Scientia Spring 2020 Edition

SCIENCE AND THE COMMUNITY SPRING 2020

SCIENTIA

A JOURNAL BY THE TRIPLE HELIX AT THE UNIVERSITY OF CHICAGO

TABLE OF CONTENTS 03

/ INQUIRY

THE BIOLOGIST: A KEYSTONE SPECIES

02

AN INQUIRY WITH DR. CATHY PFISTER Indira Khera

/ ABOUT SCIENTIA

06 INQUIRY /

SIMILARITIES AND DIFFERENCES BETWEEN ULVA SP., GRACILARIA SP., AND THE SEAWATER MICROBIOME STRUCTURE IN LITTLE SIPPEWISSETT MARSH

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LINKING THE ULTRAFAST WITH THE MACROSCOPIC

Emily Watters

AN INQUIRY WITH PROFESSOR SARAH KING Bernadette Miao

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SHAPING AN IMMUNE LANDSCAPE: MICROBIOME-DEPENDENT EFFECTS ON SUSCEPTIBILITY TO LUNG INJURY Gabriel Barrรณn

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WHAT A PIE IN THE SKY AN INQUIRY WITH DR. CHRISTINE ANDREWS Stephanie Zhang

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NOLAND’S AWAY: A CONSERVATION-BASED INVESTIGATION OF VINTAGE ACRYLIC PAINT AND COTTON DUCK CANVAS AGING IN A 1964 KENNETH NOLAND COLOR FIELD PAINTING Talia A. Ratnavale

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DIVERSITY AND SCIENCE:

AN INQUIRY WITH PROFESSOR YOUNG-KEE KIM Tori Ankel

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FULL LENGTH / UNRAVELING SUPERNOVA REMNANT DEM L71

Jared Siegel

WORK IN PROGRESS /

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ENHANCING DARK EXCITON EMISSION IN TRANSITION METAL DICHALCOGENIDES Grace Chen

ABOUT THE TRIPLE HELIX /

51 Produced by The Triple Helix at the University of Chicago / Layout and Design by Bonnie Hu, Production Director / Editors-in-Chief: Rita Khouri, Maritha Wang / Scientia Board: Josh Everts, Sweta Narayan, Molly Sun

ABOUT SCIENTIA Dear Reader, For this edition, our front cover is an artistic representation of UChicago’s campus blending into a natural landscape featuring a mountain range and a body of water with its diverse community of flora and fauna that thrive just below the surface. This image provides a snapshot of this edition’s theme: science and community. Just as a marine ecosystem is a web of dynamic relationships between organisms, UChicago is just one piece of the larger Hyde Park and Chicago ecosystems, as well as the global scientific community. We are humbled to share the work of students on campus as well as articles featuring the worldclass research and scientific service of faculty members to both the UChicago community and the broader community.

Our student researchers had the opportunity to interview professors who hail from different walks of life, are involved in rigorous scientific research, and actively contribute to the community. This issue features Professors Sarah King and YoungKee Kim as well as Drs. Cathy Pfister and Christine Andrews. These individuals have actively engaged with UChicago’s community in various ways, such as by participating in the annual South Side Pie Challenge, empowering young women to participate in STEM related fields, engaging in outreach events to

increase diversity and inclusion in science, and leading camping trips to the Indiana Dunes to supplement class material. This edition also features four impressive full-length articles on original undergraduate research ranging from topics such as the similarities and differences in microbiome structure in the Sippewissett Marsh, how the microbiome shapes an individual’s immune landscape and response to lung injuries, the components of a Kenneth Noland color field painting analyzed through the lens of conservationism, and the nuances of supernova remnant DEM L71. Additionally, this edition includes a work-in-progress that investigates the enhancement of dark exciton emission in transition metal dichalcogenides. It is truly a privilege for us to have the opportunity to highlight these pieces, and we certainly have a passionate team of writers and editors to thank.

Scientia is always looking to broaden our scope and expand the reach of our publication.

If you are completing a research project and want to see it in print, or if there is a professor performing eye-opening research that you would like to share, consider writing for us!

We encourage all interested writers to contact a member of our team, listed in the back. In the meantime, please enjoy this edition of Scientia, presented by The Triple Helix.

Sincerely, Rita Khouri and Maritha Wang Editors-in-Chief of Scientia

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THE BIOLOGIST: A KEYSTONE SPECIES

An Inquiry with Professor Cathy Pfister

INDIRA KHERA

There are few things more mesmerizing than the view from the edge of a tide pool. At a distance, the tide pool appears unassuming: a pond of scummy water, constantly beaten by the tenacity of the waves. One brave onlooker approaches the pool following a pathway of barnacles, scrambling over rocks and pieces of kelp lining the shoreline like scattered toys.

The prize awaiting a determined observer of the coast, however, is worth a lifetime. Peering over the edge of the pool, one is greeted with another universe. Soft, green fronds reach up, grazing the surface like fingertips.

Small fish dart through the crevices, and the occasional, courageous crab scuttles along

looking for food. An overwhelming number of microorganisms inch their way across the rock surface, gently twisting in the water. The longer you study the pool, the more life you see. It is a galaxy unto itself, a strange and microcosmic snapshot of the vast ocean beyond its boundaries.

Dr. Cathy Pfister is well-acquainted with this biological sense of wonder. It has carried her from lab to lab, from diving the oceanic stretch of the Appalachian Mountains off the coast of Maine, to exploring the vibrant aquatic life off Tatoosh Island in Washington, where she has been conducting research for the last 30 years.

As an undergraduate, Dr. Pfister found herself fascinated by ecology, drawn progressively more towards the dynamics of aquatic ecology. Like many young scientists, Dr. Pfister became involved with a limnology laboratory and focused on the study of inland aquatic ecosystems. After some time diving the dark quarries and lakes of the Midwest, her curiosity about the ocean began to grow.

Even in the earliest parts of her career, Dr. Pfister always had a sense of adventure.

She carried this spirit beyond her academic work, seeking out every opportunity possible

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and learning all that she could. After receiving her Master’s degree from UNC-Chapel Hill, Dr. Pfister felt like she needed more time before pursuing a PhD and found her way to the University of Maine, where she worked as a diving technician based out of the Darling Research Facility. She spent significant amounts of time exploring the oceanography of the region and cataloging the diversity of coastal Maine. From Maine, she traveled to the Caribbean, which was in the throes of a severe sea urchin die-off. At the time, the Aquarius underwater habitat was still anchored off the Virgin Islands, and Dr. Pfister spent 10 days underwater studying the dynamics of the ecosystem.

It was during this time that she was able to observe the nuanced differences and similarities between tropical and temperate ecosystems.

Dr. Pfister later found her way to Tatoosh Island during her PhD, which she completed at the University of Washington. Her advisor, famed zoologist Bob Paine, started work on the island after identifying it as a remarkable place to study long-term change: Tatoosh Island acts as a blank canvas, upon which climatic changes are incredibly stark.

Dr. Pfister’s lab runs a bit differently than what one might expect. She emphasizes the independent inquiry of her students, ensuring that each student receives the space and support to pursue their individual research projects. One of the most remarkable aspects of her lab is that every summer, for the past 30 years, Dr. Pfister and her team have traveled to the remote Tatoosh Island

Kelp forests in Bullman Beach, Washington.

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“ To solve our largest problems, we cannot focus on human well-being alone: we must view environmental well-being as a delicate dynamic between ourselves and every other living thing. ”

to work on several long-term projects. The team keeps a database on environmental changes, with a particular focus on sea water chemistry. The second aspect of Dr. Pfister’s work focuses on microbial activities, specifically relating microbiology to the macrobiology of kelp forests.

Each organism, from kelp to mussels, hosts its own unique microbiome, and Dr. Pfister is curious about how each interacts and affects the greater ecosystem. Additionally, she explores how modifications to the carbon and nitrogen cycles might alter these tailored microbiomes.

One of the lab’s most important findings was that the pH of the ocean around Tatoosh Island was declining. Dr. Pfister views the finding as almost entirely an accident, a result of noting an interesting pattern in the readings of the oceanic pH sensors. Initially, the data were disregarded, as the ocean had always been thought to be incredibly well-buffered. The reasons why are still unclear, but the effects of a changing ocean are visible. There is evidence that the shells of mussels in Washington are thinning, consistent with declines in

Dr. Pfister and her team document changes in the carbon isotopes of California mussels.

pH. There was a recent, massive die-off in the sea star population of the West Coast, and constant overfishing depleted the populations. Each of these changes has enormous implications for the trophic system in the ocean. From top to bottom, each ecosystem is uniquely structured and balanced, and each organism has a role to play. As our ocean changes, so too do the lives and roles of each living thing.

When I asked Dr. Pfister where she plans to take her research in the future, she spoke extensively on the role of technology. The information afforded to field ecologists today is incredible and can lead to profound sequencing work. In the past, it was vital for biologists to be physically present in order to collect data. Now, sensors attached to buoys and gliders can travel and record enormous amounts of oceanic data, bringing scientists closer than ever to truly understanding the ocean. However, in the field of biology, Dr. Pfister reminded me that there is no substitute for the real thing.

She urges young biologists to not be dependent on a computer, or to fall into the allure of technology. There is no substitute for being present in nature, for knowing the histories of each organism, or for seeing how each living thing in your hands will respond to the changes we are all facing.

Encouraging this perspective, Dr. Pfister has taught the undergraduate course Ecology and Conservation for close to 12 years and views it as an essential way

to connect with undergraduates. The class involves a traditional weekend camping trip in the Indiana Dunes, in which students spend the weekend collecting data which they eventually analyze in a lab setting.

I asked Dr. Pfister about what advice she has for young biologists, especially in the face of a seemingly insurmountable fight against climate change, and she provided a movingly positive perspective. She advocates for young scientists to acknowledge what is changing, but to remain focused on solutions and paths forward; they must learn as much as they can to ensure that they are capable of understanding, and ultimately solving, problems. Dr. Pfister emphasizes that protecting the environment requires not only an understanding of how humans are impacted by biological change, but one of how every organism stands to be affected. To solve our largest problem, we cannot focus on human wellbeing alone: we must view environmental well-being as a delicate dynamic between ourselves and every other living thing.

Indira Khera is a second year in The College majoring in Biology. In addition to writing for The Triple Helix, she serves as the Outreach Director of Women in Science and currently works as a research intern at the Clinical Neuroscience and Psychopharmacology Research Unit.

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Similarities and Differences between Ulva sp., Gracilaria sp., and the Seawater Microbiome Structure in Little Sippewissett Marsh Emily Watters a, Elena Lopez Peredo a, b a The University of Chicago b Marine Biological Laboratory

Microbial communities are diverse and dynamic forces within ecosystems, with the composition of these communities differing based on the host organism and environment. This project seeks to further understand the microbiome of seawater, Gracilaria sp., and Ulva sp. from the marsh in Little Sippewissett Marsh in Falmouth, Massachusetts. It is hypothesized that seawater will have more species richness and phylogenetic diversity than both genera of algae because of the seawater’s flow and freestanding environment and that Ulva sp. and Gracilaria sp. will have even more than the seawater because of its rooted environment. However, 16S sequencing suggested that microbial community composition between seawater, Gracilaria sp., and Ulva sp. might be more similar than originally thought. Specifically, there were no significant differences in richness, phylogenetic diversity, and evenness between Ulva sp. and Gracilaria sp. and only marginally significant differences between the seawater and both genera of algae.

INTRODUCTION The microbiome is composed of protists, fungi, bacteria, and archaea [1]. The microbiome is an extremely important part of ocean ecosystems and plays a vital role in denitrification, carbon cycling, and breaking down organic manner [2,3]. Generally invisible to the naked eye, the microbiome is able to conduct such important environmental functions because of its unbelievable population size. Indeed, it is suggested that there are 4.06.0 x 1030 bacteria and archaea alone on Earth, with 1.2 × 1029 existing in the open ocean and another 3.5 × 1030 residing in or on oceanic substances [4].

Despite its large size, a microbial community’s composition can be unpacked and understood based on evenness (i.e. abundance of each species), richness (i.e. number of species present), and phylogenetic diversity (i.e. summary of branch evolutionary lengths/phylogenetic differences). Evenness, richness, and phylogenetic diversity all affect a community’s stability, productivity, and trophic structure [5]. These characteristics are in turn important to consider because communities exist differently based on their composition and distribution of species [6].

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This paper will compare the microbiome of Ulva sp., Gracilaria sp., and seawater collected in Little Sippewissett Marsh in Cape Cod, Massachusetts. Specifically, each microbiome’s evenness, richness, and phylogenetic diversity will be assessed. It is hypothesized that the seawater will have more richness and phylogenetic diversity than both genera of algae because of the seawater’s flow and freestanding environment. Ulva sp. and Gracilaria sp., however, are likely to have more even than the seawater because they are located in a static and rooted environment.

This paper serves as a way to assess how the microbiomes of Ulva sp., Gracilaria sp., and seawater in Little Sippewissett Marsh coexist, and to what degree they are similar or different. Ultimately, developing an understanding of the composition of a microbial community will open the door to unraveling how it performs necessary ecological functions. Further research in this area will make it easier to discern how changes in microbiome makeup due to human actions or climate change will affect ecosystems as a whole [1].

Left: Marsh sampling site in Little Sippewissett Marsh. Right: Approximate location of sampling site within Little Sippewissett Marsh [8].

MATERIALS AND METHODS Field Collection and Site Descriptions Ulva sp., Gracilaria sp., and seawater samples were collected from one location in Little Sippewissett Marsh. Little Sippewissett Marsh is a salt marsh estuary that empties into Buzzards Bay. It is located on the western tip of Cape Cod in the town of Falmouth, Massachusetts [7].

Four samples of both algae genera and three samples of seawater were collected in the center of a flowing pool in the lower marsh area. The pool within the marsh is located at approximately 41°34’34.0”N 70°38’12.5”W [8]. The samples were collected during low tide on September 11th, 2019.

A transect was created across the marsh that measured 25 m. A random number generator was utilized to pick 4 numbers between 1 and 25 m. At each generated transect point, the closest rooted Ulva sp. and Gracilaria sp. were taken from the seawater, held in the air for one minute in order to dry, and then sampled using sterile swabs. The swabs were then placed in test tubes. The seawater was taken from the surface level of the marsh.

Three 300 mL samples were filtered through Sterivex units with 0.22 μm filters and then stored in sterile bags.

DNA Extraction, PCR, and Sequencing DNA was extracted from all samples using the commercial Maxwell® RSC PureFood GMO and Authentication Kit, Cat. #AS1600 kit (Promega, Madison, WI). The samples were disrupted with a bead beater homogenizer. Two three-minute cycles were performed at full speed. The samples were incubated at 70°C for 10 minutes in CTAB buffer. Proteinase-K and RNase were added to the samples before incubation, as instructed by the manufacturer. The DNA was quantified after the extraction with a Qubit® High Sensitivity Double DNA kit in a Fluorometer.

PCR amplification was then completed with two prepared master mixes. The master mixes for samples with a Quibet concentration of >0.6 ng/μL were created following the Bacterial/Archaeal v4v5 Amplicon developed by W.M. Keck Ecological and Evolutionary Genetics Facility at the Marine Biological Laboratory. Note that personal communication was facilitated by Aleksey Morovoz. Samples that had a Quibet concentration of <0.6 ng/μL were modified by decreasing the added H2O by 10 μL and adding 10 μL of additional DNA. PCR amplification was used to copy and highlight the 16S ribosomal gene as a prerequisite for paired-end Illumina sequencing. Subsequently, PCR quantification was completed with gel electrophoresis using a 1.5% agarose gel. Within the 11 original samples, 7 were shown to be suitable for paired-end Illumina sequencing (3 seawater samples, 2 Ulva sp., and 2 Gracilaria sp.).

Sequencing was completed in a miseq with 250-length nucleotides.

16S Sequence Analysis FastQC was used to check the quality of the forward and reverse sequences. The Fastqc score of these sequences was verified with a length of 250 base pairs using the Phred score. Because of the large data size (each sample contained anywhere from 20,000 to 300,000+ sequences) and limited processing time, every sample data set was shortened to 60,000 sequences.

