, and differential flatness.</br><p> Keywords: Exterior differential systems, nonholonomic constraints,</br>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 gymnast</br>performing on a single parallel bar. By swinging her legs, a gymnast</br>is able to bring herself into an inverted position with her center of</br>mass above the part and is able to perform manuevers about this</br>configuration. This report studies the use of nonlinear control</br>techniques for designing a controller to operate in a neighborhood of</br>the manifold of inverted equilibrium points. The techniques described</br>here are of particular interest because the dynamic model of the</br>acrobot violates many of the necessary conditions required to apply</br>current methods in linear and nonlinear control theory.</br><p></br>The approach used in this report is to approximate the system in such</br>a way that the behavior of the system about the manifold of</br>equilibrium points is correctly captured. In particular, we construct</br>an approximating system which agrees with the linearization of the</br>original system on the equilibrium manifold and is full state</br>linearizable. For this class of approximations, controllers can be</br>constructed using recent techniques from differential geometric control </br>theory. We show that application of control laws derived in this</br>manner results in approximate trajectory tracking for the system under</br>certain restrictions on the class of desired trajectories. Simulation</br>results 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 </br>physical and information systems that maintain desirable performance by sensing </br>and automatically adapting to changes in the environment. As we begin the 21st </br>Century, the opportunities to apply control principles and methods are exploding. </br>New developments in this increasingly information rich world will require a significant </br>expansion of the basic tool sets of control. This article summarizes the main </br>findings and recommendations of the Panel on Future Directions in Control, Dynamics, </br>and Systems, which has recently released its report. The report spells out some </br>of the prospects for control in the current and future technological environment, </br>describes the role the field will play in military, commercial, and scientific </br>applications over the next decade, and recommends actions required to enable new </br>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,</br>time-varying controllers which asymptotically stabilize a driftless</br>nonlinear system to be converted to homogeneous, time-varying</br>controllers which provide {\em exponential} stability. The resulting</br>controllers are smooth everywhere except the origin and are easily</br>computed given the original asymptotic stabilizer. We illustrate the</br>result 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 ‘breadboard’  + (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 time of a more traditional engineering approach can be significant. We have recently developed an in vitro Âbreadboard 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.)
• Experimental Demonstration of the Dynamics and Stability of a Low Reynolds Number Swimmer Near a Plane Wall  + (The motion of microorganisms as well as of … The motion of microorganisms as well as of tiny robotic swimmers for biomedical applications is governed by low Reynolds number (Re) hydrodynamics, where viscous effects dominate and inertial effects are negligible. This paper presents experimental results that verify theoretical predictions of our recent work which analyzed the dynamics and stability of a low-Re swimmer near a plane wall. The experimental setup uses macro-scale swimmer prototypes which are propelled by rotating cylinders in highly viscous silicone oil. The motion was recorded by a video camera and position measurements were taken by an optical tracking system. The results show good qualitative agreement with our recent theoretical predictions.t with our recent theoretical predictions.)
• Simple Delay-Based Implementation of Continuous-Time Controllers  + (The objective of this work is to study the … The objective of this work is to study the benefits that delay can provide in simplifying the control process of large-scale systems, motivated by the availability of different types of delays in man-made and biological systems. We show that a continuous-time linear time-invariant (LTI) controller can be approximated by a simple controller that mainly uses delay blocks instead of integrators. More specifically, three methods are proposed to approximate a pre-designed stabilizing LTI controller arbitrarily precisely by a simple delay-based controller composed of delay blocks, a few integrators and possibly a unity feedback. Different problems associated with the developed approximation procedures, such as finding the optimal number of delay blocks or studying the robustness of the designed controller with respect to delay values, are then addressed.spect to delay values, are then addressed.)
• Observability of a Class of Hybrid Systems on Bounded Lattices  + (The observability properties of a class of … The observability properties of a class of hybrid</br>systems whose continuous variables are available for measurement</br>are considered. We show that the discrete variables'</br>dynamics can be always extended for observable systems to</br>a lattice in such a way that the extended system has the</br>properties that allow the construction of the LU discrete</br>state estimator. Such an estimator updates two variables at</br>each step, namely the upper and lower bound of the set</br>of all possible discrete variables' values compatible with the</br>output sequence. We give an estimate of the complexity of the</br>estimator in the worst case.lexity of the estimator in the worst case.)
