The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

Our understanding of solid-fluid dynamics has been severely limited by the nonexistence of a high-fidelity modeling capability for these multiphase systems. Continuum modeling approaches overlook the microscale solid-fluid interactions from which macroscopic system properties emerge, while experimental inquiries have been plagued by high costs and limited resolution. One promising numerical alternative is to simulate solid-fluid systems at the grain-scale, fully resolving the interaction of individual solid particles with other solid particles and the surrounding fluid. Until recently, the direct simulation of these systems has proven computationally intractable. In this thesis an accurate, efficient, and robust modeling capability for the direct simulation of solid-fluid systems is formulated and implemented. The coupled equations of motion governing both the fluid phase and the individual particles comprising the solid phase are solved using a highly efficient numerical scheme based on the discrete-element (DEM) and the lattice-Boltzmann (LB) methods. Particle forcing mechanisms represented in the model to at least the first order include dynamic fluid-induced forces, buoyancy forces, and intergranular forces from particle collisions...

Robotic and embedded systems have become increasingly pervasive in every-day applications, ranging from space probes and life support systems to autonomous rovers. In order to act robustly in the physical world, robotic systems must handle the uncertainty and partial observability inherent in most real-world situations. A convenient modeling tool for many applications, including fault diagnosis and visual tracking, are probabilistic hybrid models. In probabilistic hybrid models, the hidden state is represented with discrete and continuous state variables that evolve probabilistically. The hidden state is observed indirectly, through noisy observations. A challenge is that real-world systems are non-linear, consist of a large collection of concurrently operating components, and exhibit autonomous mode transitions, that is, discrete state transitions that depend on the continuous dynamics. In this thesis, we introduce an efficient algorithm for hybrid state estimation that combines Rao-Blackwellised particle filtering with a Gaussian representation. Conceptually, our algorithm samples trajectories traced by the discrete variables over time and, for each trajectory, estimates the continuous state with a Kalman Filter. A key insight to handling the autonomous transitions is to reuse the continuous estimates in the importance sampling step. We extended the class of autonomous transitions that can be efficiently handled by Gaussian techniques and provide a detailed empirical evaluation of the algorithm on a dynamical system with four continuous state variables. Our results indicate that our algorithm is substantially more efficient than non-RaoBlackwellised approaches. Though not as good as a k-best filter in nominal scenarios...

(cont.) characterization, and kink criterion implementation, form a synergistic analysis of the mechanistic debonding behavior affected by moisture. Results have shown that moisture affected debonding is a highly complex phenomenon that involves physical changes in the bond as well as in its constituent materials. In particular, moisture can initially enhance or reduce the interface fracture toughness, depending on the epoxy formulation being used. The toughness can, however, decrease by as much as 60% and become asymptotic upon reaching a certain moisture concentration threshold, which can be attained in as short as 2 weeks in case of peel fracture. While various debonding modes have been observed for dry specimens, epoxy/concrete interface separation, which has generally been considered an unlikely debonding mode, is observed consistently in all wet fracture specimens. Interface fracture analysis indicates that this newly discovered interfacial debonding mode is attributed to various interfacial material toughening or weakening mechanisms, and has also hinted on the possible interphase formation as a consequence of moisture diffusion. The new knowledge and results obtained from this research provide a basis for further analysis directions and for design of FRP bonded concrete systems against moisture affected debonding.; The objective of this research is to develop new mechanistic understanding of moisture affected debonding failures in carbon fiber-reinforced plastic (FRP) bonded concrete systems by means of an interface fracture approach. Central to the investigation is the use of interface fracture toughness as the quantification parameter...

An experimental study was carried out to determine the feasibility of an original point of use solar water disinfection system created by the author and named "Spirasol." The study primarily focused on the comparison of microbial removal levels in the Spirasol system and the more traditional solar disinfection method called SODIS that uses a Polyethylene Terephthalate (PET) bottle. To address microbial removal capacity, the two systems were assembled and tested in Nairobi, Kenya and later in Cambridge, Massachusetts. The issue of economic feasibility and component availability were also addressed and factored in heavily during the design phase of the project. The results suggest that the Spirasol system is equally as effective as the traditional SODIS system with respect to microbial inactivation. Analysis of the costs required for continuous and semi-continuous solar disinfection system implied that such systems were not a good match for sites of extreme urban poverty such as the Kibera slum in Nairobi, Kenya. However, the overall low cost among semi-continuous point of use treatment systems and the wide availability of the required pieces made them a sustainable technology for other areas in the developing world where available capital is marginally higher.; by Brian Michael Loux.; Thesis (M. Eng.)--Massachusetts Institute of Technology...

