Physical Sciences and Mathematics Commons^™

Multi- Autonomous Vehicle Insertion-Extraction System (Mavies), Jamie C. Macbeth, Manal Habib, Armen Mkrtchyan, Missy Cummings

Computer Science: Faculty Publications

MAVIES (Multi-Autonomous Vehicle Insertion-Extraction System) is the culmination of a year-long multi-stakeholder e ort between UTRC and the Humans and Automation Lab at MIT to design a human inter- face for insertion and extraction missions with multiple UAVs and option- ally piloted rotorcraft. The design process is a successful application of the Hybrid Cognitive Task Analysis (hCTA) process that tracks dozens of tasks, decision-making processes and their associated situation aware- ness requirements to determine the proper allocation of responsibilities between the human operator and the automated mission planner.

This paper discusses the various accomplishments through several phases of a disciplined …

From Double Lie Groupoids To Local Lie 2-Groupoids, Rajan Amit Mehta, Xiang Tang

Mathematics Sciences: Faculty Publications

We apply the bar construction to the nerve of a double Lie groupoid to obtain a local Lie 2-groupoid. As an application, we recover Haefliger's fundamental groupoid from the fundamental double groupoid of a Lie groupoid. In the case of a symplectic double groupoid, we study the induced closed 2-form on the associated local Lie 2-groupoid, which leads us to propose a definition of a symplectic 2-groupoid.

Edge-Guarding Orthogonal Polyhedra, Nadia M. Benbernou, Erik D. Demaine, Martin L. Demaine, Anastasia Kurdia, Joseph O'Rourke, Godfried Toussaint, Jorge Urrutia, Giovanni Viglietta

Computer Science: Faculty Publications

We address the question: How many edge guards are needed to guard an orthogonal polyhedron of e edges, r of which are reflex? It was previously established [3] that e/12 are sometimes necessary and e/6 always suf- fice. In contrast to the closed edge guards used for these bounds, we introduce a new model, open edge guards (excluding the endpoints of the edge), which we argue are in some sense more natural in this context. After quantifying the relationship between closed and open edge guards, we improve the upper bound to show that, asymptotically, (11/72)e (open or closed) edge guards …

An Analysis Of The Effect Of Stress Diffusion On The Dynamics Of Creeping Viscoelastic Flow, Becca Thomases

Mathematics Sciences: Faculty Publications

The effect of stress diffusivity is examined in both the Oldroyd-B and FENE-P models of a viscoelastic fluid in the low Reynolds (Stokes) limit for a 2D periodic time-dependent flow. A local analytic solution can be obtained when assuming a flow of the form u=Wi-1(x,-y), where Wi is the Weissenberg number. In this case the width of the birefringent strand of the polymer stress scales with the added viscosity as ν1/2, and is independent of the Weissenberg number. Also, the " expected" maximum extension of the polymer coils remains finite with any stress diffusion and scales as Wi·ν-1/2. These predictions …

A Recognition-Based Motion Capture Baseline On The Humaneva Ii Test Data, Nicholas Howe

Computer Science: Faculty Publications

The advent of the HumanEva standardized motion capture data sets has enabled quantitative evaluation of motion capture algorithms on comparable terms. This paper measures the performance of an existing monocular recognition-based pose recovery algorithm on select HumanEva data, including all the HumanEva II clips. The method uses a physically-motivated Markov process to connect adajacent frames and achieve a 3D relative mean error of 8.9 cm per joint. It further investigates factors contributing to the error, and finds that research into better pose retrieval methods offers promise for improvement of this technique and those related to it. Finally, it investigates the …

Stress Modulation On The San Andreas Fault By Interseismic Fault System Interactions, John P. Loveless, Brendan J. Meade

Geosciences: Faculty Publications

During the interseismic phase of the earthquake cycle, between large earthquakes, stress on faults evolves in response to elastic strain accumulation driven by tectonic plate motions. Because earthquake cycle processes induce non-local stress changes, the interseismic stress accumulation rate on one fault is influenced by the behavior of all nearby faults. Using a geodetically constrained block model, we show that the total interseismic elastic strain field generated by fault interactions within Southern California may increase stressing rates on the Mojave and San Bernardino sections of the San Andreas fault within the Big Bend region by as much as 38% relative …