The Qiime2 pipeline analyzed the data set and generated graphs [9]. DADA2, a software package used for correcting nucleotide errors in sequences, shortened the parameters by 15 nucleotides in both the forward and reverse reads of the sequences. The forward reads were cut to 230 nucleotides, and the reverse reads were cut at 215 nucleotides [10].

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Figure 1. Significance test results for evenness, phylogenetic diversity, and alpha diversity metrics. Yellow highlight indicates marginal significance, and red highlight indicates insignificant differences. The majority of the data was marginally significant.

Additionally, DADA2 was used to match sequences to OTUs and remove the chimeras, singletons, and any errors. Mitochondria and chloroplasts were also removed to reduce the risk of contamination. The Green Genes Database was used to classify the sequences, and alpha and beta diversity metrics were collected using Diversity Core Metrics.

RESULTS Richness Richness was assessed by determining the number of operational taxonomic units (OTUs) present in each sample. OTUs are used to organize bacteria species based on their sequence similarity [11]. Analysis of observed OTUs found that the seawater samples had the least amount of microbial diversity with a median of 325 (range of 300-350) OTUs. Ulva sp. had a median of 837.5 (range of 725-950) OTUs, and Gracilaria sp. samples had the most OTUs with a median of 1,012.5 (range of 950 to 1,075) OTUs. Evenness Evenness ranges from 0 to 1, with 1 indicating total evenness and 0 indicating no evenness [12]. The seawater samples again had the lowest evenness, with 0.725 (0.71 to 0.74). Ulva sp. had an evenness of 0.775 (0.77 to 0.78). Gracilaria sp. had the greatest evenness with 0.86 (0.85 to 0.87). The difference in evenness between Ulva sp. and the seawater’s microbiomes appeared to be marginally significant (Kruskal-Wallis, p=0.08). Likewise, the evenness differences between Gracilaria sp. and the seawater were marginally significant (Kruskal-Wallis, p = 0.08). However, the evenness differences between Ulva sp. and Gracilaria sp. did not seem to be significant (Kruskal-Wallis, p = 0.12).

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Figure 2. A ranking of the Faith Phylogenetic Diversity results showing that Gracilaria sp. had the most phylogenetic diversity, followed by Ulva sp., and then seawater. The results were the same (order wise, in that Gracilaria sp. had the highest of each metric, followed by Ulva sp., and then seawater) for the alpha diversity and evenness data.

Phylogenetic Diversity Faith’s Phylogenetic Diversity index uses phylogenetic tree branch lengths and phylogenetic diversity between species to communicate biodiversity [13]. Seawater had the lowest phylogenetic diversity with a mean of 31 (28 to 34) (Figure 2). Ulva sp. had a phylogenetic diversity of 61 (56 to 66). Finally, Gracilaria sp. had the highest phylogenetic diversity of 64.5 (60.5 to 68). Ulva sp. and Gracilaria sp.’s difference in phylogenetic diversity was not significant (Kruskal-Wallis, p = 0.43). Ulva sp. and Gracilaria sp.’s microbiomes both had a phylogenetic diversity that was marginally significantly different from the seawater’s microbiome (Kruskal-Wallis, both p = 0.08).

Alpha Diversity Like richness, alpha diversity is the average species within a certain habitat [14]. Ulva sp. and Gracilaria sp.’s microbiomes did not have a significant difference in alpha diversity (Kruskall-Wallis, p = 0.12), and Gracilaria sp.’s microbiome was more diverse (Figure 1). The seawater and Gracilaria sp. also had a marginally significant difference in their microbiomes’ alpha diversity (p = 0.08). There was also a marginally significant difference in diversity between seawater and Ulva sp. (Kruskall-Wallis, p = 0.08).

Beta Diversity Beta diversity is the difference in species composition between samples. Beta diversity significance was tested using Permutational multivariate analysis of variance (PERMANOVA), a significance test that measures differences between groups [15]. With an unweighted-unifrac PERMANOVA test, the results indicated that Ulva sp., Gracilaria sp., and the seawater had statistically significant differences in their microbial communities (PERMANOVA, p = 0.03, pseudo-F = 4.78).

Persica made up an average of 2.85% of the Gracilaria sp microbiome and an average of 0.714% of the Ulva sp microbiome. Lewinella Persica requires one-half to double-strength seawater for optimal growth, which is interesting considering that this bacterium was not found in seawater [17].

Additionally, Phormidium priestleyi made up an average of 2.63% of the Gracilaria sp. microbiome and an average of 0.223% of the Ulva sp. microbiome.

Phormidium priestleyi is known to thrive in extremely cold temperatures and is frequently found in Antarctica, but it is apparently able to survive in Massachusetts’ marshes as well [18].

Figure 3. A taxonomic chart of the Ulva sp., Gracilaria sp., and seawater samples’ microbiomes. This taxonomic chart helps to show the subtle differences in microbiome composition between the three samples. Each color represents a different species of bacteria.

However, the test also showed that Gracilaria sp. and seawater did not have significantly different microbial communities (PERMANOVA, p = 0.11, pseudo-F = 6.62). Similarly, Ulva sp. and seawater did not have significantly different microbial communities (PERMANOVA, p = .10, pseudo-F = 6.60). Ulva sp. and Gracilaria sp. appeared to have identical microbial communities, likely an effect of a small sample size (PERMANOVA, p = 1.00, pseudo-F = .911). PERMANOVA was run with other tests (Jaccard and Bray-Curtis) as well, and the results were also insignificant.

Taxonomic Information Figure 4 shows the breakdown of bacteria species that existed in the seawater. To highlight the two species that have the highest percent composition, Coccinistipes vermicola made up an average of 7.54% of the seawater’s microbial composition, while Pelagibacter ubique made up an average of 2.78%. Unfortunately, not much appears to be known about Coccinistipes vermicola other than the fact that it is found in marine environments around the world [16].

Figure 5 shows bacterial species that existed in both algae samples, but not the seawater. Lewinella

DISCUSSION

Overall, as seen by the PERMANOVA unweightedunifrac test, the three samples—Ulva sp., Gracilaria sp., and seawater—did not have significant differences in their microbial communities. Nevertheless, there was a marginally significant difference in the evenness, phylogenetic diversity, and alpha diversity of the microbiomes between Ulva sp. and seawater. There was also a marginally significant difference between the Gracilaria sp. and seawater’s microbiomes. On the other hand, despite being entirely different genera of algae, there was no significant difference between the evenness, phylogenetic diversity, and alpha diversity of Ulva sp.’s and Gracilaria sp.’s microbiomes.

The information found contradicts almost all aspects of the proposed hypothesis, as the seawater’s microbiome was not richer or more phylogenetically diverse than the algae, and Ulva sp.’s microbial composition was not richer than Gracilaria sp’s.

However, Ulva sp. and Gracilaria sp. both had more even microbiomes than seawater, albeit marginally.

These results allow a deeper look into Little Sippewissett Marsh’s microbiome and bolster the understanding of its composition. More importantly, however, these results also open the door for further research into the marsh’s microbial composition and dynamics.

For example, the lack of significant differences between Ulva sp.’s and Gracilaria sp.’s respective microbial compositions could be a result of study limitations and a small sample size. There is also a possibility that the two genera of algae are fundamentally similar to the point that an exponentially larger sample size would still yield the same results. Gracilaria sp.’s edge in observed OTUs, evenness, and phylogenetic diversity leads to a belief that beta and alpha diversity results would be significantly different with a larger sample size, but currently, answers of that nature are unknown.

Moreover, as previously mentioned, Gracilaria

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Figure 4. A taxonomic chart of the species only present in seawater’s microbiome. The most-frequent species were Coccinistipes vermicola (pink) and Pelagibacter ubique (blue).

Figure 5. A taxonomic chart of the species only present in Ulva sp. and Gracilaria sp.’s microbiomes. The most-frequent species were Lewinella persica (purple) and Phormidium priestleyi (tan).

sp.’s microbiomes had much higher results than Ulva sp. and seawater in almost every metric. As such, these results raise the question of why Gracilaria sp.’s results were higher than Ulva sp. and what is different about Gracilaria sp.’s microbiome that causes these changes, especially considering that the beta diversity results indicated that there were no significant differences in their microbial communities.

Additionally, this study did not attempt to find how differences in evenness, phylogenetic diversity, richness/alpha diversity, or beta diversity affect the function of microbial communities. Although a small sample size was used, the results from this study present the opportunity to learn more about how changes in certain metrics can impact microbial functioning—or if it does in the first place.

In closing, while this study provides a glimpse into the Little Sippewissett Marsh microbial community and its interactions with seawater, Ulva sp., and Gracilaria sp., future studies will be needed to elucidate how the microbiome functions in an ecosystem as a whole.

REFERENCES 1. Fuhrman, J. A. Microbial community structure and its functional implications. Nature, 459(7244), 193–199. doi: 10.1038/nature08058 (2009) 2. Bowen, J. L., Ward, B. B., Morrison, H. G., Hobbie, J. E., Valiela, I., Deegan, L. A., & Sogin, M. L. Microbial community composition in sediments resists perturbation by nutrient enrichment. The ISME Journal, 1540–1548. doi: 10.1038/ismej.2011.22 (2017) 3. Kirchman, D., & Mitchell, R. Contribution of Particle-Bound Bacteria to Total Microheterotrophic Activity in Five Ponds and Two Marshes.

Applied and Environmental Microbiology, 43(1), 200–209. Retrieved from https://aem.asm.org/content/aem/43/1/200.full.pdf (1982) 4. Whitman, W. B., Coleman, D. C., & Wiebe, W. J. Prokaryotes: The unseen majority. Proceedings of the National Academy of Sciences, 95(12), 6578–6583. doi: 10.1073/pnas.95.12.6578 (1998) 5. Stirling, G., & Wilsey, B. Empirical Relationships between Species Richness, Evenness, and Proportional Diversity. The American Naturalist, 158(3), 286–299. doi: 10.1086/321317 (2001) 6. McKnight, D. T., Huerlimann, R., Bower, D. S., Schwarzkopf, L., Alford, R. A., & Zenger, K. R. Methods for normalizing microbiome data: An ecological perspective. Methods in Ecology and Evolution, 10(3), 389– 400. doi: 10.1111/2041-210x.13115 (2018) 7. Mackey, K. R. M., Hunter-Cevera, K., Britten, G. L., Murphy, L. G., Sogin, M. L., & Huber, J. A. Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping. Frontiers in Microbiology, 8. doi: 10.3389/ fmicb.2017.01496 (2017) 8. Google (n.d.). [Google Maps loction result for Little Sippewissett Marsh]. https://tinyurl.com/yy7w8ro2 (2019)

9. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et. al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37: 852–857. https:// doi.org/10.1038/s41587-019-0209-9 (2019) 10. Callahan, B., McMurdie, P., Rosen, M., Han, A., Johnson, A.J., & Holmes, S, DADA2: High-resolution sample inference from Illumina amplicon data, Nature Methods, 13, https://doi.org/10.1038/nmeth.3869. (2016) 11. Schloss, P. D., & Handelsman, J. Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness. Applied and Environmental Microbiology, 71(3), 1501– 1506. doi: 10.1128/aem.71.3.1501-1506.2005 (2005) 12. Pielou, E. C. The measurement of diversity in different types of biological collections. Journal of Theoretical Biology, 15(1), 177. doi: 10.1016/0022-5193(67)90048-3 (1967) 13. Faith, D. P. Conservation evaluation and phylogenetic diversity.

Biological Conservation, 61(1), 1–10. doi: 10.1016/0006-3207(92)91201-3 (1992) 14. Jost, L. Partitioning Diversity Into Independent Alpha And Beta Components. Ecology, 88(10), 2427–2439. doi: 10.1890/06-1736.1 (2007) 15. Kelly, B. J., Gross, R., Bittinger, K., Sherrill-Mix, S., Lewis, J. D., Collman, R. G., … Li, H. Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Bioinformatics, 31(15), 2461– 2468. doi: 10.1093/bioinformatics/btv183 (2015) 16. Zhou, Y., Su, J., Lai, Q., Li, X., Yang, X., Dong, P., & Zheng, T. Phaeocystidibacter luteus gen. nov., sp. nov., a member of the family Cryomorphaceae isolated from the marine alga Phaeocystis globosa, and emended description of Owenweeksia hongkongensis. International Journal Of Systematic And Evolutionary Microbiology, 63(Pt 3), 1143– 1148. doi: 10.1099/ijs.0.030254-0 (2012) 17. Sly, L. I., Taghavit, M., & Fegan, M. Phylogenetic heterogeneity within the genus Herpetosiphon: transfer of the marine species Herpetosiphon cohaerens, Herpetosiphon nigricans and Herpetosiphon persicus to the genus Lewinella gen. nov. in the Flexibacter-Bacteroides-Cytophaga phylum. International Journal of Systematic Bacteriology, 48(3), 731–737. doi: 10.1099/00207713-48-3-731 (1998) 18. Chrismas, N. A. M., Barker, G., Anesio, A. M., & Sánchez-Baracaldo, P. Genomic mechanisms for cold tolerance and production of exopolysaccharides in the Arctic cyanobacterium Phormidesmis priestleyi BC1401. BMC Genomics, 17(1). doi: 10.1186/s12864-016-2846-4 (2016)

Emily Watters is a third-year student at the University of Chicago majoring in Biological Sciences (specialization in Microbiology) and Russian/East European Studies. She plans to attend graduate school to study microbiology, infectious disease and global health.

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LINKING THE ULTRAFAST WITH THE MACROSCOPIC An Inquiry with Professor Sarah King

BERNADETTE MIAO

Imagine a night devoted to science.

With scientific institutions open to the general public, you might explore the latest advances in brain-machine interfaces in a molecular engineering lab or attend a lecture on cosmic ray observation. In Germany, these exploratory nights are known as Lange Nacht der Wissenschaften, or Long Night of the Sciences. This annual event held by the German government is an evening dedicated to science. Institutions invite the public to explore demonstrations and lectures on science research. Inspired as a postdoctoral fellow in Germany witnessing this active engagement of the community with science, Assistant Professor of Chemistry Sarah King envisions a similar science outreach event at the University of Chicago.

At the University of Chicago, Professor King participates in ‘Physics with a Bang!’, an outreach event presented by the University of Chicago Materials Research Science & Engineering Center (MRSEC), the interdisciplinary James Franck Institute, and Professors Sidney Nagel and Heinrich Jaeger of the University of Chicago Physics Department. This event welcomes students, families, and teachers to an open house with physics demonstrations, lectures, and

lab tours. This year, Professor King helped organize ‘Physics with a Bang!’ and led a demonstration, involving laser pointers and mirrors, to safely demonstrate scientific concepts and tools she uses in her research.

In addition to this outreach to ignite curiosity in science, Professor King participates in events to increase diversity and inclusion in science. This spring, she will be participating in the Women in STEM exhibit organized by the Physical Sciences Division of the University of Chicago. This event, titled ‘Redefining the Landscape’, highlights women in the Physical Sciences Division and Pritzker School of Molecular Engineering and their accomplishments.

In 2018, Professor King joined the Chemistry Department at the University of Chicago as a Neubauer Family Assistant Professor of Chemistry. An active member of the University’s community, she teaches chemistry classes, including graduatelevel Statistical Thermodynamics and undergraduate-level Honors General Chemistry. In addition to teaching and being involved in ‘Physics with a Bang!’, she continues to grow her physical chemistry research group. This expert skill needed to balance her teaching, research, and community outreach is one that Professor

King successfully acquired in a unique position: as an undergraduate varsity athlete at the Massachusetts Institute of Technology (MIT).

At MIT, not only did Professor King thrive as a Chemistry major, but she also balanced varsity swimming and diving with undergraduate research.

