Summer Science Research at Bryn Mawr

'2009' Archive

Visualization of the Kink-Turn Structure of RNA

Posted May 14, 2010

RNA, like proteins, folds into 3D structures, consisting of motifs such as hairpins, pseudoknots, and internal loops. This research project focuses on visualizing one such motif, which is called the kink-turn. The kink-turn region consists of Watson-Crick base pairs on either end of a short asymmetric bulge that consists of non-base paired nucleotides, which results in a sharp bend in the phosphodiester backbone. This region is of particular interest because it has been found that proteins bind to RNA selectively at this region. The figure above shows the yeast L30e protein binding to the kink-turn region of its m-RNA. The biophysical structure characterization of the kink-turn of RNA would thus give information about the nature of this motif and its importance in protein-RNA interactions. Such research will aid in studying potentially useful protein-RNA interactions as well as construction of RNA molecular units capable of self-assembling into RNA nanostructures. The goal of this research is to use Atomic Force Microscopy (AFM) to visualize and characterize RNA molecules that have a kink-turn.

Synthesis of functionalized cis-fused bicarbocyclic structures via olefin cross metathesis and tandem conjugate/Michael addition

Posted May 14, 2010

Syntheses of cis-fused bicarbocyclic systems are of great interest for constructing complex organic architectures. We report a new synthetic method to functionalized bicarbocyclic structures using the final product from the Birch-Cope sequence that has been developed by the Malachowski group. The two-step method (Scheme 1) includes an olefin cross metathesis and a tandem conjugate/Michael addition.

The Synthesis of a Solubilized [11]Phenacene Derivative

Posted May 14, 2010

[n]Phenacenes are molecules containing n aromatic rings joined together in a zigzag pattern. Since they can be thought of as graphene ribbons, which have conductive properties, they should have the potential to be used as molecular wires. The solubility of unsubstituted [n]phenacenes decreases dramatically with increasing n; [7]phenacene was found by the Mallory group to have negligible solubility. Currently the longest known [n]phenacene is an [11]phenacene derivative that was synthesized by the Mallory group with tert-butyl substituents acting as solubilizing groups, but it was found to have only modest solubility. The goal of my research is the synthesis of the [11]phenacene derivative shown below. The purpose is to test whether the long-chain alkyl groups R can provide the necessary solubility to allow the synthesis of even larger [n]phenacenes with n = 15 and n = 19.

Implementing the Birch-Cope Sequence and Rearrangement for the Synthesis of Natural Therapies

Posted May 14, 2010

Within the scope of organic synthesis, the goal of attaining biologically active compounds has proven its extensive value as well as its array of strategic challenges, specifically in the creation of enantiomerically pure carbocyclic quaternary stereocenters. However, the implementation of the three-stage Birch-Cope sequence, comprising of the Birch reduction-allylation, enol ether hydrolysis, and Cope rearrangement has become a proven method of effectively generating such chiral stereocenters, which are crucial synthetic intermediates. Expanding on the procedure’s prior successes, its discovery has stimulated a wealth of synthetic opportunity in the ultimate hopes of developing innovative therapies in the way of antibiotics, which the Malachowski research team currently seeks to explore. Within the scheme of the project, my role this summer specifically involves the production of the o-anisic acid derivative starting material possessing a chiral auxiliary, which is derived from a reaction with L-prolinol. Longer range goals include conducting the Birch-Cope sequence and contributing to the exploration of the product after the Cope rearrangement.

The Synthesis of a [7]Phenacene Derivative as a Molecular Wire

Posted May 14, 2010

Phenacenes, or graphene ribbons, are molecules containing [n] aromatic rings joined in a zigzag pattern. Because pseudo one-dimensional graphene ribbons are similar to pseudo two-dimensional graphene sheets, they may have similar conductive properties, and so could be used as bridges for electron transport within molecules. Studies have previously been reported at Northwestern University using bridges made of benzene rings connected in the pattern shown below:

Unlike these bridges, where the rings are rotated at angles to one another, phenacenes are planar, and so may conduct electrons differently and possibly more effectively. This experiment will attempt to synthesize molecules with n=7 aromatic rings in the phenacene bridge. The phenacenes will have a bromine substituted on one end, and an amine substituted on the other end. They will also have a solubilizing alkyl group substituted on either end, as shown below: R=

