Harvey Mudd College

Background: In higher education, efforts to broaden participation in computing (BPC) are typically evaluated at a single institution, which limits our ability to isolate their impacts from those of other factors at the institution.

The taxonomy of soft corals with a stoloniferous growth form is challenging. The family Clavulariidae and, more specifically, the genus Clavularia have acted as a repository for most stoloniferous corals that could not systematically be differentiated with morphology. In addition, the lack of morphological and genetic data for the type species of Clavularia, Clavularia viridis, has made a revision of the genus impossible. In this study, we use an integrative taxonomic approach combining morphological examinations and novel molecular methods to revise the taxonomy and systematics of Clavulariidae within Octocorallia. We re-describe key species of Clavularia, including C. viridis, C. inflata and C. koellikeri, resolve the position of Clavulariidae within Octocorallia, and present a revised taxonomy of the tropical, zooxanthellate species of Clavularia that includes morphological characters of each species. We further confirm the polyphyly of Clavulariidae, and resurrect the genus Hicksonia and family Hicksoniidae (Malacalcyonacea) to accommodate a new species with connecting tubes on multiple levels (H. tohrui sp. nov.). We also describe a new genus and species of Clavulariidae from Japan Bairdium iriomotejimaensis gen. nov., sp. nov. and a new Clavularia species from the Great Barrier Reef (C. brunafolia sp. nov.). This study resolves the fundamental taxonomy of Clavularia, and provides the necessary baseline for future works. ZooBank: urn:lsid:zoobank.org:pub:61754CF6-A3C9-4D1C-AC6F-4435C12BD4AD.

Emphasizing how and why machine learning algorithms work, this introductory textbook bridges the gap between the theoretical foundations of machine learning and its practical algorithmic and code-level implementation. Over 85 thorough worked examples, in both Matlab and Python, demonstrate how algorithms are implemented and applied whilst illustrating the end result. Over 75 end-of-chapter problems empower students to develop their own code to implement these algorithms, equipping them with hands-on experience. Matlab coding examples demonstrate how a mathematical idea is converted from equations to code, and provide a jumping off point for students, supported by in-depth coverage of essential mathematics including multivariable calculus, linear algebra, probability and statistics, numerical methods, and optimization. Accompanied online by instructor lecture slides, downloadable Python code and additional appendices, this is an excellent introduction to machine learning for senior undergraduate and graduate students in Engineering and Computer Science.

Abstract Massive stars in the Hertzsprung gap are a mixed population of objects in short-lived evolutionary phases: yellow supergiants (YSGs) evolving toward the red supergiant (RSG) phase, partially stripped post-RSGs, and other, rarer outcomes of stellar evolution. Studies of sufficiently large samples of these objects can constrain massive star structure and evolution during these poorly understood phases. As part of our ongoing program searching for post-RSGs, we characterized the spectral line profiles of 32 YSGs in the Large Magellanic Cloud using high-resolution spectra obtained with the Magellan Inamori Kyocera Echelle spectrograph on the Magellan 2/Clay telescope at Las Campanas Observatory. We find that the line profiles are strongly broadened by turbulent photospheric motion. After fitting the profiles to measure microturbulent and macroturbulent velocities, we identify two groups within our sample that are separated by the ratio of the two velocity scales. In both groups, the macroturbulent velocity ζ RT scales with stellar properties such as effective temperature. Additionally, we find statistically significant correlations between the macroturbulent velocity and other possible probes of large-scale photospheric motions: line profile asymmetry, as well as the amplitude and quality factor of the stochastic low frequency variability measured from Transiting Exoplanet Survey Satellite lightcurves. These correlations differ between the two groups of YSGs. Finally, we construct 1D evolutionary models of YSGs in both pre- and post-RSG phases, and find reasonable agreement between the convective velocities in these models and our measured microturbulent velocities. However, the macroturbulent velocities are much higher than the convective velocities in the models.

We synthesized a family of polynorbornenes with a widerange of cis/trans compositionsby ring-openingmetathesis polymerization (ROMP) with a variety of ruthenium catalystsand subjected these materials to ultrasonication as a proxy for mechanicaldegradation. Increasing the cis-alkene content enhancedthe degradation rate for both short (∼70 kDa) and long (∼700kDa) polynorbornenes. These data suggest that the heightened allylicstrain in cis- versus trans-polynorbornenepromotes faster degradation independent of molecular weight undermechanical stress. Our results complement existing plastics recyclingresearch by isolating the understudied relationship between backbonestereochemistry and degradability.

