2018 Faculty Research Projects:


Dr. Tim Comar, Professor, Mathematics:
tcomar@ben.edu

  • Dynamics and stochastic behavior of Integrated Pest Management Model.  This involves looking at several different models for integrated pest management using impulsive differential equations and agent based models.  We may consider systems with varying environmental or climatic conditions.  Stochastic effects are also incorporated into the models.  Questions involve finding conditions which lead to pest eradication or permanent solutions and also involve the impact of changing the timing of the impulsive pest control events.  Related to the permanence issue is that of finding optimal conditions for managing the pest populations with minimal economic and minimal negative environmental impacts.  We are also interested in selecting optimal models using stochastic and evolutionary computing techniques.
  • Dynamics of Gene Regulatory Networks.  This involves the study of the dynamics of small gene regulatory networks through discrete and stochastic models.  One of the big issues is to understand when the Boolean models sufficiently capture the behavior of the continuous models.  Another interesting issue is to understand how the continuous dynamics depends on particular parameters that influence the behavior of the systems.  A third issue is to understand how the configuration of the network (the description of which genes affect which other genes) influences the dynamical behavior in the Boolean case. We are also interested in studying stochastic versions of these models and the determination of selecting models using evolutionary computing techniques. We are also interested in the relationship between the dynamics in Boolean models using synchronous versus asynchronous update.  Finally, we would like to continue the study of the relationships between Boolean dynamics and continuous dynamics these networks.
  • Dynamics of Pulse vaccination models. A pulse vaccination strategy is method of controlling the spread of a disease by periodically vaccinating a fraction of the population. The central mathematical questions here are very similar to those of IPM: (1) Under what conditions will an epidemic die out? (2) Under what conditions will an epidemic persist? The big question is that how can an effective and efficient vaccination strategy be implemented to limit the spread of a disease.  We are interested in using modifications of impulsive differential equations systems that incorporate time delays for an exposed individual to become infective and stochasticity, particularly in the incidence rates.
    View Dr. Comar's home page
 
Dr. Anthony DeLegge, Associate Professor, Mathematics:
adelegge@ben.edu
 
  • Title: “Will Facebook be #1 ‘forever’? A Competition Analysis”
    Abstract: In the early 2000's, online social networking was dominated by two sites: Facebook and MySpace. At that time, MySpace was the #1 social network in terms of site visits and users, and Facebook was an up-and-comer. However, by 2007, their roles reversed, and Facebook not only took the #1 spot, which it has not relinquished since, but MySpace began a rapid decline in usage, eventually becoming obsolete in 2012 (though people argue it was obsolete well before then). However, there are many more online social networking sites now, such as Twitter, Snapchat, LinkedIn, and Google+, all of which are in direct competition with Facebook for users. So, the big question for fans of Facebook is: can another network come and knock Facebook off of its #1 spot, just as they did with MySpace? Or, is Facebook “here to stay”?

    To answer this question, we will work on a variation of a standard competition model that allows users to potentially be on multiple networks at the same time. The model analysis will incorporate both theoretical and computational (using MATLAB) work to see what needs to happen in order for Facebook to become obsolete, or if that’s even possible!
    View Dr. DeLegge's home page

 

Dr. Jim Fackenthal, Associate Professor, Biological Sciences:
jfackenthal@ben.edu
 
  • mRNA splice variants in BRCA2, a breast cancer tumor suppressor gene
    Background. Mutations in the BRCA2 gene are one of the two major genetic risk factors for familial Breast Ovarian Cancer Syndrome (HBOC). Individuals with strong family histories of breast and/or ovarian cancer are counseled to seek genetic testing for BRCA2 and other genes, but often DNA sequence analysis can be ambiguous because of DNA sequence variants of uncertain clinical significance (VUSs). To provide the best possible genetic counseling, it is important to characterize the potential pathogenic nature of these variants.

