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• Fast Mode Switching for a Thrust Vectored Aircraft  + (Aircraft operate in different modes during … Aircraft operate in different modes during flight, corresponding to different flight conditions and</br>control schemes. We use differential flatness of an approximate model of the pitch dynamics of a</br>thrust vectored aircraft to achieve fast switching between those modes. We investigate some</br>methods to compensate for the perturbations to flatness. Simulations and experimental data are</br>provided to validate the approach.ata are provided to validate the approach.)
• Model-Based Control of Cavity Oscillations, Part I: Experiments  + (An experimental investigation of acoustic … An experimental investigation of acoustic mode noise suppression was conducted in a cavity using a digital controller with a linear control algorithm. The control algorithm was based on flow field physics similar to the Rossiter model for acoustic resonance. Details of the controller and results from its implementation are presented in the companion paper by Rowley, et al (2002). Here the experiments and some details of the flow field development are described, which were done primarily at Mach number 0.34 corresponding to single mode resonance in the cavity. A novel method using feedback control to suppress the resonant mode and open-loop forcing to inject a non-resonant mode was developed for system identification. The results were used to obtain empirical transfer functions of the components of resonance, and measurements of the shear layer growth for use in the design of the control algorithm.se in the design of the control algorithm.)
• Population regulation in microbial consortia using dual feedback control  + (An ongoing area of study in synthetic biol … An ongoing area of study in synthetic biology has been the design and construction of synthetic circuits that maintain homeostasis at the population level. Here, we are interested in designing a synthetic control circuit that regulates the total cell population and the relative ratio between cell strains in a culture containing two different cell strains. We have developed a dual feedback control strategy that uses two separate control loops to achieve the two functions respectively. By combining both of these control loops, we have created a population regulation circuit where both the total population size and relative cell type ratio can be set by reference signals. The dynamics of the regulation circuit show robustness and adaptation to perturbations in cell growth rate and changes in cell numbers. The control architecture is general and could apply to any organism for which synthetic biology tools for quorum sensing, comparison between outputs, and growth control are available.outputs, and growth control are available.)
• System identification of phosophorylation based insulator in a cell-free in vitro transcription-translation system  + (An outstanding challenge in the design of … An outstanding challenge in the design of synthetic biocircuits is the development of a robust and efficient strategy for interconnecting functional modules. Recent theoretical work demonstrated that a phosphorylation based insulator implementing a dual strategy of high gain and strong negative feedback could potentially serve as a device to attenuate retroactivity. This research investigates the structural identifiability of the phoshorylation based insulator when implemented in an {\it in vitro} transcription-translation cell free expression system. We consider a complex model that provides an intricate description of all chemical reactions and leveraging specific physiologically plausible assumptions, we derive a rigorous simplified model that captures the output dynamics of the phosphorylation based insulator. We perform standard system identification analysis and determine that the model is globally identifiable with respect to three critical parameters. Our findings show the utility of the transcription-translation cell free expression system as a platform for system identification, as it provides extra control inputs for parameter estimation that typically are unavailable in vivo. The parameters estimated are then used as a basis for a simulation study in a parallel experimental work (also submitted to qBio-2014).mental work (also submitted to qBio-2014).)
• Nonholonomic Mechanics and Locomotion: The Snakeboard Example  + (Analysis and simulations are performed for … Analysis and simulations are performed for a simplified model of a</br>commercially available variant on the skateboard, known as the Snakeboard.</br>Although the model</br>exhibits basic gait patterns seen in a large number of locomotion problems,</br>the analysis tools currently available do not apply to this problem. The</br>difficulty is seen to lie primarily in the way in which the nonholonomic</br>constraints enter into the system. As a first step towards understanding</br>systems represented by our model we present the equations of motion and</br>perform some controllability analysis for the snakeboard. We also perform</br>some numerical simulations of the gait patterns.umerical simulations of the gait patterns.)
