Latest Discoveries & Creations

Featured Research

Vivien Hamilton talking at table

Invisible, Inevitable and Toxic

There's a new book encouraging stronger policies to ensure that people act with greater caution around creating and maintaining toxic landscapes.

In Inevitably Toxic: Historical Perspectives on Contamination, Exposure, and Expertise, editors/ authors Vivien Hamilton (history of science professor, Harvey Mudd), Brinda Sarathy (Pitzer) and Janet Farrell Brodie (Claremont Graduate University) present a collection of essays that consider exposure of humans to toxic environments that often appear innocuous.

Robot arm collecting coral sample.

Deep-Sea Surprise

As a shallow-water biologist, Catherine McFadden’s usual method of coral specimen collection is via SCUBA [...]

Vosburg and children on wall overlooking city.

Fulbright en Español

In his lab at Harvey Mudd College, chemistry professor David Vosburg seeks to make medicinally [...]

Research News

Researchers Seek Better Software Testing Techniques

Software systems in programmable items—from household appliances to cars and planes—must be reliable and high quality to avoid inconvenient or disastrous consequences. In order to [...]

Harvey Mudd Ranks High in U.S. News and World Report 2021

Harvey Mudd College ranked No. 2 for undergraduate engineering programs in U.S. News & World Report’s Best Colleges 2021, maintaining the same spot as last year. Harvey [...]

Interdisciplinary Research on Gene Histories Accepted to ACM Conference

In pursuit of developing models and algorithms for reconstructing gene histories across multiple species, Harvey Mudd College researchers have completed a paper that has been [...]

NSF Funds Interdisciplinary Engineering, CS and Biology Research

The National Science Foundation (NSF) has funded Harvey Mudd College engineering professor Chris Clark’s project “Monitoring of Marine Life Coastal Habitats via Autonomous Robot Systems.” [...]

