Research Highlights 2014


Welcome to the RIT College of Science Research Highlights page. The goal of this page is to highlight some of the college's faculty-student research projects.

Thomas H. Gosnell School of Life Sciences

Identification of three bacterial from Dioscorea sp (Yellow Yam) by whole genome sequencing and annotation


Faculty Advisor: André O. Hudson and Michael A. Savka

Student Researchers: Alexander Triassi, Biotechnology and Molecular Bioscience,

Matthew Wheatley, Biotechnology and Molecular Bioscience

Links: Faculty Website: Hudson: Savka:

Manuscript Link:

The identification of bacteria that are involved in plant growth and development in addition to plant pathogenesis are of interest in the Hudson/Savka lab. As such, we are currently investigating the role of plant-associated bacteria in a long term project using several plant species. In the plant Dioscorea sp. “yellow yam”, we have identified and sequenced the genomes of three bacteria belonging to the genus Enterobacter. Preliminary analyses from the annotated genomes suggests that the bacteria possess genes involved in the production of secondary metabolites involved in plant resistance to pathogens in addition to genes involved in the production of hormones that have an integral role in plant growth and development. Discovery and identification of the bacteria suggests a positive symbiotic relationship with the plant.  The study was done in collaboration with Dr. Han Ming Gan from Monash University in Malaysia, a 2008 graduate of the Biotechnology and Molecular Bioscience Program at RIT.   

Submission Date: March 18, 2014

 School of Physics and Astronomy

Towards A New Probe of the Distribution of Dark Matter in Galaxies

Sukanya Chakrabarti






















Faculty Advisor:  Sukanya Chakrabarti, COS Astropysical Sciences and Technology

Student Researcher:Andrew Lipnicky, Astrophysical Sciences and Technology

Galaxies contain stars, dust, gas, and dark matter.  Dark matter cannot be observed directly but we can see its impact on the surrounding matter.  Galaxies are quite large in optical light which traces the stars but radio data traces the gas in a galaxy which is much larger still.  In the above radio image of M51 the tight spiral in the center is all we can see using optical light but radio reveals many more structures including a long tidal tail. Another benefit to using radio data is that we are able to see the impacts that dark matter halos have on the outer edges of galaxies where the gas is easily influenced by perturbers.  Using large radio telescopes such as Arecibo, the Green Bank Telescope, and the Very Large Array we will obtain the masses of large spiral galaxies such as the one in the image above.  The galaxies that we are interested in are strong gravitational lenses and also close enough to use radio interferometry to map the hydrogen gas (HI). Both gravitational lensing and HI mapping give estimates for the mass of dark matter contained within a galaxy but never before have the two methods been used together. 

Submission Date: March 10, 2014

Thomas H. Gosnell School of Life Sciences

Integrin Targeted Imaging of A549 Lung Cancer Cells


Poster Presented at ASCB (American Society for Cell Biology) National Meeting-New Orleans December 2013 

Faculty Advisors:  Irene M. Evans,Thomas H. Gosnell School of Life Sciences

Hans Schmitthenner,  School of Chemistry and Materials Science

Student Researchers:  Sean Aronow  (Biotechnology),  Sarah Wang (Biotechnology with Bioinformatics Option), Yin Peng Lee  (Biotechnology, 2013 Graduate).


Irene M. Evans, Sean Aronow, Sarah Wang, Yin Peng Lee, Hans Schmitthenner, Targeted Molecular Imaging Agents for Imaging of Cancer Cells  Mol. Biol. Cell 24  (Suppl.), Abstract No. 2453.

The goals of this research are to assess the performance of new Targeted Molecular Imaging Agents (TMIAs) supplied at RIT by Hans Schmitthenner's lab. Such dyes have a role in non-invasive imaging of cancers and can be useful for detecting cancer sites in the body. Our investigations done by the undergraduate students listed above  under the direction of Irene Evans included growing, then selectively imaging the A549 human lung carcinoma cell line with three peptide dye conjugates: Cy5.5-c(RGDyK), Alexa 620-c(RGDyK) and the large Stokes shift (LSS) Dye “X-sight 640”. The targeting peptides are of the RGD family known to target the αvβ3 integrin receptors.  The dyes are near infrared (NIR) cyanine dyes related to the popular dye Indocyanine Green (ICG).   The dyes have the ability to operate in the near infrared range (NIR), and have a Large Stokes Shift (LSS). The students learned how to use confocal fluorescent microscopy to detect binding of the dye to the A549 cells. They analyzed staining patterns, and recorded fluorescent signal strength. Results with all three dyes showed cell membrane staining along with punctate vesicular dye staining, suggesting endocytosis of the dye targeting agents. The TMIA agents hold great promise for early detection of primary and metastatic cancers and should be useful in clinical imaging and diagnostics. The student's work was presented at the 2013 American Society for Cell Biology meeting held in New Orleans, LA,  December, 2013 and the abstract published in the journal, Molecular Biology of the Cell. 