The Evolution Of Function In Strictosidine Synthase-Like Proteins, Michael A. Hicks, Alan E. Barber, Lesley Ann Giddings, Jenna Caldwell, Sarah E. O'Connor, Patricia C. Babbitt

Chemistry: Faculty Publications

The exponential growth of sequence data provides abundant information for the discovery of new enzyme reactions. Correctly annotating the functions of highly diverse proteins can be difficult, however, hindering use of this information. Global analysis of large superfamilies of related proteins is a powerful strategy for understanding the evolution of reactions by identifying catalytic commonalities and differences in reaction and substrate specificity, even when only a few members have been biochemically or structurally characterized. A comparison of >2500 sequences sharing the six-bladed β-propeller fold establishes sequence, structural, and functional links among the three subgroups of the functionally diverse N6P superfamily: …

Frēstyl: Simplifying The Process Of Promoting And Discovering Local Live Music, Arianna Bassoli, Johanna Brewer

Computer Science: Faculty Publications

In this paper, we present a new service for web and iPhone for promoting and discovering live music, frēstyl. We will show how frēstyl addresses and attempts to solve the problem that emerging musicians, local promoters and small/medium venues face when publicizing their events, both on a local and global level, and the problem that music fans face when trying to gather a complete but not overwhelming understanding of local and global live music events.

Exploring Agent-Based Simulations In Political Science Using Aggregate Temporal Graphs, R. Jordan Crouser, Jeremy G. Freeman, Remco Chang

Computer Science: Faculty Publications

Agent-based simulation has become a key technique for modeling and simulating dynamic, complicated behaviors in social and behavioral sciences. Lacking the appropriate tools and support, it is difficult for social scientists to thoroughly analyze the results of these simulations. In this work, we capture the complex relationships between discrete simulation states by visualizing the data as a temporal graph. In collaboration with expert analysts, we identify two graph structures which capture important relationships between pivotal states in the simulation and their inevitable outcomes. Finally, we demonstrate the utility of these structures in the interactive analysis of a large-scale social science …

How Locus Of Control Influences Compatibility With Visualization Style, Caroline Ziemkiewicz, R. Jordan Crouser, Ashley Rye Yauilla, Sara L. Su, William Ribarsky, Remco Chang

Computer Science: Faculty Publications

Existing research suggests that individual personality differences are correlated with a user’s speed and accuracy in solving problems with different types of complex visualization systems. In this pa- per, we extend this research by isolating factors in personality traits as well as in the visualizations that could have contributed to the observed correlation. We focus on a personality trait known as “lo- cus of control,” which represents a person’s tendency to see them- selves as controlled by or in control of external events. To isolate variables of the visualization design, we control extraneous factors such as color, interaction, and labeling, …

Layer-By-Layer Fabrication Of Covalently Crosslinked And Reactive Polymer Multilayers Using Azlactone-Functionalized Copolymers: A Platform For The Design Of Functional Biointerfaces, Maren E. Buck, David M. Lynn

Chemistry: Faculty Publications

We report a method for modulating the physicochemical properties of surfaces that is based on the reactive layer-by-layer fabrication of covalently crosslinked thin films using azlactone-functionalized copolymers. We demonstrate that copolymers containing different molar ratios of methyl methacrylate (MMA) and 2-vinyl-4,4-dimethylazlactone (VDMA) can be alternately deposited with poly(ethyleneimine) to assemble covalently crosslinked thin films. Characterization using ellipsometry demonstrates that, in general, film growth and thickness decrease as the content of reactive, azlactone functionality in the copolymer used to assemble the film decreases. Reflective infrared spectroscopy experiments demonstrate that films fabricated from MMA:VDMA copolymers contain residual azlactone functionality and that these …

Spatial Correlation Of Interseismic Coupling And Coseismic Rupture Extent Of The 2011 Mw=9.0 Tohoku-Oki Earthquake, John P. Loveless, Brendan J. Meade