Research Publications

Title
Abstract
Author
Year
Dept.
The Social Rules Project​From national policies to the most minute technical design standards, social rules are the constraints that make coordinated human activity possible. The Social Rules Project is an educational initiative at Harvey Mudd College that reveals how social rules, or “institutions,” shape our planet and our lives.Program Director: Paul F. Steinberg2014 - OngoingHumanities, Social Sciences, and the Arts
Water exit dynamics of jumping archer fish: Integrating two-phase flow large-eddy simulation with experimental measurementsArcher fish jumping for prey capture are capable of achieving accelerations that can reach 12 times gravitational from a stationary start at the free surface. This behavior is associated with nontrivial production of hydrodynamic thrust. In this work, we numerically investigate the hydrodynamic and aerodynamic performance of a jumping smallscale archer fish (Toxotes microlepis) to elucidate the propulsive mechanisms that contribute to the rapid acceleration and the considerable jump accuracy. We conduct high-fidelity, two-phase flow, large-eddy simulation (LES) of an anatomically realistic archer fish using detailed jump kinematics in water, through the water/air interface, and in air. The complex fish body kinematics are reconstructed using high-speed imaging. The LES results during the water phase of the jump are compared with particle image velocimetry measurements of a live jumping archer fish, and excellent agreement is found. The numerical simulations further enable detailed analysis of the flow dynamics and elucidate for the first time the dynamics of the coherent vortical structures in both the water and air phases. In particular, the pectoral fins are shown to contribute to the initial spike in acceleration before water exit and to enhance the overall jumping performance of the fish.
Ali Khosronejad, Leah Mendelson, Alexandra H. Techet, Seokkoo Kang, Dionysios Angelidis, Fotis Sotiropoulos2020Engineering
Dynamic Control of Probabilistic Simple Temporal NetworksThe controllability of a temporal network is defined as an agent's ability to navigate around the uncertainty in its schedule and is well-studied for certain networks of temporal constraints. However, many interesting real-world problems can be better represented as Probabilistic Simple Temporal Networks (PSTNs) in which the uncertain durations are represented using potentially-unbounded probability density functions. This can make it inherently impossible to control for all eventualities. In this paper, we propose two new dynamic con-trollability algorithms that attempt to maximize the likelihood of successfully executing a schedule within a PSTN. The first approach, which we call MIN-LOSS DC, finds a dynamic scheduling strategy that minimizes loss of control by using a conflict-directed search to decide where to sacrifice the control in a way that optimizes overall success. The second approach , which we call MAX-GAIN DC, works in the other direction: it finds a dynamically controllable schedule and then attempts to progressively strengthen it by capturing additional uncertainty. Our approaches are the first known that work by finding maximally dynamically controllable schedules. We empirically compare our approaches against two existing PSTN offline dispatch approaches and one online approach and show that our MIN-LOSS DC algorithm outper-forms the others in terms of maximizing execution success while maintaining competitive runtimes.James C. Boerkoel Jr., Lindsay Popowski, Michael Gao2020Computer Science
María Acuña. Poesía descalza. Granada: Valparaíso Ediciones, 2020. (Barefoot Poetry)In 2007, the Congress of Deputies in Spain approved the Law of Historical Memory. The law sought to redress wrongs experienced by victims on both sides of the Spanish Civil War (1936-1939) and condemned the Franco regime. Since then, exhumation of the repressed past has witnessed a burgeoning. Restoration ought to include not just notables like Federico García Lorca but also the unsung voices that played a quiet yet relevant role. Within this context, I have edited the unpublished poetry of María Acuña (1928-1994). Poesía descalza is the first volume to come out. The first woman to wear pants in her village, to smoke in public, among the few to give birth out of wedlock when the Church sanctioned the harshening dictatorship, she cuts a striking figure across the somber Francoist years. My research draws on her poetry to reconstruct the postwar female experience. Women’s creativity under Franco, regional lives too often neglected, must be acknowledged and written into Spain’s intellectual history.Isabel Balseiro2020Humanities, Social Sciences, and the Arts
Decomposable Probability-of-Success Metrics in Algorithmic SearchPrevious studies have used a specific success metric within an algorithmic search framework to prove machine learning impossibility results. However, this specific success metric prevents us from applying these results on other forms of machine learning, e.g. transfer learning. We define decomposable metrics as a category of success metrics for search problems which can be expressed as a linear operation on a probability distribution to solve this issue. Using an arbitrary decomposable metric to measure the success of a search, we demonstrate theorems which bound success in various ways, generalizing several existing results in the literature.George D. Montañez, Tyler Sam, Jake Williams, Abel Tadesse, Huey Sun2020Computer Science
Minimal Complexity Requirements for Proteins and OtherHow complex do proteins (and other multi-part recognition systems) need to be? Using an informationtheoretic framework, we characterize the information costs of recognition tasks and the information capacity of combinatorial recognition systems, to determine minimum complexity requirements for systems performing such tasks. Reducing the recognition task to a finite set of binary constraints, we determine the sizes of minimal equivalent constraint sets using a form of distinguishability, and show how the representation of constraint sets as binary circuits or decision trees also results in minimum constraint set size requirements. We upper-bound the number of configurations a recognition system can distinguish between as a function of the number of parts it contains, which we use to determine the minimum number of parts needed to accomplish a given recognition task. Lastly, we apply our framework to DNA-binding proteins and derive estimates for the minimum number of amino acids needed to accomplish binding tasks of a given complexity.George D. Montañez, Laina Sanders, Howard Deshong2020Computer Science
Virtue as a framework for the design and use of artificial intelligencePractitioners are seeking information and ethical guidance related to the design and utilization of artificial intelligence (AI) across a variety of applications. Developments at Google illustrate the potential good of AI as well as potential concerns. In this article, we use Google to create a context that demonstrates the relevance of virtue for the ethical design and use of AI. We describe a set of ethical challenges encountered by Google and introduce virtue as a framework for ethical decision making that can be applied broadly to numerous organizations. We also examine support for virtue in ethical decision making as well as its power in attracting and retaining the employees who develop AI and the customers who use it. To conclude, we apply the virtue framework to Google’s AI challenges and offer suggestions for its use in other organizations.George D. Montañez, Mitchell J. Neubert2020Computer Science
