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Undergraduate Level

Primarily Undergraduate Institutions (PUI) Partnership Program

We have been collaborating for the past eight years with faculty from Morehouse, Mount Holyoke, Spelman, Smith, and Williams Colleges to provide a research opportunity for undergraduates and to provide collaboration between NSEC faculty and PUI faculty. One faculty member from Mt. Holyoke (Decatur) recently moved to Oberlin College as Dean of Science and we will continue to work with him there. Each of these colleges has outstanding undergraduate programs; the group includes two of the premier HBCUs and three of the premier women’s colleges in the U.S.  Through this collaborative effort, we have learned a great deal about how to partner with PUIs, completed some strong research, and had about 49 students (35 of them from under-represented groups in engineering ) spend time at Rensselaer. Many of the students have spent two summers involved in the project. Two of the former students are currently graduate students at Rensselaer (one from Spelman and one from Morehouse) and the majority of them have pursued graduate education. We are working on a new partnership with the University of Puerto Rico at Mayaguez and a student from UPR Mayaguez will join our summer program this year.

We budget $15K per project with about $8K/project transferring to the partner schools to cover travel, supplies, and student salary during the year. Based on assessment and discussion with partner faculty, it is clear that the students are learning a great deal, and get an opportunity to determine if they like research. This flexible program allows students to spend summers at Rensselaer or their home institution or in some cases the summer split between the two schools. We have found thatfor some projects the students are more productive if they have spent a semester or summer working at their home institution first, and for other projects, spending time at Rensselaer first works best.  We continue to try to keep the students involved for more than one year and this has been very successful when working with Morehouse and Spelman. Second, we continue to insist on an annual meeting of the faculty from the NSEC and from the partner schools early in the summer with the students present. This meeting sometimes happens face-to-face and sometimes through a conference call. This is in addition to the discussions between faculty before the students arrive for the summer.  During the first week of the summer program (Figure 1), the students give a 5 minute, 3 slide presentation of their research project. This has been an excellent way to ensure the students are clear about the goals for the summer.  Finally, we continue to develop our summer seminar series for the students that includes leadership, ethics and report writing as well as technical seminars from faculty and graduate students.

 

 

Figure 1. The 2008 PUI students and faculty meet with Prof. Schadler on the Rensselaer campus.

 

The following paragraphs give examples of the collaborative NSEC-PUI projects. Joint posters and publications resulting from the work are referenced in Section 11.5, in which undergraduates have a * after their name and both NSEC and PUI faculty names are underlined.

 

Protein Interaction with Surfaces (Decatur – Oberlin, Garcia, Dordick)

The self-assembly of polypeptide chains into bundles of nanofibrils (termed ‘amyloids’) is associated with a large number of diseases, including Alzheimer’s and type II diabetes. The mechanism of this process and the factors whichguide the self-assembly are still open questions, with significant implications in biomedical applications as well as fundamental principles of biological self-assembly. The Decatur group at Oberlin (formerly at Mount Holyoke) has synthesized many peptides, derived from naturally occurring aggregating proteins, which form amyloid fibrils in solution. One common model for self-assembly is the peptide Abeta16-22, a fragment of the Abeta polypeptide associated with Alzheimer’s disease.  This peptide forms antiparallel beta sheets, which laminate to form nanocrystallite structures.  The Decatur lab has characterized these using FTIR and X-ray fiber diffraction. Dong Zhang ’09 has introduced nitrile groups into the side chains of these peptides, and she has used the IR spectrum of the nitrile labels to probe the details of the intersheet lamination process. This year, she has been building models of the laminate structures at RPI in collaboration with the Garcia laboratory based on her IR data. Her work follows on Priscilla Yohuno’s ’08 work studying the stability of H1 aggregates using both experiment and MD modeling in Garcia’s laboratory.

 

First Principles Chromophore Formation in Green Fluorescent Proteins (Cardelino Spelman, Nayak)

 

Green fluorescent protein (GFP) is widely used as a genetic marker and biosensor. Its ability to catalyze the synthesis of its fluorescent chromophore (p-hydroxy-benzylidene-imidazolidone) from a three residue segment of its amino acid sequence (Ser-Tyr-Gly, SYG), without the use of additional enzymes or cofactors, makes it portable into any organism. Understanding this autocatalyzed reaction would fill a void in our knowledge and at the same time it would unlock the potential for the design of novel proteins with the ability to synthesize intrinsic chromophores.  Using first principles density functional method and gradient corrected approach, we have studied the initial steps of chromophore formation. Specifically, we have studied the initial cyclization step, which involves the carbonyl carbon and peptide nitrogen forming a ring structure that is a critical component for chromophore fluorescence. Starting with the uncatalyzed reaction (Figure 2), we found that carbonyl oxygen on the intermediate ring must be protonated in order to form a stable intermediate state.  The estimated energy barrier for this reaction is 14 kcal/mol with protonation (Figure 3). Without protonation of this oxygen, the ring structure opens up and returns to the initial reactant state.  This step will help in understanding which amino acids may be used for catalytic steps along the reaction path.

 

 

Figure 2. Atomic structure (left) and electronic density (right) for the GFP triad (Thr-Tyr-Gly) with catalytic groups Arg and Asp. Using density functional theory (DFT), the threshold of structural rearrangement for the catalytic side chains will be tested and used as input for determining suitable and new protein structures that may incorporate the fl uorescent triad. Three water molecules are included in the calculation. 

 

Figure 3. Energy profile for ring closure reaction, indicating protonation is necessary for a stable intermediatering structure.