Katie Solook in 2009

Posted May 12, 2010

Noting that there is a difference between young adults’ and older adults’ memory is not surprising information. Previous research has found that memory not only deteriorates with age, but that there are other differences in the application of memory between young and older adults. In recall and recognition word tasks, older adults tend to not use specific strategies to assist in memory of word lists, unlike young adults. With this study, young adults (18-25 year olds) and older adults (60-90 year olds) will be given specific strategies aimed to aid their memory of word lists. After first pre-testing their ability for recall or recognition of word lists, participants will be given four different strategies (using images, creating sentences, creating a story, and a multiple strategy approach) for assisting in word recall/recognition. The evaluation of word recall/recognition will be evaluated through comparing performance in the first session, before participants were given the strategies, and the performance in the tenth session, after they had received the strategies and have had time to practice the application in other sessions. Using a similar experimental design of a past study that only contained eight sessions for participants, this study hopes to lessen the difference between the two subjects groups through the instruction in strategy usage as well as explore if the strategy effects can be carried to other cognitions other than memory.

Monkey See, Monkey Do: Learning Symbols Through Conventionality

Posted May 12, 2010

Understanding how children learn gesture and word labels for objects provides insight into language acquisition and early cognitive development. To date, much research has focused on the importance of iconicity of gestures, or the resemblance of a gesture to its referential object. Previous literature on the subject indicates that children are able to understand iconic gestures much earlier than they understand arbitrary gestures, or gestures that do not necessarily resemble the referential object or action. However, this might have more to do with the conventionality of these gestures than their iconicity. Conventionality refers to the repetitive use of the symbol or gesture in a communicative manner during social interactions. To truly determine the roles of iconicity and conventionality, we have designed an experiment to assess children’s ability to differentiate iconic gestures used in a conventional context from those used in a non-conventional setting.

On the Boundedness of Oscillatory Integral Operators in Harmonic Analysis

Posted May 12, 2010

My summer research is in the area of harmonic analysis, the branch of mathematics which studies the representation of signals or functions as the superposition of basic waves. The basic waves are called “harmonics”, hence the name “harmonic analysis”.

In this branch of mathematics, there is great concern about examining mathematical objects by decomposing them into many simpler building blocks and studying these simpler components. This would make the study of the original object easier and more comprehensible in most cases. For instance, to study a function (a musical sound, for example) we could break it down into a sum of the pure harmonics, sine and cosine, which will allow us to study these simple graphs, to better understand our original function’s behavior. Harmonic analysis has become a vast subject with applications in areas as diverse as acoustics, optics, electrical engineering, quantum mechanics, and neuroscience.

Mathematics and the environment: A compilation of useful information

Posted May 12, 2010

Sustainability as it relates to the environment is the concept that we need to use our natural resources in such a way that future generations will still be able to live and be ‘sustained’ by our planet. This summer, I will be looking into ways that we can incorporate environmental sustainability concepts into mathematics education to better engage students in both math concepts and issues of sustainability. I will conduct research on the web to see what curriculums already exist on the subject and test the curriculums that I find by actually doing the problems associated with the various curriculums. I will also meet with Jim McGaffin, the Assistant Director for Energy and Project Management in the Facilities department at Bryn Mawr College to come up with a few topics on sustainability as it relates to Bryn Mawr for use in Professor Donnay’s spring semester Senior Conference as well as other future math courses taught at Bryn Mawr. This information could be used to incorporate sustainability concepts, as they relate specifically to our campus, into the math curriculum at Bryn Mawr. My hope is to compile a database of information including where information on sustainability curriculums can be found as well as answer keys to various curriculums and a few problem sets, which I will develop over the course of the summer about sustainability at Bryn Mawr. This database will be used as a resource for the Environmental Sustainability program for teachers that Professor Donnay is developing in conjunction with faculty from various Pennsylvania area colleges and universities spanning several different disciplines. It is my hope that in conducting this research, I will discover a potential topic of interest for me to look into in further detail in the form of a senior thesis.

Sophia Wolfenden in 2009

Posted May 12, 2010

For my summer research, I chose to analyze the shells of bivalve and other mollusca genera from the Near Eastern archaeological site of Muweilah, UAE. In order to determine the provenience of the shells found at the site of Muweilah, and specifically those found within the interior spaces of the site, it was necessary to undertake a series of dating techniques including stratigraphic dating, carbon isotope analysis and shell classifications through direct study of geographically similar collections. From this research the age and potentially, the location of origin of these shells can be determined and classified. Such research regarding the geological availabilities on hand in the region during the late Bronze age is useful when determining the likelihood of ecological and resource management practices of the early settlers.

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