Claremont, CA, United States

Harvey Mudd College
Claremont, CA, United States

Harvey Mudd College is a private residential liberal arts college of science, engineering, and mathematics, founded in 1955 and located in Claremont, California, United States. It is one of the institutions of the contiguous Claremont Colleges, which share adjoining campus grounds.Harvey Mudd College shares university resources such as libraries, dining halls, health services, and campus security, with the other institutions in the Claremont Colleges, including Pitzer College, Scripps College, Claremont McKenna College, Pomona College, Claremont Graduate University, and Keck Graduate Institute of Applied Life science, but each college is independently managed by its own faculty, board of trustees, and college endowment and has its own separate admissions process. Students at Harvey Mudd are encouraged to take classes at the other four Claremont colleges, especially classes outside their major of study. Together the Claremont Colleges provide the resources and opportunities of a large university while enabling the specialization and personal attention afforded by the individual colleges. The Bachelor of Science diploma received at graduation is issued by Harvey Mudd College.The college is named after Harvey Seeley Mudd, one of the initial investors in the Cyprus Mines Corporation. Although involved in the planning of the new institution, Mudd died before it opened. Harvey Mudd College was funded by Mudd's friends and family, and named in his honor. Wikipedia.

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Agency: NSF | Branch: Standard Grant | Program: | Phase: PHYLOGENETIC SYSTEMATICS | Award Amount: 494.48K | Year: 2015

Worldwide, humans and countless other species are dependent on coral reefs for shelter, sustenance and livelihoods. Increasing atmospheric carbon dioxide is causing the worlds oceans to become warmer and more acidic, a chemical change that may prevent corals from forming calcium carbonate skeletons. The fossil record indicates, however, that some groups of corals have survived similar environmental crises in past geological eras, and that changes in ocean chemistry may result in the evolution of different types of skeletons or of corals that lack skeletons. Understanding these past evolutionary transitions and the environmental conditions under which they occurred may help scientists predict the responses of todays reef-building corals to future climate change. This collaborative project between researchers from Harvey Mudd College, a Principally Undergraduate Institution, and the American Museum of Natural History will investigate the evolution of calcium carbonate skeletons in Anthozoa (corals, sea anemones, and relatives). They will first generate an extensive time-calibrated molecular phylogeny of the group and then use this evolutionary framework to study the evolution of skeletal characters. Students from groups underrepresented in the sciences will participate in this research through the PIs mentoring of undergraduates at the minority-serving New York City College of Technology, and the Scripps College Academy, a program for high school girls in the Los Angeles area. The project will also generate diverse outreach materials for a public display on corals at the American Museum of Natural History.

Although previous molecular phylogenetic studies have found strong support for relationships among some orders of Anthozoa, key regions of the tree remain poorly resolved, impeding efforts to understand character evolution within the group. By first sequencing complete genomes from eight distantly related taxa of Anthozoa researchers will then design a set of Ultra-Conserved Elements (UCEs) that can be used throughout Anthozoa. UCE sequences will then be generated for 192 Anthozoa species spanning diversity within the group to generate the first phylogenomic estimate of relationships within the group. The researchers will then use this phylogenetic tree and a diverse set of comparative methods to infer the direction, timing and paleoclimatic correlates of evolutionary transitions in skeletogenesis and other traits within the clade that have allowed anthozoans to engineer the largest biological structures on the planet.

Agency: NSF | Branch: Continuing grant | Program: | Phase: ATMOSPHERIC CHEMISTRY | Award Amount: 333.45K | Year: 2016

This CAREER project is focused on characterizing the formation and fate of brown carbon in the atmosphere. Ambient measurements of brown carbon will be made in Los Angeles CA over several years and laboratory studies will be conducted to better understand the fate of brown carbon in fog and clouds. The project is expected to add important insights into the sources, fate, and impact of brown carbon in the urban environment. Such knowledge could help reduce uncertainty in regards to the contribution of atmospheric aerosol to climate forcing.

