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Welcome to the
!rd A&&'a) *+,-, .&dergrad'a1e +esear34 56m8os:'m
Rose-Hulman Institute of Technology
Friday, November 3, 2006
We are honored to welcome you to the 3rd Annual IRCBC Undergraduate Research
Symposium and we sincerely appreciate your participation. The symposium is
coordinated by the Interdisciplinary Research Collaborative in Biology and
Chemistry (IRCBC), and is supported by funding from the Merck/AAAS
Undergraduate Science Research Program, the Lilly/Guidant Applied Life Sciences
Research Center, and Rose-Hulman Institute of Technology.
The IRCBC was created to encourage scientific research by undergraduate students
and to help them better understand the exciting educational and research
opportunities that lie at the interface of biology and chemistry. An appreciation for
laboratory research is central to a working understanding of experimental sciences
such as biology and chemistry. By participating in research, students add to current
knowledge and, furthermore, they enhance their education and broaden their
understanding of the scientific method and its application.
Interdisciplinary research is gaining prominence in both academia and industry, as
new techniques from one discipline are applied to problems in other disciplines. By
acquiring experience in interdisciplinary research, students become more attractive
to potential post-graduate programs and employers. The IRCBC program specifically
fosters such interdisciplinary work, and we are pleased to highlight the research of our
students, as well as the research of our colleagues in Indiana.
With this third annual event, we are delighted to welcome you. Our intention in
hosting this event is to offer students an opportunity to share their research interests
and progress with their colleagues in a nurturing and supportive environment, and to
encourage celebration of the undergraduate research experience. We hope you enjoy
the dynamic program of speakers.
Mark Brandt
IRCBC Program Coordinator
Ella Ingram
IRCBC Program Coordinator
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
3
Symposium Schedule
8:15 AM Registration
9:00 AM Welcoming Remarks – Lee Waite, Department of Applied Biology &
Biomedical Engineering, Rose-Hulman Institute of Technology
Scheduled Presentations
!hemical and Biological /unctioning of a !onstructed 5etland
Ashlee Brewer!, Jill Floyd!, Ella Ingram, Penney Miller, and Michael Robinson
Simplified Salen 8igand !ataly:ed !opolymeri:ation of !yclohexeneoxide
and !<=
Ross Poland!, 8eremy Andreatta, Wonsook Choi, Cass Richers, and >onald
>arensbourg
>fficient !oupling of Aryl Halides and Phenylboronic Acid under
>nvironmentally /riendly !onditions
Amanda Isom! and Rebecca >eVasher
<ptimi:ation of the Succinate Dehydrogenase Eital Staining Procedure for
Arbuscular Mycorrhi:as
Meagan Gallagher! and Ella Ingram
Break
Gole of T-bet in the Jeneration of Pulmonary Atopic Inflammation
A. Mae Huehls!, Sarita Sehra, and Mark HC Kaplan !
Jenetic and Biochemical !haracteri:ation of Arabidopsis thaliana
Putative Disease Gesistance Jenes
Emma Hegwood! and 8C Peter Coppinger
Anharmonic Eibrations of a LM !arbon System
Ivan Kornienko! and >aniel 8elski
12:00 PM Invited Speaker – Bruce Alberts, Department of Biochemistry &
Biophysics, University of California, San Francisco, President of the National
Academy of Sciences (1993-2005)
1:00 PM Lunch
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
2:00 PM Afternoon Session
Purification and Inhibition of Recombinant Vaccinia Virus H1 Protein
Anita Mathur*, Julia Huang and Mark Kaplan
Determining Cooperativity of the Human Estrogen Receptor Through
Tryptophan Fluorescence Quenching
Adam G. Georgas* and Mark E. Brandt
The Effect of Alcohols on the Rate of Estrogen Receptor Dimer Exchange
Rebecca J. Waltz*, David M. Knapp, Rachel Krasich, Andrei L. Edwards, and
Mark E. Brandt
The Accuracy of Laser-Induced Breakdown Spectroscopy in Quantifying
Carbon in Soils
Rachel M. Selby*, L. Edwards, I.B. Gornushkin, B.W. Smith, and J.D.
