Volume 12 Issue 1 August 2014 interactive pdf

https://doi.org/10.33697/ajur.2014.001

Design Techniques for the DNA Cubic-Lattice

Tyler Hotte and Miranda LaRocque

A Student Approach to a Mathematical Simulation of a Racing Electric Vehicle

Fernando Daniel León-Cázares and Daniel Xoconostle-Luna

Proteomic Study of Ribosomal Proteins from Escherichia coli, Saccharomyces cerevisiae, Bos taurus, Gallus gallus, and Oncorhynchus tshawytscha: Application in a Teaching Laboratory Setting

Yoshihiro Miura, Eric Yeager, James A. MacKenzie, and Kestutis Bendinskas

A Cellular Automaton Model for Traffic Flow -Investigating the Effect of Turning

Tracy Finner and Matthew A. Beauregard

On Deflection of Potentially Dangerous Asteroids

Josh Fixelle and Mikhail Kagan

 

August 2014 articles (full details and links):

1) 

Design Techniques for the DNA Cubic-Lattice

https://doi.org/10.33697/ajur.2014.002

Tyler Hotte and Miranda LaRocque

Saint Michael’s College, One Winooski Park, Colchester, VT 05439 USA

Link to PDF  Link to Supplemental Information

Abstract: We use the Watson-Crick properties of DNA and the principles of graph theory to construct origami folding designs for self-assembling cubic lattices.  Our objective is a mathematical design strategy that can be expanded systematically to any size cubic lattice.  This design consists of threading a scaffolding strand of DNA through the lattice that is secured in place by short staple strands of DNA.  We first add augmenting edges to the cubic lattice to enable a single scaffolding strand threading.   We then thread the scaffolding strand through the augmented cube in a way that minimizes the number of different vertex configurations in the structure.

Key Words: Watson-Crick, DNA Self-Assembly, Origami folding, Cubic Lattice, Scaffolding Strand, Threading, Staple Strands

Student Authors’ Bios: Miranda LaRocque graduated from Saint Michael’s College with a BS degree in Mathematics in May 2014. She is currently working as an Actuarial Systems Analyst at National Life Group, a life insurance company in Montpelier, Vermont.
Tyler Hotte graduated from the Saint Michael’s College and the University of Vermont in May 2014 with a BS degree in Mechanical Engineering (minor in math). He is currently living in Burlington, VT and works as a Timber Framer for Vermont Frames in Starksboro, VT.

Press Summary: DNA nanostructures are nanoscale structures made of self-assembling DNA, which can be used for biomolecular computing, targeted drug delivery, and biosensors. We use the Watson-Crick properties of DNA and the principles of graph theory to construct origami folding designs for a cubic lattice. Our methods involve a single scaffolding strand of DNA and short staple strands of DNA that secure the scaffolding strand into the shape of a cubic lattice. Our objective was a mathematical design strategy that could be expanded systematically for self-assembly of any size cubic lattice.

2) 

A Student Approach to a Mathematical Simulation of a Racing Electric Vehicle

https://doi.org/10.33697/ajur.2014.003

Fernando Daniel León-Cázares and Daniel Xoconostle-Luna

Instituto Tecnológico y de Estudios Superiores de Monterrey Campus Estado de México

Link to PDF

Abstract: A program was developed using the software Mathematica to simulate the dynamical behavior of an electric racing car, an electrathon. In conjunction with experimental data it is focused to allow the Borregos-CEM Racing Team decide which settings have to be adjusted in order to increase the velocity of the racing car while decreasing its energy consumption, i.e. the current demanded to the batteries.

Keywords: Model, electric, racing, vehicle, dynamic, simulation, Electrathon

Student Authors’ Bios: Fernando León-Cázares is a senior student in the area of mechanical engineering in Instituto Tecnológico y de Estudios Superiores de Monterrey Campus Estado de México. He was the Electrathon Borregos CEM Racing’s captain for two years and he has participated in a research group in the same institute dealing with the mathematical modeling of a plasma nitriding process. Daniel Xoconostle-Luna is a mechatronics engineering student who began to work full time in 2013.

