Home Town: Boulder, CO

Short peptides are strings of a few amino acids. They serve as stringent tests for our understanding of protein folding. Our goal is to experimentally understand the role of the solvent in determining peptide secondary structure. Our aim is to study several alanine- and glycine-rich model peptides using x-ray diffraction and nuclear magnetic resonance (NMR). Both solid-state and liquid-state NMR will be used to acquire information about the conformation of these molecules in forms ranging from crystalline to ideally dilute solutions. Specifically, we are interested in changes in the peptide backbone torsion angles.

X-ray diffraction data will also be taken to assess crystalline order for partially solvated states and results from the two sets of experiments compared.

Other Interests: Gardening. Reading medical literature on cancer. Playing Swedish fiddle tunes on a 16 3/4 viola. And hopefully soon I’ll resume my hobbies of instrument carving, backpacking, fishing, rock climbing, skiing, and winter camping.

Home Town: Atul, India

Short peptides are strings of a few amino acids. They serve as stringent tests for our understanding of protein folding. Our goal is to experimentally understand the role of the solvent in determining peptide secondary structure.

We are currently studying alanine dipeptide, which is the smallest molecule that has two peptide planes. The molecule is hydrated to different levels ranging from completely solvent deprived to ideally dilute. Solid-state NMR is used to acquire information about the backbone torsion angles in the various partially hydrated states. Changes in the torsion angles provide key information about the peptide’s conformation.

Our aim is to extend these studies to several alanine- and glycine-rich model peptides. Computational studies on the same molecule are being pursued by other members in the group. The experimental and computational work complement each other and provide a detailed view of peptide secondary structure and dynamics.

Other Interests: North Indian classical music, contemporary and post-colonial literature, cooking, sociological theory, traveling.

Home Town: Ithaca, NY

Home Town: Northville, MI

Home Town: Madison, WI

Home Town: Atlanta, GA

Aromatic compounds make up roughly one quarter of the atmosphere’s organic inventory. It is well known that the oxidation of aromatic compounds leads to the formation of both ground level ozone and visibility-impairing aerosols (smog). However, the specific oxidation mechanisms are not well known. We have undertaken studies of mechanism of the oxidation of benzene and toluene, the two most atmospherically abundant aromatic compounds. We are carrying out computational thermodynamics calculations that are run on Oberlin’s new supercomputer cluster and product identification experiments that are performed using the Turbulent Flow Chemical Ionization Mass Spectrometric (TF-CIMS) kinetics technique.

Other Interests: Playing French horn, good books, Pakistan, cooking, religion, long walks on the beach, pumas.

Home Town: Seattle, WA

As the available computing power continues to increase, computer models of chemical systems are becoming more and more important and informative. I am performing molecular dynamics simulations (which use pre-calculated atom, bond and angle properties to simulate molecular motion) and quantum chemical calculations (which numerically solve the Schrödinger equation) to study the effects of solvation on simple di and tripeptides. We are performing these simulations using desktop machines and Oberlin’s 70-node supercomputer. Our computational studies complement experimental NMR measurements, made locally by other members of the research group, and provide a more detailed view of the structure and dynamics of model proteins in various solvent environments. Our ultimate goal is to apply what we learn about these small peptides to larger ones and to the secondary structure of biologically significant proteins.

Other Interests: Coming of Age Movies from the ‘80s, Novel Computing, EMS, Ice Cream, Diet Pepsi, Wandering Aimlessly, Hubris, f and y.

Home Town: Phoenix, AZ

The reaction of peroxy radicals (RO ₂) with nitric oxide (NO) is the rate-limiting step in the formation of ground level ozone (smog) arising from the presence of volatile organic compounds in the atmosphere. We have undertaken studies of this reaction for methacrolein and methyl vinyl ketone, which are oxidation products of the most abundant biogenic compound in the atmosphere, isoprene. Usually, oxidation is initiated by OH radicals, but Cl radicals can be important in marine areas (due to the volatilization of chlorine by wave-breaking action). We are working on measurements of both oxidation pathways for the methacrolein and methyl vinyl ketone-derived RO₂ + NO reactions using the Turbulent Flow Chemical Ionization Mass Spectrometric (TF-CIMS) kinetics technique. We are also carrying out computational thermodynamics calculations that are run on Oberlin’s new supercomputer cluster to aid in the understanding of the oxidation mechanisms.

Other Interests: Sunshine, biking, running, skating, eating, making drinks, pilates, fireworks, tea, bread dipped in olive oil.

Home Town: Greensboro, NC

One of the aims of our research is to elucidate the secondary structure of peptides in different condensed environments using solid-state Nuclear Magnetic Resonance (NMR). Some solid-state NMR experiments, such as multiple-quantum NMR, require the presence of NMR-active nuclei above the level of natural abundance (e.g., ¹³C, 15N). In order to produce peptides with isotopic enrichment at known sites, we are chemically synthesizing the peptides using known chemistries while starting with isotopically labeled starting materials. We have successfully synthesized the alanine dipeptide, Ac-Ala-NHMe, with both the carbonyl carbons ¹³C-labeled. Our next target will be the synthesis of Ac-Ala-Ala-NHMe. Once made, the peptides are purified using reverse phase HPLC. The identity of the final product is verified using solution-state NMR and mass spectrometry.