Winefordner
Break
Method Development and Microfluidic Device Design for Separation and
Detection of Modified Nucleosides
Christian Sweeney* and Daniel L. Morris
Combustion Toolbox
Mark Vaccari* and Dan Coronell
Particle Size Effects in the Pretreatment of Wood Waste Leading to
Enhanced Ethanol Production
Amanda Grantz*, David J. Dixon, and Patrick C. Gilcrease
Prevention of Membrane Pore Formation Via P2X7R-Cx43 Interaction
Christina Chrisman*, M. Cohen, S.O. Suadicani, D.C. Spray, and E. Scemes
Additional abstract (not scheduled for presentation)
Observation of the Bioluminescent Reaction Between Aequorin and
Calcium Ions
Christina. A. Shook* and Alfred Carlson
4
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
5
Chemical and Biological Functioning of a Constructed Wetland
Ashlee Brewer*1, Jill Floyd*2, Ella Ingram2, Penney Miller1, and Michael Robinson3
1Department of Chemistry, 2Department of Applied Biology & Biomedical
Engineering, and 3Department of Civil Engineering, Rose-Hulman Institute of
Technology, Terre Haute, IN 47803
Wetlands provide a means of managing water quality because a combination of
biological, chemical and physical mechanisms work to improve water quality as
water passes through a wetland. Constructed wetlands may function differently
than natural wetlands in these respects due to constraints introduced during the
construction process, to missing components of the system, or any number of other
reasons. Our goal was to characterize the baseline water quality parameters and
biological properties of the J.I. Case Wetland and Wildlife Refuge, constructed
approximately 30 years ago by the Vigo County Parks Department, to determine if
it functions to improve the quality of surface water draining from its agricultural
watershed. Environmental monitoring stations at the inlet and outlet monitored
dissolved oxygen, pH, conductivity, turbidity, chlorophyll, temperature and depth
on a 24-hour basis. We collected water samples from the wetland inlet and outlet
three times per week, and performed chemical and algal sampling along transects
across the inlet and outlet sites to resolve spatial differences in water quality and
biological productivity. We analyzed these samples for dissolved oxygen, pH,
dissolved organic carbon (DOC), total nitrogen, and alkalinity. At both the inlet and
the outlet, dissolved organic carbon and total nitrogen content of the water were
strongly negative correlated. For water flowing into the wetland, we found no
relationship between either DOC or total nitrogen and dissolved oxygen. For water
exiting the wetland, we found a strong negative relationship between DOC and
dissolved oxygen, and a strong positive relationship between total nitrogen and
dissolved oxygen. These results suggest that both biotic and abiotic processes to
modify water quality were occurring within the wetland to create the observed
relationships by the time the water reached the outlet. In the future, we plan to
identify these processes and their controls, to eventually compare the functioning of
this constructed wetland to the functioning of similar but naturally occurring
wetlands.
6
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
Simplified Salen Ligand Catalyzed Copolymerization of Cyclohexeneoxide
and CO2
Ross Poland*, Jeremy Andreatta, Wonsook Choi, Cass Richers, and Donald
Darensbourg
Department of Chemistry, Rose-Hulman Institute of Technology, Terre Haute, IN
47803 and Department of Chemistry, Texas A&M University, College Station, TX
77842
Production of polycarbonates is a very widely
utilized industrial reaction. Polycarbonate plastic
is used in many facets of our civilization, whether
it be in automobiles, computers, or in medicine.
The reaction pathways most used in industry to
produce polycarbonates tends to utilize reagents
that are hazardous to human health and the
environment. A movement known as green
chemistry
attempts
to
develop
more
environmentally friendly reaction conditions,
reagents, and products. In this example, the
polymerization reaction is made more green by
negating the need for organic solvents. Green
routes to polycarbonate production being studied
at Texas A&M University are run in liquid CO2
with organometallic catalysts. CO2 serves as both a solvent and a monomer, as does
cyclohexeneoxide. In order to accomplish the efficient production of polymer, a
salen ligand, which is characterized by an N2O2 functionality, was synthesized in an
inert atmosphere. The salen synthesized is unique in that it doesn’t contain an
aromatic ring typical of most salens, and also has a more flexible backbone due to
the lack of doubly bound nitrogens. The ring-opening mechanism of the epoxide (2(trifluoromethyl)oxirane)) coupled with substitution on to a symmetric amine
(N1,N2-dimethylethane-1,2-diamine) produced the salen ligand in moderate
yield. Chromium(II) was complexed by the ligand after reduction of chromium(III)
to chromium(II) with KH as the reducing agent. This yielded the catalyst in a
stable, solid state which was then purified using dichloromethane. Once pure, the
catalyst and its co-catalyst (tetra-n-butylammonium chloride) were dissolved in
cyclohexene oxide. This mixture was then transferred via cannula to a high
pressure reactor and liquid CO2 was added until the pressure in the reactor was
approximately 600 psi. This reaction was allowed to run for at least 12 hours and
was monitored in situ using a ReactIR spectrometer. The general polymerization
mechanism is known, but the distinct properties of this catalyst are still unclear.