• Implementation And Simulation Of Phosphorylation-Based Insulator In Transcription-Translation Platform  + (The operational amplifier (OPAMP) is a ver … The operational amplifier (OPAMP) is a very useful insulation module in electric circuits to avoid loading effect (retroactivity). In synthetic biological circuits, we also have the same retroactivity problem, in which the biomolecular systems are not always modular due to downstream components. The output of the upstream component will be affected as the downstream component sequesters that output, which in turn impedes the process of constructing more complex biocircuits. To address this obstacle, the retroactivity needs to be attenuated by implementing a similar OPAMP device using biocircuits. Previous theoretical papers suggested a potential function of a phosphorylation based circuit in providing the feature of atten- uating retroactivity. Here we presented a successful prototyping and implementation of such a phosphorylation-based insulator (PBI) in an in vitro cell-free transcription-translation system (TX- TL). We demonstrated that retroactivity also exists in TX-TL system, if not stronger, by testing a simple negative regulation circuit. Besides we showed that the TX-TL system contains all the protein, DNA components and other resources required for the PBI circuit to work properly. We then demonstrated that the PBI circuit helps minimizing the loading effect to less than 10% compared to control circuit. With this preliminary PBI circuit design, attenuation of retroactivity while connecting two modules in vitro becomes possible. In concert with another paper from our group (E. Yeung, S. Guo, R. Murray QBIO2014) which used system identification to estimate all three essential parameters in a simplified PBI model, we showed that the simulations based on these parameters match the experimental data very well and provide an interesting insight into future designs.n interesting insight into future designs.)
• Geometric trajectory filtering via numerical conformal mapping  + (The paper studies the problem which we ref … The paper studies the problem which we refer to as geometric trajectory filtering, where only trajectories that satisfy the local safety constraints are selected from a library of trajectories. The goal is to speed up primitive-based motion planning while still maintaining a relatively a large collection of motion primitives. One way to solve this problem is to obtain a proper (preferably smooth) function, referred to as the containment indicator function, that describes the shape of the free space. To construct the containment indicator function for an arbitrary shape, the paper uses conformal mapping to transform the original shape of interest to a simpler target shape (e.g. disk, rectangle), which can then be characterized by elementary functions. Computational methods for finding the desired conformal maps are studied. It is shown that they can be formulated as convex optimization problems, whose solution can be obtained efficiently.hose solution can be obtained efficiently.)
• Learning diffeomorphism models of robotic sensorimotor cascades  + (The problem of bootstrapping consists in d … The problem of bootstrapping consists in designing agents that can learn from scratch the model of their sensori- motor cascade (the series of robot actuators, the external world, and the robot sensors) and use it to achieve useful tasks. In principle, we would want to design agents that can work for any robot dynamics and any robot sensor(s). One of the difficulties of this problem is the fact that the observations are very high dimensional, the dynamics is nonlinear, and there is a wide range of "representation nuisances" to which we would want the agent to be robust. In this paper, we model the dynamics of sensorimotor cascades using diffeomorphisms of the sensel space. We show that this model captures the dynamics of camera and range-finder data, that it can be used for long-term predictions, and that it can capture nonlinear phenomena such as a limited field of view. Moreover, by analyzing the learned diffeomorphisms it is possible to recover the "linear structure" of the dynamics in a manner which is independent of the commands representation.ndependent of the commands representation.)
• Discrete State Estimators for a Class of Nondeterministic Hybrid Systems on a Lattice  + (The problem of estimating the discrete var … The problem of estimating the discrete variables</br>in nondeterministic hybrid systems where the continuous</br>variables are available for measurement is considered. Using</br>partial order and lattice theory, we construct a discrete state</br>estimator, the LU estimator, which updates two variables at</br>each step. Namely, it updates the lower (L) and upper (U)</br>bounds of the set of all possible discrete variables values</br>compatible with the output sequence and with the systems'</br>dynamics. If the system is weakly observable, we show that</br>there always exist a lattice on which to construct the LU</br>estimator. For computational issues, some partial orders are to</br>be preferred to others.We thus show that nondeterminism may</br>be added to a system so as to obtain a new system that satisfies</br>the requirements for the construction of the LU estimator on</br>a chosen lattice. These ideas are applied to a nondeterministic</br>multi-robot system. to a nondeterministic multi-robot system.)