Mathematics for Human FlourishingFor mathematician Francis Su, a society without mathematical affection is like a city without concerts, parks, or museums. To miss out on mathematics is to live without experiencing some of humanity’s most beautiful ideas. In this profound book, written for a wide audience but especially for those disenchanted by their past experiences, an award-winning mathematician and educator weaves parables, puzzles, and personal reflections to show how mathematics meets basic human desires—such as for play, beauty, freedom, justice, and love—and cultivates virtues essential for human flourishing. These desires and virtues, and the stories told here, reveal how mathematics is intimately tied to being human. Some lessons emerge from those who have struggled, including philosopher Simone Weil, whose own mathematical contributions were overshadowed by her brother’s, and Christopher Jackson, who discovered mathematics as an inmate in a federal prison. Christopher’s letters to the author appear throughout the book and show how this intellectual pursuit can—and must—be open to all.Francis Su; With Reflections by Christopher Jackson2020Mathematics
How do I design a chemical reaction to do useful work? Reinvigorating general chemistry by connecting chemistry and societyInsights and methods from the chemical sciences are directly relevant to global challenges such as climate change, renewable energy generation and storage, water purification, and food production. However, these connections are often opaque to students in general chemistry courses, who may get lost in the weeds of stoichiometry, VSEPR, and gas laws, and fail to see the relevance of their studies to their lives and their communities. Herein we describe a redesigned first-year undergraduate chemistry course that grounds chemical content in relevant societal applications. Students engage in collaborative, inquiry-based learning through an adapted POGIL methodology, and the highly structured class activities help students learn soft skills that enable success in higher education. Significant course revisions sometimes face resistance from key stakeholders, including students, faculty, and administration. We offer a case study in framing broader disciplinary concerns through the lens of institutional values to increase buy-in among key stakeholders.Katherine M. Van Heuvelen, G. William Daub, Lelia N. Hawkins, Adam R. Johnson, Hal Van Ryswyk, David A. Vosburg2020Chemistry
Evolutionary implications of analyses of complete mitochondrial genomes across order Zoantharia (Cnidaria: Hexacorallia)Cnidarians are early‐diverging metazoans, but evolutionary aspects of some taxa are still poorly understood, as in the order Zoantharia (Anthozoa: Hexacorallia). Zoantharians have been divided into two suborders based on the arrangement of the fifth septae as complete (Macrocnemina) or incomplete (Brachycnemina). Previous molecular phylogenetic analyses have indicated the need for re‐evaluation as Macrocnemina has been found to be paraphyletic. Despite many phylogenetic studies, the recovery of complete mitochondrial genomes (mt‐genomes) for systematic and evolutionary studies of zoantharians has been limited. The present study represents the first to sequence the complete mt‐genomes of members of eight of nine zoantharian families. Although all examined mt‐genomes had the same gene order arrangement, there were variations among mt‐genomes' sizes, nucleotide substitution rates, and introns. Only two species did not have the cox1 intron, which harbors a gene coding a homing endonuclease of the LAGLIDADG type. Our mitogenomic analyses also showed relatively high nucleotide diversity in mt‐DNA regions other than the standard regions traditionally considered for DNA barcoding of this group. Phylogenetic analyses using 13 mt‐genome protein‐coding genes recovered a fully resolved tree with clear separation between macrocnemic representatives. Ancestral state reconstruction analyses revealed three main transitions in arrangement of the marginal musculature through the evolutionary history of the order. An “early” transition from reticulate mesogleal to a cteniform endodermal arrangement was followed by transitions that occurred in the common ancestor of the Brachycnemina and family Hydrozoanthidae. Our results indicate the need for clarification of higher‐level phylogeny and taxonomy of Zoantharia.Angelo Poliseno, Maria Eduarda Alves Santos, Hiroki Kise, Brooks Macdonald, Andrea M. Quattrini, James Davis Reimer, Catherine S. McFadden2020Biology
Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Sarcophyton glaucum Specimens Collected in PalauSarcophyton glaucum is one of the most abundant and chemically studied soft corals with over 100 natural products reported in the literature, primarily cembrane diterpenoids. Yet, wide variation in the chemistry observed from S. glaucum over the past 50 years has led to its reputation as a capricious producer of bioactive metabolites. Recent molecular phylogenetic analysis revealed that S. glaucum is not a single species but a complex of at least seven genetically distinct species not distinguishable using traditional taxonomic criteria. We hypothesized that perceived intraspecific chemical variation observed in S. glaucum was actually due to differences between cryptic species (interspecific variation). To test this hypothesis, we collected Sarcophyton samples in Palau, performed molecular phylogenetic analysis, and prepared chemical profiles of sample extracts using gas chromatography-flame ionization detection. Both unsupervised (principal component analysis) and supervised (linear discriminant analysis) statistical analyses of these profiles revealed a strong relationship between cryptic species membership and chemical profiles. Liquid chromatography with tandem mass spectrometry-based analysis using feature-based molecular networking permitted identification of the chemical drivers of this difference between clades, including cembranoid diterpenes (2 R,11 R,12 R)-isosarcophytoxide (5), (2 S,11 R,12 R)-isosarcophytoxide (6), and isosarcophine (7). Our results suggest that early chemical studies of Sarcophyton may have unknowingly conflated different cryptic species of S. glaucum, leading to apparently idiosyncratic chemical variation.Katherine N. Maloney, Ryan T. Botts, Taylor S. Davis, Bethany K. Okada, Elizabeth M. Maloney, Christopher A. Leber, Oscar Alvarado, Charlie Brayton, Andrés Mauricio Caraballo-Rodríguez, Jason V. Chari, Brent Chicoine, J. Chance Crompton, Sydney R. Davis, Samantha M. Gromek, Viqqi Kurnianda, Kim QuachRobert M. Samples, Vincent Shieh, Camille M. Sultana, Junichi Tanaka, Pieter C. Dorrestein, Marcy J. Balunas, Catherine S. McFadden2020Biology
Beyond treaty implementation: Multilevel governance and the politics of institutional reform in London’s transportation sector The implementation of international environmental law is often construed as a one-way process, beginning with international agenda-setting and followed by national, and eventually local reforms in laws and policies with the goal of inducing behavior change on the ground.