Geosciences: Faculty Publications

Imaging the extent to which the rupture areas of great earthquakes coincide with regions of pre-seismic interplate coupling is central to understanding patterns of strain accumulation and release through the earthquake cycle. Both geodetic and seismic estimates of the coseismic rupture extent for the March 11, 2011 MW = 8.9–9.0 earthquake Tohoku-oki earthquake may be spatially correlated (0.26 ± 0.05 to 0.82 ± 0.05) with a region estimated to be partially to fully coupled in the interseismic period preceding the earthquake, though there is substantial variation in the estimated distribution and magnitude of coseismic slip. The ∼400 km-long region estimated …

On The Lack Of Consensus Over The Meaning Of Openness: An Empirical Study, Alicia M. Grubb, Steve M. Easterbrook

Computer Science: Faculty Publications

This study set out to explore the views and motivations of those involved in a number of recent and current advocacy efforts (such as open science, computational provenance, and reproducible research) aimed at making science and scientific artifacts accessible to a wider audience. Using a exploratory approach, the study tested whether a consensus exists among advocates of these initiatives about the key concepts, exploring the meanings that scientists attach to the various mechanisms for sharing their work, and the social context in which this takes place. The study used a purposive sampling strategy to target scientists who have been active …

Star Messangers, Paul Zimet, Ellen Maddow

Kahn Institute Projects

Star Messengers is a musical theater work about two scientists, Galileo Galilei and Johannes Kepler, who changed our view of the universe. Writer Paul Zimet and composer Ellen Maddow have created a carnival of genres—opera, Com- media dell’Arte, Strindbergian Dream Play, and contemporary dance/theater—to produce a theatrical language that conveys the wonder of Galileo’s and Kepler’s discoveries.

While some aspects of Galileo’s life and discoveries are well known, hardly anything is popularly known of his scientific contemporaries. Johannes Kepler’s realization that the planets moved not in perfect circles, but in elliptical paths, was a leap of mind as extraordinary as …

Extremal Reaches In Polynomial Time, Ciprian S. Borcea, Ileana Streinu

Computer Science: Faculty Publications

Given a 3D polygonal chain with fixed edge lengths and fixed angles between consecutive edges (shortly, a revolutejointed chain or robot arm), the Extremal Reaches Problem asks for those configurations where the distance between the endpoints attains a global maximum or minimum value. In this paper, we solve it with a polynomial time algorithm. Copyright 2011 ACM.

Exact Workspace Boundary By Extremal Reaches, Ciprian S. Borcea, Ileana Streinu

Computer Science: Faculty Publications

We present the first exact, combinatorial, polynomial time algorithm for computing the description of the workspace boundary for the class of revolute jointed robot arms arising from polygonal orthogonal chains in 3D. Copyright 2011 ACM.

Springer Representations On The Khovanov Springer Varieties, Heather M. Russell, Julianna S. Tymoczko

Mathematics Sciences: Faculty Publications

Springer varieties are studied because their cohomology carries a natural action of the symmetric group Sn and their top-dimensional cohomology is irreducible. In his work on tangle invariants, Khovanov constructed a family of Springer varieties Xn as subvarieties of the product of spheres (S2)n. We show that if Xn is embedded antipodally in (S2)n then the natural Sn-action on (S2)n induces an Sn-representation on the image of H*(Xn). This representation is the Springer representation. Our construction admits an elementary (and geometrically natural) combinatorial description, which we use to prove that the Springer representation on H*(Xn) is irreducible in each degree. …

Kinari-Web: A Server For Protein Rigidity Analysis, Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu

Computer Science: Faculty Publications

KINARI-Web is an interactive web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, adding hydrogen atoms and identifying stabilizing interactions. KINARI-Web offers a quick-start option for beginners, and highly customizable features for the experienced user. Chains, residues or atoms, as well as stabilizing constraints can be selected, removed or added, and the user can designate how different chemical interactions should be modeled during rigidity analysis. The enhanced Jmol-based visualizer allows for zooming in, highlighting or investigating different calculated rigidity …

Polygonal Sandcracks: Unique Sedimentary Desiccation Structures In Bahamian Ooid Grainstone, Bosiljka Glumac, H. Allen Curran, Sarah A. Motti, Madeline M. Weigner, Sarah Pruss

