Shannon Summer Research Institute

A Temperature Control Stage for Deposition of Thin Metal Films

Today’s technology requires the use of metal films with thicknesses of only a few hundred nanometers or less. The properties of materials this small depend heavily on the history of the film and observations disagree with existing models. For instance, slight changes in the temperature at which the film was produced result in a completely different microstructure and, consequently, different mechanical and electrical properties. Much research is needed to explain this. While small temperature control stages are widely available, they are unable to provide a uniform, constant temperature throughout an entire 10 cm diameter film during deposition of hot metal. Therefore, Houghton University students Owen Fall and Luke Yelle worked alongside Dr. Brandon Hoffman to develop a temperature control stage for the deposition system that produces their films. A test chamber was set up and several experiments were conducted with different adhesion materials for mounting the sample to the stage. Silver paint performed much better than other options.

Brandon Hoffman
Professor of Physics

Low Temperature Detectors for Nuclear Safeguards

Ensuring that all nuclear material globally remains in peaceful activities like nuclear power and nuclear medicine is a multidisciplinary problem that requires constant innovation. In SRI 2022, Dr. Katrina Koehler and her student, Tim Ockrin, went to Los Alamos National Laboratory in Los Alamos, NM, to develop data analysis tools for ultra-high energy resolution low temperature detectors. With these detectors, the composition of special nuclear material can be determined more accurately, which could allow the International Atomic Energy Agency to determine whether the material has the same composition as declared. During this summer, the software tool Decay Energy Spectroscopy Analyzer (DESA) was developed to analyze uranium materials and correct for detector pathologies.

Katrina Koehler
Assistant Professor of Physics

Modeling and screening aggregation inhibition of amyloid-beta peptides by small molecules as potential drug candidates

Evan Kasper, Lydia Lagree, Emma Ryan, and Paul Martino, PhD

1. Optimization of conditions for performing photo-induced crosslinking of unmodified peptides (PICUP) experiments on Aβ42.  The peptide Aβ42’s aggregation into senile plaques is one of the Hallmarks of Alzheimer’s disease.  The aggregation process is a complex equilibrium comprised of many stabilized oligomeric states. In order to study the metastable distributions of varying oligomeric sizes, a fast photo-induced crosslinking is initiated to “freeze” the oligomeric distributions into a static state that can be measured using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) via silver staining and densitometry.  Dose-dependent aggregation inhibition by drug candidates was measured including a study with regorafenib.  Regorafenib is a current FDA approved cancer drug that was found by our work during SRI 2021 to inhibit Aβ42 aggregation.  A publication is currently in draft for this work.  Our results also indicated a clue to the potential binding site of Aβ42 because we were able to detect what appears to be competition between zinc-cations and regorafenib.  The zinc-cation binding site had been solved previously by NMR spectroscopy. This will lead to more investigations in our future.
2. Minimization of interferences during circular dichroism spectroscopy (CD) measurements.  CD experiments were attempted during SRI 2021 because they are a measure of protein secondary structure. It is widely accepted that Aβ42 undergoes a change in secondary structure  (from α-helical to β-sheet) as a requirement to aggregate.  Our CD measurements of Aβ42 (from SRI 2021) did indicate a dose-response from treatment with micromolar concentrations of regorafenib, though our data were unreliable due to interferences stemming from our solvent used for the drug (DMSO).  To rectify this issue, our CD measurements were repeated using lower concentrations of both Aβ42 and regorafenib (and consequently, DMSO) in order to generate high quality CD data.  Our efforts paid off and we were able to show a dose-dependent relationship between regorafenib and Aβ42.
3. Carbene labelling Aβ42 in the presence and absence of regorafenib.
   Due to its amphiphilic nature and high propensity for aggregation, Aβ42 has proven elusive to label using our protocol for carbene labelling that we have optimized over the years.  We continued to make minor adjustments and we were moderately successful at generating mass spectrometry data for Aβ42 in the presence of regorafenib.  Unfortunately, in the absence of regorafenib, the carbene labelling appears to increase Aβ42’s propensity to aggregate causing clogging of HPLC columns and electrospray emitters. More work needs to be done here, perhaps using a truncated form of Aβ42, now that we suspect that Aβ42 binds regorafenib at the putative zinc-cation binding site (at the N-terminus).
4. Molecular docking simulations using AutoDock Vina (Scripps Institute, La Jolla, CA) to screen for target Aβ42 binding by kinase inhibitors.  Several kinase inhibitors that were mined from literature were screened using AutoDock Vina for their ability to bind to an aqueous monomeric Aβ42 structure (PDBid: 6SZF).  This work needs to be expanded as we now have a list of 88 kinase inhibitors that currently meet FDA or EMA approval as cancer drugs.

Paul Martino
Professor of Chemistry

Investigating the Bacterial Community within the Sarracenia Purpurea Pitcher at Moss Lake Nature Preserve

Sarracenia purpurea are native to wetlands and bogs throughout the eastern United States and southern Canada. The pitcher cup shape of the “leaves” provides a unique habitat to study a contained microcosm of microorganisms, including aquatic invertebrate larvae, protozoa, bacteria, and invertebrate prey. The bacterial communities, specifically, play an essential role in aquatic food web dynamics as the pitchers develop. Nutrients from captured insects are obtained through decomposition by aquatic invertebrates and microbes in the pitchers. The ability of bacteria to decompose pitcher contents depends on the abundance of protozoa and rotifers in the trophic level, the presence of the key predator, the mosquito larvae Wyeomyia smithii, and likely other microbial members. Published research has learned much of the micro-invertebrate population, however the bacterial population and its role in establishment and maintenance of the community is still relatively unknown. Recent data has given only preliminary information on the diversity of bacteria within the micro-habitat. Our research addressed the biochemical characteristics as well as the change in the bacterial population among pitcher plants at different stages of growth. Samples were collected from older pitchers and newer pitchers at the same time points and characterized for their abundance, morphological, and biochemical characteristics. Further knowledge of the organisms and their morphological and biochemical properties will provide a greater understanding of the community dynamics of the microcosm and the broader scope of community ecology

The investigators are Samuel Calkins, Jessica Keeran, Mary Shaker, and Jamie Potter, PhD

Jamie Potter
Associate Professor of Biology

Development of a Green Oxidation Method for Alcohols

Professor of Chemistry, Karen Torraca, worked with Skye Chaapel and Abigail Young during the summer of 2022 toward the development of a “green” synthetic method for the conversion of alcohols to ketones or aldehydes.  The current standard synthetic processes require large amounts of heavy metals and generate a lot of hazardous environmental waste.  Although there is a strong research emphasis across academia to develop better oxidation processes, very few new processes have been implemented in large-scale manufacturing due to the cost of the specialized reagents required, the reactivity of the reagents required, and/or the lack of robustness of the process required in a manufacturing setting.  During the course of the summer we were able to examine various reaction conditions including the use of green solvents, transition metal catalysts, and additives.  With optimized reaction conditions employing propylene carbonate as the solvent, we were able to apply the method to a variety of alcohols as well as successfully increase the reaction scale by 10 times.