The results show that there is more to be discovered by functionalizing salen
ligands, which will lead to further opportunities for research and hopefully more
effective catalysts.
X'
O
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O
X
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X'
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O
O
O
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Optimization of the Succinate Dehydrogenase 7ital Staining Procedure for
Arbuscular Mycorrhizas
Meagan (allagher,- and Ella Ingram
2epartment of 7pplied 9iolog: ; 9iomedical Engineering- Rose?Hulman Institute
of Bechnolog:- Berre Haute- IN DE!0G
7rbuscular m:corrhizas are eJtremel: common mutualistic associations betKeen
plant roots and soil fungi. Bhese s:mbiotic fungi form structures inside the plant
roots for nutrient eJchange- Kith the plant receiving valuable nutrients in eJchange
for its carbon resources. 7ll strategies to visualize these m:corrhizal associations
use techniNues to differentiate fungal and root tissues- Kith the most common of
these methods involving the staining of chitin?containing structures. Ohile these
methods can distinguish betKeen plant material and fungal material- the: do not
distinguish betKeen the active and inactive fungal associations. Pital stain
techniNues- based on the metabolic enz:me succinate deh:drogenase hoKever- do
distinguish betKeen active and inactive fungal tissue. In this stud: the vital
staining procedure Kas applied to the arbuscular m:corrhiza of ma:apple
!"#"$%&''()* $+',-,() Q.- a common temperate forest herb. Bhe vital staining
procedure Kas tested at various points to obtain a protocol that Kould :ield more
desirable results as Kell as minimize cost and time. 9leaching roots Kith
ammonium h:droJide is recommended- but Kas found to be unnecessar: for
visualizing this m:corrhizal association. Bhe amount of time the roots Kere eJposed
to ROH for clearing purposes Kas also tested and a time of T hrs Kas found to be
sufficient- although up to 2Dhrs Kas also shoKn to be adeNuate as Kell- Kithout
significant negative outcomes for the roots. Bherefore- depending on time
constraints an: time Kithin that range Kould be effective. Voaking the roots in
lactogl:erol to destain before mounting Kas also tested and Kas found to have no
effect on cell clarit:. Bhe vital staining procedure Kas then compared to the non?
vital staining procedure using tr:pan blue to determine differences in the percent of
root colonization observed via the tKo methods- their relative costs and time
reNuired. Bhe tKo procedures resolved a similar amount of fungal tissue in the plant
roots- determined using a standard microscopic Nuantification techniNue. Bhe final
eJperiment performed shoKed that the neKest roots Kere colonized b: mid?7ugustearlier than eJpected based on data obtained via the tr:pan blue- non?vital staining
procedure. 9ased on the eJperiments performed and the comparisons made- it is
recommended that the vital staining procedure not be used for most eJperiments
Khere percent colonization or general knoKledge is sought- due to the cost- resultsand time spent performing procedure. HoKever- it Kould be useful for studies
seeking information regarding changes in the ratio of inactive and active tissue
throughout time.
Bhis Kork Kas funded in part b: the IRC9C under the auspices of the MerckY777V
Zndergraduate Vcience Research Program.
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3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
10
Genetic and Biochemical Characterization of Arabidopsis thaliana
Putative Disease Resistance Genes
Emma Hegwood*, and J. Peter Coppinger
Department of Applied Biology & Biomedical Engineering, Rose-Hulman Institute
of Technology, Terre Haute, IN 47803
NDR1 (nonrace-specific disease resistance-1) is required for pathogen resistance in
Arabidopsis thaliana. Studies have shown that null mutations in this gene result in
enhanced susceptibility to bacterial pathogens. NDR1 is flanked by two putative
genes, NDR2 and NDR3, which exhibit greater than 80% sequence similarity to
NDR1. The sequence similarity to NDR1 suggests that NDR2 and NDR3 may also
play key roles in pathogen resistance, though it is currently unknown whether
NDR2 or NDR3 are expressed in planta. In an attempt to investigate this
hypothesis, we generated epitope-tagged alleles of NDR2 and NDR3 in an
Agrobacterium 35S binary expression vector. These constructs will be transformed
into Arabidopsis and Nicotiana benthamiana to study the post-translational
processing and localization of these proteins. Concomitantly, we have initiated a
reverse genetics approach to determine the biological function of NDR2 and NDR3
in vivo. Mutant Arabidopsis lines containing “knock-out” T-DNA insertions in the
NDR2 and NDR3 ORFs were identified through published seed stocks. We are
currently testing these “knock-out” lines for an altered disease resistance
phenotype. The goal of this research is to elucidate the mechanisms of the pathogen
resistance pathways in Arabidopsis, which may ultimately enrich our
understanding of disease resistance in agriculturally significant crops.
