Computation within the context of mechanical engineering at MIT

Thesis: S.B., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2019Cataloged from the official PDF of thesis. "May 2019."Computation is undoubtedly playing a significant role in mechanical engineering both inside and outside of MIT, impacting how mechanical engineers approach and solve problems as well as how mechanical engineering is defined and evaluated. This study focuses on how computation is defined within MIT by analyzing input from both faculty and students in Course 2. Responses from faculty were collected by conducting a series of semi-structured interviews with the teaching staff while input from students were collected in a more indirect manner, by analyzing a historical data set of Course 6 classes taken by Course 2 students from 2014 to 2019 and by assessing 107 responses collected from a student survey. Based on inputs from faculty, computation takes various forms inside a Course 2 classroom, functioning as a skillset or a platform for learning and teaching. Student inputs suggest that there is a growing interest in learning various computation tools both inside and outside of their major. While most Course 2 students feel satisfied with their computational experience at MIT, there are still aspects of the Course 2 and Course 6 curriculum in need of improvement.by Kyubin Lee.S.B.S.B. Massachusetts Institute of Technology, Department of Mechanical Engineerin

Pneumatic shape-shifting fingers to reorient and grasp

We present pneumatic shape-shifting fingers to enable a simple parallel-jaw gripper for different manipulation modalities. By changing the finger geometry, the gripper effectively changes the contact type between the fingers and an object to facilitate distinct manipulation primitives. In this paper, we demonstrate the development and application of shape-shifting fingers to reorient and grasp cylindrical objects. The shape of the fingers changes based on the air pressure inside them and attains two distinct geometric forms at high and low pressure values. In our implementation, the finger shape switches between a wedge-shaped geometry and V-shaped geometry at high and low pressure, respectively. Using the wedge-shaped geometry, the fingers provide a point contact on a cylindrical object to pivot it to a vertical pose under the effect of gravity. By changing to V-shaped geometry, the fingers localize the object in the vertical pose and securely hold it. Experimental results show that the smooth transition between the two contact types allows a robot with a simple gripper to reorient a cylindrical object lying horizontally on a ground and to grasp it in a vertical pose

Dynamic modules of the coactivator SAGA in eukaryotic transcription

Gene activation: many modules make light work A protein that helps add epigenetic information to genome, SAGA, controls many aspects of gene activation, potentially making it a target for cancer therapies. To fit inside the tiny cell nucleus, the genome is tightly packaged, and genes must be unpacked before they can be activated. Known to be important in genome opening, SAGA has now been shown to also play many roles in gene activation. Daeyoup Lee at the KAIST, Daejeon, South Korea, and co-workers have reviewed recent discoveries about SAGA’s structure, function, and roles in disease. They report that SAGA’s complex (19 subunits organized into four modules) allows it to play so many roles, genome opening, initiating transcription, and efficiently exporting mRNAs. Its master role means that malfunction of SAGA may be linked to many diseases

Bone Remodeling: Histone Modifications as Fate Determinants of Bone Cell Differentiation

The bone tissue is a dynamic complex that constitutes of several interdependent systems and is continuously remodeled through the concerted actions of bone cells. Osteoblasts are mononucleated cells, derived from mesenchymal stem cells, responsible for bone formation. Osteoclasts are large multinucleated cells that differentiate from hematopoietic progenitors of the myeloid lineage and are responsible for bone resorption. The lineage-specific differentiation of bone cells requires an epigenetic regulation of gene expressions involving chromatin dynamics. The key step for understanding gene regulatory networks during bone cell development lies in characterizing the chromatin modifying enzymes responsible for reorganizing and potentiating particular chromatin structure. This review covers the histone-modifying enzymes involved in bone development, discusses the impact of enzymes on gene expression, and provides future directions and clinical significance in this area

Quantitative Trait Locus Based Virulence Determinant Mapping of the HSV-1 Genome in Murine Ocular Infection: Genes Involved in Viral Regulatory and Innate Immune Networks Contribute to Virulence.

Herpes simplex virus type 1 causes mucocutaneous lesions, and is the leading cause of infectious blindness in the United States. Animal studies have shown that the severity of HSV-1 ocular disease is influenced by three main factors; innate immunity, host immune response and viral strain. We previously showed that mixed infection with two avirulent HSV-1 strains (OD4 and CJ994) resulted in recombinants that exhibit a range of disease phenotypes from severe to avirulent, suggesting epistatic interactions were involved. The goal of this study was to develop a quantitative trait locus (QTL) analysis of HSV-1 ocular virulence determinants and to identify virulence associated SNPs. Blepharitis and stromal keratitis quantitative scores were characterized for 40 OD4:CJ994 recombinants. Viral titers in the eye were also measured. Virulence quantitative trait locus mapping (vQTLmap) was performed using the Lasso, Random Forest, and Ridge regression methods to identify significant phenotypically meaningful regions for each ocular disease parameter. The most predictive Ridge regression model identified several phenotypically meaningful SNPs for blepharitis and stromal keratitis. Notably, phenotypically meaningful nonsynonymous variations were detected in the UL24, UL29 (ICP8), UL41 (VHS), UL53 (gK), UL54 (ICP27), UL56, ICP4, US1 (ICP22), US3 and gG genes. Network analysis revealed that many of these variations were in HSV-1 regulatory networks and viral genes that affect innate immunity. Several genes previously implicated in virulence were identified, validating this approach, while other genes were novel. Several novel polymorphisms were also identified in these genes. This approach provides a framework that will be useful for identifying virulence genes in other pathogenic viruses, as well as epistatic effects that affect HSV-1 ocular virulence

Protein-protein interaction network of high scoring vQTLmap identified virulence proteins.

<p>A key is provided near the bottom of the Fig. The size of the nodes corresponds to the number of interactions. The network was produced by literature search using the GADGET tool, and the display was generated using Cytoscape 3.2.0.</p