Karen Torraca
Professor of Chemistry

How to catch stardust: simulating an ICF implosion

It is very hard to study the nuclear reactions that could take place in the core of a star, but one possible way, which has never before been attempted, is to create a tiny star, lasting for only a fraction of a nanosecond, and then collect the radioactive nuclear reaction products produced at its core.  This can be done using inertial condiment fusion (ICF) with the OMEGA laser at the Laboratory for Laser Energetics (LLE), which has sixty high power lasers that strike a tiny target capsule from every direction, heating and compressing it until nuclear reactions begin to occur.  By doping this target capsule with various materials, a range of light-ion reactions could be studied.  To test this idea, physics professor Mark Yuly and Houghton students Adam Brown, Andrew Hotchkiss, Chunsun Lei and Andrew Martin carried out an experiment to simulate this process, allowing them to test their detector system and work out unforeseen problems before attempting an experiment at LLE.  To do this, they worked with faculty and students form SUNY Geneseo to use the SUNY Geneseo Pelletron accelerator to accelerate deuterons into a lithium target.  Using the electrical energy stored in a bank of capacitors, they then vaporized the now radioactive activated lithium, collected some of the expanding gas, and detected the radioactive decays of the lithium.  Since the half-life of lithium-8 is only 840 milliseconds, the entire experiment lasted only a few seconds (but we did it more than once!) and successfully showed such an ICF experiment is feasible.

Mark Yuly
Professor of Physics

ImageNet Large Scale Visual Recognition Challenge

ImageNet Large Scale Visual Recognition Challenge (ILSVRC) is about large-scale visual database but for image recognition. In order to cope with ILSVRC, embedded image system on Jetson Nano platform has been implemented since SRI-2021. However, advanced-level intelligence capability, as well as human being’s nerve systems, requires the construction of both convolutional neural network (CNN) and deep-learning neural network (DNN) in the machine (Jetson Nano platform). Hence, we have implemented the embedded object detection system on the Jetson Nano platform in SRI-2022 and have contributed three things into the 2022’s summer research. The first thing is the implementation of the conversion from facial detection to facial recognition. Since SRI-2021, real-time facial detection has been implemented. Unlike facial detection, facial recognition not only works to detect where human’s facial area is in an image, but also identifies the person by reading the image’s human face. The second thing is making the image recognition broadens the scopes in object recognition like vehicles, vegetables and fruits. However, to concentrate the recognition accuracy, image recognition limits to identify ONE object in an image. For the intelligent needs, in the construction of Convolutional Neural Network, basically, four libraries – “alexnet”, “googlenet”, “resnet-18”, and “resnet-50” are experimented for testing the performance of the image recognition. The third thing is the exploration of using DNN for understanding the image with the complexity combined with many different types of objects like fruits combo or animal zoo. Thus, we have conducted experiments using one of DNN neural networks, which is MobileNet. After result analysis, the conclusions are drawn below:

• Animals with high confidence values are easier to be recognized.
• If animal types like dog, cat and bird are written in COCOnet (mobilenets), it has high likelihood for them to be detected.
• In future work, we have two directions to go, which are listed below:
• The exploration of the architectures of both CNN and DNN from perspective of stabilization and high performance of prediction accuracy.
• Further decipher the differences between image recognition and object detection.

The research team included Meshek Soren, Gabriel Lucena, and Jie Zhao, PhD.

Jie Zhao
Assistant Professor of Electrical Engineering

Quality assessment of Bible translations via textual similarity and entailment measurements through cross-lingual models

We identified optimal transformer-based natural language processing (NLP) models for textual similarity and entailment in Swahili. Additionally, we fine-tuned an NLP model for contradiction generation, both in Swahili and English. These models were then applied to Swahili back-translation texts and Swahili Bible translations to develop a dataset of labeled paired sentence of Biblical-style texts that provide a wide-range of textual similarity and entailment scores. This dataset is to be human scored and used for the development of quality assessment tools for future Bible translation work within SIL International. This research by Christianna Fisk and Benjamin Marmor was a collaboration between Houghton University and SIL International.

Brandon Bate, Assistant Professor of Mathematics

Laser Interferometer and X-ray Diffractometer for Experimental Study of Thin Metal Films

Computers, electronics, and optics make use of metal films that are nanometers thick. As these films heated and stressed repeatedly, their mechanical and electrical properties change in unpredictable ways. Physics Professor Brandon Hoffman and Houghton students Nathaniel Davie and Noah Klein are developing equipment that will be used to study such films and learn how and why they act the way they do. Once completed, the phase-stepping laser interferometer will measure mechanical stress in the films. The x-ray diffractometer will measure the film microstructures. Combined with information from the electron microscopes in the lab, these measurements will enable us to model the films and predict how they will respond when heated and stressed.

Brandon Hoffman, Professor of Physics

Screening FDA Approved Drugs to Repurpose for the Treatment of Alzheimer’s Disease

It is well established that it is more propitious to repurpose existing medication that already meets FDA approval than it is to synthesize drugs de novo to see through to market. With this in mind, a team of five undergraduates and one recent graduate from Houghton University embarked on ten weeks of research to find and screen for such drugs as potential to repurpose and for treatment of Alzheimer’s disease (AD).

The work was multidisciplinary and involved two faculty members as co-PI’s in biochemistry and data science and in addition to being a part of SRI, was externally supported by Robert Van Dyk. The work involved mining drug information from databases; simulation of molecular docking of drug candidates to amyloid-beta (a major player in AD pathology); in-vitro measurements of drug inhibition of amyloid-beta aggregation (a putative early step in AD pathology) by using a battery of spectroscopic techniques; mass spectrometry measurement of amyloid-beta/drug candidate binding sites (to better understand the drug's action); and in-vivo screening for reversal of modeled AD phenotype in C. elegans (to see how well it works).

Students uncovered that a drug with FDA approval for fighting metastatic cancers appears to also possess both simulated and measured activity that could be used to treat AD. This work will continue through the summer of 2022.

Paul Martino, Professor of Chemistry

Biology: Identification and Characterization of the Bacterial Microcosm of Sarracenia purpurea, Northern Pitcher Plant

To understand the diversity and colonization of the Northern Pitcher plant by bacteria found in the sphagnum moss bog of Moss Lake in Caneadea, NY, two Houghton University students, Kathryn Paschalis and Kenneth Estep, worked alongside Dr Jamie Potter (Biology) in the identification and characterization of the Sarracenia purpurea microbial community found in the pitchers of these plants. Preliminary research has characterized 67 bacterial species based on morphological and biochemical analysis, and continued research is needed to fully characterize the entire bacterial community and obtain species-level identification. Morphological, biochemical, and molecular methodologies were used to characterize 54 unique organisms. Further research on these isolates is in progress to determine the 16S RNA signature of the bacteria as well as continued sampling at different stages of pitcher development.

Jamie Potter, Associate Professor of Biology

Assessing the Effects of Electrical Stimulation on Protein Expression During Wound Healing in Vascular Smooth Muscle

In an effort to examine the therapeutic potential of electrical stimulation (ES) on wounded smooth muscle tissue, Gavin Luckey and Malachi Yeager expanded on previous work by examining several variables that might contribute to wound recovery efficacy. They explored the effectiveness of ES on recovery by performing scratch wound healing assays in rat aortic smooth muscle cell culture with and without ES. They coupled this with SDS-PAGE analysis to see if ES had any effect on protein levels.