Through working in an organic chemistry lab, she discovered her love for research. Professor King decided to pursue graduate studies in Chemistry, as she realized that many careers in science would require a PhD background. Although she was not certain that she wanted to be a faculty member, she did know that she wanted to be “in a position where she was leading the science, leading the team.” Professor King cannot be more thankful for her education at MIT. She loved being surrounded by people “truly fascinated” by their work.

In addition, she is grateful for the supporting faculty who helped her make decisions about graduate school and gave her lab tours to see the specific equipment used in different research fields.

After MIT, Professor King pursued a PhD at the University of California, Berkeley. She was a recipient of the National Science Foundation Graduate Fellowship and was part of the Chemistry graduate program for five years. She loved working with Professor Daniel Neumark, a physical chemist, and transitioned from her original field of interest in organic chemistry to physical chemistry research. A dedicated mentor, Professor Neumark gave his students the ability “to explore but not flounder.” Being in Professor Neumark’s group was an amazing experience that provided King with

the support that she needed to thrive as a graduate student.

Following her graduate work at Berkeley, she was a postdoctoral fellow at the Fritz Haber Institute of the Max Planck Society in Berlin, Germany for three years. She received the Alexander von Humboldt Foundation Postdoctoral Research Fellowship to pursue her postdoctoral research. Working at the Max Planck Institute was a great experience that provided her with the opportunity to see how “science is done somewhere else.”

Today, Professor King continues to conduct research as she leads her own physical chemistry research group, currently consisting of three graduate students and one postdoc. They set up experiments and work with lasers, vacuum chambers, and other equipment to answer important questions surrounding the field of physical chemistry. Her research focuses on the role of the nanostructure and interfacial structure in the ultimate functionality of a material. Her group probes the “mechanistic, fundamental differences” in the nanostructure of materials to understand how materials can be used in different applications. Focusing on the fundamental electronic structure and femtosecond-byfemtosecond dynamics of a material allows her group to investigate how, for example, a semiconductor can be used in energy transport, singlet fission, or catalysis.

These different applications for a given semiconductor depend on the electronic structure at the interface of materials.

Professor King’s group uses novel tools to further our current knowledge about material interfaces. These techniques include ultrafast electron microscopy to look at nanoscale dynamics and materials. In addition, her group uses interface-specific spectroscopy to analyze electronic structure and properties in situ, such as in water or under high pressure. This research on understanding a material’s fundamental structure helps guide materials scientists, synthetic chemists, and engineers, and it allows researchers to take advantage of the unique attributes of various materials.

The ultimate goal of Professor King’s research is to design materials that utilize the “defects or imperfections” of materials. These “defects” are the

“ The ultimate goal of Professor King’s research is to design materials that utilize the ‘defects or imperfections’ of materials.

These ‘defects’ are the locations where Professor King says, ‘the interesting stuff happens.’ ”

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At UChicago’s “Physics with a Bang!” outreach event, Professor King uses lasers and mirrors to show young students the tools she uses in her research.

locations where Professor King says, “the interesting stuff happens.” Specifically, these are areas where a material exhibits uncommon, often not well understood, phenomena. For example, novel functionalities of a material found in these “imperfections” could be used to emit light or for catalysis. These aspects of materials are areas of modified bonding that we currently cannot be probed experimentally and require more investigation to be fully understood.

As Professor King conducts research, participates in science teaching and outreach, and supports diversity and inclusion in STEM, she also is working toward achieving her ultimate goal of “leading the science and leading the team.” With this overarching goal in mind, perhaps it won’t be long before the community can look forward to one of Professor King’s original ideas: a UChicago-style ‘Long Night of the Sciences’ for everyone to enjoy.

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Bernadette Miao is a first-year student interested in Chemistry and Economics.

Shaping an Immune Landscape: Microbiome-dependent Effects on Susceptibility to Lung Injury Gabriel Barrรณn a, Annie I. Sperling a a Department of Pulmonary Critical Care Medicine (PCCM), University of Chicago

Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) form a spectrum of lung diseases that cause immune infiltration of the alveoli and compromise gas exchange. While the chemotherapeutic agent bleomycin (BLM) is used to model ALI in mice, its effects are variable. This raises the question of whether the microbiome of the mice may contribute to the variability of the BLM response in the lungs. The Sperling lab has found that BLM treatment of mice housed in one facility, Facility A, resulted in increased survival, decreased weight loss and decreased collagen deposition when compared to BLM treated mice in a separate facility, Facility B. To determine whether microbiome differences in the two facilities were responsible for the differential BLM response, gnotobiotic B6 (ex-germ-free) mice were conventionalized by exposure to fecal matter from Facility A or Facility B, and the initial differential response to BLM was found: Facility A mice survived while Facility B mice succumbed. To profile the microbial communities found in the two facilities, fecal samples from the ex-germ-free mice were collected and analyzed with 16S rRNA sequencing using the Illumina MiSeq platform and QIIME2. These data revealed distinct fecal microbial community membership between the mice conventionalized with Facility A vs. Facility B gut microbes. Flow cytometric analysis of lung and spleen samples showed expansion of CD4+ T regulatory (Treg) cells (CD25+ Foxp3+) at baseline in Facility A mice when compared to Facility B counterparts. These results suggest intestinal microbes harbored in separate facilities can influence adaptive immune processes and outcomes in BLM-induced lung injury. These findings implicate the microbiota in shaping adaptive immune responses in the context of lung injury and later development of fibrosis.

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INTRODUCTION Acute respiratory distress syndrome (ARDS) and the related acute lung injury (ALI) form a spectrum of lung pathologies that manifest pulmonary edema and barrier dysfunction, thereby resulting in morbidity and mortality. Lung injury is a broad term used to describe the compromised alveolar environment due to trauma, unresolved infection, and sepsis. ARDS is a more severe subset of ALI that is described by a PaO2/FiO2 ratio of less than 300 mmHg [1]. Every year, it affects around 80 patients, and those with mild to severe ARDS suffer a mortality rate of over 45% [2].

First characterized in 1967 by Ashbaugh, Bigelow, Petty, and Levine, ARDS leads to loss of compliance, hypoxemia, and tachypnoea. These conditions were only resolved with the practice of positive end-expiratory pressure (PEEP) therapy [3]. While ARDS poses serious concerns for vulnerable patient populations, it frequently goes underdiagnosed in the clinic. For instance, in one study following physicians in a US adult ICU, only 47.6% of patients who fulfilled both the clinical and pathological diagnoses of ARDS had any mention of the condition in their health chart [4].

The chemotherapy drug bleomycin has been used to model ARDS, ALI and pulmonary fibrosis, as there are similar phenotypes of pulmonary edema, increased vascular permeability, and necrosis of pulmonary epithelium [5]. The temporality of the model allows researchers to focus on specific time points, in which the peak of inflammatory responses occurs on day 5 and the peak of fibrotic responses occurs on day 17. Interestingly, BLM-induced fibrosis spontaneously resolves in mice 40+ days after initial exposure to the drug. Another model for ALI is intratracheal instillation of lipopolysaccharide (LPS), a bacterial component that activates macrophages, recruits neutrophils, and promotes the release of pro-inflammatory cytokines [6]. Both models—BLM and LPS—phenocopy neutrophil recruitment to the lung along with increased inflammatory markers. Yet, outstanding questions arise because studies from different labs exhibit great variability in lung injury results when using similar dosage and instillation of BLM to induce lung injury.

Canonically, the lungs have been characterized as a sterile environment, or inhospitable to any microbial life; however, recent advances in sequencing techniques have elucidated unique populations of microorganisms residing in the lungs. Through microaspiration, microbes residing in the oral cavity can travel on droplets of saliva into the trachea, or even deeper into the lung, colonizing the bronchi and alveoli [7]. There, the composition of microbial life in the lungs is highly similar to those found in the mouth

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and esophagus. Due to the close relationship between the oral mucosa and the gut, a semblance of the gut microbiota can also be traced to the lungs. These findings have led researchers to pursue questions elucidating the nature of the gut-lung axis and how the relationship between the two mucosal surfaces contributes to disease etiology. While previous studies have shown how the microbiome can activate specific T cell populations within the lung to confer the development of cancer [8], the role of the microbiome on inflammatory lymphocyte populations and cytokines is a burgeoning field. These studies seek to address this apparent gap in knowledge of differential responses to the same chemotherapy treatment and posit a potential role for specific microbes to drive different fibrotic and immunologic responses.

MATERIALS AND METHODS Mice

C57BL/6 mice were purchased from Harlan Laboratories (Indianapolis, Indiana). Gnotobiotic and exgerm-free mice were a generous gift from Dr. Eugene Chang (University of Chicago Medicine, Chicago, IL) and studies were conducted in collaboration with Dr. Vanessa Leone, a post-doctoral scholar in his lab. Mice were housed and bred in specific pathogen-free facilities at the University of Chicago in two different mouse housing facilities: Gordon Center for Integrative Sciences and the Knapp Center for Biomedical Discovery. Animal housing and procedures were approved by the University of Chicago Institutional Animal Care and Use Committee.

These studies were conducted according to the principles set forth by the Animal Welfare Act and the National Institutes of Health guidelines for the care and use of animals in biomedical research.

Bleomycin Model of ALI Bleomycin was purchased at 15 units/vial from Teva Pharmaceuticals USA. It was reconstituted in 5 mL of sterile PBS for a stock concentration of 3 units/ mL. Mice were grouped according to weight, using a 5-gram weight range for each group. The average weight of each group was used to calculate the appropriate volume of stock solution to be used. Mice were anesthetized by intraperitoneal injection of 300500 μL of a combined solution of ketamine (100 mg/mL) and xylazine (20 mg/mL). Once sedated, mice were administered 50 μL of the relevant bleomycin dose intratracheally. Mice were weighed every 1-3 days and weight loss was monitored. Mice were euthanized if they lost 25% or more of their starting weight.

Table 1. The following represents panels of fluorescent markers that were used to stain lung samples for flow cytometric analysis.

Lung Tissue Processing Mice were euthanized by intraperitoneal injection of 300 μL SomnaSol™ (39 mg/mL, Henry Schein, Inc.).

Lungs were perfused with PBS and then dissected and mechanically minced. Lung tissue was digested with 150 units/mL of Collagenase D (MilliporeSigma) in 10 mL complete DMEM (5% fetal bovine serum, 2.5% HEPES, 1% penicillin/streptomycin, 1% non-essential amino acids, 0.1% β-mercaptoethanol) for 1 hour to obtain a single-cell suspension. Samples were washed and red blood cells were lysed with Ammonium-Chloride-Potassium (ACK) lysis buffer. Lung samples were incubated with 1 mL ACK lysis buffer for 1 minute before adding 3 mL of complete DMEM. Flow Cytometry and Antibodies Single-cell suspensions from lung tissue were used for flow cytometry analysis. 5×105 - 1×106 cells were aliquoted into sample tubes. Cells were washed with 2 mL FACS buffer (PBS with 0.1% sodium azide and 1% bovine serum albumin). Cellular Fc receptors were blocked using 2.4G2 (α-CD16/α-CD32) for 5 mins at room temperature.

Cells were stained with surface antibodies for 30 mins at 4°C (see panels below) and then washed with FACS buffer. For intracellular staining for FoxP3+ cells, cells were surface stained and then fixed with 0.5 mL Fixation/ Permeabilization Diluent (eBioscience, Inc.) at 4°C for 45 mins. 1 mL Permeabilization Buffer (eBioscience, Inc.) was added to cells. Samples were run on an LSRFortessa (BD), which is maintained by the University of Chicago Flow Cytometry Core Facility. Data was analyzed using FlowJo software (BD Biosciences).

Microbiome Library Preparation For the stool extraction, the QIAGEN MagAttract PowerMicrobiome DNA/RNA EP Kit and the manufacturer’s protocol were followed thoroughly.

The V4 region of the 16S rRNA gene (515F-806R) was amplified with region-specific primers that included the Illumina flow cell adapter sequences and a 12-base barcode sequence. Each 25-μl PCR reaction contained the following mixture: 12.5 μl of AccuStart II PCR ToughMix (Quantabio), 9.5 μl of molecular grade water, 1 μl each of the forward and reverse primers (5 μM concentration, 200 pM final), and 1 μl of template DNA. The conditions for PCR were as follows: 94°C for 3 min to denature the DNA, with 35 cycles at 94°C for 45 s, 50°C for 60 s, and 72°C for 90 s, with a final extension of 10 min at 72°C to ensure complete amplification.

Amplicons were quantified using PicoGreen (Invitrogen) assays and a plate reader, equimolar pooled at 240 ng per reaction, followed by a cleanup using AMPure XP clean up using a 1:1 ratio of beads to PCR product, followed by a final quantification via Qubit (Invitrogen, Grand Island, USA). The 16S samples were sequenced on an Illumina MiSeq platform at Argonne National Laboratory core sequencing facility according to Earth Microbiome Project (EMP) standard protocols.

Hydroxyproline Assay Lung homogenate samples were exposed to 6M HCl/PBS mixture for 18 hours overnight in 120°F heat block. Concurrent with hydrolysis of lung samples, a hydroxyproline standard was made using 10 mg of trans-4-Hydroxy-L-proline (Sigma-Aldrich, Inc.) dissolved in 1 mL of 6M HCl/PBS solution. 10 µL of supernatant was put into a 96-well plate in triplicate along with standards. Samples were put into a 65°C incubator to dry, and they were subsequently treated with citrate acetate buffer, Chloramine T and Ehrlich’s solution. Samples were read at 562 nm using SpectraMax M2e Multilabel Microplate Reader.

Statistical Analyses Statistical tests were done using Prism (GraphPad Software), and (p<0.05) was considered statistically significant. Significance of experiments with two groups was evaluated using a Student’s unpaired t-test, unless otherwise indicated. Significance of experiments with more than two groups was evaluated using a oneway ANOVA with Tukey post-tests used for pairwise comparisons. In addition, the significance of survival cures and weight loss curves were evaluated using a log-rank (Mantel-Cox) and two-way ANOVA with Tukey post-tests, respectively.

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Figure 1. Survival response to BLM challenge is dependent upon housing facility at the University of Chicago. (A) Different strains of mice all on the WT C57BL/6 background show differential survival depending on which facility they were housed in. Data is representative of pooled experiments conducted over a period of 9 months. In all experiments, mice were observed for 17 days. (B) Age and sex-matched male C57BL/6 mice born and raised in either Facility A or Facility B were treated with BLM from the same stock on the same day. Mice were observed for 19 days.

RESULTS These studies started with a simple observation: mice housed in different facilities experienced differential weight loss and survival responses to BLM-induced lung injury (Fig. 1). It was clear that BLM exposure affected mice housed in the two facilities differently regardless of genetic strain. These findings necessitated control for genetic and microbial variables. Germ-free mice from the same set of parents were separated and transferred into the two respective facilities. Dirty specific-pathogen free (SPF) bedding from the respective facilities was transferred into the cages to allow for conventionalization over the course of two weeks. Since several cages were transferred into the housing facilities, SPF bedding was also mixed between cages to account for the cage effect. After conventionalizion was complete, fecal pellets were collected from mice and sent for 16S rRNA sequencing (Fig. 2A). Mice were also challenged with bleomycin. From the 16S sequencing, a dendrogram heatmap was created to visualize the presence or absence of specific bacterial taxa (Fig. 2B). Evidently, it was clear that mice had (1) conventionalized thoroughly to the microbiome of the respective facilities and that (2) the microbiomes of the two facilities were different.

Further studies on the sequencing data demonstrated differences in alpha and beta diversity correlating with differences in taxa diversity and microbial composition between the two rooms (Fig. 2C). Finally, weight loss and survival curves recapitulated the earlier findings of differential responses to BLM challenge (Fig. 2D).