Press Summary: An Electrathon is a custom built electric vehicle, similar in appearance to a Go-Kart but powered by an electric motor. We developed a mathematical model to simulate the performance of such vehicle under different conditions so that it is possible to predict its velocity, acceleration and energy consumption at any point of any specific track. This allows for the optimization of different parameters of the vehicle to build the best Electrathon possible.

3) 

Proteomic Study of Ribosomal Proteins from Escherichia coli, Saccharomyces cerevisiae, Bos taurus, Gallus gallus, and Oncorhynchus tshawytscha: Application in a Teaching Laboratory Setting

https://doi.org/10.33697/ajur.2014.004

Yoshihiro Miura1,2, Eric Yeager2, James A. MacKenzie2, Kestutis Bendinskas1*

1Department of Chemistry and 2Department of Biological Sciences, SUNY-Oswego

Link to PDF  Link to Supplemental Information

Abstract: Ribosomes are central to protein synthesis and our understanding of ribosomes has advanced antibiotics research. The proteomic study of ribosomes presented here utilizes a combination of differential centrifugation and matrix assisted laser desorption/ionization – time of flight mass spectrometry (MALDI-TOF MS) to analyze ribosomes from various species in a teaching laboratory setting. Five biologically varied species were used: Escherichia coli (bacteria), Saccharomyces cerevisiae (yeast), Bos taurus (cow), Gallus gallus (chicken), and Oncorhynchus tshawytscha (Chinook salmon). Samples were lysed, ribosomes were isolated via ultracentrifugation using a discontinuous sucrose gradient and the individual protein subunits were separated via sodium dodecyl sulfate polyacrylamide gel electrophoresis. Tryptic digest and MALDI-TOF MS were then conducted on fifteen bands excised from the gel, and the mass spectra of both the whole protein sample and peptides were analyzed. Five out of these fifteen bands were positively identified as various ribosomal proteins, with two uncertain identifications. Additionally, three of the five positively identified proteins that travelled the same distance on the gel were determined to be orthologous. Finally, a class of 14 Biochemistry II students utilized these protocols, identified 3 ribosomal proteins and provided their evaluations of the ultracentrifugation-proteomics teaching laboratory.

Key Words: Proteomics, MALDI-TOF MS, ultracentrifugation, ribosomes, teaching laboratory

Student Authors’ Bios: Yoshihiro Miura graduated from SUNY Oswego in December 2012 with a BS in Biochemistry and Biology. He chose to get his D.P.T. degree at Columbia University, NYC, New York.

Eric Yeager graduated from the State University of New York (SUNY) at Oswego in May, 2010 with a BS degree in Zoology (minor in Chemistry). He is currently living in Ithaca, NY, while attending the New York State College of Veterinary Medicine at Cornell University pursuing his Doctorate in Veterinary Medicine (DVM).

Press Summary: Ribosomes are central to protein synthesis and our understanding of ribosomes has advanced antibiotics research. We purified ribosomes and then ribosomal proteins and identified some of those proteins in five species: bacteria, yeast, salmon, chicken, and cow. We taught these advanced techniques to a class of biochemistry students. We suggest that other biochemists could use our protocols for teaching ultracentrifugation and proteomics in their teaching laboratories.

4) 

A Cellular Automaton Model for Traffic Flow -Investigating the Effect of Turning

https://doi.org/10.33697/ajur.2014.005

Tracy Finner1 & Matthew A. Beauregard2

1 Department of Mathematics, University of Arizona, AZ

2 Department of Mathematics, Baylor University, Waco, TX

Link to PDF 

Abstract: A cellular automaton model is proposed, modeling vehicular traffic flow on a two dimensional lattice in which the vehicles turn at an intersection with a given probability. It is shown that the introduction of turning reduces the long-term average velocity, and can be predicted by a power law depending on the probability of a vehicle turning and the density of cars. The reduction in speed decreases rapidly once the light cycle length surpasses a certain threshold, the value of which can be predicted from the observed power law.