Ransom Poythress, Associate Professor of Biology

Convenient Synthesis of Biodegradable Glycopolymers via Thiol-Ene Coupling

The surface of a cell is covered with glycoproteins, key molecules for cell-cell signaling, virus recognition, and other host-pathogen interactions. This summer, Marjorie Thornton and Peter Hwang worked on developing a convenient method for creating synthetic plastics that could mimic cell surfaces. Specifically, the desired materials were both biodegradable and readily covered with covalently bound glycoprotein mimics. These biodegradable glycopolymers have a multitude of biotech applications ranging from targeted drug delivery to implantable medical devices. Their synthetic approach utilized photo-initiated thiol-ene click reactions and air-free, zinc-catalyzed polymerization.

John Rowley, Associate Professor of Chemistry

Cost-Effective Bead-Pull System Development at Houghton University

Bead-pull system has been widely used in radio frequency (RF) cavity resonator measurement for high power particle accelerator application. The bead-pull system requires dedicated resources such as vector network analyzer (VNA), motor controller, data acquisition system, and automation software. In Summer 2021, we carried out an engineering design project of developing cost-effective bead-pull measurement system for Houghton University. Three Houghton University Engineering and Physics students, Louis Schriver, Joshua Wilson, and Matthew Bowman, were engaged in following design activities with Engineering Professor Ki R. Shin - 1) Motor control system development with data acquisition board and regulator circuit, 2) Electromagnetic and mechanical design of reference cavity model for RF model correlation work, 3) Measurement automation of VNA equipment with LabVIEW software.

Ki R. Shin, Assistant Professor of Electrical Engineering

Simulating ICF Implosions: The Exploding Wire Experiment

The nuclear processes that would occur in the core of a star or in the big bang are very hard to study – for obvious reasons! One way we might be able to learn about them is to create our own tiny star, using a process called inertial confinement fusion (ICF). The resulting nuclear reactions can be measured by trapping the reaction products and detecting their radioactive decays. To test this idea, Physics Professor Mark Yuly and Houghton students Micah Condie, Adam Brown, and Micah Christensen have designed an “exploding wire” experiment to simulate the expanding gas released in an ICF event. In this experiment, a copper plated tungsten foil was inserted into a vacuum chamber and activated with a deuteron beam using the SUNY Geneseo Pelletron accelerator. A current pulse through the tungsten then vaporized the copper to create an expanding radioactive gas, which was captured in a trap and detected.

Mark Yuly, Professor of Physics

The Implementation of the Embedded Image Recognition System on the Jetson Nano Platform

Image process and image recognition play an important role in AI implementation. For example, the image recognition with AI could make computer vision more intelligent. Traditionally, the image recognition relies on the high-performance computers, due to its requirement of high-dimensional computation. With the development of industry automation and remote sensors, however, the new generation of the image recognition is required to become an embedded system with the properties of being portable and light-weighted, catering to broader realms of research and applications. In order to implement embedded image recognition, in SRI 2021 Dr. Zhao Jie, and her students, Jonathon Zdunski and Benjamin Dostie, have considered two factors both from hardware and software, and ultimately they have chosen Jetson Nano as the platform of the embedded image recognition. In order to practically implement the image recognition in Jetson Nano, two types of cameras, stational Raspberry Pi camera and dynamic webcam, are installed in the Jetson Nano platform to capture any objects in front of the cameras. Furthermore, in order to make camera capture more precise, OpenCV with AI libraries are used to code for object tracking. After configured and tested, the embedded image recognition with AI Jetson Nano platform is proven to work well in developing object tracking and facial recognition. The implementation of Jetson Nano image recognition system is a good start to research on the embedded image recognition systems.

Jie Zhao, Assistant Professor of Electrical Engineering

Physics: Using X-Ray Diffraction to Study Imperfections in Thin Silver Films

Physics Professor Brandon Hoffman and four Houghton University students will be collaborating with Shefford Baker at the Cornell Center for Materials Research (CCMR) at Cornell University to study thin silver films. Today’s technology requires the use of metal films with thicknesses of only a few hundred nanometers or less. The properties of these films are greatly affected by imperfections that form in the crystal structure when the film is produced. One common imperfection, called a stacking fault, has been shown to be a driving force for the growth of large crystal grains in the film. However, models describing how stacking faults form and precisely how they affect the growth of grains are incomplete. This summer, thin silver films will be produced in a high vacuum deposition chamber and characterized by X-Ray Diffraction (XRD) in order to study stacking fault formation and its effects on crystal grain growth.

Biochemistry: “Spray-Painting” Biological Molecules to Understand Their Structure

Biochemistry Professor Paul Martino and Houghton University students Ellirose Edwards ’20, Hyeok Kim ’21, and Gavin Luckey ’22 will be working on developing new methodologies for the structural study of biological molecules. Techniques involving x-ray crystallography and nuclear magnetic resonance spectroscopy have long played major roles in the study of biomolecular structures. Recent advances in mass spectrometry using hydrogen-deuterium exchange rates in order to probe structure have shown great promise. This team of investigators will be studying a novel method involving rapid carbene gas labeling of biomolecules followed by mass spectrometry in order to measure structural features. The technique is analogous to spray-painting folded paper, then examining where the paint is and isn’t to infer how the paper was folded. Once developed, the technique will be utilized to examine structures that have eluded existing methods, such as early events in amyloid aggregation. The work will primarily be accomplished at Houghton University, although some work may be accomplished at the University of Rochester biological mass spectrometry facility.

Biology: Studying Bacteria Hosted by the Northern Pitcher Plant

Jamie Potter, Assistant Professor of Biology, will be working with two Houghton University students on identification and characterization of the Sarracenia purpurea microbial community. Preliminary research has characterized 75 bacterial species based on morphological and biochemical analysis. Continued research is needed to fully characterize the entire bacterial community and obtain species-level identification. Furthermore, questions remain on the ability to identify organisms that are not culturable by standard techniques or that exist in a purely symbiotic relationship with another organism where the individuals cannot be isolated into pure culture. The goal of this project is to develop molecular methods to provide genetic information on each microbe, based on 16S RNA sequencing of the unique signature of the 16S ribosome in prokaryotes.

Biology: Backpacking the Pacific Crest Trail to Assess Biodiversity

Aaron Sullivan, Associate Professor and Chair of the Department of Biology, will work with Ian Kratzer ’21 in a study to assess avian and herpetofaunal biodiversity along an approximately 500-km section of the Pacific Crest Trail (PCT) in the Sierra Nevada mountains of California. The PCT is a 4,265-km trail that extends from Mexico to Canada and passes through a variety of ecosystems. The goal of this study is to contribute to an overall project to utilize the PCT as a transect that can serve as a ‘barometer of biodiversity,’ facilitating a long-term assessment of animal distributions as well as possible altitudinal and latitudinal shifts in response to climate change. The collaborators will include the megatransect project originator and coordinator, Mike McGrann from William Jessup University; faculty from other institutions within the CCCU; and members of state entities. The project aims to document, predict, and explain patterns in biological diversity as well as to inform conservation planning. Student participation will include backpacking along the trail in 160+ km segments, as well as project planning and logistics, data collection and analysis, and writing for scientific publication. The researchers will participate in the various aspects of the megatransect project during the 2019 field season including avian point count surveys, habitat assessment, and eDNA collection over the course of the six-week project.