• Tunable integrase-mediated differentiation facilitates improved output of burdensome functions in E. coli  + (Application of synthetic biology is limite … Application of synthetic biology is limited by the capacity of cells to faithfully execute burdensome engineered functions in the face of Darwinian evolution. Division of labor, both metabolic and reproductive, are underutilized in confronting this barrier. To address this, we developed a serine-integrase based differentiation circuit that allows control of the population composition through tuning of the differentiation rate and number of cell divisions differentiated cells can undergo. We applied this system to T7 RNAP-driven expression of a fluorescent protein, and demonstrate both increased duration of circuit function and total production for high burden expression. While T7 expression systems are typically used for high-level short-term expression, this system enables longer duration production, and could be readily applied to burdensome or toxic products not readily produced in bacteria.products not readily produced in bacteria.)
• Design and implementation of a synthetic biomolecular concentration tracker  + (As a field, synthetic biology strives to e … As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we use synthetic protein scaffolds as a modular and tunable mechanism for concentration tracking through negative feedback. Input to the circuit initiates scaffold production, leading to colocalization of a two-component system and resulting in the production of an inhibitory antiscaffold protein. Using a combination of modeling and experimental work, we show that the biomolecular concentration tracker circuit achieves dynamic protein concentration tracking in ''Escherichia coli'' and that steady state outputs can be tuned.nd that steady state outputs can be tuned.)
• Toward Specification-Guided Active Mars Exploration for Cooperative Robot Teams  + (As a step towards achieving autonomy in sp … As a step towards achieving autonomy in space exploration missions we consider a collaborative robotics system with a copter and a rover. The goal of the copter is to explore an unknown environment so as to maximize knowledge about a science mission expressed in Linear Temporal Logic that is to be executed by the rover. We model environmental uncertainty as a belief space Markov Decision Process and formulate the problem as a two-step stochastic dynamic program that we solve in a way that leverages the decomposed nature of the overall system. We demonstrate in simulations that the robot team makes intelligent decisions in the face of uncertainty.gent decisions in the face of uncertainty.)
• Control of density and composition in an engineered two-member bacterial community  + (As studies continue to demonstrate how our … As studies continue to demonstrate how our health is related to the status of our various commensal microbiomes, synthetic biologists are developing tools and approaches to control these microbiomes and stabilize healthy states or remediate unhealthy ones. Building on previous work to control bacterial communities, we have constructed a synthetic two-member bacterial consortium engineered to reach population density and composition steady states set by inducer inputs. We detail a screening strategy to search functional parameter space in this high-complexity genetic circuit as well as initial testing of a functional two-member circuit.</br></br>We demonstrate non-independent changes in total population density and composition steady states with a limited set of varying inducer concentrations. After a dilution to perturb the system from its steady state, density and composition steady states are not regained. Modeling and simulation suggest a need for increased degradation of intercellular signals to improve circuit performance. Future experiments will implement increased signal degradation and investigate the robustness of control of each characteristic to perturbations from steady states.istic to perturbations from steady states.)
• Privacy Preserving Average Consensus  + (Average consensus is a widely used algorit … Average consensus is a widely used algorithm for distributed averaging, where all the agents in the network constantly communicate and update their states in order to achieve an agreement. This approach could result in an undesirable disclosure of information on the initial state of agent i to other agents. In this paper, we propose a Privacy Preserving Average Consensus (PPAC) algorithm to guarantee the privacy of the initial state and the convergence to the exact initial values, by adding and subtracting random noises to the consensus process. We characterize the mean square convergence rate of the PPAC algorithm and derive upper and lower bounds for the covariance matrix of the maximum likelihood estimate on the initial state. We further provide an algebraic condition under which the PPAC algorithm is (epsilon, delta)-differentially private. A numerical example is provided to illustrate the effectiveness of the PPAC algorithm.e the effectiveness of the PPAC algorithm.)