    One way that a DNA sequence variant could disrupt the function of the gene is by causing disruption of an mRNA splicing site. Analysis of such mutations is complicated by the large number of splice variants associated with wild type genes that appear with varying frequencies and abundances. The splice variants could give rise to alternate protein products, play regulatory roles as non-coding RNAs, or simply reflect splicing errors. Thorough understanding of all splice variant functions is critical to understanding both developmental and tumor suppressor functions of BRCA2. To begin this analysis, we will determine which splice variants are conserved between species and which are transported to the cytoplasm where translation is possible.
    View Dr. Fackenthal's home page

 

Dr. Leigh Anne Harden, Assistant Professor, Biological Sciences:
lharden@ben.edu
 
  • The Harden Lab conducts integrative ecological research on reptiles and amphibians. Our lab’s central research questions revolve around of how these organisms function and interact with their increasingly modified environment, by studying them on a physiological, behavioral, and spatial/temporal level. This research is primarily field based; however, we utilize a number of computer-based and laboratory-based techniques (e.g. biochemical assays of animal tissues, microscope slide preparation and analysis, stable isotope analysis). All research has applications for conservation and management.

    Research projects for summer 2018 will involve intensive outdoor fieldwork 4-6 days/week of trapping turtles in local wetlands to investigate their species diversity, population structure and demography. Students will have the ability to develop their own side projects of interest within this larger project. Much of this fieldwork may be done in hot, muggy, and buggy conditions, so a hardiness in this kind of weather is a must. Attention to detail is important for high quality science. Curiosity and an ability to troubleshoot will contribute substance as well as enjoyment to our shared work experience!
    View Dr. Harden's home page

 

Dr. Casey Larsen, Assistant Professor, Chemistry:
clarsen@ben.edu
 
  • My research explores the transition metal catalyzed isomerization of alkenes, which is a simple concept that involves the atom economical migration of carbon-carbon double bonds. Challenges must be met: positional and stereochemical selectivity, substrate generality, and simplicity of catalyst use. Alkene isomerization is an important process in the chemical industry that contributes to an array of applications, including the SHOP process, DuPont’s adiponitrile process, Takasago synthesis of (-)-menthol, and for the synthesis of fragrances, to name a few.

    Students will learn techniques in organic synthesis, in order to synthesize parts of the catalyst and organic substrates for catalysis; organometallic synthesis, in order to make the catalyst; and molecule characterization, to analyze the synthesized compounds and products made during catalysis. Students will not only perform chemistry in open air, but will be exposed to air free techniques (Schlenk techniques and glove box).

    Project 1: Synthesis of Royal Jelly
    Royal Jelly is a natural product synthesized by worker bees as a form of nutrition for the queen bee in a colony, where this compound has been reported to have pharmacological properties. The current synthetic route requires 6 steps for its completion, where we will look at a more economical approach to its synthesis.

    Project 2: Synthesis of Pheromones
    Pheromones are signaling molecules naturally synthesized by organisms as a social cue to impact social behaviors. Harnessing unique reactivity using the alkene isomerization catalyst has the potential to lead to a class of Lepidopteran pheromones.

    Project 3: Construction of a Catalytically Active Metal Organic Framework (MOF)
    Metal Organic Frameworks (MOFs for short) are a subclass of polymeric compounds. Organic scaffolds are linked together with structural metals to form 3-dimensional structures that have pores for molecules, solvent or substrates, to move in and out of the structure. With the right organic scaffold linker, we have the potential of making a new class of catalysts using organometallic synthesis.
    View Dr. Larsen's home page

 