Physics: Observing Nuclear Fusion Reactions Generated by High-Powered Lasers

Houghton students Tyler Kowalewski ’21, Sonny Ferri ’21, and Steven Raymond ’20 will be working with physics professor Mark Yuly and a collaboration of scientists from the State University of New York at Geneseo (SUNY Geneseo) and the University of Rochester Laboratory for Laser Energetics (LLE) on a project to develop techniques for using inertial confinement fusion (ICF) to study fundamental nuclear science.  In the ICF process at LLE, 60 extremely high-powered lasers deposit a large amount of energy into a small pellet of nuclear fuel, triggering a nuclear fusion explosion that releases energy and radiation.  Our team is developing techniques to collect the expanding neutral gas after the laser shot and detect the radioactive decay of the trapped reaction products.  Many of the nuclear reactions that could be determined this way have never been measured before, yet are important for understanding models of nucleosynthesis and in thermonuclear fusion energy research.

Biology: Evaluating Alternatives to Animal Research

Rebecca Williams, Assistant Professor of Biology, will be collaborating with Houghton students Catie (Mary) Moore ’21 and Caitlyn Cybart ’21, on a project designed to explore the use of human stem cells as an alternative to animal research. They will be working with faculty and students at the University of Windsor this summer, and anticipate continuing the research from Houghton during the next school year. The team will be working with 3-D organoid models, which use human stem cells to re-create organs with physiological features similar to organ systems in complete bodies. Applications include cancer and epithelial research, drug screening, and disease modelling. While organoid research cannot necessarily answer all questions regarding whole body outcomes, organoids offer a more ethical alternative to animal research, whilst still providing valid results. The use of organoids for testing and research furthers supports the use of stem cells in medicine, and is a more sophisticated system than simple cell culture, which relies on a 2-D matrix and not a whole organ.

Paul Martino, professor of biochemistry, and Houghton University students Ellirose Edwards and Sahara Javnerwill be working this summer on developing new methodologies for the structural study of biological molecules. Techniques involving x-ray crystallography and nuclear magnetic resonance spectroscopy have long played major roles in the study of biomolecular structures.  Recent advances in mass spectrometry using hydrogen-deuterium exchange rates in order to probe structure have shown great promise. This team of investigators will be studying a novel method involving rapid carbene gas labeling of biomolecules followed by mass spectrometry in order to measure structural features. The technique is analogous to spray-painting folded paper then examining where the paint is and isn’t to infer how the paper was folded. Once developed, the technique will be utilized to examine structures that have eluded existing methods, such as early events in amyloid aggregation. The work will primarily be accomplished at Houghton University, although some work may be accomplished at the University of Rochester biological mass spectrometry facility.

Kurt Aikens, assistant professor of physics, and Houghton University students Josiah Kratz and Jared Malone will be working to better understand the mixing performance of impellers that are operating in the transitional flow regime. This regime is in between smooth laminar flow and chaotic turbulent flow. To study the impeller mixing process, computer simulations will be performed using local computing resources, non-local supercomputing resources, and industry-leading software. This research builds on work completed last summer, where reasonable results were obtained for a canonical mixing scenario. This summer, the work will focus more specifically on transitional flow cases that have proven difficult to computationally predict. Additional simulation strategies may be utilized in an attempt to improve results. For example, Aikens, Kratz, and Malone may test alternatives to the multiple reference frames model that is commonly used in industry. The described work will be completed in collaboration with Prof. David Foster from the University of Rochester – an expert in this area of chemical engineering – and engineers at SPX Flow in Rochester.

Kelsey Barrus and Jacquelyn Lewis, biology majors at Houghton, will be working with Jamie Potter, associate professor of biology, in collaboration with Keith Perry at Cornell University, on the detection of grapevine leafroll-associated viruses (GLRaV) in wild and cultivated grapevine (Vitis sp) in Allegany and Cattaraugus counties, and the assessment and optimization of viral RNA extraction and stabilization methods. Due to the nature of viral RNA in grapevine, rapid degradation of the nucleic acid is prominent and thus current methods must be optimized to allow for greater stabilization for subsequent testing and identification. Grapevine leafroll disease (GLRD) is a significant source of cultivar loss and quality degradation in vineyards and is transmitted to the plant by cross-contamination of equipment, grafting, or insect vectors. The treatment of virally infected cultivars requires removal of the entire plant, resulting in a five to seven-year year loss for cultivated vines to produce grapes at maximum capacity again. Because of its significant impact and continued rapid spread among vineyards, epidemiological studies of GLRaVs and optimization of available techniques are needed to further development of control and prevention techniques for GLRD caused by GLRaVs.

Aaron Sullivan, associate professor and chair of the Department of Biology, and Emilia Gildemeister ’18, Lexie Reitler ’20, and Anna Trimble ’21 will spend the summer examining chemically mediated predator-prey interactions among amphibians and reptiles. More specifically, they will focus on the potential for salamander prey to identify new threats, as the capacity to recognize and assess predators via chemical stimuli may be especially beneficial for amphibians, whose populations are declining globally. The ability to learn to identify new predatory threats is especially advantageous, as introduced species can have a pronounced impact on local fauna. Through a series of experiments, an effort will be made to condition Allegheny Mountain Dusky Salamanders (Desmognathus ochrophaeus) to associate non-predatory Smooth Greensnakes (Opheodrys vernalis) with stimuli from predation events (e.g., damage-released cues, snake kairomones), and to quantify factors that contribute to the magnitude and duration of the learned response.

Ransom Poythress, assistant professor of biology at Houghton University, will be working with Kirsten Blakesleeand Keegan Frenya to assess the effects of electrical stimulation on wound recovery in smooth muscle. Despite its broad and varied use as a therapeutic modality in skeletal muscle recovery, the effects of electrical stimulation on other systems remain largely unknown. Poythress, Blakeslee, and Frenya will examine the efficacy of electrical stimulation in scratch wound healing assays in cultured rat aortic smooth muscle, as well as assess changing protein expression by western blot and LCMS. They will also be examining changes to inflammatory response and cytokine release through ELISA analysis. Finally, the research team will use Biopac force-transduction measurements in conjunction with live tissue organ baths to explore real-time effects of electrical stimulation on amphibian smooth muscle in response to injury.

Houghton students Katelyn Cook, Emma Bruce, and Sarah Hull will be working with physics professor Mark Yuly and a collaboration of scientists from State University of New York at Geneseo (SUNY Geneseo) and the University of Rochester Laboratory for Laser Energetics (LLE) on a measurement of the cross section for the ³H(t,g)⁶He radiative capture reaction. LLE is one of the largest laboratories in the world for studying inertial confinement fusion (ICF). At the facility, 60 extremely high-powered lasers deposit a large amount of energy into a small pellet of nuclear fuel, triggering a nuclear fusion explosion that releases energy and radiation. For this experiment, some of the expanding neutral gas after the laser shot will be captured with a turbo pump and a specially designed phoswich detector will count the number of ⁶He decays. This reaction has never been measured at any energy, even though it is a light nucleus reaction occurring in all DT plasma thermonuclear fusion research and is important for an understanding of nucleosynthesis in big bang models of the early universe.