• A Field-Deployable Arsenic Sensor Integrating Bacillus Megaterium with CMOS Technology  + (Bacteria innately monitor their environmen … Bacteria innately monitor their environment by dynamically regulating gene expression to respond to fluctuating conditions. Through synthetic biology, we can harness this natural capability to design cell-based sensors. Bacillus megaterium, a soil bacterium, stands out due to its remarkable heavy metal tolerance and sporulation ability, making it an ideal candidate for heavy metal detection with low transportation costs. However, challenges persist: the synthetic biology toolkit for this strain is underdeveloped and conventional whole-cell sensors necessitate specialized laboratory equipment to read the output. In our study, we genetically modified B. megaterium for arsenic detection, establishing a detection threshold below the EPA recommendation of 10 ppb for drinking water in both vegetative cell form and spore form. Additionally, we integrated both engineered B. megaterium living cells and spores with CMOS chip for field-deployable arsenic detection. We show that the limit of detection of our integrated sensor is applicable in soil and air arsenic contamination testing. As a proof of concept, this work paves the way for deploying our sensor in resource-limited settings, ensuring real-time arsenic detection in challenging environments.nic detection in challenging environments.)
• Effects of Actuator Limits in Bifurcation Control with Applications to Active Control of Fluid Instabilities in Turbomachinery  + (Bifurcations are ubiquitous in engineering … Bifurcations are ubiquitous in engineering applications.</br> Subcritical bifurcations are typically associated with hysteresis</br> and catastrophic instability inception, while supercritical</br> bifurcations are usually associated with gradual and more benign</br> instability inception. With the assumption that the bifurcating</br> modes are linearly unstabilizable, we give a constructive procedure</br> of designing feedback laws to change the criticality of bifurcations</br> from subcritical to supercritical. Algebraic necessary and</br> sufficient conditions are obtained under which the criticality of a</br> simple steady-state or Hopf bifurcation can be changed to</br> supercritical by a smooth feedback. The effects of magnitude</br> saturation, bandwidth, and rate limits are important issues in</br> control engineering. We give qualitative estimates of the region of</br> attraction to the stabilized bifurcating equilibrium/periodic orbits</br> under these constraints.</br><p></br>We apply the above theoretical results to the Moore-Greitzer model</br> in active control of rotating stall and surge in gas turbine</br> engines. Though linear stabilizability can be achieved using</br> distributed actuation, it limits the practical usefulness due to</br> considerations of affordability and reliability. On the other hand,</br> simple but practically promising actuation schemes such as outlet</br> bleed valves, a couple of air injectors, and magnetic bearings will</br> make the system loss of linear stabilizability, thus the control</br> design becomes a challenging task. The above mentioned theory in</br> bifurcation stabilization can be applied to these cases. We analyze</br> the effects of magnitude and rate saturations in active control of</br> rotating stall using bleed valves. Analytic formulas are obtained</br> for the operability enhancement as a function of system parameters,</br> noise level, and actuator magnitude and rate limits. The formulas</br> give good qualitative predictions when compared with experiments.</br> Our conclusion is that actuator magnitude and rate limits are</br> serious limiting factors in stall control and must be addressed in</br> practical implementation to the aircraft engines.</br><p>ical implementation to the aircraft engines. <p>)
• BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts  + (Biochemical interactions in systems and sy … Biochemical interactions in systems and synthetic biology are often modeled with chemical reaction networks (CRNs). CRNs provide a principled modeling environment capable of expressing a huge range of biochemical processes. In this paper, we present a software toolbox, written in Python, that compiles high-level design specifications represented using a modular library of biochemical parts, mechanisms, and contexts to CRN implementations. This compilation process offers four advantages. First, the building of the actual CRN representation is automatic and outputs Systems Biology Markup Language (SBML) models compatible with numerous simulators. Second, a library of modular biochemical components allows for different architectures and implementations of biochemical circuits to be represented succinctly with design choices propagated throughout the underlying CRN automatically. This prevents the often occurring mismatch between high-level designs and model dynamics. Third, high-level design specification can be embedded into diverse biomolecular environments, such as cell-free extracts and in vivo milieus. Finally, our software toolbox has a parameter database, which allows users to rapidly prototype large models using very few parameters which can be customized later. By using BioCRNpyler, users ranging from expert modelers to novice script-writers can easily build, manage, and explore sophisticated biochemical models using diverse biochemical implementations, environments, and modeling assumptions.s, environments, and modeling assumptions.)
