2014 SFI REUs


Final Paper: Visualizing Frustration Through the Spinning Glass 

Final Presentation: Video

Bio: My name is Randy Andrews, and I am an Engineering Physics student at NMSU in Las Cruces. I chose this degree path because of the way it ties together laws and principals of physics with concrete application. Specifically, I concentrate on mechanical engineering because it opens up doors in research, development, and analysis. Outside of class, I stay involved on my university's campus. I am active in the Outdoor Leadership Program, Phi Delta Theta, and the Society of Physics Students. Having grown up in Albuquerque, I love the desert. Summer is my favorite season because it is the best time for long boarding and backpacking. As hobbies, I am also interested in fitness, theater, and logic games.

My Science Hero: Ludwig Boltzmann

My Favorite Science Quote: "The universe works on a math equation that never even ever really even ends in the end." - Modest Mouse. "Never Ending Math Equation." Building Nothing Out of Something.

Why Science Inspires Me: Science never ceases to surprise me; one moment, everything makes sense, and the next it's found we were only almost right the whole time.

SFI MENTORS: Ruben Andrist

SFI SUMMER PROJECT ABSTRACT: Visualizing frustration through the spinning glass - Mainstream spin-glass literature tends to be very graph and equation heavy, making these systems, to some, appear incomprehensible. However, these models of disordered magnetic moments continue to show up in complex system discussions as a potential key to understanding quantum computing, neural networks, and other stochastic processes. The purpose of this presentation is to make glassy systems more accessible and to uncover unintuitive quirks in the model. I will graphically present spins, energy, and activity of spin-glasses with a short-range Edwards-Anderson model. Visualizations tend to help a wider audience understand the problem in a way that equations alone may not. Further, they may show emergent properties or inspire creative questions, deepening the understanding on these systems and the processes to which they may be applied.


Final Paper: Community Detection with the z-Laplacian 

Final Presentation: Video

Bio: Jess is a third year mathematics major at Oberlin College with research experience in graph theory and quantitative cultural geography. Born and raised in Madison, WI, Jess is a songwriter and jazz guitarist with a passion for running, overalls, and the work of Pablo Neruda, Leonhard Euler, and Erykah Badu.

SFI MENTORS:  Christopher Moore, Pan Zhang, and Ruben Andrist

SFI SUMMER PROJECT ABSTRACT: Community detection is a fundamental problem in network science, with broad applications - across the biological and social arenas. A common approach is to leverage the spectral properties of an operator related to the network (most commonly the adjacency matrix or graph Laplacian),though there are regimes where these techniques are known to fail despite the existence of theoretically detectable community structure [1]. Krzakala et al. demonstrate in [1] that a novel operator|the so-called \nonbacktracking matrix" B|is in fact amenable to spectral clustering methods in where other operators fail. This project, in collaboration with Christopher Moore and Pan Zhang, will explore yet another matrix, the \z-Laplacian" Lz = zA-D, which has been observed to share important spectral properties with B [2]. We hope build on prior work by Zhang, Moore, and Newman on Lz, in particular using techniques from the theory of random matrices to facilitate further analytic and numerical study of this matrix and it's use in community detection.

References [1] Florent Krzakala, Cristopher Moore, Elchanan Mossel, Joe Neeman, Allan Sly, Lenka Zdeborova, and Pan Zhang. Spectral redemption in clustering sparse networks. Proceedings of the National Academy of Sciences, 110(52):20935{20940, 2013. [2] Alaa Saade, Florent Krzakala, and Lenka Zdeborova. Spectral density of the non-backtracking operator. arXiv preprint arXiv:1404.7787, 2014.


Final Paper: Linguistic Divergence in Austronesian on the Island of Timor 

Final Presentation: Video

Bio: I was born in a National Forest in the great state of Colorado, where I grew up before graduating one year early to attend Central College in Pella, Iowa. Because I couldn't decide which subjects I liked most, I decided to major in as many as I could: mathematics, physics, history, and German. When I have free time, I pursue hobbies including drawing, thinking, playing guitar, hiking, writing, and reading. I also occasionally find time to sleep.

My Science Hero: James Clerk Maxwell

My Favorite Science Quote: "Research is what I'm doing when I don't know what I'm doing" - Wernher von Braun

Why Science Inspires Me: Science is an exciting puzzle with many problems to solve, the applications of which can be both beautiful and powerful. Studying it is not only fun, but gives a great insight into understanding the world.