Understanding the structure of materials, and how this structure affects their properties, is an important step towards the understanding that is necessary in order to apply computational methods to the end of designing materials to fit very specific needs. Such needs include specific optical and mechanical properties. In polymers, the ability to easily create orientation through a variety of processes allows the production of materials that, while chemically similar, exhibit a wide variety of optical and mechanical properties. The ability to illuminate the connections between structure and optical or mechanical properties depends on the ability to reliably interpret a wide variety of experimental measurements. I assert that thermodynamic consistency and energy minimization is an integral part of this endeavor; reliable analyses of structure and properties are built upon the foundation of a minimum-free-energy ensemble of configurations that reproduces the experimental results. This project encompasses three goals, which make up this thesis: 1) to show how sets of experimental measurements are integrated into simulations to produce thermodynamically consistent, minimum-free-energy ensembles; 2) to show how these ensembles can characterize the conformations of macromolecules...

With the computer hardware industry and the academic world focused on multiprocessor systems, the RAMP project is aiming to provide the infrastructure for supporting high-speed emulation of large scale, massively-parallel multiprocessor systems using FPGAs. The RAMP design framework provides the platform for building this infrastructure. This research utilizes this design framework to emulate various microprocessor memory systems through a model built in an FPGA. We model both the latency and the bandwidth of memory systems through a parameterized emulation platform, thereby, demonstrating the validity of the design framework. We also show the efficiency of the framework through an evaluation of the utilized FPGA resources.; by Asif I. Khan.; Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.; Includes bibliographical references (p. 49-50).

There are two obvious ways to map a two-dimension relational database table onto a one-dimensional storage interface: store the table row-by-row, or store the table column-by-column. Historically, database system implementations and research have focused on the row-by row data layout, since it performs best on the most common application for database systems: business transactional data processing. However, there are a set of emerging applications for database systems for which the row-by-row layout performs poorly. These applications are more analytical in nature, whose goal is to read through the data to gain new insight and use it to drive decision making and planning. In this dissertation, we study the problem of poor performance of row-by-row data layout for these emerging applications, and evaluate the column-by-column data layout opportunity as a solution to this problem. There have been a variety of proposals in the literature for how to build a database system on top of column-by-column layout. These proposals have different levels of implementation effort, and have different performance characteristics. If one wanted to build a new database system that utilizes the column-by-column data layout, it is unclear which proposal to follow. This dissertation provides (to the best of our knowledge) the only detailed study of multiple implementation approaches of such systems...

End-to-end verifiable voting systems allow voters to verify that their votes are cast as intended, collected as cast, and counted as collected. Essentially, end-to-end voting systems provide voters assurance that each step of the election worked correctly. At the same time, voting systems must protect voter privacy and prevent the possibility of improper voter influence and voter coercion. Several end-to-end voting systems have been proposed, varying in usability and practicality. In this thesis we describe and analyze Scantegrity II, a novel end-to-end verification mechanism for optical scan voting which uses confirmation codes printed on the ballot in invisible ink. The confirmation codes allow voters to create privacy-preserving receipts which voters can check against the bulletin board after the close of the election to ensure that their votes have been collected as cast. Anyone can check that votes have been counted as collected and that the tally is correct. We describe the Scantegrity II system and analyze the integrity and privacy properties it provides.; by Emily Shen.; Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.; Includes bibliographical references (p. 57-59).

Traditionally, the sampling of a signal is performed using a single component such as an analog-to-digital converter. However, many new technologies are motivating the use of multiple sampling components to capture a signal. In some cases such as sensor networks, multiple components are naturally found in the physical layout; while in other cases like time-interleaved analog-to-digital converters, additional components are added to increase the sampling rate. Although distributing the sampling load across multiple channels can provide large benefits in terms of speed, power, and resolution, a variety mismatch errors arise that require calibration in order to prevent a. degradation in system performance.In this thesis, we develop low-complexity, blind algorithms for the calibration of distributed sampling systems. In particular, we focus on recovery from timing skews that cause deviations from uniform timing. Methods for bandlimited input reconstruction from nonuniform recurrent samples are presented for both the small-mismatch and the low-SNR domains. Alternate iterative reconstruction methods are developed to give insight into the geometry of the problem.From these reconstruction methods, we develop time-skew estimation algorithms that have high performance and low complexity even for large numbers of components. We also extend these algorithms to compensate for gain mismatch between sampling components. To understand the feasibility of implementation...