Brandon Bate, assistant professor of mathematics, and Houghton University students Caleb Lyon and Nathaniel Parks will be working on classifying coadjoint orbits for the unipotent radical of minimal parabolic subgroups for the special linear group of n by n matrices. Preliminary research will focus on developing a computer program to perform this classification for given n. Data generated by this program will have applications to the theory of automorphic forms on higher rank groups leading to a detailed description of corresponding Fourier series expansions. Via the Kutznetsov trace formula, such expansions may prove helpful in better understanding the spectral theory of automorphic forms, an active area of research in number theory. Their research will also focus on determining, if possible, an explicit classification of such coadjoint orbits.

Brandon Hoffman, associate professor of physics, and Houghton students Sarah Olandt and Daniil Zhuravlev will collaborate with Shefford Baker at the Cornell Center for Materials Research (CCMR) at Cornell University to study thin silver films. Today’s technology requires the use of metal films with thicknesses of only a few hundred nanometers or less. At this thickness, crystal defects play a huge role in determining the microstructures of the film. Existing models do not adequately explain the formation of these defects or effects they have on the films. Therefore, thin films of a range of metals will be produced in a high vacuum deposition chamber and studied by x-ray diffraction (XRD) and electron backscatter diffraction (EBSD) in order to characterize the formation of defects and their effect on the microstructures. The goal of these experiments will be to improve the general model that describes similar thin metal films.

Professor of Chemistry, Karen Torraca, will work with two students this summer toward the development of a “green” synthetic method for the conversion of alcohols to ketones or aldehydes. The current standard synthetic processes require large amounts of heavy metals and generate a lot of hazardous environmental waste. Although there is a strong research emphasis across academia to develop better oxidation processes, very few new processes have actually been implemented in large-scale manufacturing due to the lack of robustness. Our ultimate goal will be to develop not only a “green” process, but one that is amenable to large-scale use where it will have the greatest environmental impact. Our research will focus on the use of palladium and other transition metal catalysts to complete the oxidation of various alcohols to ketones or aldehydes under mild conditions.

Associate Professor of Chemistry, Karen Torraca, will work with two students this summer toward the development of a “green” synthetic method for the conversion of alcohols to ketones or aldehydes.  The current standard synthetic processes require large amounts of heavy metals and generate a lot of hazardous environmental waste.  Although there is a strong research emphasis across academia to develop better oxidation processes, very few new processes have actually been implemented in large-scale manufacturing due to the lack of robustness.  Our ultimate goal will be to develop not only a “green” process, but one that is amenable to large-scale use where it will have the greatest environmental impact.  Our research will focus on the use of palladium catalysts to complete the oxidation of various alcohols to ketones or aldehydes under mild conditions.

Aaron Sullivan, Associate Professor of Biology, along with Julia Dyer and Zachary Smith are continuing a line of research that investigates how antipredator responses to chemical cues from predators are fine-tuned by prey species. More specifically, this work will examine how prior experience with a predator as well as foraging success can influence Allegany Dusky Salamander defensive behavior. Salamanders of this species are excellent models for investigating how prey use chemical cues to evaluate predation risk as they are equipped with well-developed chemosensory organs and rely on chemical cue detection for functions such as foraging, territory maintenance, and mate recognition. Furthermore, some species respond to chemical stimuli from predators and even injured salamanders. We hope to address the following questions during SRI 2014: 1) Do salamanders with recent experience related to predation respond more strongly to chemical stimuli from predators, and 2) Are ‘hungry’ salamanders willing to forage even though predation risk is relatively high?

Mark Yuly, professor of physics, and two students, Laurel Vincett and Thomas Eckert, will be working with physicists from SUNY-Geneseo on research related to inertial confinement fusion (ICF). In ICF a large amount of energy is deposited, usually with high-powered lasers, into a small pellet of nuclear fuel to initiate a fusion reaction. In order to characterize the fusion reaction, a system has been developed using ¹²C activation.  Samples of purified graphite are placed at several locations around the ICF target chamber, where they are exposed to the flux of neutrons produced in the fusion reaction. By far, the biggest remaining obstacle to the implementation of this diagnostic technique is that it depends on accurate knowledge of the ¹²C(n,2n) cross section, which has not been well-measured.  The past two summers we did an experiment at Ohio University using the tandem Van de Graaff accelerator to measure this cross section; this summer we will analyze the data that were collected, and perform a necessary side-experiment to measure the efficiency of the detectors we used the past two summers.

Jun-Koo Park, assistant professor of mathematics, and two students (August Gula and RD Marek), will continue the study of the refined Gaussian Network Model (GNM) for predicting the dynamics of biological structures. Proteins are an important class of biomolecules, and the GNM has been proved to be accurate for predicting the fluctuations. Since the X-ray structures may not directly reveal the motions of structures, we plan to use NMR data in which multiple structures of the same protein can reveal the aspects of dynamics more directly. The goal of this study is to refine a GNM and apply it to the larger set of biological structures using NMR data. This is a continuation and extension of a project that we did at SRI 2013.

Networks can model complex interactions in the real world, in which vertices are entities and edges represent the interactions between the entities. Many networks, especially social networks, exhibit community structures where vertices form different groups or communities. To date, the research on networks primarily focuses on the static networks, where vertices and edges do not change over time. However, many real networks modeling the evolving relationships between entities tend to be dynamic, which implies that the network topology, vertices, or edges could change over time. Wei Hu, professor of math and computer science, and two students, Nathan Aston and Jacob Hertzler, will create adaptive algorithms to identify local community structures to improve community detection in dynamic networks.

Brandon Hoffman, assistant professor of physics, and three students (Kyle Flemington, Paul Lashomb, and Jonathon Yuly) will be collaborating with Shefford Baker at the Center for Materials Research (CCMR) at Cornell University to study thin silver films. Today’s technology requires the use of metal films with thicknesses of only a few hundred nanometers or less. Not much is known about the properties of materials this small and the present models do not accurately describe the films. Therefore, thin silver films will be produced in a high vacuum deposition chamber and studied with x-ray diffraction (XRD), electron backscatter diffraction (EBSD), and transmission electron microscopy (TEM) in order to characterize the microstructures and transformations of the films. The goal of these experiments will be to improve the general model that describes similar thin metal films.

Jamie Potter, Assistant Professor of Biology, will be working with 2 students, Mary Grace Hollenbeck and Russell Levack, in collaboration with Dr Keith Perry, Associate Professor at Cornell University Department of Plant Pathology and Plant-Microbe Biology, on the detection of plant RNA viruses in grapevine. We will be focusing on Grapevine leaf roll-associated viruses, GLRaV, in Vitis vinifera and related Vitis species through collection and analysis of plant samples from western New York vineyards and adjacent wild cultivars using newly developed molecular macroarray diagnostic techniques. Our preliminary results show that grapevines in WNY host a variety of RNA viruses infections. In addition to continuing my research on macroarray detection of RNA virus infections in cultivated grapevines, we will also be developing virus-specific PCR protocols to confirm our results. This work is supported by the Houghton University Moreland Research Fund.

Study of the refined Gaussian Network Model (GNM) for HIV-1 protease

Jun-Koo Park, assistant professor of mathematics, and two students, Jacob Liddle and Nicholas Fuller, will continue their study of the refined Gaussian Network Model (GNM) for HIV-1 protease. The HIV-1 protease plays an essential role in the life cycle of HIV. Accurate predictions on its structural fluctuations may provide great insights into how the dynamics of the structure relate to their functions. The goal of this study is to refine the non-homogeneous GNM and apply it to the recently modeled structure, HIV-1 protease.

