A very successful summer of research.  Please feel free to click on the videos from the morning session and afternoon poster presentations.

Oral Session

Friday, August 14, 2015
10am- 11:30am
Thomas A. Steitz Hall of Science, Room 102

Modeling RNA Branching Structure with Graph Theory


Clayton Ristow, Physics

RNA, known for its role in expressing, transferring and regulating genetic code, has the property that it can fold up on itself to form a number of different branched structures. It is believed RNA can move between these different branched structures using thermal energy. When the sequence in RNA does not matter, this branching structure plays the dominant role in the RNA’s behavior. Using Graph Theory and Statistical Mechanics we have found the partition function and corresponding free energy of this branching structure allowing us to fully model its thermal behavior. This model is easily generalized to include more complicated assumptions about the likelihood of different configurations.  (Presentation Questions)

The Effects of Supernovae on Protoplanetary Disks


Rachel Mumme, Physics

As more and more extrasolar planets are discovered it has become more and more important to uncover the mechanics of their formation. We are one of many groups to use computer simulation to do so, but we are one of the only groups to take into account the violent environment of star-forming regions. While many groups let their systems evolve in isolation, we are attempting to understand the impact of environmental events on planet formation. One such potential event is a nearby star going supernova. We are attempting to discover the impact a supernova blast may have on an evolving protoplanetary disk.  (Presentation questions)

A rainbow of liquids leads to a pot of possibilities:  Structure in imidazolium-based ionic liquids.


Joe Liberko, Physics

Room temperature ionic liquids have garnered a tremendous amount of attention recently as light ion batteries are becoming more important to our energy economy.  With millions of different ionic liquids there is a need to better understand the underlying connections between the types of structures that form in the liquids and their electrochemical and transport properties.  In this talk, I will share with you the process for obtaining structural information from a liquid using X-ray diffraction, how to interpret results, and how those results inform microstructural models of these liquids. (Presentation questions)

Structural evolution of ionic liquids via X-Ray diffraction


Cody Poole, Physics

Ionic liquids are a class of substances that form ionic bonds and are liquid below 100°C. They have interesting electrochemical properties that make them possible candidates for future batteries. The ionic liquid of focus is 1-alkyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)amide, which as an alkyl chain on the cation. Our aim is to learn how both temperature and the chain length affect medium range structures in the liquid. In this talk, I’ll discuss our results that, so far, indicate the existence of a medium range structure that gets larger and more prominent with increasing temperature. (Presentation questions)

Observing Dislocations in Liquid Crystal Films


Peiying Yu, Physics

Although strain models of edge dislocations in liquid crystals have been used to estimate the depth of dislocations at a crystal interface below a free surface, the strain model has not been quantitatively tested in pure liquid crystal systems. The model predicts that in a liquid crystalline phase film, the depth of dislocation is half of the film thickness, and the step profile can be determined by the film thickness. To verify this model, we plan to image the surfaces of 4-n-heptyloxybenzylidene-4-n-heptylaniline (7O.7) films in the liquid crystal phase. To get purely liquid crystalline films, we constructed an apparatus to efficiently produce freely suspended thin liquid crystalline phase 7O.7 films between 50 and 150 layers. In combination with the calculated chromaticity diagram of 7O.7, the thickness of 7O.7 film and the predicted dislocation depth can be determined by identifying the color reflected from the film. (Presentation questions)

Using Sound to Create a Pulsed Laser


Chris Kiehl, Physics

A pulsed laser is a valuable instrument for manipulating atoms and measuring their fundamental properties. One method for creating a pulsed laser is to use a device called an acousto-optic modulator (AOM), which uses sound waves to modulate light. In this presentation, we will explore the theory behind the AOM and report the results of constructing an AOM system that can be used to measure the lifetime of an atomic excited state. (Presentation questions)

Poster Session

Friday, August 14, 2015
12pm - 1pm
Thomas A. Steitz Hall of Science Atrium

Using Open Source Hardware to Design a Device That Measures CO2 Levels and Other Environmental Factors

Meeko Trought, Chemistry

Scientific instrumentation is essential in any field of science. However, due to cost or mobility many instruments are not available to institutions or will not work for specific applications. Using electronic sensors along with a microcontroller can solve these issues and allow instrumentation to be accessible to all, due to its low cost and size. Using these electronic components, does not require any extensive background knowledge and a large community of users provides resources for troubleshooting. We have proto-typed a weather station, including temperature, relative humidity, CO2, and dust sensors that are controlled with an Arduino microcontroller. We will use this prototype to design an environmental factors monitor to be used in environmental and industrial application and a small mobile weather station which will be deployed this summer.