Keywords: cellular automaton, traffic flow, traffic light strategy, turning, dynamical systems, power law

Student Authors’ Bios:

Tracy Finner worked on this project during her senior year (2010-2011) at the University of Arizona. She finished her M.Sc. in industrial engineering in the spring of 2014. She is now an Industrial Engineer at Raytheon.

Press Summary: “Traffic flow models are central to urban planners and developers.  In this paper, a traffic flow model is proposed that models the interaction between individual vehicles and subsequent driver behavior to the traffic light system.  The model is then used to develop empirical evidence for a statistical correlation between the density of vehicles, frequency of turning vehicles, and the timing of the traffic signal.”

5) 

On Deflection of Potentially Dangerous Asteroids

https://doi.org/10.33697/ajur.2014.006

Josh Fixelle and Mikhail Kagan

Department of Science and Engineering, The Pennsylvania State University, Abington, 1600 Woodland Road, Abington, PA 19116, USA

Link to PDF 

Abstract: As has been widely discussed recently, our planet may become a target for asteroids. We consider several scenarios proposed to prevent asteroid collisions with Earth. The asteroid 99942 Apophis is considered as a typical representative. Among others, the recent “gravitational tractor” scenario is discussed. For a simplistic toy-model we obtain estimates for both the mass of the tractor and the amount of fuel required to tow a potentially dangerous asteroid off-course so as to avoid a collision with the Earth. In addition, we analyze two more scenarios titled “sling-shot” and “bumping”, and comment on their relative efficiency compared to the ‘towing” scenario. Based on the analysis, the bumping scenario looks most promising.

KeyWords: Near-Earh Objects, 99942 Apophis, Asteroid Deflection, Gravitational Tractor, “Bumping” Scenario, “Sling-shot” Scenario

Student Authors’ Bios: Joshua Fixelle graduated from the Pennsylvania State University in December, 2013 with BS degrees in Astronomy & Astrophysics and Engineering Science & Mechanics (minors in Mathematics and Physics). He is currently living in Evanston, IL, while attending Northwestern University pursuing his Doctorate in Astrophysics (PhD).

Press Summary: As has been widely discussed recently, our planet may become a target for asteroids (the asteroid 99942 Apophis is considered as a typical representative). We considered several scenarios proposed to prevent asteroid collisions with Earth, including the “gravitational tractor”, “sling-shot”, and “bumping” scenarios. We analyzed and compared the scenarios in regards to their relative efficiency compared to the “gravitational tractor”, and concluded that the bumping scenario looks most promising.

Archives

https://doi.org/10.33697/ajur.2013.001

After 10 Years: Returning to the International Connection

https://doi.org/10.33697/ajur.2013.002

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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Measuring Potassium in Muscle Tissue Utilizing an Atomic Absorption Spectrometer Validation of an Adaptation for a Whole-body Potassium Counting Method

https://doi.org/10.33697/ajur.2013.003

Author(s):

Anthony R. Horner, Rose A. Clark, Stephen M. LoRusso, and Edward P. Zovinka

Affiliation:

Department of Chemistry, Department of Physical Therapy, Saint Francis University, 117 Evergreen Drive, Loretto, Pennsylvania 15940 USA

ABSTRACT:

Potassium is a cation important for a properly functioning body. It is especially significant for nerves, kidneys, and muscles. The concentration of potassium ions in muscle tissue was determined using an atomic absorption spectrometer operating in emission mode. The meat samples were flash frozen using liquid nitrogen, further ground using a mortar and pestle and then digested by immersing the processed meat in a hydrochloric acid solution. The potassium concentrations in muscle tissue were found to range from 2.76 – 4.66 g K+/kg of beef sample.