Approved for public release; distribution is unlimited; This research provides an analysis of the training required by the Defense Acquisition University (DAU) for Defense Acquisition Workforce Improvement Act (DAWIA) certification in the Systems Planning, Research, Development, and Engineering (SPRDE) Systems Engineering (SE) career field. This training curriculum was compared and contrasted with the actual knowledge, skills and abilities needed to perform as a proficient naval acquisition systems engineer as determined by the Naval Postgraduate School SE Competency Model, as well as to DAUs own SPRDE Competency Model. Learning objectives were also compared to overarching course objectives to determine the consistency of the curriculum itself. It was found that a large gap in training exists. Only 27 percent of the KSAs needed by naval acquisition systems engineers are addressed in the SPRDE training curriculum and the SPRDE-SE curriculum does not accurately reflect the 29 competencies identified in the DAU SPRDE Competency Model. Less than half of the course objectives were consistently supported by associated learning objectives suggesting a weakness in the curriculum. Proper training of this highly specialized workforce is imperative to assure successful acquisition programs. The DAU SPRDE curriculum provides DAWIA certification and some foundation but more must be done to provide comprehensive training.

SYSTEMS ENGINEERING CAPSTONE PROJECT REPORT; Approved for public release; distribution is unlimited; The Department of the Navy (DoN) maintains an inventory of Small Tactical Unmanned Aircraft Systems (STUAS). These systems are designed for payload modularity to support user selection of multiple mission configurations in order to meet any unique mission need. Numerous mission ready payloads have been developed for each system, and only need to be integrated in order to become part of the fielded unmanned aerial system (UAS) configuration. Unfortunately, the DoN does not have a method that maintains sufficient systems engineering (SE) discipline to rapidly integrate and field new mission configurations to the fleet in support of aggressive schedules and urgent user needs. The typical fielding time frame can range from 24 to 36 months, instead of the desired 6 to 18 months. Furthermore, without a sufficient SE approach, risk to mission success is not well understood. This paper captures all applicable requirements for fielding a new capability onto an existing UAS, and using an SE approach, outlines a process to rapidly integrate payloads DoN system. The process identified provides a comprehensive list of integration requirements; a cost...

peer-reviewed; In this paper, we report on techniques for variability and evolution in Model-based Engineering of Embedded Systems. The techniques are based on an integration of domain-specific languages for embedded systems with model-driven techniques for Software Product Lines. In particular, we discuss (1) product configuration with interactive tools, (2) product derivation with model transformations, and (3) first steps towards feature-oriented evolution planning.

Deploying new healthcare technologies for proactive health and elder care will become a major priority over the next decade, as medical care systems worldwide become strained by the aging populations. This thesis presents LiveNet, a distributed mobile system based on low-cost commodity hardware that can be deployed for a variety of healthcare applications. LiveNet embodies a flexible infrastructure platform intended for long-term ambulatory health monitoring with real-time data streaming and context classification capabilities. Using LiveNet, we are able to continuously monitor a wide range of physiological signals together with the user's activity and context, to develop a personalized, data-rich health profile of a user over time. Most clinical sensing technologies that exist have focused on accuracy and reliability, at the expense of cost-effectiveness, burden on the patient, and portability. Future proactive health technologies, on the other hand, must be affordable, unobtrusive, and non-invasive if the general population is going to adopt them.; (cont.) In this thesis, we focus on the potential of using features derived from minimally invasive physiological and contextual sensors such as motion, speech, heart rate, skin conductance...

The aim of this thesis was to generate the knowledge required to represent the possible freedom topologies (motions of a mechanism) and the possible constraint topologies (flexural elements that guide the mechanism) in a form that designers can use to design parallel flexure systems. The framework that links these topologies enables designers to create three-dimensional, multi-axis flexure systems by using "Freedom and Constraint Topologies" (FACT). FACT embodies every possible design solution for parallel flexure systems. This information enables designers to consider every possible design and then select the design that is best suited for a specific application. FACT was created to improve the design processes for small-scale flexure systems and precision machines. For instance, there is a need to create multi-axis nanopositioners for emerging three-dimensional nano-scale research/manufacturing.; (cont.) Through this work the following contributions were made: (1) twenty six unique matching pairs of freedom and constraint spaces were identified; (2) it was proven that these spaces embody all possible solutions; (3) a design process was created to guide a designer from design requirements, to freedom spaces, to constraint spaces, to mechanism designs; (4) a sub-process was created to guide designers in the selection of redundant constraints that help satisfy stiffness and symmetry requirements without altering the mechanism's kinematics; (5) mathematical expressions were created to represent the freedom and constraint spaces in a form that enables computers to identify and manipulate them. In this thesis...