From a bottom-up perspective, however, the picture is considerably more complex: local governments are simultaneously implementing numerous national and international legal mandates ‒ from trade and immigration laws to public health standards, national security measures, energy and building codes, land use regulations, and more. Particularly in large cities, local governments often have independent environmental initiatives that predate international treaties. Local discretion in adjudicating trade-offs among competing policy goals, deciding how to apportion costs and benefits, and designing projects looks a lot like agenda-setting authority, rather than merely implementation.

As a result, to understand global responses to climate change requires an analytic framework that can take account of multilevel governance, combining top-down and bottom-up perspectives. This study explores how local legal reforms unfold in a context of multilevel governance, with a focus on the push for climate-friendly transportation policies in London, comparing this to my ongoing research on the political dynamics of reform in Los Angeles.
Paul F. Steinberg2020Humanities, Social Sciences, and the Arts
Linear Algebra with Applications, 10th Edition “You may have noticed something new on the cover of the book. Another author! Yes, after nearly 40 years as a “solo act,” Steve Leon has a partner. New co-author Lisette de Pillis is a professor at Harvey Mudd College and brings her passion for teaching and solving real-world problems to this revision. The focus of this revision was transforming it from a primarily print-based learning tool to a digital learning tool. The eText is therefore filled with content and tools that will help bring the entire course to life for students in new ways and help you improve instruction.”Steven J. Leon and Lisette de Pillis2020Mathematics
Mesenchymal Stem Cells Used as Carrier Cells of Oncolytic Adenovirus Results in Enhanced Oncolytic VirotherapyIn this work, we develop a mathematical model that explores aspects of a new kind of cancer treatment that harnesses the unique characteristics of stem cells loaded with a specialized virus to carry targeted therapy to a tumor site. We are very proud to have been able to publish in Nature, Scientific Reports, which has a 2 year impact factor of 4.011, and a 56% acceptance rateLisette de Pillis, K. Mahasa, R. Ouifki, A. Eladdadi, P. Maini, A.-R. Yoon, C.-O. Yun2020Mathematics
Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometryLocusts are significant agricultural pests. Under favorable environmental conditions flightless juveniles may aggregate into coherent, aligned swarms referred to as hopper bands. These bands are often observed as a propagating wave having a dense front with rapidly decreasing density in the wake. A tantalizing and common observation is that these fronts slow and steepen in the presence of green vegetation. This suggests the collective motion of the band is mediated by resource consumption. Our goal is to model and quantify this effect. We focus on the Australian plague locust, for which excellent field and experimental data is available. Exploiting the alignment of locusts in hopper bands, we concentrate solely on the density variation perpendicular to the front. We develop two models in tandem; an agent-based model that tracks the position of individuals and a partial differential equation model that describes locust density. In both these models, locust are either stationary (and feeding) or moving. Resources decrease with feeding. The rate at which locusts transition between moving and stationary (and vice versa) is enhanced (diminished) by resource abundance. This effect proves essential to the formation, shape, and speed of locust hopper bands in our models. From the biological literature we estimate ranges for the ten input parameters of our models. Sobol sensitivity analysis yields insight into how the band’s collective characteristics vary with changes in the input parameters. By examining 4.4 million parameter combinations, we identify biologically consistent parameters that reproduce field observations. We thus demonstrate that resource-dependent behavior can explain the density distribution observed in locust hopper bands. This work suggests that feeding behaviors should be an intrinsic part of future modeling efforts.
Andrew J. Bernoff, Michael Culshaw-Maurer, Rebecca A. Everett, Maryann E. Hohn, W. Christopher Strickland, Jasper Weinburd2020Mathematics
Latch-based control of energy output in spring actuated systemsThe inherent force–velocity trade-off of muscles and motors can be overcome by instead loading and releasing energy in springs to power extreme movements. A key component of this paradigm is the latch that mediates the release of spring energy to power the motion. Latches have traditionally been considered as switches; they maintain spring compression in one state and allow the spring to release energy without constraint in the other. Using a mathematical model of a simplified contact latch, we reproduce this instantaneous release behaviour and also demonstrate that changing latch parameters (latch release velocity and radius) can reduce and delay the energy released by the spring. We identify a critical threshold between instantaneous and delayed release that depends on the latch, spring, and mass of the system. Systems with stiff springs and small mass can attain a wide range of output performance, including instantaneous behaviour, by changing latch release velocity. We validate this model in both a physical experiment as well as with data from the Dracula ant, Mystrium camillae, and propose that latch release velocity can be used in both engineering and biological systems to control energy output.Sathvik Divi, Xiaotian Ma, Mark Ilton, Ryan St. Pierre, Babak Eslami, S. N. Patek and Sarah Bergbreiter2020Physics
Graphs Are Not Enough: Using Interactive Visual Analytics in Storage ResearchStorage researchers have always been interested in understanding the complex behavior of storage systems with the help of statistics, machine learning, and simple visualization techniques. However, when a system's behavior is affected by hundreds or even thousands of factors, existing approaches break down. Results are often difficult to interpret, and it can be challenging for humans to apply domain knowledge to a complex system. We propose to enhance storage system analysis by applying "interactive visual analytics," which can address the aforementioned limitations. We have devised a suitable Interactive Configuration Explorer (ICE), and conducted several case studies on a typical storage system, to demonstrate its benefits for storage system researchers and designers. We found that ICE makes it easy to explore a large parameter space, identify critical parameters, and quickly zero in on optimal parameter settings.Zhen Cao, Stony Brook University; Geoff Kuenning, Harvey Mudd College; Klaus Mueller, Anjul Tyagi, and Erez Zadok, Stony Brook University2019Computer Science
