College of Science

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. 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. Ian Hall, Assistant Professor, Biological Sciences:
ihall@ben.edu

• Research in the Hall lab focuses on integrative physiology in amphibians. Students working in the Hall lab will utilize a variety of experimental techniques- including electrophysiology, behavioral monitoring and quantification- as well as amphibian care and handling. There are multiple projects in progress and under development. Students working in the lab are likely to get involved in most, if not all of them.
  • Project 1: Endocrine regulation of osmoregulation – Fresh water organisms face two major osmotic problems – they take on water and they lose salt. To deal with these problems, amphibians will osmoregulate with their skin. These processes are regulated by the endocrine system. Students interested in this project will measure ion movements through skin and how it changes under different conditions, in particular the presence of the hormone prolactin.
  • Project 2: The role of olfaction in sexual reproduction – In amphibians, vocal communication has been widely studied as a means to communicate sexual receptivity and locate a mate. Anecdotal evidence suggests that olfactory cues are also important in the species we study in the lab, but this has never been formally quantified. Students interested in this project will monitor and quantify behavior. If results are positive, there are opportunities for collaborations with Chemistry to isolate and identify important olfactory cues that can be identified behaviorally and electrophysiologically as potential pheromones.
  • Project 3: Amphibians in the changing world – Amphibians are often seen as indicator species for the effects of ecological change. For example, pesticides and other endocrine disrupting chemicals influence amphibian development and behavior. In addition to those ecological challenges, global climate change is already having serious deleterious impacts on animal populations around the world. Students interested in these concepts will develop hypotheses and examine the effects of water composition and temperature on a variety of physiological and behavioral variables.

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 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

Transition metal-catalyzed isomerization of alkenes, which involves the atom economical migration of carbon-carbon double bonds. The challenges to be met include: positional and stereochemical selectivity, substrate generality, and simplicity of catalyst use. Alkene isomerization is an important process in the chemical industry that contributes to many 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 to synthesize parts of the catalyst and organic substrates for catalysis; organometallic synthesism 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. We are seeking 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.

Dr. Robert McCarthy, Associate Professor, Biological Sciences:
rmccarthy@ben.edu

• The McCarthy Lab concentrates on a number of areas related to human adaptation, the evolution, growth, and development of the human and primate skull, and phylogenetic theory and practice. One long-standing project on the biological basis of human vocalization and speech focuses on the structure of the human skull and vocal tract. There are also a number of other potential research projects focusing on reconstruction of Homo erectus body size, taxonomic analyses of Homo erectus skulls and teeth, integration of the primate brain and basicranium, and the relationship between tooth eruption and craniofacial size and shape in primates. I will try to match research projects to student interests whenever possible.
  View Dr. McCarthy's summer research page

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

• 1– 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.

• 2 – 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.

• 3 – 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. Grace Mirsky, Assistant Professor, Computer Science:
gmirsky@ben.edu
 

• Computer Vision / Robotics: Lightweight, inexpensive robots and drones have grown in popularity in a wide variety of applications. Being able to quickly locate and identify an object of interest using one of these platforms is challenging. These challenges arise from the limited processing capabilities of inexpensive hardware and the inability to include additional hardware due to weight requirements. This project involves designing algorithms to facilitate accurate object detection using a low-cost platform (robot or drone). Extensive programming experience is required (must have already completed CMSC 270/CMSC 274) as well as some hands-on hardware experience.
• 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. Extensive programming experience is required (must have already completed CMSC 270/CMSC 274).
• 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. Extensive programming experience is required (must have already completed CMSC 270/CMSC 274).
  View Dr. Mirsky's home page

Dr. Tiara Perez Morales, Assistant Professor, Biological Sciences:
tperezmorales@ben.edu

• Bacterial quorum sensing (QS) is a mechanism in which gene expression modulation is coordinated within a population. Bacterial populations can communicate and coordinate responses using small hydrophobic peptides or pheromones. QS regulates different genetic pathways in Gram-positive bacteria. The focus of our group is in unique stand-alone transcriptional regulators termed Rgg, and their pheromones.

  Rgg proteins contain an N-terminal DNA binding domain and a C-terminal peptide binding domain. The pheromones that interact with this domain are generally small hydrophobic peptides (termed SHP). Interaction leads to upregulation of target genes. Rgg QS pathways have been shown to regulate competence, biofilm formation, toxin production, and virulence in Gram-positive bacteria. We are interested in Rgg loci present in the probiotic and human commensal Lactobacillus acidophilus ATCC 4357.
  L. acidophilus ATCC 4357 contains three predicted Rgg proteins named herein as Rgg499, Rgg1765, and Rgg155. No pheromones have been listed for Lactobacillus species. rgg499 is in a predicted six gene operon which includes a second transcriptional regulator and it is found upstream of maltose transport genes. rgg155 is in a predicted five gene operon and all genes are of unknown function. However, rgg155 was found to have some sensitivity under stress conditions in L. acidophilus NCFM. Lastly, rgg1765 is surrounded by predicted drug transporters and cell envelope proteases. Our main research questions are: What are the QS pathways regulated by Rgg proteins in L. acidophilus ATCC 4357 and what are the signals that induce these Rgg pathways?
  Previous studies have shown Rgg positively or negatively regulate adjacent genes including itself. Most Rgg proteins are stand-alone and have been shown to be positive regulators. One negative regulator has been shown to be paired with positive regulators. Given the arrangement present in L. acidophilus, we hypothesize all Rgg(s) may be positive regulators. We have constructed luciferase transcriptional reporters to observe changes in transcription. In addition, our reporters will be used to perform phenotypic arrays to identify potential inducing environmental signals. These constructs will be expressed in L. acidophilus and a heterologous host. Results from this project will provide insight in Rgg regulation.
  View Dr. Perez Morales' 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. Stefan Stefanoski, Assistant Professor, Physics and Engineering:
sstefanoski@ben.edu
 

