Participating Faculty for Summer 2015
- Dr. Preston Aldrich, Associate Professor, Biological Sciences:
My research lab deals with systems biology, specifically with the analysis of complex biological networks. I have ongoing projects in the following areas:
Typically a student will work in two of these areas over the summer with a primary and a secondary project. Which projects are active depend on my interests and the interests and aptitude of the student. Students use a variety of software packages allowing the visualization and analysis of networks. Students also learn to write computer programs in Python allowing more refined analyses and modeling of networks. No prior programming experience is required.
- Invasive plants - analysis and modeling of invasive plant spread using networks
- Genomics - study of promoter, gene and protein networks in bacteria
- Curricular dynamics - the use of networks to understand and revise academic curricula
- Linguistics of natural languages – using networks to understand the structure and evolution of natural systems of communication.
View Dr. Aldrich's home page.
- Dr. Darya Aleinikava, Assistant Professor, Physics
- Project 1: Acoustics of natural and engineered seashells: creative fusion between emergent 3D printing technology and experimental computational explorations of the physics of sound.
The diversity of forms in living nature may lead one to a conclusion that laws governing those forms are very complex too. It can be shown, however, that the opposite may hold true and simple rules can yield complex behavior. We will explore this idea on the example of seashells, which, as we all know, can produce “ocean-like” sounds when pressed against the ear. We will investigate the possible explanations of this phenomenon, and then perform a few “experiments”: using simple geometrical rules, we will 3D print computed forms and compare acoustics of our “hand-made” shells to those of the natural seashells.
Project 2: Spiral phyllotaxis.
We will explore the phenomenon of spiral phyllotaxis. In simple terms, this is the secret that plants have been using for millions of years while they were arranging equal-size seeds in an ever-expanding pattern around a central point so that regardless of the size of the arrangement, the seeds pack evenly. The most notorious example is seed-packing of sunflowers. We will explore the geometrical rules behind this phenomenon, investigate the variety of these rules for different plants and reproduce them, and not only in flat-surface structures, but in spheres and tori as well. The final goal would be to create growth-rules for the plant with a shape of our choosing.
View Dr. Aleinikava's home page.
- Dr. Tim Comar, Associate Professor, Mathematics:
- Biological Models using Impulsive Differential Equations. The dynamics of models for integrated pest management and epidemics are investigated. Attention is paid to finding conditions for the existence and stability of total pest eradication solutions/disease free solutions and permanent solutions. Stochastic effects and delays may be incorporated into these models
- Dynamics of Gene Regulatory Networks: We primarily study small gene regulatory network via Boolean models. We are interested in how the dynamics is determined by the structure of the network. 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.
View Dr. Comar's home page.
- Dr. Pedro Del Corral, Associate Professor and Academic Program Director, Clinical Exercise Physiology:
- Our group works on the effects of exercise on energy metabolism and endocrinology in humans. It is well known that intense or prolonged endurance exercise activates the hypothalamic-pituitary –adrenal axis, leading to increases in plasma and salivary cortisol levels. Cortisol is the chief glucocorticoid in humans, it has a plethora of effects on energy metabolism, the immune and cardiovascular system, and the skeleton. The Clinical Exercise Physiology Laboratory is currently examining the effects of intense exercise on cortisol and other glucocorticoids (cortisone, corticosterone) and binding proteins (CBG) in plasma and saliva, in both men and women. We are currently analyzing data from men, and during the Spring we will analyze data collected in females. We have hypothesize that the glucocorticoid hormonal response to exercise is different between women on vs women off oral estrogens (ie., contraceptives) The findings of the female study will shape the research direction we take during the Summer 14’ and Fall 14’.
View Dr. Corral's home page.
- Dr. Peter D. Dijkstra, Assistant Professor, Biological Sciences:
- Stress and body coloration in a polymorphic cichlid fish.
The melanocortin system regulates sexual behavior, aggression, pigmentation, and the stress response. The cichlid species Astatotilapia burtoni has two distinct color types (yellow and blue) and we have evidence that the melanocortin system regulates this color variation: yellow males are more aggressive and less sensitive to stress than blue males, and α-melanocyte stimulating hormone (α-MSH, a melanocortin hormone) changes behavior and increases yellow body coloration in A. burtoni. We are interested in testing the effects of α-MSH on the stress response using hormone manipulations followed by behavioral analysis and cortisol measurements. Students use a variety of approaches (hormone manipulations, hormone measurements, behavioral analysis, statistical analysis in R).