Automatically Solving Deduction Games via Symbolic Execution, Model Counting, and Entropy MaximizationWe present a technique for automatically solving deduction games in which a player makes repeated queries to a running implementation of the game and receives a game outcome, with the goal of discovering an unknown secret value. By making multiple queries, a player iteratively reduces the uncertainty about the secret until it is known. We show how to synthesize player queries using static program analysis, model-counting, and information theory. The system we describe automatically solves deduction games implemented in a Python-based game specification language.Mara Downing, Chris Thompson, Lucas Bang2019Computer Science
The Futility of Bias-Free Learning and SearchBuilding on the view of machine learning as search, we demonstrate the necessity of bias in learning, quantifying the role of bias (measured relative to a collection of possible datasets, or more generally, information resources) in increasing the probability of success. For a given degree of bias towards a fixed target, we show that the proportion of favorable information resources is strictly bounded from above. Furthermore, we demonstrate that bias is a conserved quantity, such that no algorithm can be favorably biased towards many distinct targets simultaneously. Thus bias encodes trade-offs. The probability of success for a task can also be measured geometrically, as the angle of agreement between what holds for the actual task and what is assumed by the algorithm, represented in its bias. Lastly, finding a favorably biasing distribution over a fixed set of information resources is provably difficult, unless the set of resources itself is already favorable with respect to the given task and algorithm.George D. Montanez, Jonathan Hayase, Julius Lauw, Dominique Macias, Akshay Trikha, Julia Vendemiatti2019Computer Science
Nonadiabatic Investigation of the Electronic Spectroscopy of trans-1,3-ButadieneLow-lying UV spectroscopy of trans-1,3-butadiene has been extensively studied by experimentalists and theorists. Though a host of techniques has been applied to understand its lowest electronic states, there are still important open questions. Among these are the positions of the two lowest valence excited states and the factors responsible for the spectral shape of the lowest allowed transitions. We present results from EOM-CC calculations in extended basis sets that are used to parametrize a three-electronic-state Koppel, Domcke, and Cederbaum (KDC) model. We test the sensitivity of the KDC model to a variety of parameters and address several outstanding questions regarding the spectrum. We find that the overall shape of the spectrum is determined primarily by the Franck–Condon envelope of the 11Bu state and that the princple impact of the doubly excited 21Ag state is to broaden the 11Bu peaks. There is only modest sensitivity to the relative position of these two states. We find that the lowest Rydberg state, the 11Bg state, has an unexpected impact on the third peak in the spectrum, and its effect is considerably more energy-dependent than that of the 21Ag state.Scott M. Rabidoux, Robert J. Cave, John F. Stanton2019Chemistry
A Trypanosoma brucei ORFeome-based Gain-of-Function Library reveals novel genes associated with melarsoprol resistanceTrypanosoma brucei is an early branching protozoan that causes Human and Animal African Trypanosomiasis. Forward genetics approaches are powerful tools for uncovering novel aspects of Trypanosomatid biology, pathogenesis, and therapeutic approaches against trypanosomiasis. Here we have generated a T. brucei ORFeome consisting of over 90% of the targeted genome and used it to make an inducible Gain-of-Function library for broadly applicable forward genetic screening. Using a critical drug of last resort, melarsoprol, we conducted a proof of principle genetic screen. Hits arising from this screen support the significance of trypanothione, a key player in redox metabolism, as a target of melarsoprol and implicate novel proteins of the flagellum and mitochondria in drug resistance. This study has produced two powerful new genetic tools for kinetoplastida research, which are expected to promote major advances in kinetoplastida biology and therapeutic development in the years to come.M. Carter, H.S. Kim, S. Gomez, S. Gritz, S. Larson, D. Schultz, G.A. Hovel-Miner2019Biology
Identification of clinically approved small molecules that inhibit growth and promote surface remodeling in the African trypanosomeTrypanosoma brucei are unicellular parasites endemic to Sub-Saharan Africa that cause fatal disease in humans and animals. Infection with these parasites is caused by the bite of the tsetse fly vector, and parasites living extracellularly in the blood of infected animals evade the host immune system through antigenic variation. Existing drugs for Human and Animal African Trypanosomiasis are difficult to administer and can have serious side effects. Resistance to some drugs is also increasing, creating an urgent need for alternative trypanosomiasis therapeutics. In addition to identifying drugs that inhibit trypanosome growth, we wish to identify small molecules that can induce bloodstream form parasites to differentiate into forms adapted for the insect vector. These insect stage parasites do not vary proteins on their cell surface, making them vulnerable to the host immune system. To identify drugs that trigger differentiation of the parasite from bloodstream to insect stages, we engineered bloodstream reporter parasites that express Green Fluorescent Protein (GFP) following induction of the invariant insect-stage specific procyclin transcript. Using these bloodstream reporter strains in combination with high-throughput flow cytometry, we screened a library of 1,585 U.S. or foreign-approved drugs and identified eflornithine, spironolactone, and phenothiazine as small molecules that induce transcription of procylin. Both eflornithine and spironolactone also affect transcript levels for a subset of differentiation associated genes. We further identified 154 compounds that inhibit trypanosome growth. As all of these compounds have already undergone testing for human toxicity, they represent good candidates for repurposing as trypanosome therapeutics. Finally, this study is proof of principle that fluorescent reporters are a useful tool for small molecule or genetic screens aimed at identifying molecules or processes that initiate remodeling of the parasite surface during life cycle stage transitions.Madison Elle Walsh, Eleanor Mary Naudzius, Savanah Jessica Diaz, Theodore William Wismar, Mikhail Martchenko, Danae Schulz2019Biology
MAD-TN: A Tool for Measuring Fluency in Human-Robot CollaborationFluency is an important metric in Human-Robot Interaction (HRI) that describes the coordination with which humans and robots collaborate on a task. Fluency is inherently linked to the timing of the task, making temporal constraint networks a promising way to model and measure fluency. We show that the Multi-Agent Daisy Temporal Network (MAD-TN) formulation, which expands on an existing concept of daisy-structured networks, is both an effective model of human-robot collaboration and a natural way to measure a number of existing fluency metrics. The MAD-TN model highlights new metrics that we hypothesize will strongly correlate with human teammates' perception of fluency.James C. Boerkoel Jr., Gretchen Rice, Seth Isaacson2019Computer Science