SFI MENTOR:  Tanmoy Bhattacharya

SFI SUMMER PROJECT ABSTRACT: Linguistic Divergence in Timor - The island of Timor, located in South East Asia, experienced a wave of migration from the neighboring islands several thousand years ago, resulting in its domination by the Malayo-Polynesian branch of the Austronesian languages. The spread of these Languages and their relationships to each other remain poorly understood. Using statistical tools and computation, a data set comprised of words from 53 languages will be analyzed in order to determine how long ago the languages diverged from one another. Regular sound correspondences will be inferred and cognates will be identified to estimate the amount of time that has passed since the languages split. These new methods, incorporating linguistic knowledge, will hopefully compare favorably with current computational strategies and will contribute to a deeper understanding of the movement of the Austronesian people in Timor.


Final Paper: Entropy Maximization

Bio: Alexander Daniels is a physics major at the University of Delaware. His research interests include system dynamics and meta-mathematics. His hobbies include singing, writing, and hiking.

My Science Hero: Richard Feynman

My Favorite Science Quote:  "God does not play dice with the universe" - Albert Einstein

Why Science Inspires Me: Because science gives me a reason to imagine, -- the one thing that gave mankind power over life upon earth -- it inspires me to envision, to dream, and to continue dreaming.

SFI MENTOR: Dr. Alfred Hubler

SFI SUMMER PROJECT ABSTRACT: Arbortrons - Several systems or networks display self-organizing behavior that is characterized by a state with the maximum production of entropy. Such systems are complex in that they are open, i.e. they are not thermally isolated and therefore, the system has access to a continuous supply of energy, and dissipative, i.e. they output energy to external energy reservoirs. The nature of entropy production in these systems is explored by analyzing an example first proposed by Prigogine. An expression for the rate of entropy production in an R-C circuit will be used to demonstrate the behavior of entropy production observed in experiment. The insight provided will then be applied to the phenomena of self-organizing wires made of carbon nanotubes particles dissolved in a non-polar dielectric fluid.


Published Paper in JAMA: Epidemiological and Economic Effects of Priming With the Whole-Cell Bordetella pertussis Vaccine

Final Presentation: Video

Bio: I was born and raised in Albuquerque, NM before I moved to the Chicago area for college. At Trinity International University I am currently a junior studying mathematics and bio-ethics. Some favorite pastimes include skateboarding, coffee, and homework.

My Science Hero: René Descartes

My Favorite Science Quote: “If I have seen further it is by standing on the shoulders of Giants.” ― Isaac Newton

Why Science Inspires Me: I get inspired by the brain-picking collaboration necessary in science's pursuit uncover some new knowledge.

SFI MENTOR: Ben Althouse

SFI SUMMER PROJECT ABSTRACT: Recent evidence suggests that the current acellular Bordetella pertussis vaccine (aP) protects against whooping cough disease, but not against secondary transmission of the B. pertussis bacterium. It is likely that the aP vaccine allows for asymptomatic B. pertussis infections, allowing people to unknowingly transmit infection to other vaccinated and un-vaccinated individuals. Importantly, this includes neonatal infants too young to be vaccinated, where the mortality rate from whooping cough can be up to 3 times that of adolescents and adults. This project explores the possibility of switching back to the highly effective, yet side-affect prone, whole-cell pertussis vaccine (wP). To do this, we must answer the question: is the potential for increased transmissibility associated with aP vaccination more or less costly to the population than the side-effects associated with wP vaccination? First, we will build and run a model to determine the excess number of pertussis cases in scenarios where an aP vaccine is used, and the number of adverse events where a wP vaccine is used. Then, using literature-derived estimates of costs of infant mortality and vaccine-associated adverse events, we will run a cost-benefit analysis to determine which vaccine is more cost-effective for the population as a whole. We hypothesize that a switch back to the wP vaccine will be economically and ethically beneficial for the population.


Final Paper: Genetic Algorithm Analog Circuit Design 

Final Presentation: Video

Bio: I was born and raised in Santa Fe and went to Santa Fe Preparatory School for secondary school. For the past year, I have been attending Franklin W. Olin College of Engineering in Boston Mass. I hope to graduate with a degree in Electrical Engineering.

My Science Hero: Nikola Tesla

My Favorite Science Quote: "There is nothing new to be discovered in physics now. All that remains is more and more precise measurement" - Lord Kelvin circa 1900

Why Science Inspires Me: Science moves humanity beyond the realm of the everyday and into a place past our little world by doing the simple action of describing the everyday. In describing our world, we can better understand our limitations and possibilities and seek to create a new humanity.