Students at Benedictine University are offered the opportunity to conduct a state-of-art research by using equipment and methodologies similar to that used in modern R&D laboratories across the industry, such as potentiostats/galvanostats and solar simulators. Their research activities will meet the following objectives: analyzing the benefits from the renewable energy technologies, understanding the fundamental scientific principles behind them, learning and applying theoretical knowledge in real-time applications, hands-on measurements by using state-of-art equipment, and preparing students to enter the job market as skilled professionals or enroll in graduate schools with an advanced knowledge and experience in designing and conducting experiments.

• Project 1: Batteries for biomedical applications: Batteries can be used as power sources for motorized wheelchairs, surgical tools, cardiac pacemakers and defibrillators, dynamic prostheses, sensors and monitors for physiological parameters, neurostimulators, devices for pain relief, iontophoresis, electroporation, and related devices for drug administration. Students will investigate the types of battery chemistries used for biomedical applications and test their properties (charge/discharge cycling, internal resistance, operation in hot and humid environments, etc.).
• Project 2: Batteries for electric vehicles: This project is suitable for students majoring in engineering, physics, and/or chemistry, as it focuses on testing batteries used in electric (EV) or hybrid-electric (HEV) vehicles. Even though this project involves testing batteries on a laboratory-scale, it is intended to mimic the activities of engineers in companies and national labs who design batteries for EVs. Properties such as battery capacity and voltage will be investigated as function of cycling (charge/discharge). The effects of temperature variations and mechanical stress on the performance of the battery will be analyzed. Impedance Spectroscopy and Nyquist plot-analysis will be implemented to measure the internal resistance and assess the “state of health” of a battery.
• Project 3: Dye-sensitized solar cells (DSSCs): This is one of the latest promising solar photovoltaic (PV) technologies, focused on the design of solar cells that are light, inexpensive, transparent, and have the potential of achieving desirable efficiencies. The DSSCs will be assembled and their electrical properties measured. Various types of dyes will be tested in order to identify the inexpensive and abundant ones that will help us pave the road toward the next-generation low-cost and high-efficiency solar PV technology.
• Project 4: Standalone solar PV system for health clinics or schools in remote areas: The project will focus on designing a solar PV system for a health clinic or a school in a remote area, where no alternative sources of power are available. The project will encompass understanding of the operation and properties of solar cells, the components of a typical solar PV system (solar panels, batteries, inverters, charge controllers, etc.), and incorporating them into a final design. This project is suitable for students across a range of disciplines and majors: those interested in the engineering aspects of the design, as well as those interested in its humanitarian aspect, for example by delivering power to areas in third-world countries where power is either inaccessible or prohibitively expensive.
  View Dr. Stefanoski's home page

Dr. Matt Wiesner, Assistant Professor, Physics:
mwiesner@ben.edu

• Extraordinary Merging Galaxies in the Sloan Digital Sky Survey  In this project we will look at data from the Sloan Digital Sky Survey. We will be looking especially for extraordinary merging galaxies, that is galaxies that are gravitationally interacting. We are interested in finding merging galaxies that exhibit significant tidal bridges of stars and gas, extensive star formation and other extraordinary morphologies. Much of this project will involve visual inspection of astronomical images as well as analysis of astronomical catalogs.
• First Light for the Jurica-Havlik Telescope  In this project, you will go through the manual and learn how to use all the functions of the new 16-inch telescope and the associated CCD imager. We will be working out all the bugs to get the telescope fully operational. This project will require some early mornings or nights in order to do on-sky observing. At the end of the summer session I hope to have some good images of the Ring Nebula and other summer sky objects.\
• Looking at Galaxy Cluster Populations  In this project we will look at a sample of about 18,000 galaxy clusters and measure richness (number of galaxies in the cluster) using two different methods and then compare the results. The first method is the Voronoi Tessellation method and the second is the red sequence method. This project will require learning a few computing techniques.
• Modeling the Propagation of Pseudoscience  In this project, we will attempt to mathematically model the propagation of pseudoscientific ideas. Following on research that has modeled how rumors spread, we will take data on how false scientific ideas propagate, with a particular eye to astronomical pseudoscience. We will be investigating how these ideas are communicated and try to describe the rate and method of communication of such ideas.

Updated 02/03/2020