DREAM: An Algorithm for Mitigating the Overhead of Robust ReschedulingGenerating and executing temporal plans is difficult in uncertain environments. The current state-of-the-art algorithm for probabilistic temporal networks maintains a high success rate by rescheduling frequently as uncertain events are resolved, but this approach involves substantial resource overhead due to computing and communicating new schedules between agents. Aggressive rescheduling could thus reduce overall mission duration or success in situations where agents have limited energy or computing power, and may not be feasible when communication is limited. In this paper, we propose new approaches for heuristically deciding when rescheduling is most efficacious. We propose two compatible approaches, Allowable Risk and Sufficient Change, that can be employed in combination to compromise between the computation rate, the communication rate, and success rate for new schedules. We show empirically that both approaches allow us to gracefully trade success rate for lower computation and/or communication as compared to the state-of-the-art dynamic scheduling algorithm.Jordan R. Abrahams, David A. Chu, Grace Diehl, Marina Knittel, Judy Lin, Liam Lloyd, James C. Boerkoel Jr., Jeremy Frank2019Computer Science
Measuring and Optimizing Durability against Scheduling DisturbancesFlexibility is a useful and common metric for measuring the amount of slack in a Simple Temporal Network (STN) solution space. We extend this concept to specific schedules within an STN's solution space, developing a related notion of durability that captures an individual schedule's ability to withstand disturbances and still remain valid. We identify practical sources of scheduling disturbances that motivate the need for durable schedules, and create a geometrically-inspired empirical model that enables testing a given schedule's ability to withstand these disturbances. We develop a number of durability metrics and use these to characterize and compute specific schedules that we expect to have high durability. Using our model of disturbances, we show that our durability metrics strongly predict a schedule's resilience to practical scheduling disturbances. We also demonstrate that the schedules we identify as having high durability are up to three times more resilient to disturbances than an arbitrarily chosen schedule is.Joon Young Lee, Vivaswat Ojha, James C. Boerkoel Jr.2019Computer Science
‘Make this adult mess make sense again’: the psychic lives of gentrification’s childrenThis paper advocates for increased scholarly curiosity about the painful and hopeful psychic agency of children and youth in critiquing neoliberal urban gentrification and imagining alternative forms of city life. It performs a geographically and theoretically informed reading of American director Ira Sachs’ 2016 film Little Men, a story about a brief but intense childhood friendship that is ended by an eviction. Drawing on the gentrification and psychoanalytic geography literatures, I turn to psychoanalyst D.W. Winnicott’s key clinical observations regarding ‘antisocial’ children and youth. Bringing these tools into dialogue with Little Men, I consider the revealing differences between the film’s shooting script and the final cut, as well as the film’s reception. Little Men and its child protagonists, I argue, should inspire more fine-grained attention to gentrification’s psychic dimensions, which both animate the process and open it to contestation.David K. Seitz2019Humanities, Social Sciences, and the Arts
The Bias-Expressivity Trade-offLearning algorithms need bias to generalize and perform better than random guessing. We examine the flexibility (expressivity) of biased algorithms. An expressive algorithm can adapt to changing training data, altering its outcome based on changes in its input. We measure expressivity by using an information-theoretic notion of entropy on algorithm outcome distributions, demonstrating a trade-off between bias and expressivity. To the degree an algorithm is biased is the degree to which it can outperform uniform random sampling, but is also the degree to which is becomes inflexible. We derive bounds relating bias to expressivity, proving the necessary trade-offs inherent in trying to create strongly performing yet flexible algorithms.George D. Montañez, Julius Lauw, Dominique Macias, Akshay Trikha, Julia Vendemiatti2019Computer Science
The Labeling Distribution Matrix (LDM): A Tool for Estimating Machine Learning Algorithm CapacityAlgorithm performance in supervised learning is a combination of memorization, generalization, and luck. By estimating how much information an algorithm can memorize from a dataset, we can set a lower bound on the amount of performance due to other factors such as generalization and luck. With this goal in mind, we introduce the Labeling Distribution Matrix (LDM) as a tool for estimating the capacity of learning algorithms. The method attempts to characterize the diversity of possible outputs by an algorithm for different training datasets, using this to measure algorithm flexibility and responsiveness to data. We test the method on several supervised learning algorithms, and find that while the results are not conclusive, the LDM does allow us to gain potentially valuable insight into the prediction behavior of algorithms. We also introduce the Label Recorder as an additional tool for estimating algorithm capacity, with more promising initial results.George D. Montañez, Pedro Sandoval Segura, Julius Lauw, Daniel Bashir, Kinjal Shah, Sonia Sehra, Dominique Macias2019Computer Science
Synthesis of Tris-Heterocycles via a Cascade IMCR/Aza Diels-Alder + CuAAC Strategy6-Triazolylmethyl-pyrrolo[3,4-b]pyridin-5-one tris-heterocycles were synthesized in 43–57% overall yields. The two-stage synthesis involved a cascade process (Ugi-3CR/aza Diels-Alder/N-acylation/aromatization) followed by a copper-assisted alkyne-azide [3+2] cycloaddition (CuAAC). This efficient and convergent strategy proceeded via complex terminal alkynes functionalized with a fused bis-heterocycle at the α-position. The final products are ideal candidates for SAR studies as they possess two privileged scaffolds in medicinal chemistry: 4-substituted or 1,4-substituted 1H-1,2,3-triazoles and pyrrolo[3,4-b]pyridin-5-ones.David A. Vosburg, Manuel A. Rentería-Gómez, Alejandro Islas-Jácome, Shrikant G. Pharande, Rocío Gámez-Montaño2019Chemistry
Aqueous Dearomatization/Diels−Alder Cascade to a Grandifloracin PrecursorA green laboratory experiment has been developed in which students perform an aqueous oxidation/cycloaddition reaction to convert salicyl alcohol into a pentacyclic diepoxydione that is readily isolated by filtration. Drawing on their knowledge of periodate-mediated 1,2-diol cleavage, students propose a mechanism for the oxidation of salicyl alcohol (which is not a 1,2-diol) and the structure of the transient product (prior to a spontaneous Diels−Alder dimerization). Students then characterize salicyl alcohol and their diepoxide product by mass spectrometry, IR spectroscopy, and H, C, and twodimensional NMR spectroscopy. The only organic solvents used are small amounts for IR and NMR spectroscopy.David A. Vosburg, Emily A. Shimizu, Brett Cory, Johnson Hoang, Giovanni G. Castro, Michael E. Jung2019Chemistry