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A Case Study on Developing a Classroom Web Application Using Behavior-Driven Development

https://doi.org/10.33697/ajur.2013.004

Author(s):

Austin Vance and Trevor Cickovski

Affiliation:

Eckerd College, 4200 54th Avenue South, Saint Petersburg, Florida 33712 USA

ABSTRACT:

Behavior-Driven Development (BDD) is a software design methodology which bridges the developer-client gap by evolving software through communication between the two sides and shaping it to the goals of shareholders. As a recently published iterative development strategy, BDD is slowly being adopted as a software practice in a wide range of domains. We study the applicability of BDD to designing Narwhal, a classroom drawing application that mimics a combination of PowerPoint slides and whiteboard. Through this case study, we employ junior and senior seminar students as clients and view the effects of BDD on Narwhal’s evolution over a three-month period. We conclude with a discussion on the general applicability of BDD to the design of classroom tools following lessons learned from this case study.

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A Comparison of Skin Microbiota under Adhesive Bandages versus Uncovered Adjacent Skin

https://doi.org/10.33697/ajur.2013.005

Author(s):

Kendra Lemire, Felicia Maes, Marialis Ginart, Chris VanFleet and Tim Braun

Affiliation:

Biological Sciences Department, State University of New York at Oswego, 7060 Route 104, Oswego, New York 13126-3599 USA

ABSTRACT:

The skin is the largest organ in the human body and interacts directly with the exterior environment. It is also a habitat for bacteria. We are interested in the perturbing effects of adhesive bandages on the skin’s bacterial populations. We compared covered versus uncovered finger skin using three kinds of over the counter adhesive bandages. We found that skin covered with an adhesive bandage is home to approximately 80 fold more culturable bacteria than is uncovered skin and that type of bandage makes little difference to expansion of the bacterial population. Diversity of bacteria was measured by two different techniques: one culture dependent and one culture independent, both found no significant diversity difference between covered vs. uncovered skin in number of taxa present. The culture dependent analysis found that most samples were dominated by a single bacterium, whereas the culture independent 16S rDNA analysis found more diversity. Evidence of seasonal cycling of dominant culturable skin bacteria was observed.

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More on the Mathematics of the DLF Theory: Embedding of the Oscillator World L into Segal’s Compact Cosmos D

https://doi.org/10.33697/ajur.2013.006

Author(s):

J. Y. Feng* and A. V. Levichev

Affiliation:

Department of Mathematics, Boston University, Boston, Massachusetts 02215 USA

ABSTRACT:

The DLF theory can be understood as an attempt to modify the Standard Model by flexing the Poincare symmetry to certain 7-dimensional symmetries. The D part of the theory is known as Segal’s Chronometry which is based on compact cosmos D=U(2) with the SU(2,2) fractional linear action on it. The oscillator group is viewed as a subgroup LG of the conformal group G=SU(2,2) and certain LG-orbits L in D are studied. We prove existence of such L and of such an embedding of F=U(1,1) into D, that D differs from F by a certain torus whereas D differs from L by a circle on that torus. In the general U(p,q) vs U(p+q) case, the Sviderskiy formula is described – as a tribute to the late Oleg S. Sviderskiy (July 31 1969 – March 30 2011).

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SAR and Pharmacophore Based Designing of Some Antimalarial and Antiretroviral Agents: An INTERNET Based Drug Design Approach

https://doi.org/10.33697/ajur.2013.007

Author(s):

Soumendranath Bhakat

Affiliation:

Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi-835215 INDIA

ABSTRACT:

With the development of computational chemistry and molecular docking studies, Structure Activity Relationship or SAR- and pharmacophore-based drug design have been modified to target based drug discovery using sophisticated computational tools which is not very much user friendly and has got many incompatibility issues with many operating systems (OS) and other system configurations. In this paper SAR and pharmacophore based drug design approaches have been described by the used of free internet based tools which are very much user friendly and can almost compatible with any platform. Some antimalarial. And anti retroviral agents have been designed using pharmacophore study and their drug like properties, toxicity, metabolic sites and other parameters are predicted by the free internet based tools.