Community detection in social networks

Wei Hu, professor of math and computer science, will be researching with two computer science students, Brian Dickinson and Benjamin Valyou, and Dr. Xumin Liu from RIT, on community detection in social networks. Through learning of the community structures in social networks, we attain the knowledge of the formation, split, merge, and evolution of these communities. However, identification of communities in a real network is a challenge since the number and the sizes of communities are typically unknown. Additionally large networks of millions of nodes can bring great computational difficulty. The goal of this study is to explore an integrative approach to community detection.

Biodegradable Glycopolymers

John Rowley, assistant professor of chemistry, and students Ethan Kent and Jason Orlando will be developing methods for the synthesis of biodegradable materials.  Glycopolymers are a particularly interesting class of materials as they contain chemical functionalities that mimic signaling receptors on the surface of cells. Biodegradable glycopolymers that can degrade or be absorbed by the body have potential applications in drug-delivery, tissue engineering, and biomedical research.

Do hunger levels and prior experience with predators influence salamander responses to chemical cues associated with predation?

Salamanders within the family Plethodontidae are excellent models for investigating how terrestrial prey use chemical cues to evaluate predation risk. Members of this family are equipped with well-developed chemosensory organs and rely on chemical cue detection for functions such as foraging, territory maintenance, and mate recognition. Furthermore, some species respond to chemical stimuli from predators and even injured salamanders. In this study, Aaron Sullivan, associate professor of biology and two students including Julia Dyer will hope to address the degree to which behavioral responses by prey are fine-tuned by the internal state of the salamander (e.g., experience, hunger levels). The first line of research will evaluate how recently attacked individuals will respond to chemical cues from predators. To accomplish this we will induce tail autotomy in a subset of our salamander population to simulate predation. (Tail autotomy is commonly employed by a number of salamanders upon contact with predators as a means of escape). It is possible that salamanders with recent experience related to predation may respond more strongly to chemical stimuli from predators or that injured salamanders may be more likely to forage in the presence of predator cues because their primary energy storage organ (i.e. their tail) has been lost. The second line of research will attempt to understand how ‘hunger’ levels influence antipredator decision-making by maintaining animals on different food regimes (e.g., no food vs ad libitum feeding). Satiated individuals may be more inclined to engage in risk-averse behavior whereas ‘hungry’ salamanders may be more risk-prone and willing to forage when predation risk is relatively high.

Macroarray detection of RNA viral plant pathogens in Vitis vinifera and related grapevine species of western New York

Jamie Potter, Assistant Professor of Biology, will be working with 2 students in collaboration with Dr. Keith Perry, Associate Professor at Cornell University Department of Plant Pathology and Plant-Microbe Biology, on the detection of plant RNA viruses in grapevine. We will be focusing on Grapevine leaf roll-associated viruses, GLRaV, in Vitis vinifera and related Vitis species through collection and analysis of plant samples from western New York vineyards and adjacent wild cultivars using newly developed molecular macroarray diagnostic techniques. This work is supported by the Houghton University Moreland Research Fund.

Thin metal films

Brandon Hoffman, assistant professor of physics, and two students (Ethan Ocock and Emily Morrow) will be collaborating with Shefford Baker at the Center for Materials Research (CCMR) at Cornell University. Today’s technology requires the use of metal films with thicknesses of only a few hundred nanometers or less. Not much is known about the properties of materials this small and the present models do not accurately describe the films. Therefore, thin silver films will be produced in a high vacuum deposition chamber and studied with x-ray diffraction (XRD) and electron backscatter diffraction (EBSD) in order to characterize the microstructures and transformations of the films. The goal of these experiments will be to improve the general model that describes similar thin metal films.

Inertial confinement fusion

Mark Yuly, professor of physics, and two students, Garrett Hartshaw and Ian Love, will be working with scientists from SUNY-Geneseo and Ohio University on research related to inertial confinement fusion (ICF). In ICF a large amount of energy is deposited, usually with high-powered lasers, to a small pellet of nuclear fuel in order to initiate a fusion reaction. In order to characterize the fusion reaction, a system has been developed using ¹²C activation.  Samples of purified graphite are placed at several locations around the ICF target chamber, where they are exposed to the flux of neutrons produced in the fusion reaction. By far, the biggest remaining obstacle to the implementation of this diagnostic technique is that it depends on accurate knowledge of the ¹²C(n,2n) cross section, which has not been well-measured.  Last summer we carried out a feasibility study for a measurement of this cross section; this summer we will measure this cross section up to the highest energy possible using the tandem accelerator at the John E. Edwards Accelerator Laboratory at Ohio University.

Christopher Wells, Assistant Professor of Physics, and two students, Colin Lauer and Graeme Little, will be writing and running simulations of dark matter halo formation. It is now known, through indirect observations, that 80% of the mass in our universe is an exotic substance known as “dark matter.” It is exotic because it cannot be composed of ordinary atoms and dark because it does not produce electromagnetic radiation, i.e. light. Because it does not interact like ordinary matter does, dark matter can more easily aggregate under the influence of gravity in the early universe. These aggregations or “halos’’ act as a sort of gravitational glue that makes it possible for ordinary matter to populate galaxies and form stars. At present there are nearly a dozen distinct experiments world-wide looking for direct evidence of dark matter, that is the interaction of dark matter with ordinary matter in non-gravitational ways. These experiments and their results rely on knowing where they should be able to find the dark matter and how much momentum it should have on average. Thus, we intend to study the problem of how the dark matter organizes itself in the early universe in a variety of dark matter models. In particular, we want to study models where the dark matter has a variety of self-interactions.

Chemically-mediated Predator-prey Interactions in Larval Black Flies

Aaron Sullivan, Associate Professor of Biology, and two students, Michele Adams and Maya McElfishwill investigate chemically-mediated predator-prey interactions in larval black flies. Our recent field studies show that larvae are more likely to engage in defensive postures when they are exposed to chemical cues from wounded conspecifics and invertebrate predators versus a control stimulus (water). Our approach to the research to be done during the Summer Research Institute of 2011 is to further characterize the responses of larval black flies to cues from vertebrate as well as invertebrate predators and to determine if responses are performed in a threat-sensitive manner. The threat-sensitivity hypothesis essentially states that prey species will respond to a stimulus in proportion to the level of threat perceived as a result of that stimulus. Our research will utilize field techniques to evaluate prey responses to a variety of chemical cues related to predation as well as laboratory studies using an artificial stream apparatus.

Developing an Interferometer for Measuring Stresses in Thin Films

Brandon Hoffman, Assistant Professor of Physics, and two students, Tyler Reynolds and Nicholas Fuller, will design and construct a laser interferometer for measuring stresses in thin metal films. Nanofabricated devices have become extremely important in our ever shrinking world of technology. However, scientists have not yet developed a working model that can explain the properties of the thin films that make up such devices. For instance, thin films can support much higher stresses than their bulk counterparts. These stresses determine the microstructures which, in turn, determine the film’s properties. Most techniques used to resolve stresses in films measure the curvature of a substrate along only one or two axes and calculate the stress from the curvature. Our research group will develop an interferometer that illuminates an entire four inch substrate. Computer software will control the position of the reference mirror and generate a topographical image of the substrate. In this way, stresses can be calculated along any axis in the plane of the substrate.