The effect of size-scale on the kinematics of elastic energy releaseElastically-driven motion has been used as a strategy to achieve high speeds in small organisms and engineered micro-robotic devices. We examine the size-scaling relations determining the limit of elastic energy release from elastomer bands that efficiently cycle mechanical energy with minimal loss. The maximum center-of-mass velocity of the elastomer bands was found to be size-scale independent, while smaller bands demonstrated larger accelerations and shorter durations of elastic energy release. Scaling relationships determined from these measurements are consistent with the performance of small organisms and engineered devices which utilize elastic elements to power motion.Mark Ilton, S. M. Cox, Thijs Egelmeers, Gregory P. Sutton,d S. N. Patek, Alfred J. Crosby2019Physics
Beyond power amplification: latch-mediated spring actuation is an
emerging framework for the study of diverse elastic systems
Rapid biological movements, such as the extraordinary strikes of
mantis shrimp and accelerations of jumping insects, have captivated
generations of scientists and engineers. These organisms store
energy in elastic structures (e.g. springs) and then rapidly release it
using latches, such that movement is driven by the rapid conversion
of stored elastic to kinetic energy using springs, with the dynamics of
this conversion mediated by latches. Initially drawn to these systems
by an interest in the muscle power limits of small jumping insects,
biologists established the idea of power amplification, which refers
both to a measurement technique and to a conceptual framework
defined by the mechanical power output of a system exceeding
muscle limits. However, the field of fast elastically driven movements
has expanded to encompass diverse biological and synthetic
systems that do not have muscles – such as the surface tension
catapults of fungal spores and launches of plant seeds. Furthermore,
while latches have been recognized as an essential part of many
elastic systems, their role in mediating the storage and release of
elastic energy from the spring is only now being elucidated. Here, we
critically examine the metrics and concepts of power amplification and encourage a framework centered on latch-mediated spring actuation
(LaMSA). We emphasize approaches and metrics of LaMSA systems
that will forge a pathway toward a principled, interdisciplinary field.
M. Ilton, S. J. Longo, S. M. Cox, E. Azizi, J. P. Olberding, R. St Pierre, S. N. Patek2019Physics
Why do Large Animals Never Actuate Their Jumps with Latch-Mediated Springs? Because They can Jump Higher Without Them As animals get smaller, their ability to generate usable work from muscle contraction is decreased by the muscle’s force–velocity properties, thereby reducing their effective jump height. Very small animals use a spring-actuated system, which prevents velocity effects from reducing available energy. Since force–velocity properties reduce the usable work in even larger animals, why don’t larger animals use spring-actuated jumping systems as well? We will show that muscle length–tension properties limit spring-actuated systems to generating a maximum one-third of the possible work that a muscle could produce—greatly restricting the jumping height of spring-actuated jumpers. Thus a spring-actuated jumping animal has a jumping height that is one-third of the maximum possible jump height achievable were 100% of the possible muscle work available. Larger animals, which could theoretically use all of the available muscle energy, have a maximum jumping height that asymptotically approaches a value that is about three times higher than that of spring-actuated jumpers. Furthermore, a size related “crossover point” is evident for these two jumping mechanisms: animals smaller than this point can jump higher with a spring-actuated mechanism, while animals larger than this point can jump higher with a muscle-actuated mechanism. We demonstrate how this limit on energy storage is a consequence of the interaction between length–tension properties of muscles and spring stiffness. We indicate where this crossover point occurs based on modeling and then use jumping data from the literature to validate that larger jumping animals generate greater jump heights with muscle-actuated systems than spring-actuated systems.Gregory P Sutton, Elizabeth Mendoza, Emanuel Azizi, Sarah J Longo, Jeffrey P Olberding, Mark Ilton, Sheila N Patek2019Physics
The Long and Short of Benford’s LawN/AArthur. T Benjamin2019Mathematics
Unified Tiling Proofs of a Family of Fibonacci IdentitiesIn a recent work, Baxter and Pudwell mentioned the following identity for the Fibonacci numbers Fn and noted that it can be proven via induction: For all n ≥ 1, F2n = 1 · F2n−2 + 2 · F2n−4 + · · · + (n − 1) · F2 + n. We give a combinatorial proof of this identity and a companion identity. This leads to an infinite family of identities, which are also given combinatorial proofs.Arthur. T Benjamin, Joshua Crouch, James A. Sellers2019Mathematics
Hunting rabbits on the hypercubeWe explore the Hunters and Rabbits game on the hypercube. In the process, we find the solution for all classes of graphs with an isoperimetric nesting property and find the exact hunter number of 𝑄𝑛 to be 1+∑𝑛−2𝑖=0(𝑖⌊𝑖/2⌋). In addition, we extend results to the situation where we allow the rabbit to not move between shots.Jessalyn Bolkema, Corbin Groothuis2019Mathematics
Waring's problem in finite ringsIn this paper we obtain explicit results for Waring's problem over general finite rings, especially matrix rings over finite fields by building on analogous results over finite fields. Commutative algebra, in particular the Jacobson radical and nilpotent ideals, plays an important role in our proofs.Yeşim Demiroğlu Karabulut2019Mathematics
Expanding phenomena over matrix ringsIn this paper, we study expanding phenomena in the setting of matrix rings. More precisely, we will prove that • If A is a set of M2(Fq) and |A| ≫ q 7/2 , then we have |A(A + A)|, |A + AA| ≫ q 4 . • If A is a set of SL2(Fq) and |A| ≫ q 5/2 , then we have |A(A + A)|, |A + AA| ≫ q 4 . We also obtain similar results for the cases of A(B + C) and A + BC, where A, B, C are sets in M2(Fq).Yeşim Demiroğlu Karabulut, Doowon Koh, Thang Pham, Chun-Yen Shen, Le Anh Vinh2019Mathematics
Cayley Digraphs Associated to Arithmetic GroupsWe explore a paradigm which ties together seemingly disparate areas in number theory, additive combinatorics, and geometric combinatorics including the classical Waring problem, the Furstenberg–Sárközy theorem on squares in sets of integers with positive density, and the study of triangles (also called 2-simplices) in finite fields. Among other results we show that if 𝔽𝑞 is the finite field of odd order q, then every matrix in 𝑀𝑎𝑡𝑑(𝔽𝑞),𝑑≥2 is the sum of a certain (finite) number of orthogonal matrices, this number depending only on d, the size of the matrix, and on whether q is congruent to 1 or 3 (mod 4), but independent of q otherwise.Yeşim Demiroğlu Karabulut, David Covert, Jonathan Pakianathan 2019Mathematics
