Research Experiences for Undergraduates 2014-Participants

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Asterix = Non NSF Funded Undergraduate Intern

Randy Andrews

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 MENTOR: Ruben Andrist
SFI SUMMER PROJECT ABSTRACT:
Visualizing spin glass frustration
Spin glass theory creates a framework to model disordered magnetic systems. Analogous to the amorphous structure and competing interactions of molecules in window glass, when cooled below a critical temperature spin glasses exhibit non-ergodic evolution.
The Edwards-Anderson model represents magnetic moments as spins on a determined lattice whose interactions with each neighbor are given quenched random variables – depending on the sign, they prefer to align or anti-align with each of them. Conflicting spin interactions cause competition among multiple configurations and result in frustration of the system, especially at lower temperatures when the interactions become largely immobile. Competing interactions may give rise to complex energy landscapes with variations in local energy fields and sections of perpetually conflicting interactions.
Several glassy spin models have been studied using various different methods. However, even estimating basic properties of spin glass energy landscapes of specific instances remains very challenging. Consequently, it is not well understood what makes certain instances much more complex than others.
The purpose of this study is to develop a numerical simulation and visualization tool to gain a better understanding of the effects of frustration on the dynamics of the system. This may map and expose emergent patterns in the structure of some instances that relate to properties found in conventional applications.

Jess Banks

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: Cris 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 Cris Moore, Pan Zhang and Ruben Andrist, 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 Moore and Zhang 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 Zde- borova, and Pan Zhang. Spectral redemption in clustering sparse networks. Proceedings of theNational 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.

Riley Burkart

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.

Alexander Daniels

Bio: My name is Alexander Daniels and I currently live in Newark, DE, where I study and research at the University of Delaware.

Since my first physics course at high school, I realized the power of a well-crafted (mathematical) expression that describes a particular phenomena. I found that such statements could be employed in a number of solutions and over a range of topics, if one dared to meditate on the fundamental truths each one expressed. As a result, I developed a passion to dig for unapparent truths, to demonstrate and apply them, and to discover hidden patterns and untapped potential from a given system.

I believe there is no greater joy than to masterfully handle and delicately present such sublime truths to ensure accuracy and the finest grade of conceptual purity. This is my life's task.
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 H?ubler
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. An expression for the rate of entropy production will be derived and observed from experiment. The insight provided will then be applied to the phenomena of arbortrons - a self-organizing collection of conducting particles due to an imposed electrical current.

Haedi DeAngelis

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. My project aims to explore 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 increased transmissibility associated with aP vaccination more or less costly to the population than the side-effects associated with wP vaccination? We will build a model of pertussis transmission and compare the costs of using each vaccine. Our current hypothesis is that a switch back to the wP vaccine will be economically and ethically beneficial for the population. The first step to answering this question is a literature review on B. pertussis, its vaccines, and cost-benefit analyses in general. Such a review will reveal important details for the different wP and aP vaccines and will help us to create a model of transmission incorporating different vaccine strategies. Next, we will build and run the 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 will test the robustness of our many modeling assumptions in a series of detailed sensitivity analyses. Finally, we will write up the results in a manuscript for submission to a scientific journal.

Madeleine Fort

Bio: I'm 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:

1 Introduction

Once created simply for code and strategy development, Genetic Algorithms (from now called "GA’s") are now being applied not only in the intangible world of neural networks, but also in the very physical form of hardware. Despite the current ability to use GA’s for a diverse range of applications, there is still very little known about GA’s and the fundamentals surrounding their use in hardware design.

1.1 Previous Works

For circuit design with GA’s most work is focused around transistor arrays. This is understandable as corporations fund research on such elements because of the cost efficiency in production. A small degree of research is done in the field about analog circuit design using GA’s. The research is nearly always filter based as filters are single output single input devices. As in Sri Rama Krishna [5], the optimum use is in image processing. The majority of work on GA analog circuits seems to have been done in the late 90’s. The automation tends to use simulation programs to determine fitness (Kerr [1], Koza et al.[2]). The circuit is evaluated solely for functionality but is not characterized mathematically. Additionally, a great deal of time is put into the circuit and it’s successes, but little to no attention is given to the study of the algorithm and why it works so well for circuitry or why it fails when it does. The algorithm does not always yield a usable or significantly better than man made result. More recent attempts to automate design of analog circuits have been far more successful (Barari et al[3]). The current mode of research is in making more successful algorithms ,such as hybrid PSO and GA’s) for VLSI design (see Singh [4]).

2 Research Outline

This project aims to determine the underlying characteristics of GA circuit design. In order to accomplish this, a GA will be implemented in Matlab and the circuit it produces will be most likely be simulated in Spice (circuit analysis software developed by UC Berkeley) to evaluate fitness. The next stage will involve examining the traits similar in the process of evolution of these circuits. The type of circuit to be pursued could be either a filter or amplifier as both are single input single output circuits which are simpler to characterize. Operational amplifiers will be treated as black boxes rather than as transistor arrays. There is a plethora of available research on genetic algorithms which develop operational amplifiers.

3 Works to be Cited

[1] Kerr, Kevin E. Evolving Hardware with Genetic Algorithms. Thesis. Rochester Institute of Technology, 1998. Rochester: n.p., 1998. Web. [2] Koza, John, Forrest H. Bennett, David Andre, and Martin Keane. Proc. of Automated WYWIWYG Design of Both the Topology and Component Values of Analog Electrical Circuits Using Genetic Programming (1996), Stanford, Stanford. N.p.: MIT, 1996. 28-31. Citeseerx. Web. 2014. [3] Mansour Barari, Hamid Reza Karimi, and Farhad Razaghian, “Analog Circuit Design Optimization Based on Evolutionary Algorithms,” Mathematical Problems in Engineering, vol. 2014, Article ID 593684, 12 pages, 2014. doi:10.1155/2014/593684 [4] Singh, Rajdeep, Kumari Kalpna, and Dawindar Kumar Mishra. "Hybrid Optimization Technique for Circuit Partitioning Using PSO and Genetic Algorithm." International Journal of Emerging Trends in Electrical and Electronics 4.2 (2013): 69-71. Iret.co. Web. June 2014 [5] Sri Rama Krishna, K., A. Guruva Reddy, M. N. Giri Prasad, K. Chandrabushan Rao, and M. Madhavi. "Genetic Algorithm Processor for Image Noise Filtering Using Evolvable Hardware." International Journal of Image Processing 4.3 (2010): 240-50. Researchgate.net. Web. June 2014.

Marcus Levine

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.

Jonah Nonomaque*

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.

Cody O'Farrell*

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

Emily Robertson

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 Role of Information 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 are not fixed. A movement which is perceived to be successful is considered less risky, and thus may garner more support. Likewise, a movement that is considered unlikely to succeed is considered more risky, and thus has a higher cost. Further, individuals consider not just their own utility, but also the choices of their social group. Traditional media, social media and cell phones can increase the amount of information available, thus affecting the perceptions of a campaign’s success or failure. Three scenarios which exhibit this interaction are the Arab Spring protests of 2010 -2011, 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 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 propose to model this interaction in order to explore the role of information on patterns of social movements. In particular, whether the perception of a movement’s success can “push” a movement into actual success. And, if, so, under what conditions?

Bryan Wilder

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

Emma Wolinsky

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.