Geosciences: Faculty Publications

Sandcracks, which are ubiquitous in Holocene eolian and beach backshore carbonate grainstone on Alligator Point, Cat Island, Bahamas, resemble polygonal mudcracks, but formed in ooid sand without muddy matrix. In experiments on Cat Island beach sand, sediment surfaces cracked polygonally in the absence of mud or biofi lms while drying at room temperature due to contraction generated by capillary effects related to surface tension attraction of interstitial water. Gravitational collapse of irregular open pores and repacking of sand grains due to loss of cohesion between particles caused by evaporation of water enhance the cracking process and appearance of polygons by …

A Positive Monk Formula In The S1-Equivariant Cohomology Of Type A Peterson Varieties, Megumi Harada, Julianna Tymoczko

Mathematics Sciences: Faculty Publications

Peterson varieties are a special class of Hessenberg varieties that have been extensively studied e.g. by Peterson, Kostant, and Rietsch, in connection with the quantum cohomology of the flag variety. In this manuscript, we develop a generalized Schubert calculus, and in particular a positive Chevalley-Monk formula, for the ordinary and Borel-equivariant cohomology of the Peterson variety Y in type A_n−1, with respect to a natural S¹ -action arising from the standard action of the maximal torus on flag varieties. As far as we know, this is the first example of positive Schubert calculus beyond the realm of …

Fabrication And Selective Functionalization Of Amine-Reactive Polymer Multilayers On Topographically Patterned Microwell Cell Culture Arrays, Adam H. Broderick, Samira M. Azarin, Maren E. Buck, Sean P. Palecek, David M. Lynn

Chemistry: Faculty Publications

We report an approach to the fabrication and selective functionalization of amine-reactive polymer multilayers on the surfaces of 3-D polyurethane-based microwell cell culture arrays. "Reactive" layer-by-layer assembly of multilayers using branched polyethyleneimine (BPEI) and the azlactone- functionalized polymer poly(2-vinyl-4,4′-dimethylazlactone) (PVDMA) yielded film-coated microwell arrays that could be chemically functionalized postfabrication by treatment with different amine-functionalized macromolecules or small molecule primary amines. Treatment of film-coated arrays with the small molecule amine d-glucamine resulted in microwell surfaces that resisted the adhesion and proliferation of mammalian fibroblast cells in vitro. These and other experiments demonstrated that it was possible to functionalize different structural …

Tangible Interaction And Learning: The Case For A Hybrid Approach, Michael S. Horn, R. Jordan Crouser, Marina U. Bers

Computer Science: Faculty Publications

Research involving tangible interaction and children has often focused on how tangibles might sup- port or improve learning compared to more traditional methods. In this paper, we review three of our research studies involving tangible computer programming that have addressed this question in a variety of learning environments with a diverse population of children. Through these studies, we identify situations in which tangible interaction seems to offer advantages for learning; how- ever, we have also identify situations in which tangible interaction proves less useful and an alternative interaction style provides a more appropriate medium for learning. Thus, we advocate for …

Common Edge-Unzippings For Tetrahedra, Joseph O'Rourke

Computer Science: Faculty Publications

It is shown that there are examples of distinct polyhedra, each with a Hamiltonian path of edges, which when cut, unfolds the surfaces to a common net. In particular, it is established for infinite classes of triples of tetrahedra.

The Vlt Lbg Redshift Survey I: Clustering And Dynamics Of ≈ 1000 Galaxies At Z ≈ 3⋆, R. M. Bielby, T. Shanks, P. M. Weilbacher, L. Infante, N. H.M. Crighton, C. Bornancini, N. Bouché, P. Héraudeau, D. G. Lambas, James D. Lowenthal, D. Minniti, N. Padilla, P. Petitjean, T. Theuns

Astronomy: Faculty Publications

We present the initial imaging and spectroscopic data acquired as part of the Very Large Telescope (VLT) VIMOS Lyman-break galaxy Survey. UBR (or UBVI) imaging covers five ≈36 × 36 arcmin fields centred on bright z > 3 quasi-stellar objects (QSOs), allowing ≈210002 < z < 3.5 galaxy candidates to be selected using the Lyman-break technique. We performed spectroscopic follow-up using VLT VIMOS, measuring redshifts for 1020 z > 2 Lyman-break galaxies and 10 z > 2 QSOs from a total of 19 VIMOS pointings. From the galaxy spectra, we observe a 625 ± 510kms velocity offset between the interstellar absorption and Lyman α emission-line redshifts, consistent with previous results. Using the photometric and spectroscopic catalogues, we have analysed the galaxy clustering at z≈ 3. The angular correlation …