Other Interests: Eating good food, piano, knitting, web comics, sleeping.

Home Town: Trumbull, CT

Rotational structure in high-resolution (0.0013 cm ^-1) infrared spectra of the cis and trans isomers of hexatriene is being analyzed to obtain ground state rotational constants. These rotational constants and those for hexatriene isotopomers, yet to be synthesized, will be used to find equilibrium structures of these polyenes. From the structures we will assess the extent to which delocalization of pi-electrons is reflected in changes in bond lengths and bond angles. Some ideas for making isotopomers are being explored.

Other Interests: Music: The Fray, Counting Crows, Goo Goo Dolls, and anything Korean. My iTunes shared music library is called “passwordispyrate.”
Academic: ethics, Korean language, math, micro-biology
Recreational: socializing, hiking, dancing, dismantling computers… systematically of course.

Home Town: Baltimore, MD

The selective detection of biomolecules in serum is an important tool for basic research and clinical applications. Traditionally, such assays have relied on antibody molecules as the basis of detection. A long-term goal of research in the Whelan lab is to explore a relatively new class of affinity molecules—aptamers—and to develop analytical assays that exploit their advantages. Aptamers are single-stranded nucleic acid molecules with recognition ability comparable to antibodies. The process of aptamer selection begins with a large pool of oligonucleotides. The oligos are allowed to interact with the target protein of interest, and those that bind well to the target are separated from those that do not. Good binders are amplified by polymerase chain reaction, and the cycle of selection and amplification continues until the pool converges on a small number of excellent binders. This summer, we will optimize the processes by which candidate oligos are amplified and made single-stranded in pursuit of our goal to select a DNA aptamer that recognizes CA 125, a protein that is widely used as an ovarian cancer biomarker.

Other Interests: singing, playing the piano and the cello, biking, poetry and literature, botany, painting, listening to classical music, watching Futurama and The Daily Show

Home Town: Durham, NC

In recent years, there has been increased interest in synthesis of hybrid inorganic-organic network compounds, in which single metal atoms or metal clusters are linked by organic ligands. Because of the porosity of these compounds and the variety of functionalities that can be incorporated, they have potential as materials for catalysis and gas storage. The MS ₄^2- (M = Mo, W) anions, tetrathiomolybdate and tetrathiotungstate, are known for their ability to chelate transition metals and to act as catalysts for hydrodesulfurization and hydrodenitrogenation reactions, both of which are important in production of cleaner fuel sources. We are working to synthesize network compounds incorporating these anionic building blocks.

We are using room temperature and solvothermal methods to explore reactions among the tetrathiometallates, secondary metals, and ligands such as 4,4'-bipyridine, ethylenediamine, and terephthalic acid. Solvothermal synthesis, in which reactions are heated in sealed containers to above the boiling point of the solvent, is a useful method for growing crystalline reaction products. We are characterizing these products using both powder and single-crystal x-ray diffraction. Our goal is to synthesize new network compounds incorporating the tetrathiometallate anions and to determine their structures and catalytic activities.

Other Interests: The Spanish language, medicine and the EMS system, travel, reading, music, movies.

Home Town: North Huntingdon, PA

Fluorine substitution on carbon atoms exerts a large influence on the length of carbon-carbon bonds. We intend to assess this effect from equilibrium structures of the three isomers of 1,4-difluorobutadiene and to compare these structures with ones computed by quantum chemical methods. To obtain these structures we synthesize isotopomers, analyze high-resolution infrared spectra, and do quantum chemical calculations. The principal activity this summer is developing new syntheses of isotopomers.

Other Interests: skiing, racquetball, Rubik’s cubes, chicken pesto pizza, old James Bond movies, golf, the color red, bike rides, philosophy of science, prime numbers, Grey’s Anatomy, sudoku puzzles, Bill Nye the Science Guy, coffee, ping pong, and Arrested Development.

Home Town: Bedford, TX

Capillary electrophoresis (CE) separates biomolecules with excellent efficiency on the basis of their mobility in an applied electric field. The separation is accomplished in a glass capillary with an inner diameter on the order of tens of microns. When coupled with laser-induced fluorescence detection (LIF), CE can detect attomoles of protein or other biological analytes. In situations when the analyte of interest is non-fluorescent, it is possible to involve the analyte in a non-covalent affinity complex with another molecule—called an affinity probe—that is fluorescent. The resulting combination of affinity interaction and CE separation is called an affinity probe CE assay (APCE). In this project, an APCE assay for the ovarian cancer biomarker CA 125 will be developed. It is expected that very small amounts of this important biomarker may be detected via an APCE-LIF assay.