The objectives of the research are to (1) Determine the contribution of nitro-aromatics to ambient Los Angeles particulate brown carbon (BrC) over hourly, daily, and yearly time scales, and (2) Determine how aerosol aging during fog/cloud processing impacts aqueous secondary BrC optical and chemical properties. This project also presents a unique opportunity to engage undergraduates in timely atmospheric research with cutting-edge instrumentation.

Agency: NSF | Branch: Standard Grant | Program: | Phase: RSCH EXPER FOR UNDERGRAD SITES | Award Amount: 353.57K | Year: 2017

This award renews a highly successful CISE Research Experiences for Undergraduates (REU) Site at Harvey Mudd College. A team of computer science faculty mentors have designed a 10 week summer REU program in the broad area of computer systems. The summer research activity gives students a taste of the most compelling parts of a graduate school experience as well as an immersive experience in the field of computer science. The student research projects cover a breadth of areas in computing science. The students will gain experience in all aspects of the process of conducting research. The site will target students from 2-year schools and students early in their undergraduate studies. The faculty is committed to engaging students from groups traditionally under-represented in computing. The program features individual and group activities that create a strong common-cohort experience for students for whom the REU experience should be transformative. The program develops research ability, improves presentation and communications skills, and nurtures student interest in research-related careers.

The intellectual merit of the project revolves around the variety of systems projects through which students will be exposed to all aspects of the research process. The research focus areas include text simplification, robotics, domain-specific programming languages and systems, and active transportation planning. Each project connects with the systems theme, building atop existing platforms, melding theory and practice, and implementing designs to mitigate complexity. The projects are designed to be accessible to students early in their undergraduate careers and share principles of low-cost and overhead, external accessibility of deliverables, and narrowness of focus. The students engage in projects that are exciting, current, and externally relevant and that have clear applications. Students actively pursue the entire research process including literature search, digesting prior work, formulating new problems, designing and conducting investigations, and preparing presentations and publications of results. The REU cohorts will regularly share their work with each other and meet daily with faculty mentors. The project activities will permit students to acquire valuable professional development skills, gain a broader and deeper understanding of research, and develop greater confidence in their abilities as future computing professionals and researchers.

Agency: NSF | Branch: Standard Grant | Program: | Phase: IRES | Award Amount: 229.90K | Year: 2016

Abstract for proposal 1559403 PI: Lori Bassman

Proposal Title: IRES: US-Australia collaboration on new high strength, high ductility classes of high entropy alloys through intermetallic manipulation
Institution: Harvey Mudd College

Traditional alloys used in engineering applications consist primarily of one or two elements, with other elements added in relatively small quantities to enhance material properties. However, the inclusion of large quantities of additional elements typically causes alloys to become brittle. Recent work, including that by American undergraduate students working with researchers at the University of New South Wales (UNSW) in Australia and Prof. Lori Bassman of Harvey Mudd College (HMC), has led to the development of novel metal alloys using a new strategy. These advanced alloys, called high entropy alloys (HEAs), have carefully selected compositions with approximately equal amounts of several elements and have demonstrated excellent material properties. This project will greatly expand the range of combinations of elements that can be used to create successful HEAs. With the proposed new strategy will come increased promise for creating alloys with improved combinations of strength, ductility and cost. During ten week periods in the summers of 2017 to 2019, twelve undergraduate students will conduct experimental and computational research at UNSW towards this goal. The lead collaborators, Dr. Kevin Laws and Prof. Michael Ferry in the UNSW School of Materials Science and Engineering, and researchers in the UNSW Electron Microscope Unit have worked with HMC undergraduates for many years. They will continue to provide students with discipline-specific expertise and mentoring unavailable at HMC as well as extensive access to physical metallurgy laboratories, microscope facilities and training.