Stability And Change In Self-Reported Sexual Orientation Identity In Young People: Application Of Mobility Metrics, Miles Q. Ott, Heather L. Corliss, David Wypij, Margaret Rosario, S. Bryn Austin

Statistical and Data Sciences: Faculty Publications

This study investigated stability and change in self-reported sexual orientation identity over time in youth. We describe gender- and age-related changes in sexual orientation identity from early adolescence through emerging adulthood in 13,840 youth ages 12–25 employing mobility measure M, a measure we modified from its original application for econometrics. Using prospective data from a large, ongoing cohort of U.S. adolescents, we examined mobility in sexual orientation identity in youth with up to four waves of data. Ten percent of males and 20% of females at some point described themselves as a sexual minority, while 2% of both males and …

On Homotopy Poisson Actions And Reduction Of Symplectic Q-Manifolds, Rajan Amit Mehta

Mathematics Sciences: Faculty Publications

We present a general framework for reduction of symplectic Q-manifolds via graded group actions. In this framework, the homological structure on the acting group is a multiplicative multivector field.

Symmetric Factorization Of The Conformation Tensor In Viscoelastic Fluid Models, Nusret Balci, Becca Thomases, Michael Renardy, Charles R. Doering

Mathematics Sciences: Faculty Publications

The positive-definite symmetric polymer conformation tensor possesses a unique symmetric square root that satisfies a closed evolution equation in the Oldroyd-B and FENE-P models of viscoelastic fluid flow. When expressed in terms of the velocity field and the symmetric square root of the conformation tensor, these models' equations of motion formally constitute an evolution in a Hilbert space with a total energy functional that defines a norm. Moreover, this formulation is easily implemented in direct numerical simulations resulting in significant practical advantages in terms of both accuracy and stability.

A Stereoselective Hydroxylation Step Of Alkaloid Biosynthesis By A Unique Cytochrome P450 In Catharanthus Roseus, Lesley Ann Giddings, David K. Liscombe, John P. Hamilton, Kevin L. Childs, Dean Dellapenna, C. Robin Buell, Sarah E. O'Connor

Chemistry: Faculty Publications

Plant cytochrome P450s are involved in the production of over a hundred thousand metabolites such as alkaloids, terpenoids, and phenylpropanoids. Although cytochrome P450 genes constitute one of the largest superfamilies in plants, many of the catalytic functions of the enzymes they encode remain unknown. Here, we report the identification and functional characterization of a cytochrome P450 gene in a new subfamily of CYP71, CYP71BJ1, involved in alkaloid biosynthesis. Co-expression analysis of putative cytochrome P450 genes in the Catharanthus roseus transcriptome identified candidate genes with expression profiles similar to known terpene indole alkaloid biosynthetic genes. Screening of these candidate genes by …

Continuous Blooming Of Convex Polyhedra, Erik D. Demaine, Martin L. Demaine, Vi Hart, Joan Iacono, Stefan Langerman, Joseph O'Rourke

Computer Science: Faculty Publications

We construct the first two continuous bloomings of all convex polyhedra. First, the source unfolding can be continuously bloomed. Second, any unfolding of a convex polyhedron can be refined (further cut, by a linear number of cuts) to have a continuous blooming.

Characterizing The Iyj Excess Continuum Emission In T Tauri Stars, William J. Fischer, Suzan Edwards, Lynne A. Hillenbrand, John Kwan

Astronomy: Faculty Publications

We present the first characterization of the excess continuum emission of accreting T Tauri stars between optical and near-infrared wavelengths. With nearly simultaneous spectra from 0.48 to 2.4μm acquired with HIRES and NIRSPEC on Keck and SpeX on the Infrared Telescope Facility, we find significant excess continuum emission throughout this region, including the I, Y, and J bands, which are usually thought to diagnose primarily photospheric emission. The IYJ excess correlates with the excess in the V band, attributed to accretion shocks in the photosphere, and the excess in the K band, attributed to dust in the inner …