Dr. Brooks Maki, Assistant Professor, Chemistry:
bmaki@ben.edu

 
  • 1 – Nucleophilic Fluorination with small molecules
    We are working on developing new compounds for nucleophilic fluorination. To accomplish this we use near-aromatic heterocycles to induce the generation of F- anions which can react with other organic molecules. Fluorine is a commonly used isostere in medicinal and polymer chemistry, and it can have profound effects on stability, activity, and the physical properties of chemical compounds. Our research is focused on developing new ways of introducing fluorine to organic compounds under safe, mild conditions.
  • 2 – Pyrrole library synthesis
    Inspired by the biosynthesis of pyrraline containing natural products from sugars, we are investigating a synthetic route to libraries of pyrraline-based small molecules. This class of molecules is known to have wide-ranging bioactivity as anti-inflammatories, sleep aids, and anti-cancer compounds. The synthetic route involves an Achmatowitz / Paal-Knorr strategy, allowing access to high yields and a variety of structures.
  • 3 – Antioxidant synthesis
    Using one of the body’s natural anti-oxidants as inspiration, we look to synthesize more stable and effective antioxidant compounds that could be incorporated into proteins/enzymes and tagged to further investigate anti-oxidant pathways.
  • 4 – Bridged Heterocycle Library Synthesis
    Inspired by the novel structure of Lycojaponicumin A, we are investigating a dipolar cycloaddition reaction to allow synthetic access to this medicinally unexplored bridged heterocycle.
    View Dr. Maki's home page

Dr. Robert McCarthy, Assistant Professor, Biological Sciences:
rmccarthy@ben.edu
 
  • Neanderthal Brain Growth: In modern humans, brain growth occurs at a rapid rate but is spread out over a relatively long period of time. Growth of the brain is 80% complete by 2 years of age and 95% complete by 7 years. Recently, a 7.7-year-old Neanderthal child was discovered with a ~1330 cc brain (~87.5% complete), suggesting that Neanderthal brain growth occurred over a more extended time period. Since human brain growth studies present growth rates in terms of mean rates of growth completion, it is difficult to determine if this Neanderthal data point falls outside the range of modern human variation. In this research project, one student will be modeling brain growth in modern humans and other species, including chimpanzees, gorillas, orangutans, and Neanderthals. Requirements: Ideally, the successful candidate will be organized, independent, task-oriented, and interested in pursuing a project on brain growth and development. Tasks include data entry, database hygiene, and statistical manipulation. Familiarity with “R” software is preferred but not required.
  • Longitudinal Brain Growth: Compared to other hominins, modern humans have a brain that is large relative to cranial base length, so that the basicranium “flexes” early during development to accommodate its rapidly increasing size. Very little research has looked at the relationship between these parameters during growth and development. In this study, one student will be looking at the relationship between relative brain size (brain size divided by basicranial length) and flexion in a mixed longitudinal series of cephalometric radiographs from the Colorado Child Research Council Growth Study. If time permits, there may be opportunity to investigate the relationship between relative brain size and basicranial flexion in cross-sectional radiographic series of great apes and rabbits, and to investigate the relationship between brain and body size during development. Requirements: Ideally, the successful candidate should be able to work independently, quickly, and with great attention to detail. Tasks include literature review, radiographic data collection, geometric estimation of linear measures, and use of statistical methods including regression and multiple regression analysis. Advanced coursework in geometry or calculus is preferred but not required.
  • Vocal Tract Imaging: The vocal tract (the pharynx and oral cavity above the vocal cords) determines, to some extent, the acoustic properties of speech sounds. Radiographic studies have shown that tongue and vocal tract shape are instrumental for producing human speech sounds. However, magnetic resonance imaging (MRI) studies image patients in a supine position, which changes the position of the tongue and larynx in the neck. In this research project, one or two students will assist in the collection of MRI data using upright MRI technology. This project will teach students to collect and interpret biomedical images, to process acoustic data, and to use statistical techniques to study the relationship between vocal tract shape and the sounds of human speech. Requirements: Students interested in this project should be prepared to travel to Deerfield and Hazel Crest, two locations in Cook County, and to help recruit study participants. This project requires excellent interpersonal communication skills. Experience with human anatomy and/or physiology is preferred but not required. Priority will be given to students who can continue working on the project during fall 2018 and, ideally, spring 2019.
    View Dr. McCarthy's summer research page

 

