Thesis: S.M., Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2019 / Cataloged from the official PDF of thesis. / Includes bibliographical references (pages 42-43). / Synthetic biology is a burgeoning field with applications in medicine, agriculture, chemistry, and other fields. Synthetic biology aims to rationally engineer novel functionality into organisms, from the molecular level to whole genome scale. As an engineering discipline, synthetic biology development follows a canonical design-build-test cycle. In a typical workflow, designs are generated in computer programs, and specified at the DNA level. Subsequently, DNA encoding the design must be built to specification and tested for desired functionality in vivo or in vitro. In current practice, building DNA, by de novo DNA synthesis and related methods, is a rate limiting and costly bottleneck for researchers. State of the art de novo DNA Synthesis technologies, are trial-and-error, nondeterministic processes where turnaround times for specified DNA range on the order of weeks, and cost up to several thousand dollars per gene, multigene order. Of the many challenges inherent to building novel DNA sequences is the occurrence of truncation errors (failure to extend), and damaging side reactions during synthesis of short DNA oligonucleotide (100bp) precursors used in DNA assembly. There are also challenges in assembling oligonucleotides due to the tendency of DNA to form secondary structures and undesired annealing products during assembly reactions. Consequently, DNA synthesis companies spend upwards of 80 percent of manufacturing time sequencing thousands of DNA assemblies until a correct DNA assembly is found. This thesis describes a method for rapid, scalable, de novo DNA synthesis embodied as highly parallelized single molecule enzymatic synthesis of 10KB sequences with real time in situ sequence verification. / by Kettner J.F. Griswold Jr. / S.M. / S.M. Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences

Thesis: S.M., Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2019 / [mu] appeared in title on title page appears as lower case Greek letter. Cataloged from the official PDF of thesis. / Includes bibliographical references (pages 157-166). / We often perform activities that situationally impair us, decreasing our ability to interact with mobile devices when needed. These impairments manifest physically, by preventing us from using our hands and eyes when already being devoted to other ongoing processes (i.e., biking, driving, etc), and socially, by making certain interaction modalities inappropriate given social norms, etiquette, and rules of engagement. Researchers have investigated using jaw and teeth microgestures as a discreet hands-and- eyes-free solution for mobile device interaction while situationally impaired. However, an opportunity remains to investigate ways to wirelessly and unobtrusively sense these gestures, and further explore and evaluate the design space for jaw and teeth microgestures in the context of general-purpose Human Computer Interaction. This thesis makes four major contributions to the exploration of jaw and teeth microgestures. Through an iterative prototyping process, the work contributes attachable, miniaturized, wireless sensor nodes that are placed bilaterally behind the ears to unobtrusively sense jaw-teeth microgestures with 88% accuracy in a stationary context. The thesis also presents a hyper-personalized mobile application that permits training jaw-teeth gestures and mapping them to mobile device commands. The work further contributes a universal teeth contact and jaw-teeth gesture taxonomy, which is evaluated for its comfort and usability. Finally, it contributes an exploration of the potential use cases of jaw-teeth-gesture-based mobile device interaction. / Tomás Alfonso Vega Gálvez. / S.M. / S.M. Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences

Thesis: Ph. D., Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2019 / Cataloged from the official PDF of thesis. / Includes bibliographical references (pages 62-65). / Numerous protein variants have been made to expand the repertoire of CRISPR-Cas nucleases that can recognize protospacer-adjacent motifs (PAMs) other than the canonical NGG discovered in wild-type Streptococcus pyogenes. While Cas nuclease engineering has largely yielded proteins with enhanced specificity for NGG and variations on G-containing PAMs, we were able to construct a chimeric Cas protein with consistent specificity for a 5'-NAA-3' PAM by rationally combining the PAM-interacting domain of Streptococcus macacae with the S. pyogenes Cas9 scaffold. We have been able to demonstrate during in vitro incubations that our chimeric protein is capable of cleaving dsDNA with an NAA PAM, but a deeper biochemical understanding of the nature of these new chimeric proteins' binding and cleavage activities is of paramount importance for their practical use. Here, we use of the principles of enzyme kinetics to investigate our chimeric protein's comparative efficiency to Cas12a and the biophysical mechanism by which our grafted S. macacae segment works synergistically with the S. pyogenes Cas9 scaffold to cleave target DNA with an NAA PAM. We show that SpySmacCas9 does not bind or cleave at rates comparable to Casl2a, but its overall performance rivals that of wild-type SpyCas9 with a new PAM preference. / Lisa Nip / Ph. D. / Ph. D. Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences

Thesis: S.M., Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2019 / Cataloged from the official PDF version of thesis. / Includes bibliographical references (pages 38-40). / To circumvent the limitations of spectrally multiplexing sensors, fluorescent sensors are clustered by type and spatially separated in the cytoplasm to avoid cross-talk. Each sensor is fused to an orthogonal viral capsid protein that binds to a long, repetitive strand of its corresponding RNA sequence. All sensors fluoresce green and are indistinguishable during recording but are identified with post-hoc antibody or FISH staining for each sensor-specific puncta. This spatial multiplexing strategy will allow for easier scaling of the number of fluorescent reporters of physiological activity. / by Shannon L. Johnson. / S.M. / S.M. Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2003. / Includes bibliographical references (p. 146-150). / Woodstein is a software agent that works with a user's web browser to explain and help diagnose problems in web processes, such as purchases. It enables the user to inspect data items in ordinary web pages, revealing the processes that created them. It provides an integrated view of the processes and data associated with a user's actions at a web site, and retrieves related information on the same web site, or even on different web sites. When the user inspects data that looks incorrect, Woodstein helps manage hypotheses about causally related data and processes that look incorrect and provides guidance in the process of elimination to isolate the unsuccessful process or wrong data. / by Earl Joseph Wagner. / S.M.