This work was funded in part by the IRCBC under the auspices of the Merck/AAAS
Undergraduate Science Research Program.
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
11
Anharmonic Vibrations of a 60 Carbon System
Ivan Kornienko* and Daniel Jelski
Department of Chemistry, Rose-Hulman Institute of Technology, Terre Haute, IN
47803
The soccer ball shaped molecule, known as bucky ball, consists of 60 identical
carbon atoms positioned in a sphere. The chemically identical nature of all carbons
allows for a relatively simple mathematical model of a large, seemingly complex
system. A previously proposed equation for modeling the behavior of atoms in this
system was implemented to prove it’s validity by using a computational approach.
In order for the complex system to be rigorously tested, an efficient language had to
be chosen for the implementation. In accordance with this FORTRAN was the
choice. These proved to be a challenge because of the complexity of code required
and the inability to use modern object oriented techniques. To deal with the
problem, modern refactoring and organizational techniques were tailored to
FORTRAN to create an efficient and easily modifiable piece of code. Furthermore, to
prove the validity of the results provided by the FORTRAN code, a preliminary Java
program was written to generate 3d manifestations of the carbon atom positions of
the bucky ball.
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
12
Purification and Inhibition of Recombinant Vaccinia Virus H1 Protein
Anita Mathur-, /ulia Huang and Mark 5aplan
Department of Chemical Engineering, Rose-Hulman Institute of Technology, Terre
Haute, IN 47803 and Department of Pediatrics, Herman B. Wells Center for
Pediatric Research ! Indiana University School of Medicine, Indianapolis, IN 46202
Sariola, a member of the poxvirus family is the causative agent of smallpox and has
long been recognized has a potential threat in biowarfare. Saccinia virus is a highly
related poxvirus and is used as the vaccine for smallpox. Since smallpox has been
largely eradicated worldwide, infants and adults are no longer routinely
immunized. Both Sariola and Saccinia employ a number of immune evasion
mechanisms including blocking interferon (IFN) signaling that is required for
optimal viral clearance. SH1 is a Saccinia encoded phosphatase that is important
for the viral life cycle and disrupts IFN signaling in part by dephosphorylating
tyrosine residues of STAT proteins. Previous attempts to purify recombinant SH1
have yielded inactive enzyme. We have employed an altered protocol in the attempt
to obtain purified active enzyme that can be used for in vitro assays. We also tested
the efficacy of phosphatase inhibitors in an assay for SH1 activity using
recombinant protein bound to the purification resin with the rationale that
inhibition of the SH1 phosphatase could be a treatment for poxvirus infection. We
tested various inhibitors using the p-Nitrophenyl Phosphate (pNPP) colorimetric
assay. Six inhibitors of known phosphatase targets were tested. Significant
inhibition was only observed with a broad spectrum inhibitor. An inhibitor of the
related mammalian kinase SHR did not have an effect. Purified SH1 will be tested
with additional inhibitors and used for additional in vitro assays.
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
13
Determining Cooperativity of the Human Estrogen Receptor Through
Tryptophan Fluorescence Quenching
Adam G. Georgas* and Mark E. Brandt
Department of Chemistry, Rose-Hulman Institute of Technology, Terre Haute, IN
47803
The estrogen receptor protein plays a key role in the development of breast cancer.