Development of Green Oxidation Catalysts

Associate Professor of Chemistry, Karen Torraca, will work with two students this summer toward the development of a “green” synthetic method for the conversion of alcohols to ketones or aldehydes. The current standard synthetic process requires large amounts of heavy metals and generates a lot of hazardous environmental waste. Although there is a strong research emphasis across academia to develop better oxidation processes, very few new processes have actually been implemented in large-scale manufacturing due to the lack of robustness. Our ultimate goal will be to develop not only a “green” process, but also one that is amenable to large-scale use where it will have the greatest environmental impact. Our research will focus on the use of palladium catalysts to complete the oxidation of various alcohols to ketones or aldehydes under mild conditions.

Inertial Confinement Fusion

Mark Yuly, professor of physics, and two students, Keith Mann and Andrew Evans, will be working with scientists from SUNY-Geneseo and the Laboratory for Laser Energetics (LLE) in Rochester NY on research related to inertial confinement fusion (ICF). In ICF a large amount of energy is deposited, usually with high-powered lasers, to a small pellet of nuclear fuel in order to initiate a fusion reaction. ICF is currently studied at a number of laboratories around the world – in the United States most notably at the National Ignition Faculty (NIF) and the LLE. In order to characterize the fusion reaction, a system has been developed using activation of ¹²C. Samples of purified graphite are placed at several locations around the ICF target chamber, where they are exposed to the flux of neutrons produced in the fusion reaction. By far, the biggest remaining obstacle to the implementation of this diagnostic technique is that it depends on accurate knowledge of the ¹²C(n,2n) cross section, which has not been well-measured. Our primary goal is to develop a technique for measuring this cross section.

Gene Cloning

Associate Professor of Biology Matt Pelletier worked with two students to attempt to clone a gene encoding a protein believed to be involved in insect development. Efforts to clone and characterize this gene may lead to future discoveries of safe pesticides that could prevent herbivorous insects from destroying crops.

Computer Network Intrusion Detection Systems

Computers and the Internet are an integral part of our daily work and life. As such, computer and computer network security has become increasingly important and relevant. Malicious attacks on computers can cause different damages to organizations and homes, and computer network intrusion detection systems (IDS) are designed to detect such attacks. Most of the intrusion detection techniques developed so far build their detection model offline using the network traffic captured by some specific software, and then deploy the model in real time on the network. There are two limitations of this approach. Firstly, it cannot detect any gradual change of normal behavior, since its model is created offline. Secondly, it is impossible to store the infinite data generated by fast Internet with any finite memory storage to build a model offline. Professor of Math and Computer Science, Wei Hu, and his two students, Zachary Miller and William Deitrick, plan to create a new IDS to tackle both issues. The salient features of their IDS are to update the detection model seamlessly whenever there is a change of normal activities and to maintain the model online all the time with the capacity to process fast Internet traffic.

Chemically-mediated Predator-prey Interactions in Larval Black Flies

Aaron Sullivan, Associate Professor of Biology, and two students, Amanda Hiers and Stewart LaPan will investigate chemically-mediated predator-prey interactions in larval black flies. Our recent field studies show that individual larvae from two populations in Allegany County, NY are more likely to engage in defensive postures when they are exposed to chemical cues from wounded conspecifics versus a control stimulus (water). Furthermore, there are no differences, in terms of the type or duration of the response between these populations. Our approach to the research to be done during the Summer Research Institute of 2010 is to determine if the responses by larval black flies to cues from injured conspecifics as well as predators are performed in a threat-sensitive manner. The threat-sensitivity hypothesis essentially states that prey species will respond to a stimulus in proportion to the level of threat perceived as a result of that stimulus. The ability of invertebrates to fine-tune their defensive responses to environmental stimuli has only recently been under investigation and offers an excellent opportunity to combine field and laboratory techniques to solve biological problems. Our research will utilize field techniques to evaluate prey responses to a variety of chemical cues related to predation at different field sites and will examine diel effects on behavior.

Developing an Interferometer for Measuring Stresses in Thin Films

Brandon Hoffman, Assistant Professor of Physics, and two students, Joshua Mertzlufft and Tyler Reynolds, will design and construct a laser interferometer for measuring stresses in thin metal films. Nanofabricated devices have become extremely important in our ever shrinking world of technology. However, scientists have not yet developed a working model that can explain the properties of the thin films that make up such devices. For instance, thin films can support much higher stresses than their bulk counterparts. These stresses determine the microstructures which, in turn, determine the film’s properties. Most techniques used to resolve stresses in films measure the curvature of a substrate along only one or two axes and calculate the stress from the curvature. Our research group will develop an interferometer that illuminates an entire four inch substrate. Computer software will control the position of the reference mirror and generate a topographical image of the substrate. In this way, stresses can be calculated along any axis in the plane of the substrate.

Microbial Populations Colonizing the Feeding Apparatus of the Larval Stage of the Black fly

Jamie Potter, Assistant Professor of Biology, and students Johanna Hummelman and Hannah Gardner will investigate the microbial populations colonizing the feeding apparatus of the larval stage of the Simulium vittatum black fly. It is known that Similium sp. is a common vector of several diseases known to infect humans, birds and livestock, such as River Blindness and Pinta. However, these diseases are not found in North America despite similar habitat and vector found in endemic regions. Competition for food and habitat by other microbes in the water ecosystem and within the blackfly itself may explain the absence of the pathogenic species. To this hypothesis, we will identify and quantify common microbes found to be colonizing the feeding apparatus of the Similium organism. This information will aid researchers in understanding the microbial populations colonizing the blackfly larvae in North America, specifically in Western New York, and gain information on the potential for the migration and colonization of medically important pathogens into the local population. The research will combine field studies and basic microbiology laboratory techniques, offering a unique opportunity to study two diverse yet interconnected biological systems and fields.

Synthesizing biodegradable plastic from renewable resources

Assistant Professor of Chemistry, John Rowley, and student, Alan Stier will explore how to synthesize new types of biodegradable plastic from renewable resources. Most plastics (polymers) are synthesized from petroleum, a resource that is rapidly being consumed. One aspect of this research is to develop methods for the synthesis of polymers from alternative renewable resources, such as carbohydrates, triglycerides, and CO2. Another is to synthesize polymers that are biodegradable. Due to their low cost, polymers are used extensively in disposable products; however, as a result of their chemical structure, these materials decompose very slowly in the environment. Modifications to the chemical structure of polymers enables one to change their mechanical and material properties, including strength, toughness, flexibility, and degradability. Employing recently discovered catalyst technology, we will be designing and synthesizing new polymers that combine useful mechanical properties with the ability to degrade under the desired conditions.

This research may be extended to the field of glycopolymers – polymers that contain sugar moieties as pendant groups. Because these sugar groups engage in highly specific interactions with proteins that bind carbohydrates on the surface of cells, these glycopolymers can function as cell surface mimics, promoting cell-polymer adhesion, and may be very useful in implantable medical devices. Thus, our research will explore the possibility of extending our synthetic methods to create a new class of biodegradable glycopolymers with applications in biomedical research.