https://doi.org/10.33697/ajur.2012.006

After 10 Years: Back to Undergraduate Research Advisors

https://doi.org/10.33697/ajur.2012.007

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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The Effects of Hypergravity on Xenopus Embryo Growth and Cardiac Hypertrophy

https://doi.org/10.33697/ajur.2012.008

Author(s):

Bryce Joseph Duchman and Darrell Wiens

Affiliation:

Department of Biology, University of Northern Iowa, Cedar Falls, Iowa 50614-0421 USA

ABSTRACT:

All life on earth has developed and evolved in a unity gravity (1G) environment. Any deviation below or above 1G could affect animal development, a period when much change occurs and sensitivity is high. We imposed simulated hypergravity through centrifugation and analyzed the effects on the overall body length and cardiac growth of Xenopus laevis embryos. We predicted that increased contractile force would be required from the heart to adequately circulate blood, dispersing nutrients, and that this would inhibit organism growth and possibly induce a state of hypertrophy. Embryos reaching gastrulation stage were exposed to a 7G or 1G (control) field via centrifugation for 96 hours. We then recorded behavior, mortality and took body length measurements. We found no significant differences in behavior or mortality, however, body length was significantly reduced by an average of 6.8% in the 7G group. We then fixed, embedded, sectioned and stained embryos in order to investigate the dimensions of cardiac tissue and of the cardiac region of the body using image analysis software. We found the 7G group had a significantly reduced average body cross-sectional area (-18%) and yet a significantly larger ventricular cross-sectional area (+36%) when compared to the 1G group. The average ratio of ventricle cross-sectional area to average body cross-sectional area was significantly higher in the 7G group when compared to the 1G. From these data, we conclude that hypergravity has a significant inhibitory impact on the Xenopus laevis embryo growth and causes a significant increase in ventricle size.

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Observing Program Calculator for Eclipsing Binary Star Systems

Appendix: ephemeris calculator

https://doi.org/10.33697/ajur.2012.009

Author(s):

Colby Neal and Michael Braunstein

Affiliation:

Central Washington University, Department of Physics, Ellensburg, Washington 98926 USA

ABSTRACT:

A Microsoft Excel application has been developed to utilize eclipsing binary elements to calculate binary ephemerides that are useful in a program of observing binary systems. Binary star systems consist of two stars orbiting a common center of mass. Consistent monitoring of eclipsing binary stars is important for establishing fundamental astronomical parameters, such as mass and composition of the stellar system. The application that was developed supports effective use of resources in such monitoring applications. The main quantities computed by the application at the time of the eclipse include: local time, Julian date, starting Epoch, altitude of the system, phase of the moon, Local Mean Sidereal Time, and Local Hour Angle. Other quantities computed by the application include current Universal Time (UT), UT/Local Time correction, Julian Date, and current moon phase/percent illuminated. The observing application has been demonstrated to be effective in practical application to obtain differential photometry data for SV Camelopardalis, a system of interest because of variability in its period caused by a third body. The application can be easily modified for use with other highly periodic astronomical systems, for instance transits of extrasolar planets.

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Isospectral Domains in Euclidean 3-Space

https://doi.org/10.33697/ajur.2012.010

Author(s):

Christopher Cox

Affiliation:

Department of Mathematics, Iowa State University, Ames, Iowa 50011 USA

ABSTRACT:

The question as to whether the shape of a drum can be heard has existed for around fifty years. The simple answer is ‘no’ as shown through the construction of isospectral domains. Isospectral domains are non-isometric domains that display the same spectra of frequencies of sound. These frequencies, deduced from the eigenvalues of the Laplacian, are determined by solving the wave equation in a domain omega , where alpha-omega is subject to Dirichlet boundary conditions. This paper presents methods to expand the already existing two dimensional transplantation proof into Euclidean 3-space and, through these means, provides a number of three dimensional isospectral domains.