- Oxidative stress in East African cichlid fish.
Oxidative stress is an indicator of an imbalance between the production of reactive oxygen metabolites (reactive waste products resulting from normal metabolism) and the antioxidant system. The level of oxidative stress is an indicator of the rate of aging and general stress levels. Cichlids are the most diverse group of vertebrates on the planet and are an excellent system to test how oxidative stress varies across cichlid lineages that differ in behavior, body coloration and ecological specialization. Our goal is to measure both reactive oxygen metabolites and the antioxidant defense in blood plasma collected from four cichlid species from Lake Victoria.
View Dr. Dijkstra's home page
- Dr. Cheryl Heinz, Associate Professor, Biological Sciences:
- The China Pollination Project. A team of students and two faculty will again travel to China for 3.5 weeks in May/June 2015 to study pollinators in the Shenyang and Beijing areas. Much of the research consists of observing, recording, and identifying pollinators. In 2015 we will also try to elucidate the basic biology of some of the common pollinators in these areas, based on observations from 2014. Upon return to Benedictine, data and image analyses will occur, with the possibility of local observations. More information about the China Pollination Project can be found here: http://bucpp.wordpress.com.
View Dr. Heinz's home page.
- Dr. Robert McCarthy, Assistant Professor, Biological Sciences:
- Anterior cranial fossa morphology in hominoid primates. . In modern humans, a flexed cranial base is thought to be an adaptation to fit the brain into a limited space. However, little is known about the scaling relationships of the anterior cranial fossa, the part of the cranial base that is limited in size in larger primates. We will be collecting qualitative and quantitative data from the cranial base in great apes, modern humans, and fossil hominin specimens in order to assess the relationship between the bones in the anterior cranial fossa and between anterior cranial fossa size and basicranial flexion and length.
- A phylogenetic test of homoplasy in the mammalian skeleton. . Craniodental, but not postcranial, data are often used to reconstruct phylogenies in extinct groups of mammals, a practice which reduces the number of morphological characters available to test phylogenetic hypotheses in the absence of genetic data. This practice stems from the idea that postcranial data are more prone to homoplasy than are craniodental data, an untested assumption. In this study, we will compare phylogenetic signal in cranial, dental, and postcranial data partitions from published morphological datasets using partitioned Bremer support and other phylogenetic data partitioning algorithms.
View Dr. McCarthy's summer research page
- Dr. Scott Meyer, Assistant Professor, Chemistry:
- In vitro selection:
Knowledge about the relationship between a biological molecule’s structure and its functions is central to the understanding of biochemistry. In an effort to develop systems to study the structure/function relationships of proteins and their binding partners, we will use a method called in vitro selection to discover peptide ligands for various protein targets. In our research, we will develop new approaches to phage display, a type of in vitro selection, that will facilitate the discovery of novel protein/ligand pairs. These approaches include the development of novel library architectures and the development of a real-time monitoring system for phage display.
- Biosensors Development:
DNA is a vital carrier of genetic information in multicellular organisms. As such, modifications to DNA, such as mutations and covalent modifications, are of intense interest in the biochemical and medical fields. We will use a method known as SEER (SEquence Enabled Reassembly of proteins) to develop biosensors to detect covalent modifications of DNA. Using SEER, we will be able to detect DNA damage (in the form of covalent modifications) adjacent to specific sequences of double stranded DNA. As an entry into this field, our goal is to detect DNA damage caused by the chemotherapeutic agent cisplatin. Once we construct a functional biosensor for cisplatin, we will look to develop biosensors for other kinds of DNA damage.
- Synthesis of Bile Acid Derivatives: In a collaboration with Dr. Jayashree Sarathy, we have begun the synthesis of bile acid derivatives to facilitate the study of this important class of biological molecules. The bile acid derivatives that we synthesize will be used to isolate the cellular targets of these compounds as well as tracking their interactions in isolated cell cultures.
View Dr. Meyer's home page
- Dr. Grace Mirsky, Assistant Professor, Computer Science:
- 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. Prior programming experience in Matlab, C++ or Java is required.
- 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. Prior programming experience in Matlab, C++ or Java is required.
- 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. Prior programming experience in Matlab, C++ or Java is required.
