"It's education and fun wrapped in one good bundle!"

—Theresa Kimmitt

Participating Faculty for Summer 2013

Please consult faculty members before making selections on your application!

Faculty below will have research programs this summer:

Dr. Preston Aldrich(paldrich@ben.edu) Associate Professor and Chair, Biological Sciences

Gene regulatory networks, promoter networks, and/or protein similarity networks and the evolution of natural languages

Dr. Timothy Comar (tcomar@ben.edu) Associate Professor, Mathematics

1.      Biological Models using Impulsive Differential Equations. The dynamics of models forintegrated pest management and epidemics are investigated.  Attention ispaid to finding conditions for the existence and stability of total pesteradication solutions/disease free solutions and permanent solutions.Stochastic effects and delays may be incorporated into these models

2.       Dynamics of GeneRegulatory Networks:  We primarily study small gene regulatory network viaBoolean models.  We are interested in how the dynamics is determined bythe structure of the network.  We are also interested in the relationshipbetween the dynamics in Boolean models using synchronous versus asynchronousupdate.  Finally, we would like to continue the study of the relationshipsbetween Boolean dynamics and continuous dynamics these networks

Dr. Anthony DeLegge (adelegge@ben.edu) Assistant Professor,Mathematics

 1.   "An Epidemic Model with a Multi-Stage Vaccine" This project will be a continuation of work done with Reema Khatri, KiranMunir, and Katie Hunzinger over the past two summers.  So far, we haveconstructed mathematical models to help us study the spread of a diseasethrough a population such that immunity can be given through a series of multiplevaccines.  A perfect example of such a disease would be Hepatitis B, whichrequires three vaccines for immunity.  Up to this point, however, we haveproven that, assuming the population has births and deaths, it is not possibleto completely eradicate a disease unless the disease was going to die outanyway.  So, this summer, I hope to extend this to looking at repeatingthe vaccination cycle numerous times and/or changing how the vaccine is givenso that we can kill the disease off, or even better, suppress it for a longerperiod of time.  If time permits, we may also try to build in morerealistic contact patterns.

2. "A Model for Disease Spread With Different Susceptibility Levels" For some diseases, such as the common cold, it really seems like certain individualsjust have a much better chance of getting sick than others (or even not gettingsick at all!) when coming into contact with an infected individual.  Thisproject will concern constructing and studying a model for disease spread suchthat people are placed into different susceptibility groups, where some groupsare more likely to get sick by coming into contact with infectives than others,and some people may even have full immunity to the disease.  Specifically,we want to study how sensitive the spread of disease throughout a population isbased on how the make-up of the susceptible groups is.  That is, if onegroup is pretty much the driver toward having a disease become endemic, can wequarantine the group (or some similar strategy) to stop the spread of thedisease?

 3. "Monopoly:  The Speed Die" Monopoly is arguably one of the world's most popular board games.  It isso popular that, every so often, a world championship tournament is held. In the past tournament, however, a new rule was introduced, which has also madeits way into the home game:  the "Speed Die."  Rolling thespeed die not only, as its name suggests, speeds up the game play, but it canalso affect strategy greatly.  A player could simply move extra spaceswith it, could have the choice to move using only one die as opposed to two, orend up getting to purchase two properties in a single turn (or, even worse,paying rent on two properties in a single turn).  The strategy for theclassic game of Monopoly has been extensively studied, but this project willinvestigate if those strategies are still the best ones to do when playing withthe "Speed Die."  If time permits, we will also investigateplaying under tournament rules (games are timed) to see if those strategiesshould be adapted in the tournament setting at all. 

Dr. Cheryl Heinz (cheinz@ben.edu) Associate Professor, Biological Sciences

Ecologicalfield work including surveys and samples of plants and butterflies in the localarea. Behavioral observations on the host-plant choices of the blackswallowtail butterfly. Physiological plant ecology of native prairie plants.Preference and performance assays with caterpillars and moths, continuing astudy to look at the effects of plant nutrient status with these insectbehaviors. 

Dr. Manhoman Kaur (mkaur@ben.edu) Associate Professor, Mathematics

1. Cryptography Elliptical Curve cryptography isused in small hand held devices like the Blackberry to ensure secure transferof information. Recently the security of certain Elliptic curve cryptosystemshas been challenged. We will look study the security of Elliptic CurveCryptosystems. Preferred: students who have completed Math 385, Introduction to Modern Cryptology.
2. Quantum Information SystemsThistopic is at theintersection of Quantum information systems, Real Analysis and Linear Algebra.Preferred: Students who have completed Linear Algebra and Real Analysis.