Project ZOLO: Synthesizing and testing potential antimalarial compounds

Charlie Martin, Chemistry

Malaria is an infectious disease caused by parasites that is widespread in tropical regions. It is one of the leading causes of death in developing countries. The parasites that cause malaria are developing drug resistance, so new anti-malarial drugs are needed. This project is the basis for a classroom module spanning two Lawrence courses. In Organic Chemistry II, students synthesize a potential anti-malarial drug in two to three steps; in Biochemistry I, they use standard biochemical techniques to assess their drug’s functionality. I performed and optimized a 6-step synthesis to an important synthetic intermediate, characterizing each reaction product by infrared and proton nuclear magnetic resonance spectroscopy. Specifically, I optimized the nucleophilic aromatic substitution of hydrazine to a chloropyrazine. Cell toxicity tests revealed that the compounds are relatively non-toxic. In the future, I will complete the last step of the synthesis to form the desired product, test the toxicity and functionality of the compound, and repeat the synthesis with different side groups to determine how they affect the functionality of the compound. More broadly, it is hoped that one or more compounds in this family could prove to be effective anti-malarial drugs.

Electrochemistry of an electron-rich subporphyrazine

Tyler Herman, Chemistry

Tris-(1,2,5-thiadiazole)-subporphyrazine (S3N6SubPz) is an unusual example of an electron-rich subphthalocyanine homologue. Bearing peripheral five-membered thiadiazole groups, the compound’s weakened aromatic stabilization produces an electronic spectrum intermediate between those of the more common aliphatic subporphyrazines and subphthalocyanine. In this poster, we present preliminary electrochemical analysis of this unusual macrocycle.

Pigment analysis of a 14th century illuminated book of hours by Raman microscopy

Caren Sullivan, Chemistry

A book of hours is a medieval devotional manuscript containing prayer text, pigment decoration, and gold leaf illuminations. The origins of a manuscript can be partly ascertained through pigment identification using analytical techniques. Confocal Raman microscopy provides a non-invasive, non-damaging, and highly sensitive method that can help characterize the compounds used within works of art. The collaboration of the Art History and Chemistry departments provided an opportunity to study a 14th c. book of hours. Red and blue pigments are investigated as well as the ink used within the text . This particular work also has several pages which may not be original to the manuscript as a whole. We present Raman spectra of multiple pigments and compare them to synthesized pigments from medieval recipes. Due to the fragile nature of the manuscript, we also present our experimental approach of handling the manuscript in data acquisition.

Application of the compensated Arrhenius formalism to temperature-dependent fluidity and self-diffusion coefficients of 1-alcohol and 3-alcohol systems

Grant Forsythe, Chemistry

A molecular level picture of mass transport is crucial in developing better materials for industrial applications. The compensated Arrhenius formalism (CAF) has been shown to model temperature-dependent self-diffusion coefficients, and fluidity (the inverse of viscosity) of protic and aprotic polar liquid systems. The CAF assumes transport to be a thermally activated process, with a corresponding energy of activation, Ea. The CAF includes the solution dielectric constant in the exponential prefactor of an Arrhenius-like model, which varies with the extent of hydrogen bonding for the protic systems. Here, we apply the CAF to temperature dependent fluidity data of 1-alcohol and 3-alcohol systems to investigate the effect of hydrogen bonding on the Ea, where 3-alcohol liquids have a weaker hydrogen-bonding network than 1-alcohol liquids. The CAF results describe the temperature-dependent behavior of the fluidity data between the 1- and 3-alcohols—the Ea values are similar, but the exponential prefactors are significantly different due to the difference in hydrogen bonding. The CAF is also applied to temperature-dependent self-diffusion coefficients for 1- and 3-alcohols and compared to the results for fluidity.

Mass and charge transport in pyrrolidinium cation-based and alkyltrimethylammonium cation-based ionic liquids

Augustus Lowry, Chemistry

Room-temperature ionic liquids (RTILs) offer great promise in the electrochemical industry. Application of these materials is limited, however, because the accepted empirical descriptions of mass and charge transport do not provide a molecular-level picture of the mechanism governing transport. An alternative model, the compensated Arrhenius formalism (CAF), successfully models mass and charge transport in RTILs providing this molecular-level picture. The CAF uses an Arrhenius-like expression to model transport as a thermally activated process by incorporating the dipole density into the exponential prefactor. The activation energy and exponential prefactor provide insight into the intermolecular interactions that govern transport. This work demonstrates the versatility of the CAF in describing temperature dependent self-diffusion, fluidity, and conductivity of pyrrolidinium cation-based RTILs and alkyltrimethylammonium cation-based RTILs and offers a comparison of the different systems.

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