View Dr. Mirsky's home page
- Dr. Jeremy Nadolski, Associate Professor, Mathematics:
- A continued statistical look into the Tree of Heaven and possible eradication strategies.
This project is a continuation of summer research conducted two years ago in conjunction with Dr. Aldrich. Since that time, more variables and real data have been obtained to assist in judging validity of results.
- An investigation into the use of statistical trigonometry, phase and shift relationships, with emphasis on biological/physiological data.
This project will investigate how trigonometry and vectors can be used to analyze data. We will attempt to analyze two experiments conducted on crayfish (an experiment conducted at the University of Kentucky under Dr. Robin Cooper). One experiment was on the behavior of crayfish interactions and the second experiment was to look at the relationship between heart rate and ventral rate under different stimulus to determine synchronicity.
- An investigation into methods to detect outliers using Stalactite Plots and other mechanisms.
This project is a completion of a project started years ago. This project will involve programming and analysis of baseball data. The goal is to find and remove real outliers from the data based on an overall, multiple variable, approach.
View Dr. Nadolski's home page
- Dr. Peter Nelson, Professor, Physics and Biology:
There is a growing movement to transform undergraduate science education. A major goal is for students to learn how to think like a scientist. My contribution has been to develop learning modules that engage students in research activities using a “guided-inquiry” process. I have been pioneering this active-learning approach in my recent physics and biology courses (University Physics I and II, Biophysics and Physiological Modeling). This modular approach begins with a scientific investigation into the properties of a prototypical kinetic Monte Carlo simulation – “the marble game”. The marble game is a realistic simulation of Brownian motion and molecular diffusion that is inherently interdisciplinary. It provides a conceptual framework that can be applied to systems ranging from single molecules (ligand binding) to organisms (drug elimination) and entire ecosystems (population dynamics). The mathematical and computational framework provided by the marble game has universal applicability across all of science, technology, engineering and math (STEM). It can be applied to physics and engineering problems ranging from Newtonian mechanics and automotive engineering through to quantitative molecular biology and biomedical engineering. Students are engaged in an authentic research experience. They have gone on to graduate school at institutions such as Georgetown, Harvard, Northwestern and Yale. This summer, my plan is to focus on membrane transport and molecular dynamics.
For more information, visit the Biophysics and Physiological Modeling web page http://circle4.com/biophysics or contact Dr. Nelson directly.
- Two areas of membrane transport received the 2003 Nobel Prize in Chemistry – the transport of water molecules (osmosis) and potassium ions (ion channel permeation). These two processes are central to all life on earth. The marble game can be modified in a very simple way to model both of these processes in a quantitatively accurate manner at different levels of molecular detail. This project will focus on research activities that can be developed into guided-inquiry modules.
- Molecular dynamics (MD) simulations are the foundation of quantitative molecular biology (biophysics). Newton’s laws of motion are used to predict how the molecules of life behave. MD simulations can be applied to simple ions and molecules, enzymes, transporters and even small cellular machines such as ribosomes and motor proteins. This project will focus on engaging students in research activities about the fundamentals of molecular dynamics.
- Dr. David Rubush, Assistant Professor, Chemistry:
- Dr. Jayashree Sarathy, Assistant Professor, Biological Sciences:
My research goal is to identify the specific processes involved in bile acid-mediated fluid secretion. There are approximately 10 million cases of bile-induced diarrhea worldwide. Thus, it is crucial to identify the mechanisms mediating bile acid effects on intestinal barrier function, ion transport and fluid secretion. The effect of individual bile acids on ion secretion has been studied in various mammalian models. However, a combinatorial effect of primary and secondary bile acids on tight junction function and/or ion transport has not yet been studied in the presence of inflammation. Further, the second messenger pathway involved in bile acid signaling has not been delineated.
- So in project 1, the students will measure Cl- secretion and intracellular calcium levels in human colon carcinoma cells + bile acids + proinflammatory cytokines using Cl- -sensitive and calcium sensitive fluorescent dyes. Ca2+ signals and Cl- secretion will be captured using the newly acquired spectrofluorometer and/or a fluorescence microscope.
- In project 2, if there is a change in [Ca2+]i upon bile acid exposure, the source of this calcium will be further examined. To confirm the role of Ca2+ in bile-acid induced Cl- secretion (Cl- is the major ion that aids in fluid secretion in the colon), [Ca2+]i can be chelated with agents such as BAPTA and the effect of bile acid on Cl- secretion will be observed in an Ussing chamber or using MQAE fluoremetry.