Subsequent studies sought to elucidate the adaptive immune responses at baseline, day 5 (the peak of inflammation) and day 17 (the peak of fibrosis) within the context of BLM-induced lung injury. Mice born and raised in either Facility A or Facility B were harvested for

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lung samples and stained with T cell markers presented in Table 1 (Fig. 3A). Mice housed in different facilities exhibited differential ratios of specific CD3+ lymphocyte populations as well as ratios between the CD4+ and CD8+ cells, which can provide a possible explanation for the variable outcomes (Fig. 3B). Implementing machine learning algorithms to analyze the high-dimensional flow cytometry data allowed for visualization of differences in lymphocyte populations (Fig. 3C). Furthermore, specific populations of lymphocytes were shown to be differentially abundant (Fig. 3D). In-depth analysis demonstrated that a CD25+Foxp3+ population of CD3+ cells were more abundant in the lungs of mice housed in Facility A compared to those in Facility B. The CD25+Foxp3+ phenotype canonically defines a T regulatory cell (Treg), which is responsible for suppressing immune functions in the body. Therein, this data implicates that the gut microbiome of different mice could correlate with different adaptive immune responses in the lung, perhaps implicating a mechanism of protected and exacerbated lung injury.

Germ-free mice from UChicago gnotobiotic facilities were transferred into both housing facilities as founder populations. F1 progeny from these mice were genetically identical and had only been exposed to the microbiome of either Facility A or Facility B. 5 females from each of the facilities were injected with 1 U/kg of BLM and lungs were harvested at day 5 to interrogate immune responses at the peak of inflammation (Fig. 4A). Quantification of CD4+ and CD8+ population of cells recapitulated previous findings of different ratios of these lymphocytes between the two facilities (Fig. 4B). Analysis of specific CD4+ T cell subsetsâ&#x20AC;&#x201D;such as TH2 and Tregs cells, which are anti-inflammatory and suppressive, respectivelyâ&#x20AC;&#x201D;revealed increased ratios

Figure 2. (A) Method to examine the microbiome effect in lung injury. Littermate gnotobiotic mice were conventionalized with â&#x20AC;&#x2DC;dirtyâ&#x20AC;&#x2122; SPF bedding from Facility A or Facility B and challenged with BLM. (B) Heatmap dendrogram displaying relative abundance of bacterial species from fecal matter samples collected at day 0. (C) Alpha diversity and PCA plots from 16S rRNA data before BLM challenge (A0, B0) or 7 days post-challenge (A7, B7). (D) Weight loss over time and survival of conventionalized mice housed in either facility.

of TH2 cells in the lungs of mice from Facility A and increased Tregs in the lungs of mice from Facility B (Fig. 4C). These findings hint at a possible mechanism by which the phenotype manifests: microbes in Facility A elicit an anti-inflammatory response, whereas microbes in Facility B are unable to do so as a result of the expansion of suppressor cells.

To investigate the role of the gut microbiome in fibrotic aspects of BLM-induced injury, germ-free female mice were transferred into either Facility A or B and left to conventionalize to the microbiome of the respective facilities for two weeks (Fig. 5A). Mice were treated with 1 U/kg of BLM, observed for 17 days, and subsequently sacrificed to quantify levels of collagen via hydroxyproline assay. Over the time course, mice housed in Facility B suffered more weight loss compared to those in Facility A (Fig. 5B). Quantification of hydroxyproline, the major component of the collagen

protein, revealed that the lungs of mice from Facility B were more fibrotic than those from Facility A (Fig. 5C).

Taken together, these results suggest a role for the microbiome in dictating fibrogenic mechanisms of the lung during BLM-induced injury.

DISCUSSION The results presented here implicate the role of the gut microbiome in influencing the composition and activity of the lung immune landscape. In the current body of literature, much is known about the composition, activity, and mutability of the gut microbiome, yet this is not true for other mucosal surfacesâ&#x20AC;&#x201D;namely, the lung. Comprising more than 70 sq. ft of surface area, the lungs are one of the largest mucosal surfaces in the body but have a significantly smaller biomass of microbes compared to that of the gut and skin. Though the lung has canonically

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Figure 3. (A) Method to examine the baseline immune landscape of mice raised in two different housing facilities. Littermate, age-matched male mice were taken â&#x20AC;&#x2DC;off the shelfâ&#x20AC;&#x2122; for flow cytometric analysis of the lungs. (B) Frequencies of CD4+ and CD8+ cells from mice housed in the two different facilities. (C) t-SNE density maps pre-gated on live

CD3+ cells in either Facility A or Facility B. Using PhenoGraph, an unsupervised learning algorithm, population 9 was identified and found to be consistent with a regulatory T cell (Treg). (D) Frequency of population 9 in the down-sampled live CD3+ t-SNE from mice housed in the two facilities. (E) Conventional flow cytometry gating of Foxp3+CD25+ CD4+.

Figure 4. (A) Method to examine microbiome effect within the fibrotic aspect of lung injury. Mice from gnotobiotic conditions were set up as breeders in in either Facility A or Facility B. The F1 progeny of the breeders were used in this experiment. Appropriate littermate, age- and sex-matched controls were used. At day 0, mice were treated with either 1.0U/kg of BLM or PBS control. (B) Total cell numbers of CD4+ and CD8+ cells are depicted here. (C) Intracellular markers GATA3 and Foxp3 were stained and depicted are both fraction of CD4+ as well as total numbers of cells.

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Figure 5. (A) Method to examine the microbiome effect in lung injury. Littermate gnotobiotic female mice were conventionalized with ‘dirty’ SPF bedding from Facility A or Facility B and challenged with BLM. Lungs were harvested at day 17 to determine collagen levels. (B) Weight loss in ex-germ-free female mice that were conventionalized to the microbiome of either Facility A or Facility B. *** denotes a p value less than 0.001 and that the statistic was done using a Student’s t-test. (C) Hydroxyproline assay was conducted on lung samples collected from mice upon sacrifice. Amount of hydroxyproline was standardized to weight of original lung sample assayed. ** denotes a p value less than 0.01 and that the statistic was done using a Student’s t-test.

been characterized as a sterile place, this paradigm has shifted in recent literature through samples from the lung microbiome of swine and mice [10, 11]. The findings herein focus solely on the gut microbiome, implicating cross-talk between the gut and lung mucosal surfaces; however, what is missing is the depiction of the lung microbiome–– the local microbial environment that lung dendritic, T, and B cells are directly interfacing with to mount an immune response.

Studies from the past decade have addressed the link between commensal bacteria and how they influence the immune landscapes and programs of their microenvironments. For example, segmented filamentous bacteria (SFB) has been shown to elicit a strong Th17 response in the gut lamina propia [12]. These studies have demonstrated the correlation between SFB colonization of the gut and an expansion of CD4+ helper T cells that secrete IL-17A and IL-22 cytokines,

which are commonly associated with inflammation and anti-microbial defenses [13]. Interestingly, this is not an isolated case. Other, distinct sets of microbes correlate with specific subsets of CD4+ T cells, suggesting that a microbe can influence, shift, and activate transcriptional programs within the immune system [14-16]. These programs have been suggested to be plastic even though these T-cells are non-naïve and differentiated.

Taken together, these studies elucidate how the immune system is educated by the host microbiome. While distinct subsets of Th1, Th17 and Treg cells have been shown to arise from colonization of specific microbes, gaps in the literature remain when it comes to what composition of microbiota correlates with a strong Th2 response. The work presented here will contribute to the growing body of knowledge regarding how subsets of bacteria can shape an immune response.

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Gabriel Barrón is a 4th year undergraduate in The College studying Biological Sciences and specializing in Immunology. His interests lie largely in lymphocyte development and differentiation and how these processes are shaped by microbes, metabolites, or other small molecules.

REFERENCES 1. Villar, J., Pérez-Méndez, L., Blanco, J., Añón, J. M., Blanch, L., Belda, J., … Spanish Initiative for Epidemiology, Stratification, and Therapies for ARDS (SIESTA) Network. (2013, April). A universal definition of ARDS: the PaO2/FiO2 ratio under a standard ventilatory setting--a prospective, multicenter validation study.

2. Pham, T., & Rubenfeld, G. D. (2017). Fifty Years of Research in ARDS.The Epidemiology of Acute Respiratory Distress Syndrome. A 50th Birthday Review. American Journal of Respiratory and Critical Care Medicine, 195(7), 860–870. doi: 10.1164/rccm.201609-1773cp 3. Hardin, C. C. & Hibbert, K. ECMO for Severe ARDS. N Engl J Med 378, 2032-2034, doi:10.1056/NEJMe1802676 (2018).

4. Frohlich, S., Murphy, N., Doolan, A., Ryan, O. & Boylan, J. Acute respiratory distress syndrome: underrecognition by clinicians. J Crit Care 28, 663-668, doi:10.1016/j.jcrc.2013.05.012 (2013).

5. Parker, J. C. Acute lung injury and pulmonary vascular permeability: use of transgenic models. Compr Physiol 1, 835-882, doi:10.1002/cphy. c100013 (2011).

6. Asti, C. et al. Lipopolysaccharide-induced Lung Injury in Mice. I. Concomitant Evaluation of Inflammatory Cells and Haemorrhagic Lung Damage. Pulmonary Pharmacology & Therapeutics 13, 61-69, doi:https:// doi.org/10.1006/pupt.2000.0231 (2000).

7. Dickson, R. P., Martinez, F. J. & Huffnagle, G. B. The role of the microbiome in exacerbations of chronic lung diseases. Lancet (London, England) 384, 691-702, doi:10.1016/s0140-6736(14)61136-3 (2014).

8. Jin, C. et al. Commensal Microbiota Promote Lung Cancer Development via gammadelta T Cells. Cell 176, 998-1013.e1016, doi:10.1016/j.cell.2018.12.040 (2019).

9. Moffatt, M. F. & Cookson, W. O. The lung microbiome in health and disease. Clinical medicine (London, England) 17, 525-529, doi:10.7861/ clinmedicine.17-6-525 (2017).

10. Siqueira, F. M. et al. Microbiome overview in swine lungs. PLoS One 12, e0181503, doi:10.1371/journal.pone.0181503 (2017).

11. Kostric, M., Milger, K., Krauss-Etschmann, S., Engel, M., Vestergaard, G., Schloter, M., & Schöler, A. (2017). Development of a Stable Lung Microbiome in Healthy Neonatal Mice. Microbial Ecology, 75(2), 529– 542. doi: 10.1007/s00248-017-1068-x 12. Ivanov, I. I. Atarashi, K. Manel, N., Brodie, E. L., Shima T., Karaoz, U., …

Littman, D. R. (2009). Introduction of Intestinal Th17 Cells by Segmented Filamentous Bacteria. Cell, 139(3), 485-498. doi:10.1016/j.cell.2009.09.033 13. Ivanov, II et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139, 485-498, doi:10.1016/j.cell.2009.09.033 (2009).

14. Atarashi, K. et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331, 337-341, doi:10.1126/science.1198469 (2011).

15. Clemente, A. M. et al. Differential Th17 response induced by the two clades of the pandemic ST258 Klebsiella pneumoniae clonal lineages producing KPC-type carbapenemase. PLoS One 12, e0178847, doi:10.1371/journal.pone.0178847 (2017).

16. Ramakrishna, C. et al. Bacteroides fragilis polysaccharide A induces IL-10 secreting B and T cells that prevent viral encephalitis. Nat Commun 10, 2153, doi:10.1038/s41467-019-09884-6 (2019).

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TEACHING, ADVISING, AND BAKING? WHAT A PIE IN THE SKY An Inquiry with Dr. Christine Andrews STEPHANIE ZHANG

Over the past twenty years, Dr. Christine Andrews’ commitment to the University of Chicago and its students means that she and the University have grown alongside each other, changing and adapting to generations of unique student bodies. Between Dr. Andrews and the University, however, one thing remains constant: a shared commitment to learning.

After receiving her bachelor’s from Cornell University and her PhD from Stony Brook University, Dr. Andrews joined the University of Chicago’s Biological Sciences Collegiate Division to run labs in ecology and evolution. Two decades later, she serves as the Senior Advisor and a Senior Lecturer in the division. She juggles advising students on their curriculum choices and coordinating labs for courses in evolution, ecology, and biodiversity with teaching a variety of her own courses, ranging from Evolutionary Adaptation to two courses in the pre-med biology sequence.

Walking into Dr. Andrews’ office, her roots in evolution and biodiversity are obvious: the walls are lined with her daughter’s bird drawings,

and a toy horseshoe crab accompanies her at her desk. Through college, she eliminated the prospects of majoring in another subfield of biology after realizing that she cared the most for the larger-scale, behavioral aspects of biology. She took a variety of classes exposing her to the various aspects of ecology, including an animal behavior course where she censused birds, a herpetology course (reptiles and amphibians!), and a course in functional and comparative anatomy. During her graduate studies, Dr. Andrews investigated how the morphology of threespine stickleback fish evolved based on the different environmental conditions in a series of lakes located in Alaska.

From the loss of armor due to relatively low predation pressure to disparate diets, the lakes’ independent populations teemed with distinct adaptations for evolutionary fitness. It is this research on morphometric divergence in threespine stickleback fish across independently colonized lakes that continues to inform how she thinks like a scientist today.

By integrating experimental methods and perspectives into her lectures and exam questions, Dr. Andrews stresses the

Every spring, Dr. Christine Andrews teaches Biodiversity labs with Dr. Michael LaBarbera. Here, as photographed by Dr. LaBarbera, Dr. Andrews explores the Jackson Park lagoon, the site of the class’ annual field trip.

importance and benefits of research in her teaching.

Initially brought into the pre-med biology sequence due to her background in teaching comparative anatomy in graduate school, Dr. Andrews went from giving just two lectures on evolution and providing consultations for the fetal pig dissection laboratory exercise to running the Cell Biology course with Dr. Elizabeth Kovar the next year and eventually Physiology as well.

Speaking fondly of her work with Dr. Kovar, Dr. Andrews recalls how they intentionally built the Microbial and Human Cell Biology course together from scratch to ensure that their partnered teaching felt like one unified course for students. Notably, Dr. Andrews’ annual collaboration with Dr. Kovar is a direct example of the interplay between scientists of different backgrounds.

Bantering with her more computationally and chemistryoriented friend, Dr. Kovar, during lectures, Dr. Andrews hopes that the team lecture style humanizes the two of them. They hope to put students at ease with their abilities—in no way are they “out to get them.”

Dr. Andrews’ career at the University is varied and exciting by nature. Midway through the past two decades, it was natural for Dr. Andrews to take on the additional role of senior advisor to assist students with changes made to the curriculum at the time, given how fluent

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she had become with the curriculum’s intricacies after ten years. I was able to witness her advising firsthand midway through our interview. In this particular case, it was geographic advising instead of biology, as a student briefly interrupted to ask how to find the building that her statistics office hours was in. Although the student was clearly not familiar with the Biological Sciences Learning Center and erroneously stumbled upon it, Dr. Andrews must have exuded enough of a welcoming air for the student to feel comfortable popping in.

As an advisor, Dr. Andrews cherishes the privilege of meeting such a diverse array of students. The perspective she gains from helping them put together

“ Notably, Dr. Andrews’ annual collaboration with Dr. Kovar is a direct example of the interplay between scientists of different backgrounds. Bantering with her more computationally and chemistryoriented friend, Dr. Kovar, during lectures, Dr. Andrews hopes that the team lecture style humanizes the two of them. ”

a schedule that is just right for them allows her to improve her own teaching and better contribute to the Biological Science Collegiate Division’s overarching mission. Through her interactions with students, she is all the more aware of how her duty as an instructor is to “meet people where they are then and get them to the same place”—grading not on how students come in, but on how they have learned during their time with her.

To accomplish this goal, Dr. Andrews supplements the bare-bones lecture and textbook readings with a variety of active learning methods: daily in-class exercises, weekly learning objectives, videos, and optional review questions. By the time students take her Evolutionary Adaptation class, Dr. Andrews is so familiar with students and their niche interests that she is ready to deliberately pair students based on differing backgrounds—say, by matching an aspiring biophysicist with an aspiring ornithologist.

Beyond the BSLC, Dr. Andrews continues to connect with students’ on-campus activities and the South Side of Chicago as a whole through her love for baking mouthwatering pies out of basic ingredients.