Dr. Robert McCarthy (rmccarthy@ben.edu) Assistant Professor, Biological Sciences

The Role of the Vocal Tract in Speech Production. The supralaryngeal vocal tract (the pharynx and oral cavityabove the vocal cords) determines, to some extent, the acoustic properties ofspeech sounds. Radiographic studies have shown that the shape of the tongue,vocal tract, and lips is instrumental in producing the unique sounds of humanspeech. However, recent magnetic resonance imaging (MRI) studies image patientsin a supine position, which changes the position of the tongue and larynx inthe neck. These images have been used to inform clinical diagnoses and toreconstruct the size and shape of the vocal tract in Neanderthals and otherextinct human species. In this project, students will be assisting in thecollection of MRI data using a new technology, upright MRI, which has thecapability of imaging a patient in multiple views, including while sitting orstanding. Students will then: (1) compare MR images of subjects in sitting andsupine position; (2) record audio for subjects reading lists of words and shortpassages; (3) process and analyze acoustic data; and (4) statistically assessthe relationship between vocal tract morphology and acoustic data. This projectwill teach students to collect and interpret MR images, to process acousticdata, and to use statistical techniques to study the relationship between vocaltract morphology and the sounds of human speech.

Dr. Scott Meyer (smeyer@ben.edu) Assistant Professor, Chemistry

1. In vitro selection Knowledge about the relationship between a biologicalmolecule's structure and its functions is central to the understanding ofbiochemistry.  In an effort to develop a system with which to study the structure/functionrelationship of proteins and their binding partners, we will use a methodologycalled in vitro selection to discover peptide ligands for an importantprotein called NeutrAvidin. NeutrAvidin is a variant of a biotin-bindingprotein called avidin that is widely used in biotechnological techniques. For our project, we will explore the idea of changing the shape of a peptidefrom a cyclic peptide (constrained by an intramolecular disulfide bond) to apeptide with a well-defined secondary structure.  Using phage display, atype of in vitro selection, we will probe libraries that containhundreds of millions of different peptides to see what binds toNeutrAvidin.  Once we have discovered NeutrAvidin binding peptides, wewill synthesize the peptides in the lab and interrogate their binding(function) in relation to their amino acid sequences (structure). 
2. Biosensors Development DNA is a vital carrier of genetic information inmulticellular organisms.  As such, modifications to DNA, such as mutationsand covalent modifications, are of intense interest in the biochemical andmedical fields.  We will use a method known as SEER (SEquence EnabledReassembly of proteins) to develop biosensors to detect covalent modificationsof DNA.  Using SEER, we will be able to detect DNA damage (in the form ofcovalent modifications) adjacent to specific sequences of double strandedDNA.  As an entry into this field, our goal is to detect DNA damage causedby the chemotherapeutic agent cisplatin.  Cisplatin is known to deform orkink DNA by covalently binding to adjacent nucleotide bases.  Thedeformation of DNA is thought to be the cause of cisplatin's toxicity andtherefore its efficacy as a chemotherapeutic agent.  Because of thedeformation, a protein called High Mobility Group Box Domain 1 (HMGB1) can bindto the cisplatin/DNA adduct more tightly than it can to unmodified DNAalone.  This binding selectivity should allow us to eventually use HMGB1in SEER biosensors to detect where in the human genome cisplatin is damaging DNA. 

Dr. Jeremy Nadolski (jnadolski@ben.edu) Associate Professor,Mathematics

The investigation using a Bayesian Occupancy model to detect the dispersion and possible eradication of the tree of heaven from West Virginia.

Dr. Jayashree Sarathy (jsarathy@ben.edu), Assistant Professor,Biological Sciences

1.Does bile acid modulate tight junction to increase paracellular permeability?Cells will be grown on inserts to form a monolayer, challenged with variousdoses of bile acid. Transepithelial resistance will be measured usinganelectrical resistance system and paracellular permeability measured viamucosal to basolateral flux of 10-kDa fluorescence tagged dextran.

2.Is the drop in resistance due to cytotoxic effects of bile acids? This will beassessed by measuring lactate dehydrogenase activity in the supernatant ofcells treated with various doses of bile acids. Cytotoxicity is indicated ifthe LDH activity is increases in the solution. This is measured using acolorimetric assay.

Dr. Kari Stone (kstone@ben.edu), Assistant Professor,Chemistry

Bioinorganic Chemistry: My research program seeks an alternative to multi-electronsmall molecule transformations by utilizing transition metal complexescoordinated to redox-active ligands in order to make new nitrogen-containingmolecules.Information obtained from these studies will be applied toward thedevelopment of catalysts.The aim of this endeavor is to prepare metal complexeswith catecholate ligands with oxygen, nitrogen, or sulfur donor atoms that areknown to have low-lying redox states to exploit their reactivities.We aremoving away from metals in high oxidation states and utilizing novel ways ofachieving electron transfer to perform desirable chemicaltransformations.Asymmetric nitrene transfer will be the target reaction whereazides will be the nitrene reagent.Transition metal complexes with redox-activeligands will be synthesized and their reactivity will be surveyed with respectto catalytic nitrene transfer via environmentally benign methods.