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2008. / Includes bibliographical references (v. 2, leaves 248-253). / In this work, a system for recognizing activities in the home setting that uses a set of small and simple state-change sensors, machine learning algorithms, and electronic experience sampling is introduced. The sensors are designed to be "tape on and forget" devices that can be quickly and ubiquitously installed in home environments. The proposed sensing system presents an alternative to sensors that are sometimes perceived as invasive, such as cameras and microphones. Since temporal information is an important component of activities, a new algorithm for recognizing activities that extends the naive Bayes classifier to incorporate low-order temporal relationships was created. Unlike prior work, the system was deployed in multiple residential environments with non-researcher occupants. Preliminary results show that it is possible to recognize activities of interest to medical professionals such as toileting, bathing, and grooming with detection accuracies ranging from 25% to 89% depending on the evaluation criteria used. Although these preliminary results were based on small datasets collected over a two-week period of time, techniques have been developed that could be applied in future studies and at special facilities to study human behavior such as the MIT Placelab. The system can be easily retrofitted in existing home environments with no major modifications or damage and can be used to enable IT and health researchers to study behavior in the home. Activity recognition is increasingly applied not only in home-based proactive and preventive healthcare applications, but also in learning environments, security systems, and a variety of human-computer interfaces. / by Randy Joseph Rockinson. / S.M.

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2003. / Pages 98 and 99 blank. / Includes bibliographical references (p. 75-81). / This work builds an infrastructure called Location Linked Information that offers a means to associate digital information with public, physical places. This connection creates a hybrid virtual/physical space, called glean space, that is owned, managed, and rated by the public, for the benefit of the populace. Initially embodied by an interactive, dynamic map viewed on a handheld computer, the system provides two functions for its urban users: 1) the retrieval of information about their surroundings, and 2) the optional annotation of location for communal benefit. Having the ability to link physical location with arbitrary information is an essential function to building immersive information environments and the smart city. Public computing systems such as Location Linked Information will enhance the urban experience, just as access to transportation dramatically altered the sensation and form of the city. / by Matthew William David Mankins. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 131-135). / Robotic vehicles walk on legs, roll on wheels, are pulled by tracks, pushed by propellers, lifted by wings, and steered by rudders. All of these systems share the common character of momentum transport across their surfaces. These existing approaches rely on bulk response among the fluids and solids. They are often not finely controllable and complex approaches suffer from manufacturing and practical operational challenges. In contrast I present a study of a dynamic, programmable interface between the surface and its surrounding fluids. This research explores a synthetic hydrodynamic regime, using a programmable surface to dynamically alter the flow around an object. Recent advances in distributed computing and communications, actuator integration and batch fabrication, make it feasible to create intelligent active surfaces, with significant implications for improving energy efficiency, recovering energy, introducing novel form factors and control laws, and reducing noise signatures. My approach applies ideas from programmable matter to surfaces rather than volumes. The project is based on covering surfaces with large arrays of small cells that can each compute, communicate, and generate shear or normal forces. The basic element is a cell that can be joined in arrays to tile a surface, each containing a processor, connections for power and communications, and means to control the local wall velocity The cell size is determined by the characteristic length scale of the flow field ranging from millimeters to centimeters to match the desired motion and fluidic system. Because boundary layer effects are significant across fluid states from aerodynamics to hydrodynamics to rheology, the possible implications of active control of the boundary layer are correspondingly far reaching, with applications from transportation to energy generation to building air handling. This thesis presents a feasibility study, evaluating current manufacturing, processing, materials, and technologies capabilities to realize programmable surfaces. / by Amy Sun. / Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 79-81). / The purpose of this thesis is to present the design and evaluation of a new type of socially assistive robot, one that can interact with people and collect various types of sensory input while being small enough to hold in one's arms. This project is a completely new revision of the Huggable project created by Dan Stiehl and Cynthia Breazeal, which features a new mechanical design, a revamped electronics structure, and a polished control system based off of its sister project, DragonBot (developed by Adam Setapen). This thesis describes the process of how this new design came to be, and provides extensive content on how it was designed, along with all major components that were included. An evaluation is also presented as a test run for the new Huggable, in the form of an online survey. The results, along with much of the work done with the initial prototype, showed that there is still much work to be done to be convincing as a robust research robot. Improvements are listed, as well as its future work with Boston Children's Hospital. This new design hopes to finally bring the Huggable project out into the field for actual use with people. / by Kristopher B. Dos Santos. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Program in Media Arts & Sciences, 1996. / Includes bibliographical references (p. [223]-238). / Kristinn Rúnar Thórisson. / Ph.D.