• How to model DNA replication in stochastic models of synthetic genetic circuits (and why)  + (Biocircuit modeling sometimes requires exp … Biocircuit modeling sometimes requires explicit tracking of a self-replicating DNA species. The most obvious, straightforward way to model a replicating DNA is structurally unstable and leads to pathological model behavior. We describe a simple, stable replication mechanism with good model behavior and show how to derive it from a mechanistic model of ColE1 replication. a mechanistic model of ColE1 replication.)
• Synthetic circuit for exact adaptation and fold-change detection  + (Biological organisms use their sensory sys … Biological organisms use their sensory systems to detect changes in their environment. The ability of sensory systems to adapt to static inputs allows wide dynamic range as well as sensitivity to input changes including fold-change detection, a response that de- pends only on fold changes in input, and not on ab- solute changes. This input scale invariance underlies an important strategy for search that depends solely on the spatial profile of the input. Synthetic efforts to reproduce the architecture and response of cellu- lar circuits provide an important step to foster under- standing at the molecular level. We report the bottom- up assembly of biochemical systems that show exact adaptation and fold-change detection. Using a malachite green aptamer as the output, a synthetic tran- scriptional circuit with the connectivity of an incoherent feed-forward loop motif exhibits pulse generation and exact adaptation. A simple mathematical model was used to assess the amplitude and duration of pulse response as well as the parameter regimes required for fold-change detection. Upon parameter tuning, this synthetic circuit exhibits fold-change detection for four successive rounds of two-fold input changes. The experimental realization of fold-change detection circuit highlights the programmability of transcriptional switches and the ability to obtain predictive dynamical systems in a cell-free environment for technological applications.nvironment for technological applications.)
• Systematic Design and Implementation of a Novel Synthetic Fold-Change Detector Biocircuit In Vivo  + (Biological signaling systems not only dete … Biological signaling systems not only detect the absolute levels of the signals, but are also able to sense the fold-changes of the signals. The ability to detect fold-changes provides a powerful tool for biological organisms to adapt to the changes in environment. Here we present the first novel syn- thetic fold-change detector (FCD) circuit built from ground up in vivo. We systematically designed the FCD circuit in silico, prototyped it in cell-free transcription-translation platform (TX-TL), and eventually implemented it in E. coli cells. We were able to show that the FCD circuit can not only generate pulse-like behavior in response to input, but also produce the same pulse response with inputs of the same fold-change, despite of di�erent absolute signal levels.espite of di�erent absolute signal levels.)
• An analytical approach to bistable biological circuit discrimination using real algebraic geometry  + (Biomolecular circuits with two distinct an … Biomolecular circuits with two distinct and stable steady states have been identified as essential components in a wide range of biological networks, with a variety of mechanisms and topologies giving rise to their important bistable property. Understanding the differences between circuit implementations is an important question, particularly for the synthetic biologist faced with determining which bistable circuit design out of many is best for their specific application. In this work we explore the applicability of Sturm's theorem—a tool from nineteenth-century real algebraic geometry—to comparing ‘functionally equivalent’ bistable circuits without the need for numerical simulation. We first consider two genetic toggle variants and two different positive feedback circuits, and show how specific topological properties present in each type of circuit can serve to increase the size of the regions of parameter space in which they function as switches. We then demonstrate that a single competitive monomeric activator added to a purely monomeric (and otherwise monostable) mutual repressor circuit is sufficient for bistability. Finally, we compare our approach with the Routh–Hurwitz method and derive consistent, yet more powerful, parametric conditions. The predictive power and ease of use of Sturm's theorem demonstrated in this work suggest that algebraic geometric techniques may be underused in biomolecular circuit analysis.nderused in biomolecular circuit analysis.)
• Vehicle Motion Planning Using Stream Functions  + (Borrowing a concept from hydrodynamic anal … Borrowing a concept from hydrodynamic analysis, this paper presents stream functions which satisfy Laplace's equation as a local-minima free method for producing potential-field based navigation functions in two dimensions. These functions generate smoother paths (i.e. more suited to aircraft-like vehicles) than previous methods. A method is developed for constructing analytic stream functions to produce arbitrary vehicle behaviors while avoiding obstacles, and an exact solution for the case of a single uniformly moving obstacle is presented. The effects of introducing multiple obstacles are discussed and current work in this direction is detailed. Experimental results generated on the Cornell RoboFlag testbed are presented and discussed.oFlag testbed are presented and discussed.)