Progress in the HEA field so far has focused on identification of specific systems of elements that can form one or two simple solid solution phases with high thermal stability and no brittle intermetallic phases. In this project new HEAs will be developed by increasing the ductility of intermetallic phases that occur in other systems. Through this alloy development, the students and their UNSW mentors will refine the fundamental principles that govern HEA formation and atomic ordering and explore the deformation mechanisms associated with greatly enhanced strength and ductility in HEAs over conventional alloys. The specific experimental projects to be performed by HMC undergraduates include alloy design, alloy fabrication, mechanical characterization and microstructural characterization. Computational projects will involve first-principles modeling of alloy structures and properties. These experiences will contribute to the maturation of the students into confident, enthusiastic researchers who are prepared for science and engineering careers in international research environments. At least half of the participating students will be female, and underrepresented minority students will be specifically recruited.

This research is funded by the IRES program of the NSF Office of International Science and Engineering.

Agency: NSF | Branch: Standard Grant | Program: | Phase: Theory, Models, Comput. Method | Award Amount: 261.08K | Year: 2016

Robert Cave of Harvey Mudd College is supported by an award from the Chemical Theory, Models and Computational Methods program in the Chemistry division to develop computational methods for studying electron transfer reactions. Electron transfer reactions are the simplest chemical reactions but have central roles in biological systems and in human-engineered devices that seek to harness solar energy as alternative sources. The initial stages of plant photosynthesis are exquisitely engineered to transfer electrons across large distances, wasting as little energy as possible, in order to make high-energy molecules for later use. The mitochondria in the cells of animals use an analogous reverse electron transfer pathway to synthesize molecules that allow muscle movement from high-energy precursors. As we seek to mimic the effectiveness of plants in harnessing solar energy it is critical to understand electron transfer processes at a detailed level. The rate of electron transfer depends on many quantities, but the factor that controls the distance- and orientation-dependence of the rate is called the electronic coupling element, a quantity that has the potential to yield unprecedented control of rates if we can understand it at a fundamental level. Cave and his coworkers develop new methods for the calculation of the electronic coupling that are more accurate than existing approaches. The new methods and results are used to better design new synthetic solar energy conversion devices and understand mechanisms of biological electron transfer. The work is carried out Harvey Mudd College, an undergraduate institution. The work provides an excellent educational opportunity for students likely to pursue graduate work in chemistry and also supports the annual presentation of a theoretical chemistry workshop to the Society of Women Engineers? On-Campus Day for high school women, where 100-150 high school women are introduced to opportunities in science, engineering and mathematics.

Great strides have been made over the past two decades in developing diabatization techniques for extracting the electronic coupling from standard quantum chemical approaches. However, because of the poor scaling of correlated quantum chemistry methods with system size one is often faced with the choice between accuracy and tractability, especially for large electron transfer systems. Given the success of these diabatization methods, it is imperative to turn attention to developing new electronic structure theory approaches, tailored to the electron transfer problem, which are accurate and able to treat considerably larger systems. This work addresses this challenge by developing a series of approximate methods that include correlation in a balanced fashion for all of the zeroth-order states relevant to the electron transfer process. These approaches greatly extend the size of electron transfer systems for which the coupling can be obtained accurately and thus provide useful guidance about the suitability of more approximate methods. In particular a family of correlated methods is developed to calculate the electronic coupling element based on approximations to the Equation of Motion Coupled Cluster approach. The methods scale no worse than MP2/MBPT2, giving access to dramatically larger systems than available to CI or CCSD. Use of PT-based coefficients in place of CCSD coefficients in the similarity transformed Hamiltonian, coupled with truncated excitation spaces tailored to electron transfer systems, lead to the increased scope and speed. Tests of these new methods include a series of model systems where high-accuracy calculations can also be performed, application to calculate the electronic coupling in near-degenerate donor/acceptor and bridge systems, and the study of through-solvent electron transfer. Both of the latter two computational targets have been studied experimentally.