Years ago, she dressed up in a self-proclaimed “pie ninja outfit” complete with an apron, pie servers for weapons, and a sign broadcasting the first iteration of the South Side Pie Challenge, an annual event supporting amateur baking and local hunger programs. Since then, the event has become a tradition for not only her family but also students in her classes to attend and compete in. From there, her involvement with the local pie scene only snowballed: to date, she has added donating pies to the on-campus a cappella group Medusa’s “Pie School Musical,” trading recipes with students, and judging for The Great Renee Bake Off to her impressive pie repertoire.

Yet, Dr. Andrews’ support of students’ pursuits outside of the classroom is not just limited to pie. She consistently participates in Phoenix Biology’s activities, helping facilitate heart dissections and leading trips to the Field Museum. Forever grateful for the unique privilege she has to focus on students, Dr. Andrews looks forward to seeing how her instructional and mentoring roles will continue to evolve. Evolution, after all, occurs on grand timescales, so a couple of decades is just a couple of drops in the bucket. Nevertheless, in these past twenty years, Dr. Andrews has already made a significant impact. One can only imagine what else is still in store. In keeping the University of Chicago ecosystem in balance, Dr. Andrews’ passion, generosity, and loyalty empower students to carve their own unique paths in biology—and, of course, baking.

Stephanie Zhang is a second-year student planning to study Chemistry and Comparative Human Development. Outside of the classroom, she enjoys researching cancer vaccines in the Hubbell Lab, supporting families impacted by cancer through Camp Kesem, promoting entrepreneurship on campus, and trying her hand at beekeeping. After college, she hopes to attend medical school and tackle cancer in one way or another.

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Noland’s Away: A Conservation-Based Investigation of Vintage Acrylic Paint and Cotton Duck Canvas Aging in a 1964 Kenneth Noland Color Field Painting Talia A. Ratnavale a a The University of Chicago

In this paper, Noland’s pioneering yet under-appreciated work Away (1964) is examined from the standpoint of a technical art historian. Technical art history aims to combine non-invasive methods of scientific analysis with art historical considerations of materials’ aesthetic significance. In Away, the focus of the study, the aim was to determine the cause of various stains on the cotton canvas. The methods used for this investigation involved a comparative literature review, visual examination, IR photography, and UV photography, all of which indicated that exposure to extreme humidity conditions has been the main cause of mold growth, canvas aging, and migration of components of the paint. Prolonged exposure of the surface to UV light is also likely to have caused photodegradation of these components, which in turn may have sped up the degradation of the cellulose polymer. These effects would cause an overall brownish darkening of unpainted areas and areas in which “bleeding” occurred. For these reasons, it is likely that Away no longer appears as bold and striking as was intended by Noland.

INTRODUCTION Author Biography and Painting History Kenneth Noland (1924-2010) was an American artist best known for his influence on the late modernist movement via his optically intriguing color field paintings.

Color field paintings are known for their uniquely large swaths of single-hued regions; these regions force the viewer to confront the power inherent in color. After World War II, Noland studied at the famed Black Mountain College, through which he was able to associate with a host of influential and prominent artists.1 Noland was compelled by the primary concern with materiality which both Frankenthaler and Pollock evinced in their works.2 Soon after meeting with Frankenthaler, he would begin his renowned exploration of circular motifs, in which paint was “stained” into unprimed cotton duck canvas.3 Indeed, much like Frankenthaler and Pollock, Noland painted on unstretched canvas.4 He continued to work with staining and unprimed cotton duck throughout his painting career.5 His 1964 work Away is a particularly strong example of such techniques.

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Noland also met paint manufacturer Leonard Bocour through association with the painter Morris Louis.6 Bocour, who would found Golden Artist Colors in the 1980s, made one of the first acrylic paints, Magna acrylics.

These paints were novel in their incorporation of a nonbiological, synthetic polymer (an “acrylic resin”) into the binder which carried the inorganic pigment. This paint would remain highly saturated when diluted with the traditional organic solvents. However, this paint differs from contemporary water-solvated acrylics in that the resin was instead solvated in organic solvents.7 Noland used this paint throughout his works from the mid 1950s to the early 1960s.8 Historically, it can be inferred that his 1964 painting Away is one of his first pieces which we can be certain was made from the water-solvated AquaTec acrylic paints rather than the organically solvated Magna acrylics.9,10 Noland’s diamond series also launched him into his experimentation with non-square canvas forms.

This innovation would become incredibly influential to

Figure 1. Kenneth Noland, Away, 1964, acrylic on canvas, 69’’x 69’’, Chicago, the Smart Museum of Art.

countless late-modern and postmodern artists. Thus, this work is pioneering from both a material and conceptual standpoint and invites further analysis.

Noland saw his ability to succeed with his postpainterly aspirations to create “color fields” as crucially dependent on the unique material properties of acrylic paints: “color field curiously enough, or perhaps not, became a viable way of painting about exactly the time that acrylic paint—the new plastic paint—came into being. Oil paint would always leave a slick of oil, a puddle of oil, around the edge of the color, whereas acrylic paint stops at its own edge.”11 Thus, Noland found it crucial to create hard edges as conferred upon him by the new acrylic medium. Furthermore, for Noland, the appearance of a painted area was fundamentally “tactile” (i.e., related to its thickness, opacity, and finish). Another material advantage of acrylics was their ability to be differentially diluted and intermingled with the canvas in various ways.12 Noland was known to thin his water-based acrylic paint with both water and detergent to increase the intermingling of the canvas and the paint.

Within two years of its creation, Away was acquired

by Walter and Dawn Clark Netsch for their private

collection, where it was likely hung in their upper OldTown Triangle home until 2013.13,14 This Chicago open floor plan home was within close proximity of Lake Michigan and featured multiple skylights and large windows.15 Thus, it can be assumed that the piece was exposed to cycles of high and low humidity as well as periods of intense, non-archival lighting. From 2014 onwards, the piece has been stored in substantially better conditions in the Smart Museum of Art and was only exhibited for four months at the beginning of 2018.16 Still, these non-ideal conditions attest for the need of a condition examination of the work.

MATERIALS AND METHODS Given Noland’s essential concern with materiality, it seemed that a direct examination of the work would be especially crucial for understanding the phenomenology of the piece. From afar, it was difficult to tell if there were any major conservation issues with the piece (see Fig. 1). However, up-close, a host of unexpected potential irregularities confronted the eye. Firstly, the canvas overall appeared to be fairly dark, although from visible examination alone, it was difficult to tell whether this was

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Figure 2. Example of patchlike discoloration seen throughout the canvas.

Figure 4. Away under raking light.

Figure 3. Discoloration along top edge of canvas.

due to the unprimed nature of the canvas or a sign of aging. Furthermore, throughout the unpainted portions of the canvas, there were many small, round discolored patches of a faded orange-tan color which were less than one centimeter in diameter (see Fig. 2). Some patches were darker in color than others. Along the top edge of the canvas, a similar type of discoloration was seen in larger proportions (see Fig. 3). Examination under raking light proved useful in identifying uneven coloration in both painted and unpainted areas of the canvas (see Fig. 4). Due to the irregularity and patch-like aspects of the discoloration on the proper left bottom of the canvas, it can be inferred that the dark patches were not due to irregularities in the flatness of the canvas surface. Finally, especially pronounced darkening was noticed around the edges of painted stripes in what appeared to be an outwards bleeding or wicking of a particular material (see Figs. 5 and 6). These were not considered to likely be a result of the artist’s process due to the high variation and prominence of the feature.

Inspection under long and short wave UV light yielded valuable information. UV-visible fluorescence examination can be used to distinguish the particular pigments and substances whose chemical structures

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allow them to “glow”, or emit intense visible light, when subjected to ultraviolet light. An Analytik Jena Handheld UV Lamp (model UVGL-58) was used with a UVA wavelength of 365 nm and a UVB wavelength of 254 nm. First, it was noticed that the round patches of tan discoloration seen under visible light appeared significantly darker under UV (see Fig. 7). Second, an unusual, quite pronounced greenish yellow-white fluorescence was seen around the stripes in the areas where the bleeding effect was seen under visible light (see Fig. 8). Examination of the back of the canvas showed that this fluorescent material in fact ran throughout the painted stripes, which confirms that it is a component of the paint rather than an accretion of foreign material (see Figs. 9 and 10).

An IR photograph of Away was taken using an optical filter which only passes light of wavelength above 720 nm. IR photography makes use of a filter which blocks much of the visible spectrum from reaching the camera sensor; this allows conservators to distinguish the particular pigments and substances which better absorb and reflect infrared light. This photograph showed elimination of the appearance of bleeding while the inconsistency of paint throughout the stripes remained (see Fig. 11). This indicates that the inconsistencies within the stripes are more likely to be inherent to Noland’s process as an artist; however, this assertion will be revisited in the results section. Furthermore, the tonality of the various greys in the IR photograph provided some indication as to the type of pigment which might be

Figure 5. Visible discoloration around painted stripes of Away.

Figure 7. Darkening of patchlike discoloration under longwave UV light.

Figure 6. Close-up image of visible discoloration around painted stripes of Away.

present in each area of the canvas. It was hypothesized that the canvas contained cadmium yellow in its innermost stripe.17 This information was cross-checked with a list of known AquaTec paint colors and contemporary Golden paint swatches to preliminarily identify the paint used as cadmium yellow medium.18,19 (Note that Golden Artist Colors is the second company founded by Leonard Bocour). The same process was used to determine that the third most outward stripe likely contained ultramarine or phthalocyanine blue (termed â&#x20AC;&#x153;Bocour blueâ&#x20AC;?).20-2 However, it must be noted that this information is not definitive since the tonalities of colors under IR are highly dependent on the opacity of the paint mixture used and the exposure time of the camera.23 Still, under UVA, the yellow stripe became dark-orange in color, the orange stripe became reddish-brown, and the blue stripe darkened substantially whereas the third innermost stripe did not appear to change color (see Fig. 12). These color changes are consistent with some

Figure 8. Pronounced greenish yellow-white longwave UV fluorescence around the two middle stripes.

of the pigment identities determined by the infrared method. For example, it has been noted that cadmium yellow light changes color to orange under UVA, which might indicate that cadmium yellow medium responds similarly.24

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Figure 9. Pronounced greenish yellow-white longwave fluorescence throughout backs of painted stripes.

Vintage paint samples were spectrophotometrically analyzed in comparison with freshly dried cadmium orange and cerulean blue heavy body Golden acrylic paints (see Fig. 13). Though Noland diluted his paints, these thicker Golden acrylics were chosen because his pre-diluted AquaTec paints were similar in thickness. Spectrophotometry essentially measures the quality and temperature of light reflected by a particular sample of color. A Cary 5000 UV/ NIS/NIR Spectrophotometer with a sample angle of 30.00 degrees was used so that a spectrum of the paintsâ&#x20AC;&#x2122; visible reflectance could be obtained (see Figs. 14 and 15). From the similarities between the reflectance curves, it can be seen that both paints prove to be good matches for their respective AquaTec colors, though the Golden cerulean blue reflected approximately 0.05% more light in the blue region of the spectrum and the Golden cadmium orange reflected approximately 0.05% more light in the orange region of the spectrum. These differences are negligible and can be attributed to the darkening of AquaTec over time or the slight adjustment of pigment concentration in the newer acrylics made by Golden.

RESULTS A review of previously existing literature on the conservation issues of unprimed cotton canvases proved

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Figure 10. Pronounced greenish yellow-white shortwave fluorescence throughout backs of two outermost painted stripes.

Figure 11. IR reflectance photograph of Away using a Hoya 720+ nm passing filter. Photograph was taken with a Canon EOS 5D Mark II DSL using a 50mm lens with the f-stop set to 3.5. Exposure time was between 104-120 seconds.

useful in refining analytical conclusions. For example, in humid conditions, cotton is particularly prone to mold growth, which destabilizes the cellulose structure. This destabilization results in a tan-brown discoloration which is quite similar in color and form to that seen on the unprimed canvas of Away (see Fig. 16).25,26. However, although some spots appeared darker under UV examination, they exhibited no definitive fluorescence that would be indicative of active mold growth.27 The staining on the canvas therefore indicates past mold growth.

Figure 12. Color changes in stripes under longwave UV light.

While this mold growth no longer exists in substantial proportions, it left the canvas stained and degraded. This suggests that the piece was likely exposed to conditions of high humidity for substantial periods of time, which affirms the provenance-based assertion that Away likely experienced repeated cycles of high and low humidity.

As noted earlier, a similar (though more pronounced) staining in a more elongated shape was seen to emerge from the top edge of the canvas. This also attests to the contact of the canvas with high levels of humidity. This staining may be due to either mold growth (as discussed above) or oxidation-catalyzed degradation of the cellulose material. Oxidation of cellulose is often caused by continued exposure to ultraviolet light which causes homolysis of the polymer.28,29 This homolysis results in the production of acid which makes it more favorable for the canvas to degrade via hydrolysis (water-induced scission).30 The result is a darkening and weakening of the material. Due to similarities in the chemical mechanisms, the discoloration appears very similar to stretcher burn. Stretcher burn involves degradation of the fabric through contact with highly acidic wood which has absorbed moisture from the air.31,32 Thus, examples of stretcher burn were analyzed to determine whether the cellulose structure had been oxidized and hydrolyzed (see Fig. 17). Though it was not possible to

observe the full edges of the canvas, it was determined that a very similar type of large-scale discoloration was present around the painted portions of the canvas where the staining phenomenon was seen to occur.

Thus, a material in the areas with staining may have catalyzed the degradation of the canvas. Once again, it is also highly likely that these areas were exposed to conditions of high humidity.

A return to the material composition of the AquaTec paints was made in order to assess the bleeding phenomenon seen around the edges of the paint stripes. Aside from containing an acrylic resin, water (as a solvent), and various inorganic pigments, AquaTec paints are highly likely to contain a “non-ionic polyethoxylatetype surfactant such as “polyethylene glycol,” or PEG.33 Surfactants such as PEG are used in paints in order to increase the water solubility of the acrylic resin.34 PEG is known to increase the fluorescence of other materials and can break down to create acid. This explains the increased strong fluorescence and marked darkening of the areas in consideration.35 Furthermore, it explains why the verso, or backside of the canvas was seen to fluoresce in the areas which had been painted on the other side. However, it remains yet to be explained how the surfactant would be able to migrate out of the paint film and why the fluorescence was greenish-yellow.

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Figure 13. Tubes of vintage cadmium orange and cerulean blue AquaTec acrylic paints; samples of dried paint were obtained using a small x-acto knife.

Figure 14. Reflectance curves of cadmium orange AquaTec acrylic paint sample (Series1) and cadmium orange Heavy Body Golden acrylic paint sample (Series2) from a Cary 5000 UV/NIS/NIR Spectrophotometer with a sample angle of 30.00 degrees.

The conditions under which surfactant migration is possible were found through literature review. It turns out that in conditions of high relative humidity (RH) (where the RH is greater than 40%), acrylic paint films are able to absorb water and swell in volume, allowing surfactants to migrate inwards. The strength of this effect increases with an increase in RH.36 In contrast, when the RH drops, the surfactant is able to migrate out of the paint film.37 Furthermore, the movement of water caused by paint film formation may allow transportation of surfactants.38 Thus, it can be concluded that humidity cycles and the drying of the paint likely caused this observed surfactant migration. Furthermore, DigneyPeer et al. noted that once non-ionic surfactants such as a polyethylene oxide have migrated to the surface, they are light sensitive and subject to photodegradation.39 Since polyethylene oxide is a PEG, this would explain how the surfactant would remain outside the paint film and become acidic through aging. Furthermore, since the canvas is unprimed, greater integration of the surfactant into the canvas structure would be possible, much like the higher absorptivity of paper towels in contrast to wax-coated paper.