Development of Green Oxidation Catalysts

Associate Professor of Chemistry, Karen Torraca, will work with two students this summer toward the development of a “green” synthetic method for the conversion of alcohols to ketones or aldehydes. The current standard synthetic process requires large amounts of heavy metals and generates a lot of hazardous environmental waste. Although there is a strong research emphasis across academia to develop better oxidation processes, very few new processes have actually been implemented in large-scale manufacturing due to the lack of robustness. Our ultimate goal will be to develop not only a “green” process, but also one that is amenable to large-scale use where it will have the greatest environmental impact. Our research will focus on the use of palladium catalysts to complete the oxidation of various alcohols to ketones or aldehydes under mild conditions.

Nuclear Physics Experiments

Mark Yuly, professor of physics, and three students, Katrina Koehler, Adam Silvernail and Nick Fuller, will be collaborating with researchers from Los Alamos National Laboratory (LANL), Massachusetts Institute of Technology (MIT), and the University of Kentucky on two nuclear physics experiments at the Los Alamos Neutron Science Center (LANSCE). The first experiment is an active target measurement of n+p → d+γ neutron capture cross sections at low energies, which are important for Big Bang nucleosynthesis models. For the second experiment, a Time Projection Chamber is being constructed that will allow measurement of high precision fission cross sections needed for advanced nuclear reactor design codes.

Investigation of correlation of host-shift markers in Influenza viruses

The pandemic (H1N1) 2009 was a clear reminder that influenza A viruses remain a global health threat. The genes of the novel 2009 H1N1 flu virus consist of those from avian, human, and swine viruses. In particular, the two surface glycoproteins, haemagglutinin and neuraminidase, of the 2009 H1N1 virus are of classical swine and Eurasian swine origins, respectively. When avian or swine influenza viruses cross host species barriers to infect humans, it can lead to pandemics. Therefore, identifying the genetic modifications that would lead to a host switch is of fundamental importance. Research to date has uncovered several key molecular differences between bird/swine flu and human flu, which could be used as markers to monitor changes in bird/swine flu that could threaten humans. Wei Hu, Professor of Math and Computer Science, and two computer science students, Keli Fancher and Zachary Miller, will investigate the correlation of the host-shift markers, because these individual markers tend to function in concert for their biological purposes.

Molecular markers of tumor sensitivity and resistance to cancer therapeutics

Wei Hu, Professor of Math and Computer Science, and two students David King and Thomas Keane, will be studying an integrative approach to discover molecular markers of tumor sensitivity and resistance to cancer therapeutics. The phenotype of cancer is a dynamic interplay of changes at the DNA, RNA, and protein levels. To improve cancer treatment, we need to deepen our knowledge of how these different factors interact with each other. The complexity of DNA-RNA-protein relationships provides challenges as well as opportunities for an integrative approach to study cancer. In the past, researchers have employed two kinds of datasets, either DNA and RNA, or RNA and proteins, to tackle the issue of sensitivity and resistance of cancer drugs. Their focus was to find the molecular markers that affect the effectiveness of cancer drugs, which is a hot topic these days. In this study, we plan to use all three levels of data, DNA, RNA, and proteins, to study the same issue. With more data, we are hopeful that our machine learning techniques will uncover more informative molecular markers than those published in the literature.

Predator-prey interactions in Red-backed Salamanders

Aaron Sullivan, Associate Professor of Biology, and two students, Nathaniel Smith and Stewart LaPanwill investigate chemically-mediated predator-prey interactions in Red-backed Salamanders. As it turns out, this species of salamander is able to evaluate the risk of predation based primarily on chemical cues deposited in their habitat from predators or wounded conspecifics (other Red-backed Salamanders). Our specific approach for the research to be done during the Summer Research Institute of 2009 is to determine if the responses by salamanders to cues from predation support the threat-sensitivity hypothesis. The threat-sensitivity hypothesis essentially states that prey species will respond to a stimulus in proportion to the level of threat perceived as a result of that stimulus. The ability of so-called “lower vertebrates” to fine-tune their responses to environmental stimuli has only recently been under investigation and offers an excellent opportunity to combine field and laboratory techniques to solve biological problems.

Cornell Center for Materials Research

Assistant Professor of Physics, Brandon Hoffman, and students Adam Silvernail and Lindsay Timianwill travel to Cornell University to collaborate with Shefford Baker, professor at the Cornell Center for Materials Research. The group will use X-ray diffraction, various electron microscopy techniques, and an ultra-high vacuum laser stress measurement system to study the microstructures of thin silver films used in nanotechnology. Applications range from tiny microchips in personal computers to the huge mirrors used by NASA.

Synthesizing biodegradable plastic from renewable resources

Assistant Professor of Chemistry, John Rowley, and two students, Zachary Adam and Kelly Harty, will explore how to synthesize new types of biodegradable plastic from renewable resources. Most plastics (chemically known as polymers) are synthesized from petroleum, a resource that is rapidly being consumed. One aspect of this research is to develop methods for the synthesis of polymers from alternative renewable resources, such as carbohydrates, triglycerides, and CO2. Another is to synthesize polymers that are biodegradable. Due to their low cost, polymers are used extensively in disposable products; however, as a result of their chemical structure, these materials decompose very slowly in the environment. Modifications to the chemical structure of polymers enables one to change their mechanical and material properties, including strength, toughness, flexibility, and degradability. Employing recently discovered catalyst technology, we will be designing and synthesizing new polymers that combine useful mechanical properties with the ability to degrade under the desired conditions.

This research may be extended to the field of glycopolymers – polymers that contain sugar moieties as pendant groups. Because these sugar groups engage in highly specific interactions with proteins that bind carbohydrates on the surface of cells, these glycopolymers can function as cell surface mimics, promoting cell-polymer adhesion, and may be very useful in implantable medical devices. Thus, our research will explore the possibility of extending our synthetic methods to create a new class of biodegradable glycopolymers with applications in biomedical research.

Development of Green Oxidation Catalysts

Associate Professor of Chemistry, Karen Torraca, will work with two students, Kaitlin Smith and Hillary Chartrand, this summer toward the development of a “green” synthetic method for the conversion of alcohols to ketones or aldehydes.  The current standard synthetic process requires large amounts of heavy metals and generates a lot of hazardous environmental waste.  Although a significant amount of research is currently focused on the development of better processes, very few of those developed have actually been implemented in large-scale manufacturing due to the lack of robustness.  Our ultimate goal will be to develop not only a “green” process, but also to study it and adapt it to make it amenable to large-scale use where it will have the greatest environmental impact.  Research work will focus on the use of palladium catalysts to complete the oxidation of various alcohols to ketones or aldehydes under mild conditions.

Nuclear Physics Experiments

Mark Yuly, professor of physics, and three students, Katrina Koehler, Peter Kroening and Jonathan Slye, will be collaborating with researchers from Los Alamos National Laboratory (LANL), Massachusetts Institute of Technology (MIT), the University of Kentucky, and Bogazici University (in Turkey) on a several nuclear physics experiments at the Los Alamos Neutron Science Center (LANSCE). The group will be using neutrons produced by the Clinton B. Anderson linear accelerator to study the interactions of neutrons with deuterium nuclei and the induced fission of the unstable isotope Am-243.