SFI MENTOR: Alfred Hubler

SFI SUMMER PROJECT ABSTRACT: In genetic algorithm circuit design, analog circuits can be made with a great degree of difficulty. The algorithm must both specify the location of components and the values of the components. It was found that a variable mutation rate that is dependent upon the fitness requires less time to find an acceptable answer, but risks premature determination. For Matlab to do these algorithms with an acceptable population size and number of generations is also extremely computationally expensive taking over several hours.


Final Paper: Final Paper in Publication Process - Coming Soon

Final Presentation: Video

Bio: I hail from sunny South Florida, but attend college at Columbia University in New York City. To facilitate my broad academic interests, I chose to double major in astrophysics and philosophy. My elective coursework focuses on the intersection between physics and philosophy, employing critical reason to make sense of foundational issues in physics ranging from the arrow of time to the interpretation of quantum mechanics. Outside my formal studies, I have worked as a professional theater technician since high school; my speciality is lighting. Since freshman year I have been an active member of Columbia's swing dance club, along with the wider NYC swing dance community, and I look forward to seeking out the Santa Fe swing dance scene. I also volunteer occasionally with the Columbia Astronomy department's public outreach program, operating rooftop telescopes for public observing. I am happy to go stargazing with anyone on a clear night — I imagine the skies in Santa Fe are much darker than New York's!

My Science Hero: Carl Sagan

My Favorite Science Quote: "Any sufficiently advanced technology is indistinguishable from magic." - Arthur C. Clarke

Why Science Inspires Me: Sciences inspires me because it renders the seemingly incomprehensible behavior of physical reality accessible to the human mind.

SFI MENTORS: David Wolpert, Eric Libby, and James O’Dwyer

SFI SUMMER PROJECT ABSTRACT: Challenges for Inferring Partial Interaction Matrices in Generalized Lotka-Volterra Models of Microbial Communities Several recent attempts to model the dynamics of the human microbiome from metagenomic time series have relied on the standard ecological framework of generalized Lotka-Volterra equations. I demonstrate using simulated data that interaction matrices inferred for a subset of the community are not in general consistent with the full interaction matrix. I also suggest future directions for applying this analysis to empirical metagenomic data.


Bio: Although I am a Texas native, I have long looked upon Santa Fe in the light of a second home. I am currently a sophomore at Marlboro College in Vermont, where I intend to pursue a degree in anthropology. Chief among my subjects of interest are cultural anthropology, history, religion (specifically religious change), identity, and politics. I am particularly interested in south-central Vietnam and hope to conduct work among the Cham and such upland-dwelling minorities as the Raglai, Jarai, Sre, and Sedang. My primary geographic areas of focus include Indochina, Malaya and the Malay Archipelago, sub-Saharan Africa, Myanmar, the Baltic States, and eastern Germany. In my private life, I enjoy traveling, writing, reading, seeing films, creating thematic maps, collecting African and Oceanic art, hiking, and spending time with family, friends, and pets.

SFI MENTORS: Dr. Luis Bettencourt, Dr. Christa Brelsford, Joe Hand, and Dr. Deborah Strumsky

SFI SUMMER PROJECT ABSTRACT: As an REU, I have been collaborating with Dr. Luis Bettencourt, Dr. Christa Brelsford, Joe Hand, and Dr. Deborah Strumsky on the Cities, Scaling and Sustainability project, whose principal aim is to advance a quantitative approach to the study of complex urban forms. Our findings will serve to cast some light upon the nature of cities and kindred forms of human social organization and lay the foundation for future academic work in this important area. I am concerned with, inter alia, collecting low-level socioeconomic census data; using spatial analysis to understand urban transformation (for which purpose I have been digitizing cadastral maps); and employing statistical models to evaluate the properties of various urban systems.


Bio: I am from California, but I currently live in Santa Fe, where I attend St. John's College. My current interests are 3D printing and daydreaming about difficult math problems. In my free time, I like to go hiking and read. My research interests are broad, I hope to solidify questions that will lead into lines of inquiry that span multiple disciplines. I am excited to study at SFI because the collaborative and mixed culture will help me generate new ideas and new questions.

My Science Hero: Michael Faraday

My Favorite Science Quote: "Questioning builds a way." Martin Heidegger, The Question Concerning Technology

Why Science Inspires Me: If I'm alive, I might as well try to explore the world around me. "Science" is just a methodical way of exploring, so that I can hopefully say something with greater certainty after my observations than before them.