Agency: NSF | Branch: Standard Grant | Program: | Phase: RSCH EXPER FOR UNDERGRAD SITES | Award Amount: 358.07K | Year: 2014

This funding renews a Research Experience for Undergraduate (REU) site at Harvey Mudd College. The site brings 10 undergraduates in order to engage them in research and encourage graduate study in computer science. The intellectual focus of the site is research in computer systems. The program provides a microcosm of the graduate experience through four broadly-scoped systems projects. Students have a chance to gain experience in all aspects of the research process, including its social aspects. The site focuses on recruiting a sufficiently diverse pool of students, including women and underrepresented minorities.

The intellectual merit of the proposal rests with the leadership of an experienced team of mentors with excellent expertise and experience in the research areas. The site focuses on four main projects. The first project develops algorithms for estimating cophylogenetic trees based on biological host/parasite data. Students work is encapsulated in a software package named Jane, currently in use by dozens of biology research groups. The second effort investigates approaches for automatic synthesis of music scores, furthering our understanding of computational music research. It leverages the Impro-Visor software, which has many thousands of users. The third project explores program analyses to support new, accessible domain-specific languages, secure information flow in industry-standard languages such as Javascript, and visualization tools for both sides of that programming spectrum. The fourth project tests machine-learning and computer vision-based algorithms that improve the state-of-the-art of performance of low-cost robots, such as sub-$300 quadcopters and laser-guided wheeled platforms.

The broader impacts include the sites emphasis on the broad human and research impacts of pursuing computer science at the graduate level -- especially for participants who had not previously considered graduate work. Challenging research problems prompt students guided development of research skills: investigation, presentation, and publication. One-on-one introductions by advisors transition to student-led talks and culminate with publications and conference experiences during or after the summer. The programs most important impact is its cultivation of the next generation of creative and enthusiastic computer science researchers. The evaluation plan and the student research artifact archiving plan should contribute to educational research on effective structures for involving undergraduate students in research.

Agency: NSF | Branch: Standard Grant | Program: | Phase: | Award Amount: 249.99K | Year: 2015

This International Research Experiences for Students (IRES) project aims to develop an Autonomous Underwater Vehicles (AUV) system for intelligent shipwreck search, mapping and visualization. The proposed system will improve on current approaches to marine archeology, and in doing so develop novel techniques that can be applied to a general class of robot exploration tasks. First, an investigation will be launched into probabilistic algorithms that identify regions of high likelihood of containing unexplored shipwrecks that offline and online AUV planning algorithms can use to maximize information gain when searching for wrecks. Second, the development of visualization techniques dedicated to surface reconstruction that merge side scanning sonar and stereo image disparity maps while incorporating volume visualizations of marine site science data. Third, and finally, these techniques will be applied in actual AUV shipwreck search experiments in previously unexplored and under-explored areas of the Mediterranean.

The robotic exploration technology developed in this project will be applicable to a wide range of applications in archaeology, oceanography, biology, homeland security, and defense. The Principal Investigators and student participants will disseminate research findings via publications and professional conferences, and to local community members and public internet portal. A digital archive of sites will be created for the archeological community. This project aims to use the research findings to introduce these robotic technologies to a broad audience including elementary school children in both the US and Malta, and especially to groups typically underrepresented in computer science and engineering. As part of the project, robotics workshops will be run at elementary schools located in Malta and Sicily.

Agency: NSF | Branch: Standard Grant | Program: | Phase: IUSE | Award Amount: 298.34K | Year: 2016

Computer Sciences traditional role in the university setting has been to develop skilled software engineers and computing professionals. Eclipsing, not replacing, that role is the growing need for computing expertise in non-computing disciplines. The CS for Insight project at Harvey Mudd College will develop a curriculum that will serve as a bridge from a typical introductory computer science course (CS1) to discipline-specific courses in computing for many fields. In the CS for Insight curriculum students will use existing computing resources, first to gain confidence in learning new interfaces, and then will apply these resources to address challenges within their discipline. The projects broader goal will be to better understand the pathways that non-computing disciplines may follow to provide their students with the appropriate computing skills for their specific discipline.