Submission Date: February 3, 2014

 School of Physics and Astronomy


Measuring the size of a galactic nucleus

Faculty Advisor: Michael Richmond, SoPA, Laboratory for  Multiwavelength Astrophysics (LAMA)

Student:  Billy Vazquez, Ph.D. student in the Astrophysical Sciences and Technology (AST) program

Clouds of gas and dust orbit around a black hole at the center of many galaxies.  How far are the clouds from the black hole?  We can find out by observing these galaxies in ordinary visible light, and at infrared wavelengths.  Some visible light from the black hole's outskirts comes straight to us, and some shines into the clouds, heating them so that the dust emits infrared light. The infrared light is thus delayed, and appears as an "echo".  We measure visible and infrared radiation from galaxies and look for the time delay.

Submission Date: January 17, 2014

School of Chemistry and Materials Science


SD Spencer, C Bougher, PJ Heaphy, VM Murcia, CP Gallivan, A Monfette, JD Andersen, JA Cody, BR Conrad, CJ Collison “The effect of controllable thin film crystal growth on the aggregation of a novel high panchromaticity squaraine viable for organic solar cells.
Solar Energy Materials and Solar Cells  112, 202–208, (2013).

A description of the synthetic procedure is provided for a new squaraine molecule, DiPSQ(OH)2. This molecule is an interesting target molecule for organic photovoltaics (OPV) because of its unusually broad panchromaticity, suggesting a tighter molecular packing than would be expected, given its bulky alkyl side groups. UV-VIS-NIR absorption data provides evidence for the presence of both H- and J-aggregates. Thin Film X-Ray Diffraction (TFXRD) data supports the presence of one dominant crystal structure. Further interpretation of TFXRD results and complementary Atomic Force Microscopy (AFM) characterization for pure and blended samples provides a comprehensive explanation of how DiPSQ(OH)2 aggregates are affected by annealing and crystal growth. The described aggregation properties of donor-acceptor blends for solar cells are strongly dependent on annealing. Influencing phase separation, local crystallinity, and macroscopic crystallization, these physical properties are known to significantly impact charge dissociation, exciton diffusion rates, and bulk charge transport in devices. The strategy of systematically varying annealing times has resulted in improved bulk heterojunction crystallinity and regions of increased phase separation, both necessary to achieve the long term goal of morphological control for commercially viable NIR-active OPV devices.


A direct comparison of TFXRD intensity at 9.25° 2θ (black squares) with the relative absorbance intensity of the assigned J-aggregate peak, J-aggregate to monomer, (blue circles) in a 1:2 DiPSQ(OH)2:PCBM blend film.

(5 µm)2 AFM images of a DiPSQ(OH)2:PCBM blends that are (a) pristine and (b) annealed for 20 minutes at 150 °C. Height ranges are 29 nm and 38 nm respectively for (a) and (b). Pixel size is 9.8 nm.














Submission Date: January 17, 2014

 School of Chemistry and Materials Science


A greenhouse gas silicon microchip sensor using a conducting composite with single walled carbon nanotubes

Sensors and Actuators B 191 (2014) 545– 552

Faculty Advisor: K.S.V. Santhanam

Student Researchers: D. Olneya , L. Fullera

A new silicon substrate microsensor has been developed using a composite made of carbon nanotube andBaytron-P that senses the greenhouse gas carbon dioxide gas at 22◦C. The sensor was constructed with a Sichip by depositing the composite between two gold electrodes. Two identical Si chips were connected in aparallel configuration to reduce the initial resistance of the sensor. The resistance of the sensor decreasesupon exposure to the greenhouse gas that is proportional to the concentration of carbon dioxide. Thesensor showed a semiconducting behavior with a negative temperature coefficient. The response time ofthe sensor is about 40 s. The Fourier transform infrared spectroscopy showed peaks for the nanocompos-ite at 1056 cm−1, 1195 cm−1, 1296 cm−1, 1635 cm−1, 2083 cm−1, 2345 cm−1and 3278 cm−1. The carbondioxide adsorption on the composite results in the polystyrene sulfonate absorption band shifting from1195 cm−1to 1176 cm−1suggesting a phase separation occurring in the nanocomposite that result in theincreased conductivity.© 2013 Elsevier B.V. All rights reserved.