As noted above, it is yet unclear what caused the greenish cast of the fluorescence which was seen on the backside of all four painted stripes and in the areas of bleeding around the stripes. It was posited that the acrylic resin may have been deposited into the canvas due to a combination of aging and humidity-induced film movement. This was corroborated by the discovery from the literature that aged synthetic polymers (or resin) often fluoresce greenish-white or greenishyellow.40 The yellow aspect of this fluorescence may also be partly due to a weakly visible yellowing of

the resin.41 Furthermore, synthetic resins increase in fluorescence as they age.42 Finally, since detergent and optical brighteners fluoresce blue-white, they are unlikely to be the source of the fluorescence.43,44 These facts all support the conclusion that these vintage resins are the source of the fluorescence.

Still, it is important to recall that despite the likelihood that the surfactant and resin migrated outward, the cause of the inconsistencies in the paint opacity within the stripes are as of yet unknown.

Although the prolonged exposure of Away to extreme humidity cycles suggests partial movement of the film and migration of surfactant and resin around the edges of the stripes, it is unlikely that this effect is so substantial as to cause large-scale changes in the opacity of the dried paint which are situated in the centers of the stripes.

An analysis of similar Noland works proved useful for confirming these assertions. One of Noland’s 1964 works can be seen to exhibit minimal edge bleeding and subtle intra-stripe color inconsistency (see Fig. 18).45 However, another 1964 work of Noland’s shows substantial edgebleeding and intra-stripe inconsistency (see Fig. 19).46 Furthermore, a 1961 work of Noland’s (painted with Magna acrylic) shows marked bleeding and intra-stripe inconsistency (see Fig. 20).47 From these similarities and differences it can be concluded that the inconsistency within the stripes was likely part of Noland’s process. In contrast, the bleeding phenomenon can be considered a conservation issue related to the aging process rather than a quality of the original work. However, it must be noted that this canonical information only serves as support for rather than proof of these assertions, since the images which were viewed were obtained indirectly

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Figure 15. Reflectance curves of cerulean blue AquaTec acrylic paint sample (Series1) and cerulean blue Heavy Body Golden acrylic paint sample (Series2) from a Cary 5000 UV/NIS/NIR Spectrophotometer with a sample angle of 30.00 degrees.

Figure 16. Example of canvas staining from mold.

from the websites of museums and auction houses with photographic processes that are unknown.

CONCLUSION Visual examination and photography of Away combined with the spectrophotometric testing of vintage paint and review of supplementary literature indicate that exposure to extreme humidity conditions has been the main cause of mold growth, canvas aging, and migration of the surfactant and resin. Prolonged exposure of the surface to UV light is also likely to have caused photodegradation of the surfactant and resin, which in turn may have sped up the degradation of the cellulose polymer. These effects would cause an overall brownish darkening of unpainted areas as well as areas where “bleeding” occurred. The presence of the tancolored sporadic stains can be attributed to the past presence of mold, while the edges of painted stripes are likely muddied in appearance due to surfactant migrations and increasing acidity of the canvas. These changes are likely to have detracted from Noland’s intention to minimize the apparent role of the artist’s hand in favor of the prominence of the “materiality” of the paint. Still, it must be noted that some of the inconsistencies in paint application, especially those which are seen deeply within the painted stripes, are part of Noland’s staining process.

Going forward, it is recommended that this work be stored in an area with stable and moderate levels of relative humidity in which oxygen levels and light intensity are kept to a minimum. In order to determine whether future treatments of this piece are necessary, it is recommended that the piece be unframed so that it can be determined if stretcher burn has occurred due

Figure 17. Example of stretcher burn.

Figure 18. Kenneth Noland, Sarah’s Reach, 1964, acrylic on canvas, 93 3/4 x 91 5/8 in, Smithsonian American Art Museum.

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Figure 19. Kenneth Noland, Sand, 1964, acrylic on canvas, 34’’x 34’’, Private Collection.

to prolonged contact with moist acidic wood. If such an effect has occurred, it is recommended that the piece be reframed. From this study, however incomplete, it is clear that art history and science have much to learn from each other when it comes to the investigation of materials. From non-invasive techniques alone, substantial information has been gleaned regarding the aging of Noland’s Away.

With invasive methods or more highly technical forms of spectroscopy, the potential for understanding light, color, and aging are endless. It is the researcher’s hope that the Away may be further investigated with these advanced techniques.

Figure 20. Kenneth Noland, An outside red, 1961, Magna acrylic on canvas, 86 x 87.5 cm, Private Collection.

REFERENCES 1. Taylor, Alex, “The Painting,” Tate Research Publication (2017) https:// www.tate.org.uk/research/publications/in-focus/gift-kenneth-noland/thepainting.

2. Marontate, Janet Lee Ann, “Synthetic Media and Modern Painting: A Case Study in the Sociology of Innovation,” National Library of Canada (1996) http://www.collectionscanada.gc.ca/obj/s4/f2/dsk2/ftp03/ NQ26696.pdf.

3. Taylor.

4. Fenton, Terry. “Kenneth Noland: master of color abstraction,” Appreciating Noland (2001) http://www.sharecom.ca/noland/materials. html.

5. Dixon, Glenn. “Hirshhorn Presents “Gravity’s Edge”,” Hirshhorn Museum and Sculpture Garden (2014) https://hirshhorn.si.edu/explore/ hirshhorn-presents-gravitys-edge/.

6. Taylor.

7. Rogge, Corina E. and Bradford A Epley, “Behind the Bocour Label: Identification of Pigments and Binders in Historic Bocour Oil and Acrylic Paints,” Journal of the American Institute for Conservation 56:1 (2017): 15-42 https://tandfonline.com/doi/full/10.1080/01971360.2016.1270634?scr oll=top&needAccess=true.

8. Taylor.

9. Waldman, Diane, “Kenneth Noland, A Retrospective,” The Solomon R. Guggenheim Museum Foundation (1977) https://archive.org/stream/ kennethnolandret00wald/kennethnolandret00wald_djvu.txt.

10. Rogge & Epley.

11. Marontate.

12. Ibid.

13. Lloyd, Frank, “Craig Kauffman and Chicago Architects,” Frank Lloyd’s Blog (2017) https://franklloydgallery.wordpress.com/tag/dwan-clarknetsch/.

14. Smart Museum of Art.

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39. Digney-Peer et al.

15. Rodkin, Dennis, “See the inside of famed architect Walter Netsch’s house,” Crain’s Chicago Business (2015) https://www.chicagobusiness. com/article/20150402/CRED0701/150409984/buyers-of-walter-anddawn-clark-netsch-s-house-in-chicago-celebrate-its-eccentricities.

16. Smart Museum of Art. 17. “Pigments Checker,” Cultural Heritage Open Source (2015) https:// chsopensource.org/pigments-checker/.

18. Rogge & Epley.

19. “Heavy Body,” Golden Artist Colors (2017) https://www.goldenpaints. com/products/colors/heavy-body.

20. Rogge & Epley.

21. “Bocour blue,” Conservation and Art Materials Encyclopedia Online (2016) http://cameo.mfa.org/wiki/Bocour_blue.

22. “Pigments Checker.”

23. Ibid.

24. Measday, Danielle, “A summary of ultra-violet fluorescent materials relevant to Conservation,” Australian Institute for the Conservation of Cultural Material (2017) https://aiccm.org.au/national-news/summary-ultraviolet-fluorescent-materials-relevant-conservation. Accessed 18 March 2019. https://www.goldenpaints.com/products/colors/heavy-body.

25. Skelton, Samantha, James, Erica ESH (ed.), and Stephenson, Erin (ed.), “Raw Canvas,” AIC Conservation Wiki (2017) http://www. conservation-wiki.com/wiki/Raw_Canvas.

26. Gridley, Mary, “White Surface Hazes,” AIC Conservation Wiki (2019) http://www.conservation-wiki.com/wiki/White_Surface_Hazes#Mold.

27. Measday.

28. Melo, M.J., S. Bracci, M Camaiti, O. Chiantore, and F. Piacenti, “Photodegradation of acrylic resins used in the conservation of stone,” Polymer Degradation and Stability 66 (1999): 23-30.

29. Skelton.

30. Hackney, Stephen “Paintings on Canvas:Lining and Alternatives,” Tate Research Publication (2004) https://www.tate.org.uk/research/ publications/tate-papers/02/paintings-on-canvas-lining-and-alternatives.

40. Measday.

41. Whitmore, Paul and Val G. Colaluca, “The Natural and Accelerated Aging of an Acrylic Artists’ Medium” Studies in Conservation 40:1(1995):5164 https://www.jstor.org/stable/15066114c.

42. Measday.

43. Ibid.

44. Bajpai, Divya and V. K. Tyagi, “Laundry Detergents: An Overview” Journal of oleo science 56(7):327-40 https://www.researchgate.net/ publication/5945251_Laundry_Detergents_An_Overview.

45. “Sarah’s Reach,” Smithsonian American Art Museum https:// americanart.si.edu/artwork/sarahs-reach-18771.

46. “Kenneth Noland: Sand,” Sotheby’s Contemporary Art Day Auction (2018) http://www.sothebys.com/en/auctions/ecatalogue/2018/ contemporary-art-day-sale-n09933/lot.130.html?locale=en.

47. “Kenneth Noland (1924-2010): An outside red” Christie’s https:// www.christies.com/lotfinder/paintings/kenneth-noland-an-outside-red5755096-details.aspx?from=searchresults&intObjectID=5755096&sid=74 f61baa-fbad-4b98-bc59-ba5ae33d6329.

Talia Ratnavale is a third year student at the University of Chicago majoring in chemistry and anthropology and minoring in art history. She has worked as a conservation intern or volunteer at the Smart Museum, The Smithsonian, and The Getty Conservation Institute. She has carried out two independent research papers on conservation topics through her studies at UChicago. She is originally from LA and discovered her interest in art history and art conservation by exploring Los Angeles’ museums.

31. Davis, Ellen “The Unfurling of Margaret Watherston’s Method: Research into the Re-Treatability of Morris Louis’s Alpha (1960),” Association of North American Graduate Programs in Conservation (2015) http://resources.conservation-us.org/anagpic-student-papers/wp-content/ uploads/sites/11/2016/01/2015ANAGPIC_Davis_Paper.pdf.

32. Skelton.

33. Rogge & Epley.

34. Digney-Peer, Shawn, Aviva Burnstock, Tom Learner, Herant Kanjian, Frank Hoogland and Jaap Boon, “The Migration of Surfactants in Acrylic Emulsion Paint Films,” Studies in Conservation 49:2 (2004): 13-17.

35. “PEG Stability: A Look at pH and Conductivity Changes over Time in Polyethylene Glycols,” Hampton Research Corporation (2012) https:// hamptonresearch.com/documents/growth_101/27.pdf .

36. Ziraldo, Ian, Kristen Watts, Arnold Luk, Anthony F. Lagalante, and Richard C. Wolbers, “The influence of temperature and humidity on swelling and surfactant migration in acrylic emulsion paint films,” Studies in Conservation 61:4 (2016): 209-21.

37. Ziraldo et al.

38. Schantz, Staffan, Hans T. Carlsson, Thomas Andersson, Stefan Erkselius, Anders Larsson, and Ola J Karlsson, “Poly(methyl methacrylateco-ethyl acrylate) Latex Particles with Poly(ethylene glycol) Grafts: Structure and Film Formation,” Langmuir 23 (2007): 3590-3602.

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DIVERSITY AND SCIENCE An Inquiry With Professor Young-kee Kim TORI ANKEL

Some people grow up knowing exactly what they want to be, but Professor Young Kee Kim was not one of them. As a child growing up in a small village in South Korea, all she wanted to do was “sing, dance and do math.” Her love of math evolved into a love of physics, which led her to become a professor at the University of Chicago for the last 17 years, and the chair of the Physics department since 2016. While at UChicago, Professor Kim’s impact on the department has been remarkable. Her research has been critical to the development of new physics, and she is well-known not only for her devotion to her students within the undergraduate and graduate physics programs, but also for her engagement with the scientific community at large. Her outreach work includes educating middle school girls about STEM opportunities, hosting an undergraduate physics conference, and creating an inclusive environment for physics students of all backgrounds.

Professor Kim’s research is in particle physics, meaning that she seeks to understand the fundamental building blocks of the world around us, and how they interact.

Her extensive career has taken her to particle accelerators across three continents—from

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Japan’s KEK, to Fermilab’s Tevatron and finally to CERN’s Large Hadron Collider. Each accelerator brought with it a different physics focus and approach, and Professor Kim appreciated the chance to do research in such different environments and cultures. While working at Fermilab in the 90’s, Professor Kim was the leader of the CDF (Collider Detector at Fermilab) Experiment, through which the top quark was discovered. Quarks, along with other elementary particles such as Leptons and Bosons make up the Standard Model of particle physics: a system used by physicists to classify known elementary particles. Now working for CERN, she seeks to further our understanding of the Standard Model in relation to dark matter. In particular, Professor Kim focuses on uncovering what gives mass to dark matter.

Within the physics department at the University, Professor Kim’s main goal is to create a welcoming environment. From undergraduate students to faculty, she fosters a community in which everyone feels like they belong and can get the support they need.

“When [students] come to lecture rooms, or lecture buildings, I like them to be happy to come in.” Part of this initiative is her involvement

with the Society of Women in Physics, or SWiP. For her, SWiP is about giving both support and self- confidence to a community she knows is capable. “If they have a dream, I just want to make sure that their dreams come true.”

Part of this involves hosting the annual Conference for Undergraduate Women in Physics (CUWiP), which is held in late January. First hosted here in 2014, she brought the regional conference back to UChicago this past year.

CUWiP’s goal is to provide information to undergraduate physics majors about future career and graduate school opportunities over the course of a long weekend. At UChicago, students engaged with speakers and attended lab tours arranged by graduate student volunteers. This interaction between physicists of all levels is crucial in building a supportive network that benefits all—something Professor Kim stresses is important. Building a strong and inviting community of women in physics is not one person’s responsibility. All voices, from undergraduate to faculty, need to be heard, and Professor Kim is always eager to hear opinions and take suggestions from students. She hopes her attentiveness to students’ needs “makes them feel that [building a stronger community is] not something I do, but something that we do together.

We make this place better.”

While her interest in math goes back as far as she can recall, Professor Kim was not introduced to the physical sciences until middle school. In fact, this introduction was one of the turning points in her life, though she says she didn’t recognize its significance until later. Despite having no prior background in science, her teachers encouraged her to compete

in a statewide physical science competition. To her surprise, she was a finalist, and eventually won first place. Competition organizers announced her win over the radio and in the newspapers that night. The radio announcer explained that “Kim Young Kee Kun” had won. But there was one issue. Because no girl had ever won this prize, reporters assumed that she must have been a boy, and attached the suffix Kun (meaning ‘boy’) to her name. Someone had to correct them on air, explaining that the winner was actually Kim Young Kee Yang. Nonetheless, Professor Kim was not deterred, and now looks back on the incident as the start of her future in science.

Professor Kim’s teachers introduced her to science during middle school, and the middle school demographic is one that she still tries to connect with.

Although she believes that outreach and support should be provided to women at every stage of their careers, the transition to middle school is key. Before working in Chicago, Professor Kim worked at UC Berkeley, where one of her postdocs learned about a program called “Expanding your Horizons” that introduces middle school girls to STEM opportunities.

As soon as her postdoc mentioned the program, Professor Kim immediately knew that she wanted to get involved and became the deputy chair of the first committee in 2012. Although all were welcome, she specifically reached out to middle school aged girls on the South and West sides of Chicago. During the day-long conference, girls have the opportunity to interact with women at the top of their fields, through workshops with mentors and hands-on activities. The first year they opened registration, more than 200 girls signed up within three days. This was far more than the program could accommodate at that time. Eight years later, the program has grown, and continues to introduce middle school girls and their parents to the exciting career opportunities in STEM. Throughout her years of leadership, Professor Kim has also made diversity paramount in her own research teams. When she was the leader of CDF, she led more than 700 researchers from all over the world, with varying backgrounds and skills. This diversity was deeply beneficial because whenever the team faced a problem, the variety of perspectives led to

“ But there was one issue. Because no girl had ever won this prize, reporters assumed that she must have been a boy, and attached the suffix Kun (meaning ‘boy’) to her name. ”

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Professor Kim chaired the 2014 Midwest Conference for Undergraduate Women in Physics, an effort to support women in physics.

a wide array of creative approaches to solutions. In fact, Professor Kim has also built her current research group to embody this principle as well. The research teams that she has led are testaments to the critical role of diversity in the scientific endeavor. Professor Kim is highly optimistic about improving the future of the physics establishment. Looking at the generation before her, she notes that the community of women in physics was once much smaller and more isolated.