Other Interests: Music, books, nature, cuisine, tennis, movies, trips.

Home Town: Lansdale, PA

Aptamers are single stranded oligonucleotides—DNA or RNA—that are selected out of a large, random pool on the basis of a particular function. Often aptamers function as high-affinity binders to biological molecules. The process of selecting aptamers relies on repeated cycles of selection and amplification until a small number of oligos with the desired binding property dominate the pool. Selection can occur in one of two formats, on a stationary phase or in free solution. My contribution to this project is the development and optimization of a selection process based on the microscale separations method of capillary electrophoresis that will identify candidate oligos that bind to the ovarian cancer biomarker CA 125. It is hoped that such aptamers may form the basis of new detection methods for ovarian cancer.

Other Interests: Playing/teaching violin, tropical ecology, Brazil, languages, cooking, gardening, making jewelry.

Home Town: Mulhall, OK

FtsZ is a bacterial protein essential for cell division. In vivo, FtsZ assembles into a ring at the center of the cell; this ring then constricts as the cell divides in two. In vitro, FtsZ forms polymers whose stability and curvature depends on whether FtsZ subunits are GTP or GDP-bound. Controlling which nucleotide is bound to FtsZ subunits is essential to regulating the timing, localization, and properties of FtsZ structures in the cell. In vivo, a protein called EzrA prevents Z-rings from forming at incorrect locations in the cell; in vitro EzrA interacts directly with FtsZ to destabilize polymers. We are studying how EzrA affects FtsZ’s GTP hydrolysis cycle in order to distinguish between different mechanisms of polymer destabilization.

Other Interests: Batman, flip-flops, friends, tempera paint to put on the friends, Doris Day, parafilm, folk music, country music, my music, Auntie Mame, Liz Wheeler, hearty cheers, Yay!!, Teen Witch, Star Trek, orange, Those Terrible Twisters, B. C. Clark’s Anniversary Sale, the green-house gas theory of gin flavor, sopapillas, OKLAHOMA!!!, Wednesdays with Mia, King kong kitchie kitchie ki-me-o.

Home Town: South Kingstown, RI

FtsZ is a bacterial protein essential for cell division. In vivo, FtsZ assembles into a ring at the center of the cell; this ring then constricts as the cell divides in two. In vitro, FtsZ forms polymers whose stability and curvature depends on whether FtsZ subunits are GTP or GDP-bound. Controlling which nucleotide is bound to FtsZ subunits is essential to regulating the timing, localization, and properties of FtsZ structures in the cell. In vivo, a protein called EzrA prevents Z-rings from forming at incorrect locations in the cell; in vitro EzrA interacts directly with FtsZ to destabilize polymers. We are studying how EzrA affects FtsZ’s GTP hydrolysis cycle in order to distinguish between different mechanisms of polymer destabilization.

Other Interests: Viola, Classical Music, cooking, drawing, science fiction and fantasy books, Buffy the Vampire Slayer!!, movies, making jewelry.

Home Town: Livonia, MI

Surface Plasmon Resonance Spectroscopy (SPR) provides a means of detecting protein-protein interactions in real time and without the need for labels. One important application of SPR is in the context of assays to detect proteins that are biomarkers of disease. In this project, an antibody molecule that recognizes the ovarian cancer biomarker CA125 will be immobilized onto the sensing surface of an SPR instrument, creating a specific test for CA125. The SPR instrument we will be using is the miniaturized Spreeta sensor. Using this sensor, which about as large as a quarter, may enable this sensitive and selective assay to be transportable, for eventual use in clinical settings or field hospitals.

Other Interests: Hiking and generally being outside, biology and evolution, electronica, and international politics.

Home Town: The Netherlands

Around the world, pipes in historic organs are suffering from damaging corrosion that eventually causes formation of cracks and holes, robbing valuable instruments of their ability to produce sound. Organ pipes are most commonly made from lead-tin alloys, ranging in composition from pure lead to pure tin. We are studying corrosion of these alloys with the goal of learning how deterioration of organ pipes can be prevented or slowed. Specifically, we are studying how alloy composition affects the susceptibility of pipe metal to attack by acetic acid, which is emitted in appreciable quantities by the wood of organ cases.

We are using laboratory exposure experiments in which metal coupons of specific compositions are exposed to low, controlled concentrations of acetic acid vapor. The extent of corrosion is monitored through gravimetric analysis, and corrosion products are characterized using powder x-ray diffraction and scanning electron microscopy. Finally, in collaboration with the Center for Surface Analysis of Materials at Case Western Reserve University, we will use focused ion beam milling to cut cross-sections through corrosion sites, allowing chemical mapping of the corrosion products and underlying metal. Together, these methods will allow us to identify alloy compositions that are most resistant to acetic acid corrosion and to identify the role of each of the alloying elements in the corrosion process.

Other Interests: Organ building, organ design, organ playing, organ tuning, musical temperaments, travel, fitness, cooking, opera.