• Nonlinear Trajectory Generation for Unmanned Air Vehicles with Multiple Radars  + (The problem of finding a real time optimal … The problem of finding a real time optimal</br>trajectory to minimize the probability of detection (to maximize</br>the probability of notbeingdetected, pnd, function) of</br>unmanned air vehicles by opponent radar detection systems</br>is investigated. This paper extends our preliminary results</br>on low observable trajectory generation in three ways. First,</br>trajectory planning in the presence of detection by multiple</br>radar systems, rather than single radar systems, is considered.</br>Second, an overall probability of detection function is</br>developed for the multiple radar case. In previous work, both</br>probability of detection by a single radar and signature were</br>developed in the theory section, but the examples used only</br>signature constraints. In this work, the use of the overall</br>probability of detection function is used, both because it</br>aids in the extension to multiple radar systems and because</br>it is a more direct measure of the desirable optimization</br>criteria. The third extension is the use of updated signature</br>and probability of detection models. The new models have a</br>greater number of sharp gradients than the previous models,</br>with low detectability regions for both a cone shaped areas</br>centered around the nose as in the previous paper, as well as a</br>cone-shaped area centered around rear of the air vehicle. The</br>Nonlinear Trajectory Generation method (NTG), developed</br>at Caltech, is used and motivated by the ability to provide</br>real time solutions for constrained nonlinear optimization</br>problems. Numerical simulations of multiple radar scenarios</br>illustrate UAV trajectories optimized for both detectability and</br>time.optimized for both detectability and time.)
• Model reduction of interconnected linear systems  + (The problem of model reduction of linear s … The problem of model reduction of linear systems with certain interconnection structure is considered </br>in this paper. To preserve the interconnection structure between subsystems in the reduction, special </br>care needs to be taken. This problem is important and timely because of the recent focus on complex </br>networked systems in control engineering. Two different model-reduction methods are introduced and </br>compared in the paper. Both methods are extensions to the well-known balanced truncation method. </br>Compared to earlier work in the area these methods use a more general linear fractional transformation </br>framework, and utilize linear matrix inequalities. Furthermore, new approximation error bounds that </br>reduce to classical bounds in special cases are derived. So-called structured Hankel singular valueso-called structured Hankel singular values)
• Formal Test Synthesis for Safety-Critical Autonomous Systems based on Control Barrier Functions  + (The prolific rise in autonomous systems ha … The prolific rise in autonomous systems has led to questions regarding their safe instantiation in real-world scenarios. Failures in safety-critical contexts such as human-robot interactions or even autonomous driving can ultimately lead to loss of life. In this context, this paper aims to provide a method by which one can algorithmically test and evaluate an autonomous system. Given a black-box autonomous system with some operational specifications, we construct a minimax problem based on control barrier functions to generate a family of test parameters designed to optimally evaluate whether the system can satisfy the specifications. To illustrate our results, we utilize the Robotarium as a case study for an autonomous system that claims to satisfy waypoint navigation and obstacle avoidance simultaneously. We demonstrate that the proposed test synthesis framework systematically finds those sequences of events (tests) that identify points of system failure.s) that identify points of system failure.)
• 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 computational protein design and screened in a cell-free transcription-translation (TX-TL) system for responsiveness to a new targeted effector. The modified repressors target vanillin, a growth-inhibiting small molecule found in lignocellulosic hydrolysates and other industrial processes. Promising candidates from the in vitro screen were further characterized in vitro and in vivo in a gene circuit. The screen yielded two qacR mutants that respond to vanillin both in vitro and in vivo. While the mutants exhibit some toxicity to cells, presumably due to off-target effects, they are prime starting points for directed evolution toward vanillin sensors with the specifications required for use in a dynamic control loop. We believe this process, a combination of the generation of variants coupled with in vitro screening, can serve as a framework for designing new sensors for other target compounds.ng new sensors for other target compounds.)
• 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.)