Yet with each passing generation, she sees the percentage of women in the field increasing due to intentional steps taken by leaders to break down barriers. To continue these large- scale changes, we need to continue being proactive. We need to understand the challenges and hurdles ahead of us and deliberately tackle them as a community.

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Tori Ankel is a first year student at the University of Chicago majoring in Physics and Math. She participated in this yearâ&#x20AC;&#x2122;s CUWiP, run by Professor Kim, and is also a member of SWiP.

Unraveling Supernova Remnant DEM L71 Jared Siegel a a The University of Chicago

Supernovae are cataclysmic stellar explosions that produce most of the elements in the universe other than hydrogen and helium. These explosions expel an expanding shell of gas and dust that will form supernova remnants (SNRs) that live for many thousands of years. Here we apply Smoothed Particle Inference (SPI) to the X-ray emission of the supernova remnant DEM L71. This novel computational technique can characterize the structure, dynamics, morphology, and abundances of an entire remnant with a single analysis, as well as infer the masses of nucleosynthesis yields from the supernova. Through this procedure, we characterized the temperature, elemental abundances, and morphology of DEM L71, as well as the individual element masses. For each of these parameters, we present the posterior parameter distribution histograms and parameter maps across the entire remnant. We then compare the observed abundance pattern with the predictions of supernova explosion models, in order to constrain the explosion mechanism of DEM L71. We find that the abundances of DEM L71 are consistent with a Type Ia explosion scenario, while also highlighting the complexity and irregular structure of the remnant.

INTRODUCTION Following a supernova explosion, either the corecollapse of a massive star (mass > 10 where is the mass of the sun) or the thermonuclear explosion of a white dwarf in a binary system (Type Ia), a super-sonic shock propagates outwards. This shock sweeps up the surrounding medium, and heats the material to millions of degrees Kelvin, causing the plasma to emit X-rays [1]. Studying this emission presents a remarkable opportunity to characterize the remnant and study not only the explosion mechanism, but also the explosionsâ&#x20AC;&#x2122; interaction with the circumstellar medium.

However, there are significant challenges to this analysis. The emission of SNRs contains numerous components due to the contribution of both the shocked surrounding medium and reverse-shocked ejecta in the plasma, which complicates the spectral analysis. Moreover, SNRs have complex, three-dimensional morphologies that can only be observed as a two-dimensional projection.

Here we aim to address that complexity by applying the novel Smoothed Particle Inference (SPI) technique to SNR DEM L71.

Located in the Large Magellanic Cloud, DEM L71 is an approximately four-thousand-year-old SNR at a distance of 50 kiloparsec (kpc) from Earth [2]. Prior X-ray studies of DEM L71 have revealed a regular, ring-like morphology, with an enhanced outer region and diffuse interior (see Figure 1) [3]. The outer ring is generally interpreted as the

forward and reverse shock of DEM L71, while the diffuse central region contains the reverse-shocked ejecta.

Previous studies have also identified enhanced iron abundances in the central region, potentially suggesting a Type Ia origin for DEM L71 [3, 4].

Figure 1. XMM-Newton combined EPIC-pn and MOS exposure-corrected image of DEM L71 in the 0.2â&#x20AC;&#x201C;8.0 keV band.

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Figure 2. Observed X-ray spectrum of DEM L71 (black) in comparison to the SPI model spectrum (blue).

Studying remnants like DEM L71 provides a powerful tool for modern astrophysicists. As the primary producer of all elements heavier than helium and a central source of energy in the interstellar medium, supernovae play an important role throughout astrophysics. In particular, by studying the remnants of these explosions, we can gain a unique understanding of how supernovae operate and more accurately characterize the interstellar medium.

Here we applied the SPI technique to a 2003 XMMNewton x-ray observatory observation of DEM L71. Our analysis and full results can be found in Frank et al.

(2019) and Siegel et al. (2020) [5, 6]. Through this work, we further constrained the explosion mechanism of DEM L71 and characterized the remnant’s morphology.

METHODS Smoothed Particle Inference (SPI) models the plasma as a collection of independent ‘smoothed particles’ or blobs [7]. The physical profile of each blob is assumed to be a three-dimensional Gaussian, with the plasma in each blob assigned a unique set of parameters including temperature, abundances, spatial position, and size. The SPI process takes these blobs and forward-folds them through the XMM-Newton instrument using a Markov chain Monte Carlo (MCMC) to predict detector positions and energies for each model photon. The resulting artificial emission can then be compared with the observed data, in order to select new blob parameters. This fitting process is then repeated until convergence has been reached between the artificial emission and the observation. This process is

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shown in Figure 2, where the observed spectrum of DEM L71 is compared with the artificial spectrum produced using SPI. Once convergence has been reached, SPI then returns the set of blobs, which we utilized in our study of DEM L71.

This method is extremely powerful in the study of SNRs because they are complex, three-dimensional objects composed of plasma containing both ejecta material and swept-up medium. In contrast to traditional analysis techniques, which select sample regions in an SNR and must assume a geometry and level of homogeneity, SPI treats the geometry as a free parameter and can model multi-phase plasma, by combining the emission of multiple blobs along the same line of sight. Additionally, SPI characterizes the emission across the entire remnant, which enables us to study the plasma through the creation of histograms and maps showing global properties of the remnant. These capabilities were originally demonstrated

by Frank et al. (2019) [5].

Density and Mass The density of an individual blob can be calculated using the following relations:

Figure 3 shows the mean-molecular weight of the plasma, and are the number-densities (the number of the given particle per unit volume) of electrons, ions, and hydrogen, respectively. Since the SPI model fits a

Figure 3. Emission-measure weighted maps of oxygen, neon, and iron. The white contours are taken from the emission-measure map.

value of emission measure and volume for each blob, we can extract the total hydrogen density by finding a relation between the values of and and calculating the mean-molecular weight. We can then estimate the total ion density, by using the abundance of hydrogen in the plasma. In order to estimate these values, we consider three approaches.

We first consider the case where all emission is entirely from swept-up material and there is no enrichment from ejecta. In this case, the material is assumed to have elemental abundances characteristic of the Large Magellanic Cloud. From these adopted abundances we are able to calculate the ratios of and , as well as the value of , which in turn allows us to estimate the density within each blob.

We next consider the case where the emitting material has non-local abundances. Abundance enhancements in SNRs are likely the result of mixed-in ejecta and are of significant interest in studying these objects. From the SPI fit, each blob has its own values for elemental abundances, which results in unique values in each blob. As in the first case, we use these values to calculate the density of each individual blob.

We finally consider our third and final case, which assumes that all emission arises from ejecta material with no hydrogen present. The distinct lack of hydrogen in this case drastically impacts the density and mass estimates because the SPI spectral fitting process assumes a hydrogen emission continuum. As a result, it would be inappropriate to utilize the SPI abundances in this case. Instead, we employ the predictions of supernova explosion models. Using the predicted yield of each element and assuming full ionization, we compute the ratio of and the value of . Although relative mass abundances are adopted from the supernova models, the

total inferred mass still depends on the emission measure and volume of the SPI fit.

In all three scenarios, we infer the total remnant mass by summing over all the blobs after the density and mass has been calculated. We then extract the individual element masses, by using element mass fractions within the blobs. In the first two scenarios, these fractions are derived from the adopted abundances (either the local abundance or the abundances of the SPI fit) and in the third, the fractions are adopted from the corresponding supernova model.

Given the complex nature of SNRs, with emission from both ambient material and the supernova ejecta, the ability to infer masses using these three cases provides substantial flexibility in our analysis. In particular, we can attempt to isolate pure ejecta material and make estimates of the associated mass. By allowing for comparison with an array of supernova explosion models, these estimates of the ejecta mass provide a powerful metric for studying the progenitor system.

RESULTS We first extract the emission-measure weighted summary statistics for DEM L71. These quantities reflect the general properties of the remnant, including elemental abundances, ionization age, and temperature.

We find a substantial difference between the medians and modes for several parameters, as well as large standard deviations. This suggests a highly complex distribution. To study this variation, we also produce posterior distributions for the parameters. These histograms reveal a wide range of values across the remnant, consistent with complex multi-component plasma.

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Element Figure 4. The mass of each element over the entire remnant, derived using the smoothed particle inference (SPI) measured abundances (red circle) and the Typical LMC scenario (blue triangle), in comparison with the range of values predicted by the core-collapse (purple bar) and Type Ia (green bar) models listed in Table 1. All masses are in units of solar mass.

Additionally, because each blob has a location and size, we are able to study the spatial distribution of the blobsâ&#x20AC;&#x2122; and their parameters. In Figure 3, we present the maps of oxygen, neon, and iron. Maps are created by dividing the remnant into spatial bins. In each spatial bin, a value is assigned by combining the contributions of all overlapping blobs in that bin [5]. Similar to the parameter distributions, these maps reveal a complex composition with an inhomogeneous spatial distribution.

DISCUSSION From the maps, we find the central region features significant iron enhancement and higher temperatures, but a lower emission measure than the outer shell. This elevated iron abundance and temperature of the central region suggests the emission is from shocked ejecta, [5, 6] rather than swept-up ambient medium. To investigate this scenario, we isolate the emission by selecting all blobs with kT > 1 keV, iron > 1, and blob radius less than 26â&#x20AC;&#x2122;â&#x20AC;&#x2122;, the approximate radius of the central emission region.

In order to study the origin of DEM L71, we first consider the emission from the entire remnant. Using the methods described above we calculate the masses of oxygen, neon, magnesium, silicon, sulfur and iron in the remnant. For each element, the mass is inferred

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using both the SPI fit abundances and the typical LMC abundances. The resulting masses are shown in Figure 4, along with the range of masses predicted by core collapse and Type Ia models [8, 9, 10, 11, 12, 13, 14].

Although it appears the masses inferred for oxygen, neon, and magnesium are compatible with the core collapse models, the masses derived using SPI abundances are near the masses found using LMC abundances. This suggests the levels of oxygen, neon, and magnesium we find are associated with swept-up ambient medium, rather than the supernova ejecta. Thus, the masses of oxygen, neon, and magnesium are not indicative of a core collapse origin. Moreover, there is considerable overlap between the core collapse and Type Ia predictions for silicon and sulfur, so these elements have little discrimination power.

However, the high iron abundance is consistent with a Type Ia origin and is significantly elevated from the LMC material. Therefore, the iron abundance has the most discriminating power and suggests a Type Ia origin. This finding is consistent with previous studies [3, 4], although with SPI we have the capability to further study the ejecta material.

Using only the ejecta blobs, we calculate the mass in each blob using the pure Type Ia scenario outlined in our methods. We follow this procedure for each Type Ia model [8, 9, 11, 13]. In the Type Ia explosion scenario, the

Element Figure 5. The mass yield (in solar masses) predicted by DDT (dark blue bar) and pure deflagration (dark red bar) Type Ia models, as listed in Table 1, in comparison with the ejecta mass calculated from the SPI results by assuming pure Type Ia ejecta composition using DDT (light blue bar) and deflagration (light red bar) models.

supernova is caused by the explosive nuclear burning of a binary white dwarf pair. These explosions are theorized to occur in either a double degenerate system (where two white dwarfs instigate the supernova by merging), or the single degenerate channel (where the white dwarf accretes mass from a companion star until the explosion is triggered). These supernovae can be further subdivided by the mechanics of the explosion itself.

Here we consider two explosion mechanisms: those that model a pure deflagration (i.e. a subsonic burning front), and those that incorporate a deflagration-to-detonation transition (DDT) (i.e. a transition from a subsonic burning front to a supersonic front). Our sample of models includes both explosion mechanisms, as well as varied progenitor metallicity and ignition sites. Additionally, we note that although this procedure adopts the relative abundances of each element from the chosen model, the total mass is still dependent on the blob emission-measure and volume.

For each model, we compare the predicted mass with the mass derived from the ejecta blobs. The results of this comparison are shown in Figure 5. Notably, we find general agreement between the predicted and measured masses for the DDT models, while the deflagration models are not consistent with the measurements. As Figure 5 demonstrates, each element holds considerable

discrimination power and the agreement with the DDT models are consistent across all elements.

CONCLUSION In this study, we review the SPI analysis of DEM L71 performed by Frank et al. 2019 and Siegel et al. 2020 [5,6]. We first confirmed the Type Ia origin of DEM L71 and then isolated the ejecta material within the remnant.

We then constrained the explosion mechanism of DEM L71, by estimating the ejecta mass using an array of Type Ia explosion models. We found that the ejecta distribution of DEM L71 is compatible with deflagration-todetonation explosion models and incompatible with pure deflagration models. Moreover, we identified considerable inhomogeneities within DEM L71 and demonstrated the range of parameter values within the remnant.

We are now applying the SPI technique to other SNRs observed with XMM-Newton. We are particularly interested in the application of SPI to remnants interacting with complex surrounding mediums. The unique capabilities of SPI will allow us to better understand the morphologies and explosion mechanisms of these remnants.

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REFERENCES 1. Vink, J. Supernova remnants: the X-ray perspective. Astron Astrophys Rev 20, 49 (2012). https://doi.org/10.1007/s00159-011-0049-1 2. Ghavamian, P., Rakowski, C. E., Hughes, J. P., & Williams, T. B. 2003, ApJ, 590, 833.

3. Van der Heyden, K. J., Bleeker, J. A. M., Kaastra, J. S., & Vink, J. 2003, July, A&A, 406, 141-148.

4. Hughes, J. P., Ghavamian, P., Rakowski, C. E., & Slane, P. O. 2003, Jan, ApJ, 582(2), L95-L99.

5. Frank, K. A., Dwarkadas, V., Panfichi, A., Crum, R. M., & Burrows, D. N. 2019, April, ApJ, 875, 14.

6. Siegel, J., V. Dwarkadas, K. Frank, D. N. Burrows, and A. Panfichi (2020), SPI Analysis and Abundance Calculations of DEM L71, and Comparison to SN explosion Models, Astr. Nach.

7. Peterson, J. R., Marshall, P. J., & Andersson, K. 2007, ApJ, 655, 109.

8. Bravo, E., Badenes, C., & Mart´ınez-Rodr´ıguez, H. 2019, MNRAS, 482, 4346. doi: 10.1093/mnras/sty2951 9. Leung, S.-C., & Nomoto, K. 2018, ApJ, 861, 143. doi: 10.3847/1538-4357/ aac2df 10. Maeda, K., & Nomoto, K. 2003, ApJ, 598, 1163. doi: 10.1086/378948 11. Maeda, K., R¨opke, F. K., Fink, M., et al. 2010, ApJ, 712, 624. doi: 10.1088/0004-637X/712/1/624 12. Nomoto, K., Tominaga, N., Umeda, H., Kobayashi, C., & Maeda, K. 2006, NuPhA, 777, 424. doi: 10.1016/j.nuclphysa.2006.05.008 13. Seitenzahl, I. R., Ciaraldi-Schoolmann, F., R¨opke, F. K., et al. 2013, MNRAS, 429, 1156. doi: 10.1093/mnras/sts402 14. Sukhbold, T., Ertl, T., Woosley, S. E., Brown, J. M., & Janka, H. T. 2016, ApJ, 821, 38. doi: 10.3847/0004-637X/821/1/38

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Jared Siegel is a second year at the University of Chicago studying Physics and Astrophysics.

His research currently focuses on the Smoothed Particle Inference technique and its application to supernova remnants.