SFI MENTORS: Sam Scarpino and Ben Althouse


Final Paper: Kickstarting Memes and Movements: A Distribution-Based Threshold Model 

Final Presentation: Video

Bio: Hi, I'm Emily, an economics major and math minor at Portland State University. I'm currently in my junior year. I grew up in the San Francisco Bay area, and have lived in Portland for the last five years or so. I'm all about the "social" aspect of social sciences, and I'm interested in exploring the ways that our social habits and connections are connected to our financial ones. I've also been a professional baker for the last 8 years, and am totally on Team Cake. In my spare (ha!) time I enjoy hiking in the beautiful Pacific Northwest and wandering around antique shops. While in Santa Fe, I plan on eating about a million sopapillas.

My Science Hero: My high school chemistry teacher, Mr. Mainieri

My Favorite Science Quote: "If you wish to make an apple pie from scratch, you must first invent the universe." -Carl Sagan, Cosmos

Why Science Inspires Me:  I think there's something incredibly beautiful about the search for knowledge. It's this exploration of our place in the universe that makes us human, and it's both very personal and at the same time very humbling.

SFI MENTOR: John Miller

SFI SUMMER PROJECT ABSTRACT: The Importance of Population Characteristics in Threshold Models: The Arab Spring, Kickstarter Campaigns and Internet Memes - The decisions of individual agents to participate in a social movement have collective effects. Each agent faces certain costs and benefits associated with their participation. When enough agents decide to participate, the movement is successful. However, these costs and benefits often vary based on the number of participants. More popular movements are considered more likely to succeed, and thus are less risky for the individual. Three scenarios which exhibit this interaction are the Arab Spring protests of 2010­2011, Kickstarter campaigns, and the spread of internet memes. In the Arab Spring, protesters faced high participation costs and uncertain success. However, the success of the Tunisian protests and their high visibility on social media influenced action in other countries. In Kickstarter campaigns, projects are only funded when they reach a specified goal. Potential donors can view the progress toward that goal before deciding to donate. Internet memes tend to spread primarily through social media, and the “utility” of continuing a meme includes its perceived popularity among a particular social group. I develop a model of this process, based on Granovetter’s (1978) threshold model of collective action. In this model, each agent must see a “threshold” level of participation before joining a movement. Crucial to this process is the distribution of thresholds within a population. Small changes to either the mean threshold level or the variance in thresholds can have strong effects. This explains why some countries seemingly on the brink of social change maintain the status quo, while others break into full onrevolution. My model supports Granovetter’s theory, and extends the theory to explore the relationship between a population’s mean threshold and the critical level of variance needed to push a movement into success. This analysis provides key implications for agents seeking to either promote or deter social movements.


Bio: I’m studying computer science at the University of Central Florida, with a minor in math. My interests lie in simulations of cultural evolution, as well as models of how evolvability and complexity come about in biological systems such as gene regulatory networks. Generally, I want to use simulation to study the emergent properties of biological and social systems with an emphasis on the role of evolution and network dynamics. Outside of academics, I enjoy fencing, video games, and sci-fi/fantasy novels, as well as coaching high school debate.

SFI MENTORS: Anne Kandler and Laura Fortunato


Final Paper: Final Paper in Publication Process - Coming Soon

Final Presentation: Video

Bio: Born and raised in Santa Fe, New Mexico, I am now a student at UC Berkeley. I am interested in studying biological systems through computation, and learning as much as I can. I like roller skating and spicy food.

SFI MENTOR: Eric Libby

SFI SUMMER PROJECT ABSTRACT: The Evolutionary Origins of Developmental Programs

Organisms may exhibit stochastic variation in phenotypes as an evolved strategy to survive in fluctuating environments. These phenotypic variations can have different advantages in different environments; for example, a fast-growing antibiotic-sensitive type and a slow-growing antibiotic-resistant type of bacteria each have different advantages. When growth of an organism population is coupled with changes in environmental fluctuations, it becomes possible to optimize the switching strategy between different phenotypes. This optimal is largely independent of the specific environmental conditions; it is resistant to changes in carrying capacity and competitor organisms’ switching strategies. This project aims to investigate how a deterministic strategy evolves and competes with an optimized stochastic strategy, with the hypothesis that even a rudimentary deterministic strategy would out-compete a stochastic one. This will be done using computer models to simulate competition between organisms with different switching strategies. Investigating this sort of developmental program may provide clues into the emergence of multicellular life as a form of life cycle which develops from cooperation in the growth of single-celled organisms.




*Non NSF Funded Undergraduate Intern