Carbon dioxide sensor responses to different concentrations of methane.Y = sensor response; Z = concentration. Group 1 a: CO2concentration, 390 ppm, b.Ratio of carbon dioxide/methane, c: methane concentration 1.8 ppm; Group 2 a:CO2concentration, 390 ppm, b. Ratio of carbon dioxide/methane, c: methane con-centration 4.25 ppm; Group 3 a: CO2concentration, 390 ppm, b. Ratio of carbondioxide/methane, c: methane concentration 18 ppm; Group 4 a: CO2concentration,390 ppm, b. Ratio of carbon dioxide/methane, c: methane concentration 40 ppm;Group 5 a: CO2concentration, 390 ppm, b. Ratio of carbon dioxide/methane, c:methane concentration 80 ppm; Group 6 a: CO2concentration, 390 ppm, b. Ratioof carbon dioxide/methane, c: methane concentration 100 ppm.


Submission Date: January 15, 2014

School of Chemistry and Materials Science


Efficient and Regioselective Nickel-Catalyzed [2 + 2 + 2] Cyclotrimerization of Ynoates and Related Alkynese

Faculty Advisor: Michael G. Coleman, School of Chemistry and Materials Science

Organic & Biomolecular Chemistry201311(44), 7653-7657. DOI: 10.1039/C3OB41872C

A nickel-based catalytic system has been developed for [2 + 2 + 2] cyclotrimerization of various alkynes, especially ynoates. This catalytic system enables facile construction of substituted aromatic compounds in excellent yields with high regioselectivity.

Submission Date: January 15, 2014

 School of Physics and Astronomy


Using an Elastic Tracking method to find steep tracks in the MINERvA neutrino detector

Faculty Advisor: Aaron McGowan, School of Physics and Astronomy
Student Researcher:  Andrew Carley, major in physics, minor in computer science

McGowanAndrew Carley is a senior physics major who joined the MINERvA experiment this fall through Dr. Aaron McGowan's affiliation with the University of Rochester's neutrino group. For his senior capstone research, Andrew is developing a new implementation of the elastic tracking algorithm for the purpose of finding and fitting short and steep tracks left by the passage of charged particles through the detector. While other reconstruction algorithms are successful at finding long and shallow tracks in this neutrino detector, a novel approach is required to find short and steep tracks. A successful algorithm will benefit existing physics analyses in the MINERvA experiment and allow for new analyses to be developed.

Submission Date: January 15, 2014

School of Chemistry and Materials Science


One-Vessel synthesis of iron oxide nanoparticles prepared in non-polar solvent

Faculty Advisor: Thomas Allston, School of Chemistry and Materials Science

Student Researchers: Carly Augustine Biomedical Sciences – graduated May, 2013

AlstonThis research presents a simple, reliable, and efficient method to produce a stable suspension of monodisperse maghemite (g-Fe2O3) nanoparticles that are highly crystalline and 3 nmto 3.5 nm in diameter. Particles were characterized by X-ray diffraction to determine the crystal phase of the particles and transmission electron microscopy with images used to size the particles. Iron oxide nanoparticles were synthesized through the thermal decomposition of an organic mixture of iron(II) acetate, oleic acid, and 1-octadecene, with particular emphasis on the molar ratio of oleic acid to iron content. These unique conditions produce nanoparticles with physical properties ideal for application as an automotive combustion catalyst in diesel engines and numerous other applications. The one-vessel synthesis method creates an efficient procedure to synthesize iron oxide nanoparticles readily miscible, as made, with Kensol-50H for example, or other petroleum products; producing a ready-made material for mass production with no waste in materials nor subsequent chemical work-up.