Enhancing Dark Exciton Emission in Transition Metal Dichalcogenides Grace Chen a, Amy Butcher a, Alexander High a a Pritzker School of Molecular Engineering, Pritzker Nanofabrication Facility, The University of Chicago

Excitons are electron-hole pairs that determine many optical properties of transition metal dichalcogenides (TMDs). Due to optical selection rules, excitons can be classified as either “bright” or “dark,” where “dark” excitons prohibit the direct recombination of the electron-hole pair for the emission of a photon. These dark excitons with out-of-plane transition dipole moments in TMDs like WSe 2 and MoSe 2 are difficult to detect due to decoupling from light and being drowned out by bright excitons. Thus, we propose an optical cavity constructed of two parallel plane mirrors whose tunable spacing allows for selective suppression or enhancement of specific wavelengths.

Simulations show that this geometry allows for exclusive detection of out- of-plane dark excitons that couple to similarly polarized surface plasmon polaritons (SPPs). SPPs, electromagnetic excitations that exist at the surface of metals, are propagated to outcoupling trenches for far-field detection across single-crystalline silver mirrors.

Photoluminescence scans and spectra show that light with similar features as the WSe 2 monolayer spectra was scattered by the trenches, confirming the orientation and coupling of excitons to SPPs. Improvements to the structural geometry and fabrication of the top silver mirror can yield promising new ways to study dark exciton lifetimes and interactions with applications for quantum information storage.

INTRODUCTION TMDs are MX2 type semiconductors where M is a transition metal and X is a chalcogen. The benefit of TMDs is that, like graphene, they can be exfoliated into an atomically thin monolayer, but they also have a directbandgap with strong spin-orbit coupling that makes them favorable for applications in quantum optoelectronics [1]. Due to the van der Waals forces between atomically thin layers, TMDs can be stacked into specifically layered heterostructures. We focus on WSe2 and MoSe2 to study exciton interactions. In these atomically thin layers of TMDs, the bright excitons, whose optical transitions are “allowed,” become polarized in the plane of the semiconductor. Correspondingly, the optically “forbidden” dark excitons are polarized perpendicular to the plane of the semiconductor. Because these out-of-plane electronhole transitions are optically forbidden, dark excitons have much longer lifetimes than bright excitons, making them exciting candidates for applications in quantum information storage.

Previous studies [2] have shown that dark exciton emission wavelengths in WSe2 can be detected by coupling out-of-plane dark excitons to similarly polarized surface plasmon polaritons (SPPs). Surface plasmon polaritons are electromagnetic excitations that exist at the surface of metals. SPPs decay exponentially with propagation distance across the surface and can only be observed in the far-field if they are converted into light by scattering off of surface inhomogeneities (Fig. 1) [3].

The propagation of SPPs across the surface of the silver was made possible by the lack of grain boundaries in epitaxially grown single-crystalline silver. Epitaxy is the growth of a crystal structure in a specific orientation that is dependent on the crystal orientation of the underlying substrate. In this way, we engineered single-crystalline silver outcoupling trenches that enabled the far-field detection of SPPs [2].

In comparison to WSe2, dark excitons in MoSe2 are especially challenging to detect using only the

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Figure 2. Diagram of optical cavity.

MATERIALS AND METHODS

Figure 1. Diagram of SPPs propagating to outcoupling trenches (reproduced from [2]).

aforementioned methods because of the TMDâ&#x20AC;&#x2122;s unique band ordering, which results in the dark exciton having a slightly higher emission energy than the bright exciton.

Moreover, the exciton peaks in MoSe2 are difficult to discern from each other due to the closeness of their energy levels. A recent study [4] demonstrates that by applying a strong in-plane magnetic field to a hexagonal boron nitride (hBN) encapsulated monolayer of MoSe2, the bright and dark exciton energies are split, allowing for accurate spectroscopy of their respective energies.

On the other hand, the novel geometry of our optical cavity will allow us to selectively enhance the emission of dark excitons in MoSe2 while cutting off the emission of bright excitons with a high level of specificity. This will allow us to study dark exciton interactions and make lifetime measurements without emission interference from the bright exciton.

Thus, to construct our optical cavity for dark exciton emission in MoSe2, we propose an optical cavity constructed of two parallel plane mirrors. The TMD monolayer encapsulated in hBN will be stacked in-between parallel plane mirrors, and the SPPs will be scattered off outcoupling trenches located on either side of the TMD (Fig. 2). The parallel orientation of the optical cavity will suppress the emission of light from the in-plane bright exciton. The optical cavity will modulate the orientation of light emission by employing atomic angular momentum effects to suppress parallel polarized light while also selectively enhancing or suppressing light wavelengths by tuning intra-mirror distances [5]. Longer wavelengths or lower energies are suppressed, selectively enhancing the emission of higher energy states.

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We used Lumerical software to simulate the emission of light from both a parallel and a perpendicular dipole between two silver mirrors. By simulating varying distances between the silver planes, we were able to determine the necessary thickness of the optical cavity that would suppress the longer wavelengths of the parallel polarized bright exciton (Fig. 3a), yet also enhance the emission from the perpendicular dark exciton (Fig. 3b). These optical simulations were also greatly beneficial in providing guidelines for other process design parameters, such as the distance from the dipole to the silver surface and the expected emission intensity from the outcoupling trenches.

We then proceeded to the epitaxial growth of singlecrystalline silver. In order to support the propagation of SPPs, the silver needed to have no grain boundaries in the crystal structure and have sub-nanometer roughness.

Although the growth of single-crystalline silver can be achieved through various methods like sputtering or colloidal chemistry, we ran a heated thermal deposition on top of a mica substrate. Mica is a favorable substrate because it is lattice-matched to silver, is easily cleaved by manual methods to reveal a smooth surface, and is obtained at a relatively low cost. Literature [6] shows that the conditions for single-crystalline silver growth involve heating the substrate above 300ÂşC and maintaining a deposition rate above 1.5 nm/s. Thermal evaporation is a method of physical vapor deposition that evaporates material in a thin film onto a substrate. By manually adjusting the power output of the thermal evaporator, we were able to maintain depositions at 350ÂşC and 1.8-2.0 nm/s. Subsequent measurements of surface roughness using Atomic Force Microscopy (AFM) showed that there were no grain boundaries on the surface of the silver and that the RMS roughness of the silver surface was as low as 0.35 nm (Fig. 4).

Following our growth of single-crystalline silver, we employed two different methods to fabricate the outcoupling trenches. We first used electron-beam lithography to pattern the trenches straight into the

A

B

Figure 3. (A) Cutoff emission for parallel dipole with varying distance between mirrors. Horizontal axis measures different wavelengths of light from 500 nm to 1000 nm. The vertical axis shows the varying distance between the mirrors. The color bar indicates intensity of light transmitted. Simulation shows that as distance between mirrors is increased, longer wavelengths of light are able to be transmitted. (B) Enhanced emission from perpendicular dipole with varying distances. Horizontal axis measures different wavelengths of light from 500 nm to 1000 nm. The vertical axis shows the varying distance between the mirrors.

The color bar indicates intensity of light transmitted. This simulation shows that the intensity of light from the perpendicular dipole will not be affected by the varying distance between mirrors.

A

B

Figure 4. (A) Atomic Force Microscopy (AFM) on left shows grown silver that has visible grain boundaries. These boundaries would scatter SPPs before they can reach the scattering trenches. (B) AFM on right shows single-crystalline silver with RMS roughness of 0.407nm. There are no visible grain boundaries in the AFM scan.

silver. In order to do this, we spin-coated ~275 nm of polymethyl methacrylate (PMMA A4), a polymer used as e-beam resist, on top of the silver (Fig. 5a).

The exposure of PMMA to the electron beam and the development of the sample in a solution of methyl isobutyl ketone (MIBK) and isopropyl alcohol (IPA) created the desired trench pattern in the resist that acts as a soft mask during the etching stage (Fig. 5b).

When etching the trenches into the silver, we used Inductively Coupled Plasma (ICP) Etching with an argon gas (Fig. 5c). Although ICP Etching typically uses gases that combine both chemical reactions and a physical

ion-induced etch, we employed argon gas for physical, non-reactive etch. This is because single-crystalline silver is highly reactive, and we wanted to preserve its quality throughout the etching process (Fig. 5d). After the trenches were etched into the silver, we used an overnight acetone soak to remove the top layer of PMMA from the silver structures (Fig. 5e).

Through experimentation, we encountered several issues with this etch-process. If we did not pattern the trenches into the silver soon after deposition, the quality of the single-crystalline silver decreased. Additionally, the argon etching process accelerated the ions at such

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Figure 5. Process diagram for fabricating outcoupling trenches

A

B

Figure 6. (A) Photoluminescence scan over flake. (B) Photoluminescence scan over flake.

a voltage that the PMMA polymers were burned and melted non-uniformly, making the removal process in acetone extremely difficult. In an attempt to circumvent these issues, we grew a 10-12 nm passivation layer of alumina (Al2O3) on top of the silver. This passivation layer was designed for two purposes: to protect the surface of the single-crystalline silver from environmental contamination and general degradation over time and to serve as a hard mask during the etching process of the outcoupling trenches. We followed the same electronbeam lithography steps above. During the etching step, we first did an Al2O3 ICP etch followed by removal of the top layer of PMMA with an overnight acetone soak.

This prevented the PMMA polymers from burning up and allowed for its easy removal. Since alumina is not

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easily etched by argon, we used the same argon etch as before to etch the pattern into the single-crystalline silver. Ideally, this remaining layer of alumina would easily be removed by an HF soak or aluminum wet etchant, but the chemistry of the mica and silver reacting with these acids prevented its simple removal. Thus, without a reliable method of removing the alumina passivation layer, we were unable to immediately employ this new fabrication process.

To collect the necessary WSe2 and hBN flakes, we exfoliated bulk crystals with tape, peeling apart the layers of each material. We then used an optical microscope to identify flakes by color that fell within the correct thickness range as determined by the simulations. For a precise measurement of the flake heights, we used AFM to

X0: Neutral exciton XD: Dark exciton

Figure 7. Photoluminescence spectra comparing emission from flake to emission from outcoupling trench. Neutral exciton (X0) and dark exciton (XD) are labelled by comparing to literature [2].

measure that the hBN flakes were 24nm and 33nm thick.

Finally, we assembled the hBN-WSe2-hBN heterostructure using a Computer-Aided Positioning (CAP) stamping process. This system allows for a high degree of precision when lining up the flakes.

RESULTS The goal of our preliminary measurements with WSe2 was to verify the concept of dark exciton coupling to SPPs and the propagation of SPPs towards the outcoupling trenches for far-field detection of dark excitons. Fig. 6a shows a photoluminescence map of photon counts detected in the far field while the excitation laser is focused on the WSe2 monolayer (brightly illuminated flake). This confirmed that the WSe2 flake we found was indeed a monolayer. Other thicknesses of WSe2 would not have such high photon counts. However, we observed that there was an inhomogeneity in the bright emission from the flake. We were also able to see that there were

faint edge outlines and bright spots in the hBN where the light was being scattered off before it reached the outcoupling trench. In Fig. 6b, the green excitation laser was still focused on the WSe2 monolayer, and faint photon counts were detected from the dimly illuminated line where the outcoupling trench was located. These results confirm that the outcoupling trenches are successful in scattering SPPs excited from the flake into the far-field for detection. The next measurement we made was to compare the photoluminescence spectra (intensity over a range of wavelengths) emitted from the monolayer to the spectra emitted from the trench. Fig. 7 shows PL spectra measured over the trench (orange) versus the monolayer itself (blue). Each spectrum was normalized to unit intensity and superimposed on top of each other to compare features at corresponding wavelengths. We were able to identify exciton features in the PL spectra from the monolayer (blue) by referencing previous literature [2] of a similar experimental set-up.

49 / SPRING 2020

REFERENCES DISCUSSION From these PL spectra we can see that although the signal measured over the trench was attenuated and noisy compared to the signal measured from the flake, similar key features confirm the coupling of outof-plane dark excitons to SPPs. In Fig. 7, a similar feature appears in both the trench spectrum and the monolayer spectrum at ~733nm, confirming that the peak at 733 nm in the spectra from the flake corresponds to the dark exciton peak. We can be fairly certain that the feature detected from the trench corresponds to the dark exciton because the surface plasmon polaritons are perpendicularly polarized and thus can only couple to perpendicularly polarized dark excitons. It is possible that the thicker bottom layer of hBN allowed us to observe a sharp dark exciton peak in the spectra taken over the flake without the addition of the top layer of silver. The signal-to-noise ratio of the spectra from the trench can be improved by choosing TMD monolayers that are more uniform across their surfaces to limit the inhomogeneity of the signal. This can be accomplished

by AFM of the surfaces of the monolayers to make sure that there are no large bubbles or debris across the surface. Additionally, we can pick hBN flakes that are also relatively smooth and flat with no wrinkles or edges near the trenches to prevent the early scattering of SPPs. Finally, we can decrease the distance between trenches from 20 um to 5um in order to increase the intensity of the SPPs when they are scattered. This is especially important due to the strong SPP decay with propagation distance.

NEXT STEPS We are working on creating heterostructures of MoSe2 to try to repeat the same measurements we made with WSe2. These new trenches will have a slightly different geometry with SiO2 grown as an additional layer between the silver and hBN. This addition of a lower-index dielectric inside the cavity should yield sharper transmission cutoffs at the desired wavelengths. This sharp cutoff at the desired wavelength is paramount for detection of dark excitons in MoSe2 because the bright and dark excitons are very close in energy. From there, we will move forward with growing the top layer of silver in order to make use of the optical cavity’s geometric selectivity of wavelengths

50 / SCIENTIA

1. Manzeli, S. et al. (2017). 2D transition metal dichalcogenides. Nat Rev Mater 2, 17033. https://doi.org/10.1038/natrevmats.2017.33 2. Zhou, Y., et al. (2017). Probing dark excitons in atomically thin semiconductors via near-field coupling to surface plasmon polaritons.

Nature Nanotechnology, 12(9), 856-860. doi: 10.1038/nnano.2017.106 3. Zayats, A. (2004). Nano-optics of surface plasmon polaritons. Physics Reports, 408(3-4). https://doi.org/10.1016/j.physrep.2004.11.001 4. Lu, Z., et al. (2019). Magnetic field mixing and splitting of bright and dark excitons in monolayer MoSe2 . 2D Materials, 7(1), 015017. Doi: 10.1088/2053-1583/ab5614 5. Jhe, W., et al. (1987). Suppression of Spontaneous Decay at Optical Frequencies: Test of Vacuum-Field Anisotropy in Confined Space.

Physical Review Letters, vol. 58, no. 14, pp. 1497–1497., doi:10.1103/ physrevlett.58.1497.2.

6. Park, J.H., et al. (2012). Single-Crystalline Silver Films for Plasmonics.

Advanced Materials, 24(29), 3988-3992. doi: 10.1002/adma.201200812

Grace Chen is a second-year student at the University of Chicago majoring in Physics and Molecular Engineering (Quantum Track). She hopes to attend graduate school to study Quantum Engineering and eventually go into a related academic or industrial field.

THE TRIPLE HELIX Dear Reader, The Triple Helix, Inc. (TTH) is the world’s largest student-run organization dedicated to evaluating the true impact of historical and modern advances in science. Of TTH’s more than 20 chapters worldwide, The University of Chicago chapter is one of the largest and most active. Our TTH chapter continues to proudly share some of the most distinct publications and events on campus, engaging the minds and bodies of our institution and the public as “a global forum for science in society.”

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51 / SPRING 2020

ACKNOWLEDGEMENTS The Triple Helix, Inc. (TTH) is the world’s largest student-run organization dedicated to evaluating the true impact of historical and modern advances in science. Of TTH’s more than 20 chapters worldwide, The University of Chicago chapter is one of the largest and most active. Our TTH chapter continues to proudly share some of the most distinct publications and events on campus, engaging the minds and bodies of our institution and the public as “a global forum for science in society.” Our mission, to explore the interdisciplinary nature of the sciences and how they shape our world, remains the backbone of our organization and the work we do. In addition to Scientia, we publish The Science in Society Review (SISR) and an online blog (Spectrum), while also creating events to discuss the most current, pressing topics at the intersection of science and our society.

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