In order to learn more about the disease and its treatment, the effect of ligands such
as the commonly prescribed anti-cancer pharmaceutical, tamoxifen, on the receptor
protein must be understood. By measuring the amount of tryptophan fluorescence
quenching through fluorescence spectroscopy, the amount of ligand bound to the
receptor can be determined. Previous experiments showed that methanol, which is
required for Tamoxifen solution preparation, affects the protein’s conformation less
than other solvents. Under these conditions, the experimental reproducibility
increased. Usual methods of curve fitting were not robust, yielding to non-unique
fitting parameters. By employing a highly iterative least squares optimization
method written in Matlab, unique solutions for the Hill coefficient and K0.5 fitting
parameters were achieved. Analysis shows that the human estrogen receptor
exhibits positive cooperativity with the Hill coefficient being 1.41 ± 0.07 and K0.5
being 0.024 ± 0.006 µM. Determining the effects of ligand on the estrogen receptor
will give us greater insight in how this protein functions, and may allow researchers
to develop improved pharmaceuticals for the treatment of breast cancer.
This work was funded in part by NSF MRI Program Award CHE-0521430.
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
14
The Effect of Alcohols on the Rate of Estrogen Receptor Dimer Exchange
Rebecca J. Waltz*, David M. Knapp, Rachel Krasich, Andrei L. Edwards, and Mark
E. Brandt
Department of Chemistry, Rose-Hulman Institute of Technology, Terre Haute, IN
47803
The ligand-binding domain (LBD) of the estrogen receptor protein can be expressed
in Escherichia coli as an independently folding peptide covalently attached to
maltose binding protein. This 70 kDA fusion protein is cleaved during purification
to release the 30 kDa LBD. Both the fusion protein and the isolated LBD form noncovalently associated dimers in solution; the two interacting polypeptides exchange
partners with a half-life dependent on the strength of the interaction. Previous
studies have suggested that binding of both physiological and non-physiological
ligands has a significant effect on the protein dimer exchange half-life. Because
estradiol and other ligands have limited solubility in water, these compounds are
typically dissolved in organic solvents prior to use. Full characterization of the
effects of ligand binding requires an understanding of the effect of organic solvents
on the protein. The kinetics of dimer exchange were measured using HPLC gel
filtration chromatography following pre-incubation of the homodimeric LBD and
fusion protein homodimers in the presence of low concentrations of organic solvent.
The half-life of wild-type protein in buffer was about two hours. Low concentrations
(0.1 to 0.5% by volume) of small mono-functional alcohols ranging from methanol to
1-butanol reduced the half-life in a concentration-dependant manner. The decrease
in half-life was positively correlated with the boiling point of the alcohol tested,
suggesting that the effect is mediated by non-polar interactions with the protein.
Because changes in the dimer exchange half-life imply perturbations of the protein
structure affecting the dimer interface, characterizing these effects may improve
understanding of the estrogen receptor protein. The low concentrations of alcohols
used further suggest possible physiological significance to these studies.
This work was funded in part by the IRCBC under the auspices of the Merck/AAAS
Undergraduate Science Research Program.
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
15
The Accuracy of Laser-Induced Breakdown Spectroscopy in Quantifying
Carbon in Soils
Rachel M. Selby*, L. Edwards, I.B. Gornushkin, B.W. Smith, and J.D. Winefordner
Department of Chemistry, Rose-Hulman Institute of Technology, Terre Haute, IN
47803 and Department of Chemistry, University of Florida, Gainesville, Florida
32611
The purpose of this research is to use Laser-Induced Spectroscopy (LIBS) to
determine the most accurate method of quantifying carbon in soils by comparing the
integrated areas of the carbon (C) and the carbon-nitrogen molecular bands (CN).
LIBS Advantages
Possibility of remote sensing
In-situ analysis
Little to no sample preparation
Micro-destructive
Applicability to all media (solids, liquids, aerosols)
Simultaneous multi-element detection capabilities
LIBS Disadvantages
Poor precision (typically 5-10%)
Relatively high detection limits
Difficulty in preparing matrix-matched standards
Spectral Interferences
Carbon is a key element for all living organisms, but carbon-containing gases in the
atmosphere affect the earth’s climate, known as the Greenhouse Effect, which could
be detrimental to us if nothing is done. The amount of carbon uptake in soils can
represent an important mechanism in the cycling of carbon. By knowing the carbon
concentrations in different soils and climates, the effect of global warming may be
better understood. In order to complete such research, an easier method and
applicable instrument will be needed to gather the immense amounts of
measurements required.
Soil is very complex when considering its components; it contains inorganic and
organic atoms, ions, and molecules. LIBS is capable of identifying carbon without
spectral emission interferences. This, coupled with the above-mentioned
advantages explains why LIBS is the forerunner in field analysis, although its
precision continues to create problems.