Dr. Grace Mirsky, Assistant Professor, Computer Science:
gmirsky@ben.edu
 
  • Prediction of Acute Hypotensive Episodes:  Patients in the intensive care unit (ICU) are under constant monitoring, using a variety of physiological signals.  An Acute Hypotensive Episode (AHE) is a rapid, sudden decrease in blood pressure, which typically indicates that a life-threatening event is imminent.  Accurate prediction of an AHE can ensure that interventions are in place prior to the event, in order to minimize or prevent severe organ damage or death.  While techniques do currently exist to make these predictions, they are often either computationally intensive and require a relatively long training period, or are relatively simple but restrict the prediction to a relatively short time window.  In either case, practical clinical utility is reduced or eliminated.  In this project, we will investigate machine learning techniques to make accurate, real-time predictions of future AHE. 
  • Reconstruction of Absent or Corrupt Physiologic Signals: Signal corruption or dropout can cause issues in continuous patient monitoring in the ICU.  As a result, the ability to accurately reconstruct absent or corrupt signals as well the ability to detect if a signal is becoming corrupt as a result of noise, drift, etc. can greatly enhance critical patient care.  Continuous monitoring is important because in the ICU, patient condition can quickly degrade, and continuous monitoring is necessary in order to detect problems and administer treatment immediately.  In this project, we will work with a variety of different signals (electrocardiogram (ECG), respiratory rate, blood pressure, etc.) to determine how to best reconstruct the lost signal data.  An important application of this work, in addition to providing robust, continuous patient monitoring, is the continuous estimation of heart rate, even when the ECG signal is missing.  This project will be accomplished using predictive analytics techniques from machine learning. 
  • Reduction of False Arrhythmia Alarms: Frequent false cardiac arrhythmia alarms in the ICU have been shown to result in reduced patient care by diminishing attentiveness of the staff, due to the so-called “crying wolf” effect.  In addition, these alarms often negatively affect the patient’s ability to sleep, thus also interfering with the patient’s recovery.  As such, reduction of false alarms could potentially greatly improve care, but the criterion of not removing any true alarms creates a difficult constraint.  In this project, we will work with the electrocardiograms and their associated alarms to develop robust algorithms to reduce the frequency of false alarms, while ensuring that no true alarms are removed.  This project will use Matlab to develop and test appropriate machine learning algorithms.
  • Educational Robots in Computer Science: Robots have the potential to facilitate learning a wide range of Computer Science concepts including: programming fundamentals, operating systems, networking, systems architecture, and much more.  Nevertheless, making robots accessible at a variety of educational levels requires overcoming a number of hurdles.  In this study, we will look at how robots can be used most effectively to teach a variety of concepts while maintaining cost effectiveness to keep the lessons accessible to a wide variety of institutions. 
    View Dr. Mirsky's home page
     

Dr. David Rubush, Assistant Professor, Chemistry:
drubush@ben.edu

My research group explores new organic chemistry reactions and catalysts which are in turn used to create novel biologically active molecules. Students will learn techniques in organic synthesis, purification and molecule characterization (HPLC, NMR and IR spectroscopy).
 
  • Project 1: Artemisinin, an endo-peroxide containing molecule, is currently the frontline treatment for malaria; however, high production costs have limited its availability in underdeveloped countries. Additionally, artemisinin resistant parasites have been found in Southeast Asia. Synthetic endo-peroxides could potentially offer advantages over artemisinin. In addition to treating malaria, artemisinin has also shown potential as a chemotherapeutic. My group has recently developed a reaction to synthesize new endo-peroxides called 1,2,4-dioxazinanes.
    Project goals:
    1. Expand the scope of this reaction to make new endo-peroxides
    2. Synthesize endo-peroxides on a larger scale and send them to collaborators at St Jude Children’s Research Hospital who will screen them for antimalarial activity.
       