 

Characterization of Metal Encapsulated Multiwall Carbon Nanotubes (Ravi – Spelman, Schadler)

This new project this year focused on the characterization of metal encapsulated multiwall carbon nanotubes using X-ray diffraction and electron microscopy. Transition/rare earth metal encapsulated multiwall carbon nanotubes were synthesized by the pyrolysis of hydrocarbon using an intermetallic alloy as the catalyst. While electron microscopy confirmed the presence of the nanotube structure (Figure 4), X-ray diffraction data indicate encapsulation of metal atoms in the tube. Diffraction peaks corresponding to the metals are seen in addition to conventional peaks due to carbon.  From the characterization studies of the materials prepared at different conditions, it is concluded that encapsulation is possible only when the operating temperature is above 900C, but below 1000C.  This project resulted in a presentation at the National Society of Black Physicists in Nashville, TN, February 10-13, 2009 by Jasmine Hargrove. This past summer was primarily spent training Jasmine on microscopy and the X-ray diffraction equipment, teaching her the fundamentals behind the techniques and gathering preliminary data. In the future, she will complete a more comprehensive study of the structures of the tubes under different processing conditions.

 

 

Figure 4. A TEM micrograph of nickel encapsulated in multiwall carbon nanotubes.

 

The Structure of Water on Nanoscale Surfaces (Queeney – Smith, Schadler)

 

For cells to adhere and grow on a surface, it has been shown that pre-adsorption of proteins is an essential fi rst step. The amount of adsorbed proteins on a surface will, to some extent, determine the quantity of cells that will adhere. Certain qualities of a surface promote increased protein adsorption that leads to cell adherence. Experimental data suggest that proteins adsorb in greater amounts to various oxide surfaces with nanoscale, rather than conventional micron-scale, features.  This study focuses on the size-dependent surface chemistry of α-alumina. Specifically, we have examined the hydroxyl groups on this surface and their relationship, if any, to particle size.  Alumina (aluminum oxide) is a ceramic that has many phases, of which α-alumina (commonly known as corundum) is the most stable. The goal is to look at differences in the surface chemistry and determine if smaller particles, specifically nanoscale alumina particles, promote the adsorption of proteins better than larger, conventional sized particles. By depositing alumina particles of varying sizes on substrates cut from silicon wafers, transmission infrared (IR) spectroscopy can be used to look at the different hydroxyl groups that are on the surface of the alumina particles.  IR spectra taken show a defi nitive difference in the hydroxyl groups of silicon wafers that have been coated with 0.9-2.2 μm (conventional) particles and those that have been coated with 27-43 nm (nanoscale) particles. The smaller particle size has a higher relative intensity than the larger particle size.  This suggests that there is a different distribution of hydroxyl groups, depending on the size of the particles.  The difference in surface chemistry as a function of size may therefore be influenced by the distribution of hydroxyl groups on the particle.

 

Undergraduate Nanotechnology Research

We have hired 7 undergraduates from UIUC and RPI to conduct research inside the Center this year. These are in addition to students involved in the partnerships with PUIs. These students were closely allied with NSEC research and in several cases their work has resulted in excellent publications.


Ekandrea Miller, a junior in Chemical Engineering at UIUC, synthesized fluorescently dyed silica microspheres and characterized them using scanning electron microscopy under Prof. Lewis's guidance. In her work she developed a method to scale up colloidal synthesis to create large volume batches. She further studied the effect of a comb copolymer dispersant on the stability of colloids as a function monovalent salt additions. She characterized the coated particles using zeta potential measurements, and imaged the resulting colloidal structure with confocal laser scanning microscopy.


Evelyn Huang, a Junior in Materials Science and Engineering at UIUC, worked on peptide-directed membrane reconstructions under the guidance of Prof. Wong. In collaboration with a graduate student mentor, she measured how deeply a prototypical class of antimicrobials embed themselves in membranes of different composition. This is an important determinant of how much the membrane initially thins, and whether the membrane thus restructured can undergo addition self assembly. To do this, Evelyn had to learn to analyze the scattering form factor of membrane vesicles with high and low cholesterol content at a synchrotron. We anticipate that these results will be published this year.


Meghan McKelvey, a Senior in Materials Science and Engineering at UIUC, explored various methods to synthesize and functionalize magnetic iron oxide nanoparticles of different shapes under the guidance of Prof. Shim. In addition to UV-Vis spectroscopy and other chemical analysis, she worked with a graduate student mentor to characterize the nanoparticles with transmission electron microscopy. She successfully synthesized nearly spherical and cubic shaped nanoparticles and exchanged their surface capping molecules to achieve water soluble nanoparticles.


Arianne Collopy, a Sophomore in Physics at CalTech, under the guidance of Prof. Braun studied the effect of exposure dose on the formation of holographically defined photonic crystals. She used optical microscopy and FTIR microscopy to characterize the optical properties of these holographic structures, and was able to identify the parameters necessary to reproducibly fabricate the photonic crystal structures.


Dan Scheffler, a Junior in Materials Science and Engineering at RPI, under the guidance of Prof. Schadler and senior NSEC graduate student Doug Dukes, is processing lead zirconium titanate nanoparticles for use in polymer nanocomposites. He uses microscopy and dynamic light scattering to characterize the nanoparticles.


Shannon Johnson, a Junior in Materials Science and Engineering at RPI, under the guidance of Prof. Schadler explored the use of high energy lasers to break up agglomerates of InSnO nanoparticles. She worked with a graduate student to characterize the size of the particles as a function of laser power, nanoparticle concentration, and time. The work resulted in a poster presentation at the Fall 2008 MRS meeting.


Nicolas Profita, a Junior in Information Technology at RPI worked with the NSEC and our Molecularium(R) Project under the guidance of Prof. Siegel on implementation of new Web sites.