Chow Rings of Heavy/Light Hassett Spaces via Tropical GeometryWe compute the Chow ring of an arbitrary heavy/light Hassett space M¯0,w. These spaces are moduli spaces of weighted pointed stable rational curves, where the associated weight vector w consists of only heavy and light weights. Work of Cavalieri et al. exhibits these spaces as tropical compactifications of hyperplane arrangement complements. The computation of the Chow ring then reduces to intersection theory on the toric variety of the Bergman fan of a graphic matroid. Keel has calculated the Chow ring A∗(M¯0,n) of the moduli space M¯0,n of stable nodal n-marked rational curves; his presentation is in terms of divisor classes of stable trees of ℙ1's having one nodal singularity. Our presentation of the ideal of relations for the Chow ring A∗(M¯0,w) is analogous. We show that pulling back under Hassett's birational reduction morphism ρw:M¯0,n→M¯0,w identifies the Chow ring A∗(M¯0,w) with the subring of A∗(M¯0,n) generated by divisors of w-stable trees, which are those trees which remain stable in M¯0,w.Siddarth Kannan, Dagan Karp, Shiyue Li2019Mathematics
Advection and Autocatalysis as Organizing Principles for Banded Vegetation PatternsWe motivate and analyze a simple model for the formation of banded vegetation patterns. The model incorporates a minimal number of ingredients for vegetation growth in semiarid landscapes. It allows for comprehensive analysis and sheds new light onto phenomena such as the migration of vegetation bands and the interplay between their upper and lower edges. The key ingredient is the formulation as a closed reaction–diffusion system, thus introducing a conservation law that both allows for analysis and provides ready intuition and understanding through analogies with characteristic speeds of propagation and shock waves.Jasper Weinburd, Richard Samuelson, Zachary Singer, Arnd Scheel2019Mathematics
A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of coralsOur ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia. Results: Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of > 6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia. Conclusions: A genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.Andrea M. Quattrini, Tiana Wu, Keryea Soong, Ming-Shiou Jeng, Yehuda Benayahu, Catherine S. McFadden2019Biology
Relating Level of Inquiry in Laboratory Instructions to Student Learning OutcomesThis research paper will describe the results of an experiment in which the level of inquiry in a laboratory manual is varied from guided inquiry to open inquiry by reducing the specificity of the instructions in the lab manual. The hypothesis is that less specific instructions will cause students to reflect on their actions in lab and, as a result, circle further around Kolb’s experiential learning cycle during each step of the lab. This should result in improved recall and better integration of laboratory and classroom understanding. Student learning outcomes are assessed using an in-lab, direct assessment which evaluates both students’ laboratory skills and their ability to relate experiences in the laboratory to classroom learning. Student attitudes are also assessed with surveys.Spencer Rosen, Sabrine Griifith, Eli Byrnes, Steven Michael Santana, Dr. Laura Palucki Blake, Matthew Spencer2019Engineering
A mathematical model for DC vaccine treatment of type I diabetesMathematical modeling of Type I Diabetes (T1D) is a new path in my research journey, and was initiated through a discussion with folks from a startup biotech company developing treatments for skin grafting and T1D. There is currently no cure for T1D. In this paper we develop a new mathematical model of onset and progression of Type I Diabetes (T1D), and explore the potential use of dendritic cell immune-modulating therapy to manage the disease. Our analysis and computational simulations indicate that there are immune-state related windows of opportunity in which treatment intervention is more likely to be beneficial in protecting an individual from entering a diabetic state. Lisette De Pillis, Blerta Shtylla, Marissa Gee, An Do, Shahrokh Shabahang, Leif Eldevik2019Mathematics
Canvass: A Crowd-Sourced, Natural-Product Screening Library for Exploring Biological Space
Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The assay data generated were analyzed using a variety of quality control metrics, and the resultant assay profiles were explored using statistical methods, such as clustering and compound promiscuity analyses. Individual compounds were then sorted by structural class and activity profiles. Differential behavior based on these classifications, as well as noteworthy activities, are outlined herein. One such highlight is the activity of (−)-2(S)-cathafoline, which was found to stabilize calcium levels in the endoplasmic reticulum. The workflow described here illustrates a pilot effort to broadly survey the biological potential of natural products by utilizing the power of automation and high-throughput screening.S. E. Kearney, G. Zahoránszky-Kőhalmi, K. R. Brimacombe, M. J. Henderson, C. Lynch, T. Zhao, K. K. Wan, Z. Itkin, C. Dillon, M. Shen, D. M. Cheff, T. D. Lee, D. Bougie, K. Cheng, N. P. Coussens, D. Dorjsuren, R. T. Eastman, R. Huang, M. J. Iannotti, S. Karavadhi, C. Klumpp-Thomas, J. S. Roth, S. Sakamuru, W. Sun, S. A. Titus, A. Yasgar, Y. Zhang, J. Zhao, R. B. Andrade, M. Kevin Brown, N. Z. Burns, J. K. Cha, E. E. Mevers, J. Clardy, J. A. Clement, P. A. Crooks, G. D. Cuny, J. Ganor, J. Moreno, L. A. Morrill, E. Picazo, R. B. Susick, N. K. Garg, B. C. Goess, R. B. Grossman, C. C. Hughes, J. N. Johnston, M. M. Joullie, A. Douglas Kinghorn, D. G.I. Kingston, M. J. Krische, O. Kwon, T. J. Maimone, S. Majumdar, K. N. Maloney, E. Mohamed, B. T. Murphy, P. Nagorny, D. E. Olson, L. E. Overman, L. E. Brown, J. K. Snyder, J. A. Porco Jr., F. Rivas, S. A. Ross, R. Sarpong, I. Sharma, J. T. Shaw, Z. Xu, B. Shen, W. Shi, C. R.J. Stephenson, A. L. Verano, D. S. Tan, Y. Tang, R. E. Taylor, R. J. Thompson, D. A. Vosburg, J. Wu, W. M. Wuest, A. Zakarian, Y. Zhang, T. Ren, Z. Zuo, J. Inglese, S. Michael, Anton Simeonov, W. Zheng, P. Shinn, A. Jadhav, M. B. Boxer, M. D. Hall, M. Xia, R. Guha, J. M. Rohde2018Chemistry
Divergent Diels–Alder Reactions in the Biosynthesis and Synthesis of Endiandric-Type Tetracycles: A Computational StudyEndiandric acids and related polyketide natural products arise from polyene precursors and occur naturally as fused and bridged tetracycles. In some cases, the intramolecular Diels–Alder reactions that produce fused and bridged tetracycles result from a diene tether that may act as either a 4π or 2π component in the cycloaddition. To examine the preference for fused or bridged products, we applied density functional theory (using the M06-2X and B3LYP functionals) to reactants with various substituents for both fused and bridged transition states. Fused products were generally preferred except when disfavored by extreme steric hindrance (e.g., a tert-butyl group). These computational results are consistent with experimental data and suggest the existence of as-yet undiscovered natural products.David A. Vosburg, Kareesa J. Kron, Mikaela KosichRobert J. Cave2018Chemistry
An Information-Theoretic Perspective on Overfitting and UnderfittingDaniel Bashir '20, Sonia Sehra '20, Julius Lauw '20, Pedro Sandoval Segura '19, Dominique Macias '192020Computer Science
A Castro Consensus: Understanding the Role of Dependence in Consensus FormationJarred Allen '22, Cindy Lay CMC '22, George D. Montañez2020Computer Science