Property:Abstract
From Murray Wiki
Jump to navigationJump to search
This is a property of type Text.
A
Substantial reductions in aircraft
size are possible if shorter, more aggressive, serpentine inlet ducts are used
for low-observability constrained propulsion installations. To obtain this benefit,
both inlet separation and compressor stall dynamics must be controlled. In this
paper the integrated control of this coupled inlet/compression system is considered.
Initial results are shown using separation point actuation to control both separation
and stall dynamics. Calculations show that separation can be substantially reduced
with approximately 1.2% core flow, based on scaling previous results. Simulation
results using a medium fidelity model show that proportional control of distortion
has little effect on stall behavior. +
S
Successful high-speed autonomous navigation requires integration of tools from robotics, control theory, computer vision, and systems engineering. This thesis presents work that develops and combines these tools in the context of navigating desert terrain.
A comparative analysis of reactive, behavior-based, and deliberative control architectures provides important guidelines for design of robotic systems. These guidelines depend on the particular task and environment of the vehicle. Two important factors are identified which guide an effective choice between these architectures: dynamic feasibility for the vehicle, and predictability of the environment. This is demonstrated by parallels to control theory, illustrative examples, simulations, and analysis of Bob and Alice---Caltech's full-scale autonomous ground vehicle entries in the 2004 and 2005 Grand Challenge races, respectively.
Further, new model-based methods are developed for constructing and maintaining estimates of terrain elevation and road geometry. These are demonstrated in simulation and in fully autonomous operation of Alice, including accurate detection and tracking of the centerline of desert roads at speeds up to 5 m/s. Finally, Alice's navigation architecture is presented in full along with experimental results that demonstrate its capabilities. +
C
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. +
B
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. +
D
Data-driven network models for genetic circuits from time-series data with incomplete measurements +
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. +
M
Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking +
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. +
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. +
N
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. +
D
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. +
O
Temporal logics have proven effective for correct-by-construction
synthesis of controllers for a wide range of
applications. Receding horizon frameworks mitigate the
computational intractability of reactive synthesis for temporal
logic, but have thus far been limited by pursuing a single
sequence of short horizon problems to the current goal. We
propose a receding horizon algorithm for reactive synthesis that
automatically determines a path to the currently pursued goal at
runtime, in response to a nondeterministic environment. This is
achieved by allowing each short horizon to have multiple local
goals, and determining which local goal to pursue based on the
current global goal, currently perceived environment and a
pre-computed invariant dependent on each global goal. We
demonstrate the utility of this additional flexibility in
grant-response tasks, using a search-and-rescue
example. Moreover, we show that these goal-dependent invariants
mitigate the conservativeness of the receding horizon approach. +
N
The Caltech Multi Vehicles Wireless Testbed (MVWT)
is a platform designed to explore theoritical advances
in multi-vehicle coordination and control, networked
control systems and high con�dence distributed
computation. The contribution of this report is to
present simulation and experimental results on the
generation and implementation of optimal trajectories
for the MVWT vehicles. The vehicles are nonlinear
and spatially contrained with bounded input control.
The trajectories are generated using the NTG software
package developed at Caltech. Minimum time trajectories
and the application of Model Predictive Control (MPC)
are investigated.
can actually follow i.e. trajectories that satisfy every
constraint of the testbed. Those constraints can either
be linear, like the boundaries of the testbed or nonlinear
like the constraints on the input. The main di�erence and
also di�culty in our case is that the system is not linearly
controllable around its equilibrium.
In Section 2 we will give a quick description of the systems
properties and in Section 3 and 4 we will describe the
progression which led us from the optimization problem
to the implementation on the real vehicles. In Section
5 other optimization problems such as minimum time
trajectory generation and model predictive control are
investigated. +
M
The Caltech Multi-Vehicle Wireless Testbed is
an experimental platform for validating theoretical advances
in multiple-vehicle coordination and cooperation, real-time
networked control system, and distributed computation. This
paper describes the design and development of an additional
fleet of 12 second-generation vehicles. These vehicles are
hovercrafts and designed to have lower mass and friction as
well as smaller size than the first generation vehicles. These
hovercrafts combined with the outdoor wireless testbed provide
a perfect hardware platform for RoboFlag competition. +
R
The Electrostatically Suspended Gyroscope (ESG) is a two-axis inertial orientati on
sensor manufactured by Boeing and currently in use on U.S. Navy submarines. The additi
onal ability of the ESG to act as an accelerometer is well known, but extraction of
precision acceleration measuremen ts from an ESG has not been achieved. The major
obstacles to precision accelerometry are the nonlinear dynamics of the ESG rotor and param
etric variation of the ESG electronics. In this paper, we derive a model for the ESG
dynamics with an eye toward efficient representation of the uncertainties in the model. We
represent the model uncert ainties and nonlinearities in a framework amenable to
mu-analysis and analyze ESG accelerometer precision using $\mu$-analysis tools. Finally,
we discuss the implementation of a digital ESG control architecture for use in ESG system
identification and testing of suspension control and acce lerometer algorithms. +
A
The Goursat normal form theorem gives conditions under which an
Pfaffian exterior differential system is equivalent to a certain
normal form. This paper details how the Goursat normal form and its
extensions provide a unified framework for understanding feedback
linearization, chained form, and differential flatness.
<p> Keywords: Exterior differential systems, nonholonomic constraints,
chained form, feedback linearization, differentially flat. +
O
Optimizing protein expression in the One-Pot PURE system: Insights into reaction composition and translation efficiency +
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. +
T
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. +
A
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 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. +
R
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. +
S
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. +
A
The acrobot is a simple mechanical system patterned after a gymnast
performing on a single parallel bar. By swinging her legs, a gymnast
is able to bring herself into an inverted position with her center of
mass above the part and is able to perform manuevers about this
configuration. This report studies the use of nonlinear control
techniques for designing a controller to operate in a neighborhood of
the manifold of inverted equilibrium points. The techniques described
here are of particular interest because the dynamic model of the
acrobot violates many of the necessary conditions required to apply
current methods in linear and nonlinear control theory.
<p>
The approach used in this report is to approximate the system in such
a way that the behavior of the system about the manifold of
equilibrium points is correctly captured. In particular, we construct
an approximating system which agrees with the linearization of the
original system on the equilibrium manifold and is full state
linearizable. For this class of approximations, controllers can be
constructed using recent techniques from differential geometric control
theory. We show that application of control laws derived in this
manner results in approximate trajectory tracking for the system under
certain restrictions on the class of desired trajectories. Simulation
results based on a simplified model of the acrobot are included. +