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
16
Method Development and Microfluidic Device Design for Separation and
Detection of Modified Nucleosides
Christian Sweeney* and Daniel L. Morris
Department of Chemistry, Rose-Hulman Institute of Technology, Terre Haute, IN
47803
The DNA base guanine is by far the most vulnerable to oxidative damage by
reactive oxygen species (ROS), forming 8-OH-Deoxyguanosine (8-OH-dG), a
compound known to be linked to at least 50 diseases and clinical conditions.
Therefore, it is of great relevance to develop fast and effective means of separating
and detecting of 8-OH-dG from oxidatively damaged DNA.
Capillary Electrophoresis (CE) provides a powerful and fast means of separation on
the basis of charge and size by means of an applied electric field, and is readily
interfaced with UV/Vis absorption detection. Unfortunately, the sensitivity of
UV/Vis detection in CE is limited by the small internal diameters of the capillaries.
However, stacking of analytes in the capillary can be achieved when employing
electrokinetic injection (EK), thereby decreasing the detection limits. We have
employed stacking using a cholate based run buffer in a Micellar Electrokinetic
Chromatographic (MEKC) separation. The cholate micelles contribute a
partitioning dimension to the separation and allow the separation of neutrals in the
sample. We report the results of altering individual parameters in the MEKC
separation (concentrations, injection times, injection types, etc.) to achieve an
optimal set of separation parameters for unmodified nucleosides and 8-OH-dG. We
present the results of reactions involving double stranded calf thymus DNA and
ROS separated using MEKC and demonstrate the successful separation and
detection of 8-OH-dG in the reaction mixtures.
The results from the MEKC separations were employed to the design of a
microfluidic device for performing the separations. The advantages of microfluidic
devices for chemical analysis include short analysis times and minimal sample
requirements, and we report a design that incorporates a z-shape detection channel
allowing for an elongated path length for performing UV/Vis absorption detection.
In addition, microfluidic device designs are being evaluated which incorporate a
solid phase extraction step prior to separation as a means of preconcentrating the
analytes. In addition, a device designed for the reaction of DNA and ROS that
integrates the reaction, extraction, and separation steps, preventing sample loss as
well as degradation is being developed.
This work was funded in part by the IRCBC under the auspices of the Merck/AAAS
Undergraduate Science Research Program.
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
17
Combustion Toolbox
Mark Vaccari* and Dan Coronell
Department of Chemical Engineering, Rose-Hulman Institute of Technology, Terre
Haute, IN 47803
The CHEMKIN software package was developed by Sandia National Laboratories
in the early 1980’s to model combustion chemistry at the elementary reaction level.
Its format for describing detailed chemical mechanisms has been adopted as an
industry standard, resulting in the publication of numerous CHEMKIN combustion
mechanisms in scientific journals and on the internet. In 1997, the CHEMKIN
software package was commercialized and could no longer be obtained through the
public domain. The objective of this work was to develop a combustion chemistry
simulator that replicates the primary features of the CHEMKIN package, and
which can make use of the large number of CHEMKIN-formatted mechanisms
available in the literature. The Combustion Toolbox that resulted from this effort is
an Add-In that is seamlessly integrated into the Microsoft Excel environment. The
graphical user interface was developed using Visual Basic for Applications, and the
computational models were developed using Matlab. The Combustion Toolbox
solicits input from the user, translates the selected CHEMKIN mechanism and
associated thermophysical property files, dispatches the computational task to
Matlab, and performs a variety of graphical post-processing tasks. Models have
been developed to simulate detailed combustion chemistry in batch reactors,
continuous flow (plug, well-mixed) reactors, well-mixed reactors in series, and
homogeneous charge compression ignition (HCCI) engines. The numerical results
predicted by the Combustion Toolbox have compared favorably with published
experimental data (autoignition delays) and CHEMKIN simulations (composition
and thermal profiles).