Worldwide electricity consumption will nearly double between 2001 and 2025 but the projects to increase electricity production and transport will not be enough to fulfill the demand. In the future, most of the power demand will be produced by Distributed Generation (DG) systems. DG refers to power generating technologies independent from the electrical grid, located at or near the location where electricity is consumed. Fuel Cells have become very attractive DG systems in recent years, however, Fuel Cells are still in their early stages of deployment and the advantages and disadvantages of such systems for commercial applications are unclear. A study to learn how Fuel Cells perform in commercial buildings was conducted. To compare the effectiveness of fuel cells to other prime movers the study looked at Phosphoric Acid and Molten Carbonate Fuel Cells, microturbines, and lean burning reciprocating engines. First, the hotel's natural gas and electricity load data was analyzed to understand the requirements and adequately size the DG systems. After, the economics and efficiency of the plant was looked at with and without opportunity for cogeneration. Finally, a sensibility analysis was conducted to assess the variability of the plant's savings if some of the assumed parameters changed PAFC and MCFC...

The complexity of the systemic inflammatory response and the lack of a treatment breakthrough in the treatment of pathogenic infection demand that advanced tools be brought to bear in the treatment of severe sepsis and trauma. Systems medicine, the translational science counterpart to basic science's systems biology, is the interface at which these tools may be constructed. Rapid initial strides in improving sepsis treatment are possible through the use of phenomenological modelling and optimization tools for process understanding and device design. Higher impact, and more generalizable, treatment designs are based on mechanistic understanding developed through the use of physiologically based models, characterization of population variability, and the use of control-theoretic systems engineering concepts. In this review we introduce acute inflammation and sepsis as an example of just one area that is currently underserved by the systems medicine community, and, therefore, an area in which contributions of all types can be made.

A crowdsourced stream processing system (CSP) is a system that incorporates crowdsourced tasks in the processing of a data stream. This can be seen as enabling crowdsourcing work to be applied on a sample of large-scale data at high speed, or equivalently, enabling stream processing to employ human intelligence. It also leads to a substantial expansion of the capabilities of data processing systems. Engineering a CSP system requires the combination of human and machine computation elements. From a general systems theory perspective, this means taking into account inherited as well as emerging properties from both these elements. In this paper, we position CSP systems within a broader taxonomy, outline a series of design principles and evaluation metrics, present an extensible framework for their design, and describe several design patterns. We showcase the capabilities of CSP systems by performing a case study that applies our proposed framework to the design and analysis of a real system (AIDR) that classifies social media messages during time-critical crisis events. Results show that compared to a pure stream processing system, AIDR can achieve a higher data classification accuracy, while compared to a pure crowdsourcing solution...

The purchase of medical devices involves engaging various stakeholders as well as balancing clinical, technical and financial requirements. Failure to consider these requirements can lead to wider consequences in the delivery of care. This study first builds a general knowledge base of current purchasing practice in a sample of NHS Trusts, which confirms the direction and guidance given by policy documents and literature as to the extent of the challenges faced by purchasing stakeholders. This then leads to an analysis to identify inefficiencies in the purchasing process, and how such practice can lead to risks in the delivery of care. These risks range from injury to individuals, impacts to the healthcare delivery service, and financial and litigation risks. Finally, a framework that highlights these potential risks in the life-cycle of medical devices in hospitals is presented. Key policy guidance has encouraged both researchers and implementers of healthcare services to approach patient safety from a systems perspective, acknowledging that medical device errors are not only directly related to device design, but to the design of the healthcare delivery service system in which the device operates. Little evidence exists of successfully applying systems approaches specifically to medical device purchasing practice. Medical device purchasing...

The need for systems engineering training is steadily increasing, as both the defense and commercial markets take on more complex "systems of systems" work. A variety of universities and commercial training vendors have assembled courses of various lengths, format, and content to meet this need. This presentation looks at the requirements for systems engineering training, and discusses techniques for increasing its effectiveness. Several format and content options for meeting these requirements are compared and contrasted, and an experience-based curriculum is shown.