• Uniting local and global controllers for the Caltech ducted fan  + (Caltech's ducted fan experiment is used as … Caltech's ducted fan experiment is used</br>as a case study to investigate the properties of</br>an algorithm for uniting local and global controllers</br>proposed in (Teel and Kapoor, 1997)</br>To simplify the control design process and to illustrate robustness,</br>the ducted fan is</br>modeled as a linear system with input rate limits.</br>The local controller is an (fairly aggressive) LQR state feedback while</br>the (semi-)global controller is a much less aggressive</br>LQR state feedback. Closed-loop simulation results</br>are provided</br>using a fully nonlinear model of the ducted fan derived</br>from wind tunnel data. Experimental results are also</br>provided using the actual Caltech ducted fan.vided using the actual Caltech ducted fan.)
• A chemical reaction network model of PURE  + (Cell-free expression systems provide a met … Cell-free expression systems provide a method for rapid DNA circuit prototyping and functional protein synthesis. While crude extracts remain a black box with many components carrying out unknown reactions, the PURE system contains only the required transcription and translation components for protein production. All proteins and small molecules are at known concentrations, opening up the possibility of detailed modeling for reliable computational predictions. However, there is little to no experimental data supporting the expression of target proteins for detailed protein models PURE models. In this work, we build a chemical reaction network transcription model for PURE protein synthesis. We compare the transcription models using DNA encoding for the malachite-green aptamer (MGapt) to measure mRNA production. Furthermore, we expand the PURE detailed translation model for an arbitrary set of amino acids and length. Lastly, we combine the transcription and the expanded translation models to create a PURE protein synthesis model built purely from mass-action reactions. We use the combined model to capture the translation of a plasmid encoding MGapt and deGFP under a T7-promoter and a strong RBS. The model accurately predicts the MGapt mRNA production for the first two hours, the dynamics of deGFP expression, and the total protein production with an accuracy within 10%.in production with an accuracy within 10%.)
• Metabolic perturbations to an E. coli-based cell-free system reveal a trade-off between transcription and translation  + (Cell-free transcription-translation (TX-TL … Cell-free transcription-translation (TX-TL) systems have been used for diverse applications, from prototyping gene circuits to providing a platform for the development of synthetic life, but their performance is limited by issues such as batch-to-batch variability, poor predictability, and limited lifetime. These issues stem largely from the fact that cell lysate contains an active and complex metabolism whose effect on TX-TL has remained largely uncharacterized.</br></br>Motivated by a minimal model of cell-free metabolism, this work explored the effects of energy molecules, which power TX-TL, and fuel molecules, which regenerate energy by harnessing core metabolism, on an E. coli -based TX-TL system. This work reports a compensatory interaction between TX-TL components Mg2+ and 3-phosphoglyceric acid (3-PGA, used to regenerate ATP), where if one component’s concentration is increased, the other’s must likewise be increased to maintain optimal translation. Furthermore, maximum mRNA and protein production occur in opposite concentration regimes of Mg+2 and 3-PGA, suggesting a TX-TL trade-off. To explore the observed phenomenon, transcription and translation were decoupled. Under translation inhibition, transcriptional output was uniform across Mg2+ and 3-PGA concentrations, but in a translation-only system, maximum protein production occurred in the previously found optimal regime of Mg2+ and 3-PGA. Using alternative fuels to regenerate energy, this work found that the trade-off is universal across the different fuel sources, and that a system’s position along the trade-off is determined strongly by Mg2+. The location and slope of the trade-off curve are determined strongly by DNA concentration, cell lysate batch, and the fraction of cell lysate in a reaction. Finally, in systems where additional energy is supplied and where a fuel source is absent, the trade-off is absent.</br></br>Overall, these results suggest the trade-off arises from limitations in translation regulation and efficient energy regeneration. This work represents a significant advancement in understanding the effects of fuel and energy metabolism on TX-TL in cell-free systems and lays the foundation for improving TX-TL performance, lifetime, standardization, and prediction.lifetime, standardization, and prediction.)