Paper Citation:  RSC Adv., 2014, 4, 5228-5235

Submission Date: January 8, 2014

School of Chemistry and Materials Science

UV photo-chlorination and –bromination of single-walled carbon nanotubes

Faculty Advisor:  Dr. Gerald A. Takacs, Professor of Chemistry

Student Researcher(s):Luciana Oliveira, MS Chemistry, Fei Lu, MS Materials Science & Engineering, Lisa Andrews, MS Materials Science & Engineering

Electron-withdrawing halogen atoms are often bonded to he surface of carbon nanotubes to assist in the conversion from metallic to semiconducting properties. Single-walled carbon nanotubes (SWCNTs) ere surface modified using UV photolysis with: (1) a broad band of wavelengths from ca. 250 to 400 nm having a maximum intensity at ca. 300 nm for photolysis of Cl2, (2) low-pressure Hg lamps emitting 53.7 nm photons for photo-decomposition of HBr, and (3) low-pressure Hg lamps emitting both 253.7 and 184.9 nm for photo-dissociation of HCl and HBr, and analyzed by X-ray photoelectron spectroscopy. Chlorine atoms adhered more readily than bromine atoms with the p-conjugation of the SWCNTs. The dominant increase with treatment was observed in the singly bonded chlorine moiety. Chlorine atoms, generated by UV photolysis of Cl2, produced a higher Cl saturation level of ca. 36 atomic % (at%) than previously observed for multi-walled carbon nanotubes (13 at%).The degree of chlorination depended on the amount of oxygen on the surface of the SWCNTs. Photo-dissociation of gaseous HCl and HBr showed lower amounts of halogenation on SWCNTs (ca. 5.8 at% Cl and 2.5 at% Br, respectively) than photolysis of Cl2.

Manuscript: Journal of Materials Research, in press (2014).

Submission Date: January 3, 2014

 School of Physics and Astronomy

Spiral phase plate characterization for optomechanics

Faculty Advisor: Mishkat, School of Physics & Astronomy

Student Researchers: Michael Eggleston (Physics), Tyler Godat (Physics), Hao Shi (Physics), Eugene Munro (Mathematics)



The spiral phase plate is an important element in modern optics as it can impart well-defined orbital angular momentum to any photon that it transmits or reflects. Spiral phase plates are widely employed in laser physics, for rotating microparticles and nanomechanical elements, in microscopy, astronomy, and in tests of quantum mechanics. We present a ray transfer matrix for a spiral phase plate. Using this matrix we determine the stability of an optical resonator made of two spiral phase plates and trace stable ray orbits in the resonator. Our results should be relevant to laser physics, optomechanics and quantum information.





M. Eggleston, T. Godat, E. Munro, M. A. Alonso, H. Shi and M. Bhattacharya, “Ray Transfer Matrix For a Spiral Phase Plate”, Journal of the Optical Society of America A, 30, 2526-2530 (2013). (Included in top ten JOSA A downloads for November 2013).


Submission Date: January 3, 2014

School of mathematical Sciences


Modeling the RIT Facebook Social Network

Longo, D.J, Brooks, B.P., (2013). Modeling the RIT Facebook Social Network, RIThink, Vol 3, 74-78.

Facebook-logoOur paper describes and analyzing the RIT Facebook network from a mathematical viewpoint. My research is in mathematically modeling the propagation of rumors over social networks. I needed the RIT Facebook network analyzed so I could have a real network to which to calibrate my artificially generated networks. My undergraduate research student David J Longo is first author. He created the algorithm that gathered the data and he performed the analysis under my direction. The funding for this research came from the National Science Foundation under Award No. BCS-0527371 where Nick Difonzo was the PI and I was a CoPI; the rumor propagation grant. 


ABSTRACT. The friendship information of Rochester Institute of Technology students was collected through a custom Facebook survey. A social network was then constructed using that friendship data. The RIT Facebook network will provide a target network to which randomly simulated networks will be calibrated in order to repeatedly conduct Monte Carlo experiments on rumor propagation through a social network.  Properties of the RIT Facebook network were analyzed with a specific focus on assorta¬tive mixing patterns of degree and similari¬ties to the neuroscience co-authorship network studied by Barabàsi. Community structure was found through the Newman modularity maximization algorithm. The flow over the RIT Facebook network of the GBN-Dialogue model of rumor transmission was explored. The RIT Facebook network was found to be best replicated by an evolving neighborhood model.

Submission Date: January 2, 2014



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