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
18
Particle Size Effects in the Pretreatment of Wood Waste Leading to
Enhanced Ethanol Production
Amanda Grantz*, David J. Dixon, and Patrick C. Gilcrease
Department of Chemical Engineering, Rose-Hulman Institute of Technology, Terre
Haute, IN 47803 and Department of Chemical and Biological Engineering South
Dakota School of Mines and Technology Rapid City, SD
A twin screw extruder and a ball mill were explored as means of physical
pretreatment in the conversion of wood waste to ethanol. Sieve analyses were
performed to compare the particle size distributions of wood subjected to different
pretreatment methods. Enzymatic hydrolysis was employed to quantify glucose
recoveries for particular pretreatment schemes. While particle size distribution
analyses show milling to be a more effective particle size reduction method than
extrusion, extrusion proved more successful than simple grinding in enhancing
cellulase enzyme recovery of glucose for fermentation to ethanol. Extruded wood
produced glucose recoveries 10 times greater than those obtained from raw feed
material and 25 percent greater than those obtained from ball-milled wood.
Scanning electron microscopy revealed significant structural differences among
untreated, extruded, and ball-milled wood. The twin screw extruder shears wood to
mechanically breaking apart fiber structure. Compared to traditional particle size
reduction methods, the effects of using a twin screw extruder in the pretreatment of
biomass leading to enhanced ethanol production are unique.
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
19
Prevention of Membrane Pore Formation Via P2X7R-Cx43 Interaction
Christina Chrisman*, M. Cohen, S.O. Suadicani, D.C. Spray, and E. Scemes
Department of Neuroscience, Albert Einstein College of Medicine of Yeshiva
University, New York, NY
P2X7Rs are ATP-gated ion channels expressed in brain, colon, heart, prostate, and
skeletal muscles. Activation of these receptors leads to the opening of large pores,
permeable to molecules of up to 900 Da. This membrane pore may be responsible
for exacerbating cell damage during pathological conditions such as inflammation,
ischemia, spreading depression, and trauma. Previous studies indicate that
interactions between P2 receptors and gap junctions may occur. Gap junctions are
clusters of intercellular channels that connect the intracellular milieu of adjacent
cells and allow the passage of molecules of up to 1 kDa in size. Each cell of an
adjacent pair contributes six connexins (Cxs) to form a hemi-channel (connexon),
and the pairing of two connexons forms the gap junction channel.
The aims of this study were to determine the proteins of the Cx43-P2X7R complex
using antibody arrays; to determine if there was an interaction between P2X7R and
Cx43 in the brain, and, if so, to determine the role played by Cx43 in the P2X7Rinduced pore formation. Using antibody array technique we found that in the brain
Cx43 and P2X7R interact, result confirmed by immunoprecipitation assays. Dye
uptake experiments performed on Cx43-null neuroblastoma (N2A) cells and two
subclones of a macrophage cell line, J774 (G8 – a subclone where Cx43 binds to
P2X7R, and A1 – a subclone where Cx43 does not bind to P2X7R) showed that Cx43null N2A cells over-expressing P2X7R and J774-A1 cells took up 30% more dye than
J774-G8. These results suggest that Cx43-P2X7R interaction prevents membrane
pore formation.
3rd Annual IRCBC Undergraduate Research Symposium
November 3, 2006
2"
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3rd Annual IRCBC Undergraduate Research 5ymposium
November 3, 2006#
21
University of Evansville
MESCON
Math, Engineering, and Science CONference
SATURDAY MARCH 31, 2007
PRIZE MONEY FOR TOP PRESENTATIONS!
Call for Abstracts
ABSTRACT DEADLINE: JANUARY 20, 2007
Undergraduate students in science, math
and engineering are invited to present the
results of their research at the 3rd Annual
MESCON on Saturday March 31, 2007 at
the University of Evansville.
To be eligible for a cash prize, students
must submit an abstract by January 19,
2007. Based on the review of abstracts,
participants will be notified via email by
March 1st as to whether to present a poster
or give a presentation.
PRIZES
Monetary prizes in all major disciplines;
Biology, Chemistry, Physics/Math, and
Engineering.
$100 Best poster
TENATIVE SCHEDULE
8:00 am:
Registration/Breakfast
8:30 am:
Opening Remarks
9:00 am:
Presentations
NOON:
Lunch
1:00 pm:
Keynote Address
2:00 pm:
Awards
Visit http://csserver.evansville.edu/mescon for
information concerning abstract guidelines and
instructions, paper and poster format, judging
criteria, money allocation and directions to UE.
For questions or more information contact:
Mark S. Davis Ph.D.
Email: md7@evansville.edu
Phone: 812-488-2024
FEE
Presenter
$20.00
Non presenter
$15.00
Fee includes a continental breakfast, lunch,
and a copy of the publication of
proceedings.
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