• Proof of concept continuous event logging in living cells  + (Cells must detect and respond to molecular … Cells must detect and respond to molecular events such as the presence or absence of specific small molecules. To accomplish this, cells have evolved methods to measure the presence and concentration of these small molecules in their environment and enact changes in gene expression or behavior. However, cells don’t usually change their DNA in response to outside stimuli. In this work, we have engineered a genetic circuit that can enact specific and controlled genetic changes in response to small molecule stimuli. Known DNA sequences can be repeatedly integrated in a genomic array such that their identity and order encodes information about past small molecule concentrations that the cell has experienced. To accomplish this, we use catalytically inactive CRISPR-Cas9 (dCas9) to bind to and block attachment sites for the integrase Bxb1. Therefore, through the co-expression of dCas9 and guide RNA, Bxb1 can be directed to integrate one of two engineered plasmids, which correspond to two orthogonal small molecule inducers that can be recorded with this system. We identified the optimal location of guide RNA binding to the Bxb1 attP integrase attachment site, and characterized the detection limits of the system by measuring the minimal small molecule concentration and shortest induction time necessary to produce measurable differences in array composition as read out by Oxford Nanopore sequencing technology. by Oxford Nanopore sequencing technology.)
• Feedback Stabilization of Steady-State and Hopf Bifurcations: the Multi-input Case  + (Classification of stabilizability is obtai … Classification of stabilizability is obtained for multi-input nonlinear systems</br>possessing a simple steady-state or Hopf bifurcation with the critical mode being linearly</br>uncontrollable. Stabilizability is defined as the existence of a sufficiently smooth state</br>feedback such that the bifurcation for the closed loop system is supercritical, and in the</br>meantime, the linearly controllable modes are locally asymptotically stable. Necessary and</br>sufficient conditions of stabilizability are derived under certain nondegeneracy</br>conditions. Explicit construction of stabilizing feedbacks is obtained for the cases when</br>the system is stabilizable.the cases when the system is stabilizable.)
• Multi-Hop Relay Protocols for Fast Consensus Seeking  + (Consensus protocols in coordinated multi-a … Consensus protocols in coordinated multi-agent systems are</br>distributed algorithms. Just using local information</br>available to each single agent, all agents converge to an</br>identical consensus state and the convergence speed is</br>determined by the algebraic connectivity of the</br>communication network. In order to achieve a faster</br>consensus seeking, we propose multi-hop relay protocols</br>based on the current ``nearest neighbor rules'' consensus</br>protocols. By employing multiple-hop paths in the network,</br>more information is passed around and each agent enlarges</br>its "available" neighborhood. We demonstrate that these</br>relay protocols can increase the algebraic connectivity</br>without physically adding or changing any communication</br>links. Moreover, time delay sensitivity of relay protocols</br>are discussed in detail. We point out that a trade off</br>exists between convergence performance and time delay</br>robustness. Simulation results are also provided to verify</br>the efficiency of relay protocols. verify the efficiency of relay protocols.)
• Pacti: Scaling Assume-Guarantee Reasoning for System Analysis and Design  + (Contract-based design is a method to facil … Contract-based design is a method to facilitate modular system design. While there has been substantial progress on the theory of contracts, there has been less progress on scalable algorithms for the algebraic operations in this theory. In this paper, we present: 1) principles to implement a contract-based design tool at scale and 2) Pacti, a tool that can efficiently compute these operations. We then illustrate the use of Pacti in a variety of case studies.use of Pacti in a variety of case studies.)
• Graph Laplacians and Stabilization of Vehicle Formations  + (Control of vehicle formations has emerged … Control of vehicle formations has emerged as a topic of significant interest to the controls</br>community. In this paper, we merge tools from graph theory and control theory to derive</br>stability criteria for formation stabilization. The interconnection between vehicles (i.e., which</br>vehicles are sensed by other vehicles) is modeled as a graph, and the eigenvalues of the Laplacian</br>matrix of the graph are used in stating a Nyquist-like stability criterion for vehicle formations.</br>The location of the Laplacian eigenvalues can be correlated to the graph structure, and therefore</br>used to identify desirable and undesirable formation interconnection topologies.able formation interconnection topologies.)