Dr. Ellen Ziliak (eziliak@ben.edu), Assistant Professor, Mathematics

1.      Magic Graphs and Quasigroups: A Quasigroup is a set ofelements with a binary operation whose multiplication table forms a Latinsquare.  Latin squares are precisely whatyou get when you solve a Sudoku game.  ALatin square is in a class of special combinatorial objects called magicsquares.  In fact a Latin square isa semimagic square.  In graphtheory semimagic squares can be identified with a super magic labeling ofthe complete bipartite graph on n points. In group theory a graph which describes the multiplication table for agroup is called a Cayley Graph. Unfortunately for quasigroups it seems that manydifferent Cayley graphs can be constructed for one quasigroup.  In this project I want to study these supermagic labeled graphs to see if one can use them to construct a graph similar tothe Cayley Graph for a group.  Thehope is that this new graph would be more useful for answering severalquestions about quasigroups. 

2.      Cryptography and Quasigroups: A quasigroup is a set ofelements with a binary operation whose multiplication table forms a Latinsquare.  Latin squares are precisely whatyou get when you solve a Sudoku game. These algebraic structures have applications in many areas including thefield of Cryptography.  Cryptography isthe study of secure communication when a third party is present.  Recently quasigroups have been used inseveral cryptographic applications including Message Authentication Codes.  In this project we will continue the work ofa former student to study properties of this algebraic object to determinewhy quasigroups are useful in this field.

3.   Cryptography in Group Theory: Publickey cryptosystems have been used for secure communication between twoparties.  This system is used most oftenwhen the two individuals who wish to communicate have not met prior to thecommunication.  It is used often inonline transactions.  Most of thealgorithms currently used rely on modular arithmetic in Zp however theneed to ensure security has led to explorations in the fieldof noncommutative groups.  In thisproject we will study how noncommutative groups are used for developingnew approaches and study several of the open questions associated with theiruse. 

4.   The Algebra of Rewriting: In mathematics, one method of defining a group is by a presentation.  Everygroup has a presentation.  A presentation is often the most compact way ofdescribing the structure of the group.  However there are also somedifficulties that arise when working with groups in this form.  One of theproblems is called the word problem which is an algorithmic problem of decidingwhether two words represent the same element.  I want to study the wordproblem on group extensions.   Currently there is a procedurecalled coset enumeration which can be used to address this problem,however it has difficulties with memory when the groups reach a certainsize.  In this project we will continue the work of a former student tocompute in the group extension using a modified coset enumerationtechnique.  This method is derived using the Cayley graphs for thetwo smaller groups.

Dr. Robin Rylaarsdam (rrylaarsdam@ben.edu) Associate Professor, Biological Sciences

McCune-Albright Syndrome is a genetic disease caused by a mutation that permanently activates the Gs alpha protein in cells. Previous work in the laboratory identified several secondary mutation in the G alpha gene of yeast that can reverse the     permanent activation caused by the MAS mutation. Summer students will systematically introduce the homologous amino acid substitutions into the human Gs alpha gene to investigate the structural requirements for inactivating the McCune-Albright mutation. The work will involve  site-directed mutagenesis, mammalian cell culture and transfection, western blotting, ELISA assays, and microscopy. Students may also work on microarray experiments that identify gene expression changes in human     osteoblasts that are associated with activation of the Gs protein.

Dr. Andrew Wig (awig@ben.edu) Associate Professor, Physics

1. Optical Tweezers: Research will be conducted to use the BU optical tweezers instrument to study biological systems. Optical tweezers use focused light to trap and manipulate small objects. The initial study is focused on the trapping and  analysis of E. coli bacteria. The project is experimental and  involves learning about optics, lasers, and the interaction of light with matter.

2.  Scanning Probe Microscopy: A Scanning Tunneling Microscope (STM) is a device used to image surfaces of materials with atomic resolution. This project will involve building and testing an STM. It is an experimental project and will involve computer     programming and electronics.

Dr. Peter H. Nelson (phnelson@ben.edu), Associate Professor, Physics

BiophysicsTeaching Materials: As part of an NSF grant I'm developing new biophysics teaching materials.Topics include: oxygen, water, glucose, ion and drug transport; ion channelgating (neuroscience); motor proteins; DNA and RNA dynamics and more. I'mlooking for research students to determine the current state of knowledge andto find the numerical data required for biophysical models. Right now I'mlooking for students to help me investigate water
transport through aquaporins.In the process, we learn some basic physiology,including such things asosmosis and homeostasis of erythrocytes (red blood cells) from a biophysicsperspective! There are many other topics available —
for more information visitthe project web page http://circle4.com/biophysics-or contact Dr. Nelson directly.