Departments at schools across the country are exploring the many pathways for leveraging computation for their specific purposes. Two paradigms have begun to emerge. Some disciplines adapt and assimilate, integrating their own computing curriculum from the very start. Others collaborate to factor-out-then-follow-up, choosing to build discipline-specific skills atop a computing-based CS1. The consortium of Claremont Colleges, simultaneously widely varied and close-knit, offers a laboratory uniquely suited for comparing these paradigms head-to-head and exploring the hybrid approaches that will arise alongside. This project will leverage this disciplinary diversity to draw a more representative cohort of students to computing. The PI team will carefully track the demographics and computational identities of the participants to develop knowledge that can be used by others to create a model by which all disciplines can leverage computing as part their own unique culture.

Agency: NSF | Branch: Continuing grant | Program: | Phase: ROBUST INTELLIGENCE | Award Amount: 465.52K | Year: 2014

Periodic migration patterns can be found throughout the natural world. Examples of periodic movements have been observed in humans, terrestrial and aquatic animals, insects, even bacteria. Understanding such patterns can provide researchers with essential information to making decisions that affect environment, health, finances, and safety. Developing better tools for accurately measuring periodic movements is essential for developing more sophisticated movement models. This project focuses on the development of a mobile, multi-robot sensing system capable of monitoring individuals and populations that share common behaviors resulting in periodic movement patterns. The project uses multiple Autonomous Underwater Vehicles (AUVs) for monitoring, tracking, and modeling fish populations in their coastal habitat. The specific goals of the project are to (1) develop mathematical models of a populations periodic migratory motion, (2) develop strategies based on these models for real-time estimation of the state of individuals and the population, (3) construct multi-robot control strategies for tracking populations, and (4) conduct continuous monitoring of fish populations using AUVs. To accomplish these goals, a multi-AUV system is deployed to autonomously track and follow acoustic tagged fish populations in Big Fisherman?s Cove in Catalina Island. This test site is a Marine Protected Area abundant with several species of fish that follow periodic migration patterns. Results from experiments are expected to validate the system and generate models that are useful to marine biologists and policy makers.

Agency: NSF | Branch: Continuing grant | Program: | Phase: ADVANCES IN BIO INFORMATICS | Award Amount: 331.27K | Year: 2014

Reconciliation analysis is a fundamental method in the study of species and genes, hosts and parasites, and geographical areas and species. While these applications are different, the underlying mathematical and computational problems are analogous. Genes and species interact through complex evolutionary processes such as gene duplication, horizontal gene transfer, and gene loss. Parasites and their hosts coevolve through processes including both contemporaneous and independent speciation, host switch, and extinction. And, species and their geographical habitats interact over geological time scales through vicariance, sympatric speciation, dispersal, and extinction. Consequently, the phylogenetic trees for genes and species, parasites and hosts, and species and their geographic regions are inherently incongruent. This research will develop new algorithms, visualization methods, and software tools for studying the evolutionary histories of pairs of entities such as genes and species, hosts and parasites, and species and their geographical habitats and also help to train the next generation of researchers.

Genes and species interact through complex evolutionary processes such as gene duplication, horizontal gene transfer, and gene loss. Parasites and their hosts coevolve through processes including both contemporaneous and independent speciation, host switch, and extinction. And, species and their geographical habitats interact over geological time scales through vicariance, sympatric speciation, dispersal, and extinction. Consequently, the phylogenetic trees for genes and species, parasites and hosts, and species and their geographic regions are inherently incongruent. Phylogenetic tree reconciliation seeks to reconstruct the evolutionary histories of pairs of related entities by positing the evolutionary events that explain their incongruence. Traditional maximum parsimony methods for tree reconciliation require the user to select costs for each type of evolutionary event. These cost parameters are notoriously difficult to estimate and their values can substantially affect the results and conclusions. This approach uses a Pareto-optimal methodology that does not require the user to select event costs a priori, thereby providing a systematic view of the set of all possible optimal reconciliations. This work will ultimately result in software tools with applications across the life sciences including genomics, parasitology, virology, and biogeography. In addition, this project will involve a substantial number of undergraduates, thereby helping prepare the next generation of researchers in computational biology.

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