• Optimal and Cooperative Control of Vehicle Formations  + (Control of vehicle formations has emerged … Control of vehicle formations has emerged as a topic of significant </br> interest to the controls community. In applications such as microsatellites </br> and underwater vehicles, formations have the potential for greater functionality </br> and versatility than individual vehicles. In this thesis, we investigate two </br> topics relevant to control of vehicle formations: optimal vehicle control and </br> cooperative control.ehicle control and cooperative control.)
• An Experimental Comparison of Tradeoffs in Using Compliant Manipulators for Robotic Grasping Tasks  + (Controllers developed for control of flexi … Controllers developed for control of flexible-link robots in hybrid</br>force-position control tasks by a new singular perturbation analysis</br>of flexible manipulators are implemented on an experimental two-robot</br>grasping setup. Various performance criteria are set up and</br>experimental results are discussed within that setting to show</br>tradeoffs in using flexible link robots for grasping. We conclude that</br>large flexibility can be controlled without too much additional</br>effort, has performance comparable to rigid robots and possesses</br>enhancing properties which make it attractive for use in certain types</br>of applications. for use in certain types of applications.)
• Robust Estimation Framework with Semantic Measurements  + (Conventional simultaneous localization and … Conventional simultaneous localization and map- ping (SLAM) algorithms rely on geometric measurements and require loop-closure detections to correct for drift accumulated over a vehicle trajectory. Semantic measurements can add measurement redundancy and an alternative form of loop closure. We propose two different estimation algorithms that incorporate semantic measurements provided by vision-based object classifiers. An a priori map of regions where the objects can be detected is assumed. The first estimation framework is posed as a maximum-likelihood problem, where the likelihood function for semantic measurements is derived from the con- fusion matrices of the object classifiers. The second estimation framework is comprised of two parts: 1) a continuous-state estimation formulation that includes semantic measurements as a form of state constraints and 2) a discrete-state estimation formulation used to compute the certainty of object detection measurements using a Hidden Markov Model (HMM). The advantages of incorporating semantic measurements in these frameworks are demonstrated in numerical simulations. In particular, the proposed estimation algorithms improve upon the robustness and accuracy of conventional SLAM algorithms. Also, the certainty metric of object detection measurements derived from the HMM in our simulation are greater than the certainty levels provided by the confusion matrix in object classification algorithms.atrix in object classification algorithms.)
• Convergence Properties of Dynamic Agents Consensus Networks with Broken Links  + (Convergence properties of distributed cons … Convergence properties of distributed consensus protocols on networks of dynamical agents have been analyzed by combinations of algebraic graph theory and control theory tools under certain assumptions, such as strong connectivity. Strong connectivity can be regarded as the requirement that the information of each agent propagates to all the others, possibly with intermediate steps and manipulations. However, because of network failures or malicious attacks, it is possible that this assumption no longer holds, so that some agents are </br>only receiving or only transmitting information from other subsets of agents. In this case, strong connectivity is replaced by weak connectivity. We analyze the convergence properties of distributed consensus on directed graphs with weakly connected components. We show conditions for which the agreement is reached, and, for the cases in which such conditions do not </br>hold, we provide bounds on the residual disagreement. </br>in terms of the number of agents that must fail for thehe number of agents that must fail for the)
• Variable Elimination for Scalable Receding Horizon Temporal Logic Planning  + (Correct-by-construction synthesis of high- … Correct-by-construction synthesis of high-level re- active control relies on the use of formal methods to generate controllers with provable guarantees on their behavior. While this approach has been successfully applied to a wide range of systems and environments, it scales poorly with the increasing size of the environment. A receding horizon framework was recently proposed to mitigate this computational blowup, by decomposing the global control problem into several tractable subproblems. The existence of a global controller is ensured through symbolic checks of the specification, and local controllers are synthesized when needed, using the current state of the environment as the initial condition. This reduces the size of the synthesized strategy, but does not provide much improvement for problems with large dynamic environments, because the large number of possible global environment strategies. Ad hoc methods to locally restrict the environment have previously been used, at the risk of losing correctness. This paper presents a method of reducing specifications by eliminating locally redundant variables, while maintaining the correctness of controllers. We demonstrate the method using an autonomous car example, on problem sizes that were previously unsolvable due to the number of variables in the environment. We also demonstrate how the reduced specifications can be used to identify opportunities for reusing the synthesized local controllers.reusing the synthesized local controllers.)