Abstract At high eccentricities, tidal forcing excites vibrational modes within orbiting bodies known as dynamical tides. In this paper, we implement the coupled evolution of these modes with the body’s orbit in the REBOUNDx framework, an extension to the popular N-body integrator REBOUND. We provide a variety of test cases relevant to exoplanet dynamics and demonstrate overall agreement with prior studies of dynamical tides in the secular regime. Our implementation is readily applied to various high-eccentricity scenarios and allows for fast and accurate N-body investigations of astrophysical systems for which dynamical tides are relevant.

Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) provides insights into both the genomic location occupied by the protein of interest and the difference in DNA occupancy between experimental states. Given that ChIP-seq data are collected experimentally, an important step for determining regions with differential DNA occupancy between states is between-sample normalization. While between-sample normalization is crucial for downstream differential binding analysis, the technical conditions underlying between-sample normalization methods have yet to be examined for ChIP-seq. We identify three important technical conditions underlying ChIP-seq between-sample normalization methods: balanced differential DNA occupancy, equal total DNA occupancy, and equal background binding across states. To illustrate the importance of satisfying the selected normalization method's technical conditions for downstream differential binding analysis, we simulate ChIP-seq read count data where different combinations of the technical conditions are violated. We then externally verify our simulation results using experimental data. Based on our findings, we suggest that researchers use their understanding of the ChIP-seq experiment at hand to guide their choice of between-sample normalization method. Alternatively, researchers can use a high-confidence peakset, which is the intersection of the differentially bound peaksets obtained from using different between-sample normalization methods. In our two experimental analyses, roughly half of the called peaks were called as differentially bound for every normalization method. High-confidence peaks are less sensitive to one's choice of between-sample normalization method, and thus could be a more robust basis for identifying genomic regions with differential DNA occupancy between experimental states when there is uncertainty about which technical conditions are satisfied.

Abstract The traditional approach to analyzing mean motion resonances (MMRs) is through the canonical perturbation theory. While this is a powerful method, its generality leads to complicated combinations of variables that are challenging to interpret and require looking up numerical coefficients particular to every different resonance. In this paper, we develop simpler scaling relations in the limit where orbits are closely spaced (period ratios ≲2), and interplanetary interactions can be approximated by only considering the close approaches each time the inner planet overtakes the outer at the conjunction. We develop geometric arguments for several powerful results: (i) that p:p − q MMRs of the same order q are all rescaled versions of one another, (ii) that the general case of two massive planets on closely spaced, eccentric, coplanar orbits can be approximately mapped onto the much simpler case of an eccentric test particle perturbed by a massive planet on a coplanar circular orbit, and (iii) that, while the effects of consecutive conjunctions add up coherently for first-order (p:p − 1) MMRs, they partially cancel for p:p − q MMRs with order q > 1, providing a physical explanation for why these higher-order MMRs are weaker and can often be ignored. Finally, we provide simple expressions for the widths of MMRs and their associated oscillation frequencies that are universal to all closely spaced MMRs of a given order q, in the pendulum approximation.

Abstract Ever since the discovery of the invasive soft coral species Xenia umbellata (Anthozoa, Octocorallia, Malacalcyonacea, Xeniidae) on the reefs of southwestern Puerto Rico, ongoing surveys have documented its spread and potential impacts on native marine fauna. During benthic surveys conducted by scientific divers from Puerto Rico’s DNER and the Department of Marine Sciences at UPRM, colonies of xeniid soft corals were observed with morphological and color characteristics distinct from those of X. umbellata . Morphological and genetic barcoding analyses of four gene regions confirmed the presence of a second invasive xeniid species, Latissimia ningalooensis , in the southern reefs of Puerto Rico. Originally described in Western Australia, L. ningalooensis has recently been reported in southeastern Brazilian waters, marking its expansion into the Atlantic. The discovery of a second xeniid species in Puerto Rico following the recent introduction of X. umbellata , is both surprising and concerning. Highly disturbed reefs, such as those along the southern coast of Puerto Rico and the wider Caribbean, seem highly susceptible to invasive species. Recent reports of invasive soft corals and other marine species in Puerto Rico highlight the potential for some species to become a regional issue, requiring coordinated management actions across the Caribbean.