Overall this study will contribute to the greater understanding of bile acid physiology and will offer novel insights into therapeutic targets for the treatment of bile acid-induced diarrheas, as seen in inflammatory bowel diseases.
View Dr. Sarathy's home page
- Dr. Sarah Shaner, Assistant Professor, Chemistry:
Research in my lab applies the techniques and strategies of inorganic and electrochemistry to develop materials with interesting properties and functionalities. Student researchers in my lab will learn to perform electrochemical experiments and gain experience in the synthesis and characterization of molecules, metal complexes, and materials.
- Electrografting of molecules and metal complexes onto conductive surfaces.
The development of high-yield routes to attach organic molecules and metal complexes to surfaces is important in many areas of science, such as electrode protection, attachment of catalysts and biomolecules, dye-sensitized solar cells, sensors, and the formation of single-molecule junctions. Covalent bonds provide robust, well-defined linkages between substrate surfaces and organic or inorganic moieties. One method for introducing molecules onto surfaces is electrografting, which typically involves the electrochemical generation of a relatively stable radical with subsequent bond formation with the surface. Our efforts will focus on:
(1) identifying and developing new classes of molecules that are suitable electrografting precursors, and (2) exploring post-surface-attachment functionalization reactions.
- Earth-abundant metal oxide catalysts for the water oxidation reaction.
There is much interest in harnessing solar energy to produce chemical fuels, such as hydrogen, which can serve as environmentally friendly alternatives to fossil fuels. One approach to this challenge is the optimization of the water splitting reaction, which splits water molecules into H2 and O2. Catalysts are necessary to facilitate this reaction, but the best catalysts often are made of very expensive and rare metals. Our research will focus on identifying and developing alternative catalysts that are made from combinations of earth-abundant metals that can compete with their expensive counterparts.
View Dr. Shaner's home page
- Dr. Kari Stone, Associate Professor, Chemistry:
- 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
- Dr. Ellen Zilliak, Assistant Professor, Mathematics:
- Computing the Structure of Generalized Symmetric Spaces: For over 100 years symmetric spaces have been of interest to geometers, group theorists, physicists and topologists. These spaces have been generalized and many open questions exist concerning the characterization and classification of various symmetric spaces. In this project we will choose one of the open groups and classify the involutions, compute the fixed point group, generalized symmetric space and extended symmetric space. We will determine if our group follows the patterns that have been found for other groups. Finally we can study the orbit decomposition of the generalized symmetric space by various subgroups. The project will be computational by nature, using the software GAP to investigate and classify these groups.
- Cayley Graphs and Colored Graphs: A Cayley graph is a directed graph that encodes the multiplication table for an algebraic structure. These graphs can be used to study many interesting problems including constructing group extensions and cryptosystems based on algebraic structures. In this project I would like to study a related graph called a Colored graph which is a graph that generalizes the notion of distance. It was first introduced in the paper “Groups of graphs of groups” by Sibley, Byrne, and Donner. In this project we will investigate properties of these two graphs. Interesting questions include which Cayley graphs have the same Colored graph, and how this classification is related to the algebraic structure encoded by the graphs.
- Cryptography in Group Theory:
Public key cryptosystems have been used for secure communication between two parties. This system is used most often when the two individuals who wish to communicate have not met prior to the communication. It is used often in online transactions. Most of the algorithms currently used rely on modular arithmetic in Zp however the need to ensure security has led to explorations in the field of noncommutative groups. In this project we will study how noncommutative groups are used for developing new approaches and study several of the open questions associated with their use.
- The Algebra of Rewriting: In mathematics, one method of defining a group is by a presentation. Every group has a presentation. A presentation is often the most compact way of describing the structure of the group. However there are also some difficulties that arise when working with groups in this form. One of the problems is called the word problem which is an algorithmic problem of deciding whether two words represent the same element. I want to study the word problem on group extensions. Currently there is a procedure called coset enumeration which can be used to address this problem, however it has difficulties with memory when the groups reach a certain size. In this project we will continue the work of a former student to compute in the group extension using a modified coset enumeration technique. This method is derived using the Cayley graphs for the two smaller groups.
View Dr. Ziliak's home page