• Quantification and Minimization of Crosstalk Sensitivity in Networks  + (Crosstalk is defined as the set of unwante … Crosstalk is defined as the set of unwanted interactions among the different entities of a network. Crosstalk is present in various degrees in every system where information is transmitted through a means that is accessible by all the individual units of the network. Using concepts from graph theory, we introduce a quantifiable measure for sensitivity to crosstalk, and analytically derive the structure of the networks in which it is minimized. It is shown that networks with an inhomogeneous degree distribution are more robust to crosstalk than corresponding homogeneous networks. We provide a method to construct the graph with the minimum possible sensitivity to crosstalk, given its order and size. Finally, for networks with a fixed degree sequence, we present an algorithm to find the optimal interconnection structure among their vertices.connection structure among their vertices.)
• Design and application of stationary phase combinatorial promoters  + (Current bacterial synthetic circuits rely … Current bacterial synthetic circuits rely on the fast dilution and high protein expression that occurs during exponential phase. However, constant exponential phase is both difficult to ensure in a lab environment and almost certainly impractical in any natural setting. Here, we characterize the performance of 13 E. coli native 38 promoters, as well as a previously identified 38 consensus promoter. We then make tetO combinatorial versions of the three strongest promoters to allow for inducible delayed expression. The design of these combinatorial promoters allows for design of circuits with inducible stationary phase activity that can be used for phase-dependent delays in dynamic circuits or spatial partitioning of biofilms.cuits or spatial partitioning of biofilms.)
• System-level studies of a cell-free transcription-translation platform for metabolic engineering  + (Current methods for assembling biosyntheti … Current methods for assembling biosynthetic pathways in microorganisms require a process of repeated trial and error and have long design-build-test cycles. We describe the use of a cell-free transcription-translation (TX-TL) system as a biomolecular breadboard for the rapid engineering of the 1,4-butanediol (BDO) pathway. We demonstrate the reliability of TX-TL as a platform for engineering biological systems by undertaking a careful characterization of its transcription and translation capabilities and provide a detailed analysis of its metabolic output. Using TX-TL to survey the design space of the BDO pathway enables rapid tuning of pathway enzyme expression levels for improved product yield. Leveraging TX-TL to screen enzyme variants for improved catalytic activity accelerates design iterations that can be directly applied to in vivo strain development.tly applied to in vivo strain development.)
• Prototyping 1,4-butanediol (BDO) biosynthesis pathway in a cell-free transcription-translation (TX-TL) system  + (Current methods for assembling metabolic p … Current methods for assembling metabolic pathways require a process of repeated trial and error and have a long design-build-test cycle. Further, it remains a challenge to precisely tune enzyme expression levels for maximizing target metabolite production. Recently it was shown that a cell-free transcriptional-translation system (TX-TL) can be used to rapidly prototype novel complex biocircuits as well as metabolic pathways. TX-TL systems allow protein expression from multiple DNA pieces, opening up the possibility of modulating concentrations of DNA encoding individual pathway enzymes and testing the related effect on metabolite production. In this work, we demonstrate TX-TL as a platform for exploring the design space of metabolic pathways using a 1,4-BDO biosynthesis pathway as an example. Using TX-TL, we verified enzyme expression and enzyme activity and identified the conversion of 4-hydroxybutyrate to downstream metabolites as a limiting step of the 1,4-BDO pathway. We further tested combinations of various enzyme expression levels and found increasing downstream enzyme expression levels improved 1,4-BDO production.ession levels improved 1,4-BDO production.)