  • Project 2: The ability to synthesize organic molecules in high optical purity using sustainable methods is a significant yet challenging goal for chemists. The use of organocatalysts has eliminated stoichiometric reagents and expensive or toxic metals in many instances. However, there is much room for improvement and further applications of these technologies. This project investigates polymer bound chiral organcatalysts that will allow for the rapid and economical synthesis of complicated organic molecules.
    Project goals:
    1. Develop novel chiral acid catalysts with improved reactivity and selectivity
    2. Create a library of reusable solid-supported acid catalysts
    3. Apply newly developed catalysts to unsolved reaction methodologies and synthesize biologically important molecules
    View Dr. Rubush's home page

Dr. Jayashree Sarathy, Assistant Professor, Biological Sciences:
jsarathy@ben.edu
 
  • Project 1: An increase in epithelial permeability has been repeatedly demonstrated in patients with active inflammatory bowel disease and we have shown a possible role for bile acids and IL-8 in this process. The exact pathway on how bile acids stimulate the release of IL-8 is not known. Increased reactive oxygen species (ROS) production is associated with inflammatory conditions as seen  in Crohn's disease. Further, ROS has been suggested to stimulate the release of cytokines from epithelial cells. Thus, student(s) goal this summer is to investigate if bile acids can modulate ROS production by colonic epithelial T-84 cells, by using fluorescein and calcein as cell-permeant indicators for ROS and a hydrogen peroxide colorimetric detection kit. The student will detect ROS production or hydrogen peroxide release in the presence or absence of CDCA, LCA or both by monitoring the increase in fluorescence with a flow cytometer.  Further, since T84 cells can be stimulated to release mucus, the effect of ROS release on mucin (Muc-2) expression will also be assessed using fluorescence and Western blotting. 
  • Project 2: This project will focus on delineating the effects of bile acids on tight junction function and integrity of intestinal epithelial barriers. Barrier function is compromised in pathological conditions such as inflammatory bowel diseases, potentially resulting in bile acid-diarrhea.  Our studies have identified a potential role for cytokine, IL-8 in bile acid induced barrier dysfunction. However, cytokines are not the only mediators that alter barrier integrity. Inflammatory cytokines and other luminal agents could stimulate the release of nitric oxide (NO) which could be cytotoxic in high, but protective in small quantities.   Further, a role for another local mediator, reactive oxygen species generation (which interact with NO to release peroxynitrates), has also been indicated in the inflammatory process and alterations in tight junctions. Thus, the student will involve identify the role, if any, for nitric oxide and nitrates/nitrites in bile acid-induced regulation of barrier function.
    View Dr. Sarathy's home page


Dr. Kari Stone, Associate Professor, Chemistry:
kstone@ben.edu
 

  • Protein project: Utilizing the potential of metal-replaced hemoproteins in order to promote new types of reactivity and catalysis.:  The design of metalloenzymes in order to produce new types of biocatalysts has received ongoing attention in the industrial community.  The major aim of this project is to utilize hemoproteins as protein scaffolds to introduce new active sites that are produced by synthetic methods in order to improve functionality.  Many of these types of proteins have robust protein structures and their heme cofactors can easily be replaced.  This proposal has two main themes: (1) replacement of metal ions in the porphyrins of hemoproteins and (2) the incorporation of porphyrin derivatives into the protein matrix with the goal of promoting new reactivity and catalysis in order to make new oxygen-containing molecules.
  • synthesis project: Exploring metal complexes with redox-active ligands to promote new types of reactivity and catalysis.:  Transition metal complexes that perform small molecule transformations utilize multi-electron processes.  Two-electron oxidations include C-H bond oxidation and reduction of protons to dihydrogen, while oxidation of water is a four electron process and reduction of dinitrogen is a six electron process. To perform multi-electron transformations many times one or more transition metals are implicated invoking a change in oxidation states of the metal or metals.  Redox-active ligands containing oxygen, nitrogen, and sulfur have gained considerable attention recently as ligands for transition metals to become involved in electron donation that is typically assigned to metal redox processes.  This research project seeks to employ an alternative to a many-electron process involving transition metals by including redox active ligands coordinated to the metal center to supply the necessary oxidative or reducing equivalents to perform desirable chemical transformations.
    View Dr. Stone's home page
     

Updated 2/16/18

   
Dr. Ziliak 

 Student researcher 


 Dr. Rubush and summer research students with NMR 

  Summer Research 

 BenU Pollination Project at Tiananmen



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