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Memory Accuracy for Emotional and Neutral Narratives: Investigating the Influence of Suggestive Misinformation on the Frequency of False Memories

https://doi.org/10.33697/ajur.2012.011

Author(s):

Laura E. Paige and Elizabeth A. Kensinger

Affiliation:

Psychology Department, Boston College, Chestnut Hill, Massachusetts 02467 USA

ABSTRACT:

Memory is a reconstructive process, impressionable and not always vigilant in detecting devices working against its accuracy. False memory occurs when memory for an event is infiltrated by new information or alterations are made to the information that was previously stored. The present study investigated the effect of emotional valence on false memory occurrence through the misinformation effect – memory errors that arise as a consequence of exposure to misleading information – by presenting participants with narratives in one of three valence conditions (negative, positive, neutral) and subjecting them to suggestive questions providing credulous misinformation following a one-hour delay. Results revealed that when collapsing across negative and positive conditions, overall false memory occurrences were significantly reduced for these narratives compared to the neutral condition. Some of the effects of emotion on memory accuracy were more pronounced for negative information than for positive or neutral information; response rates in the negative condition, as compared to the two other valence conditions, revealed an increase in hits and a decrease in false alarms suggesting negative valence enhances discriminability.

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Diffusion of Water and Diatomic Oxygen in Poly(3-hexylthiophene) Melt: A Molecular Dynamics Simulation Study

https://doi.org/10.33697/ajur.2012.012

Author(s):

Julia Deitz, Yeneneh Yimer, and Mesfin Tsige

Affiliation:

Department of Polymer Science, University of Akron, 302 Buchtel Common, Akron, Ohio 44325 USA

ABSTRACT:

Diffusion behavior of water, diatomic oxygen, and a mixture of both into a poly(3-hexylthiophene)[P3HT] melt were investigated using Molecular Dynamics Simulation. Once simulations were complete, the data was analyzed to determine the diffusion coefficient of those molecules in P3HT using Fick’s law. The diffusion coefficient values were then plotted as a function of concentration and temperature to determine if trends existed. For both water and oxygen, no dependence was observed of the diffusion coefficient on concentration and temperature for the ranges studied. However, a variation in the diffusion coefficient on concentration was observed due to the expected inhomogeneity of the P3HT melt. In the presence of O2, the diffusion of H2O decreased significantly by a factor between four and five, while in the presence of H2O, the diffusion of O2 slightly decreased.

https://doi.org/10.33697/ajur.2012.001

After 10 Years: Back to Where We Began

https://doi.org/10.33697/ajur.2012.002

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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A New Vectorization Technique for Expression Templates in C++

https://doi.org/10.33697/ajur.2012.003

Authors and Affiliations:

J. Progsch and Y. Ineichen
Department of Computational Science, ETH-Zürich, CAB H 83.2, Universitätstrasse 6, 8092 Zürich SWITZERLAND

A. Adelmann
Paul Scherrer Institute, 5232 Villigen PSI, SWITZERLAND

ABSTRACT:

Vector operations play an important role in high performance computing and are typically provided by highly optimized libraries that implement the Basic Linear Algebra Subprograms (BLAS) interface. In C++ templates and operator overloading allow the implementation of these vector operations as expression templates which construct custom loops at compile time and providing a more abstract interface. Unfortunately existing expression template libraries lack the performance of fast BLAS implementations. This paper presents a new approach – Statically Accelerated Loop Templates (SALT) – to close this performance gap by combining expression templates with an aggressive loop unrolling technique. Benchmarks were conducted using the Intel C++ compiler and GNU Compiler Collection to assess the performance of our library relative to Intel’s Math Kernel Library as well as the Eigen template library. The results show that the approach is able to provide optimization comparable to the fastest available BLAS implementations, while retaining the convenience and flexibility of a template library.

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Determining the Efficacy of IonatorEXP™ Activated Tap Water on Growth of Staphyloccocus aures and Escherichia coli.

https://doi.org/10.33697/ajur.2012.004

Author(s):

Sara Schiedler, Rachelle Peterson, and Sasha Showsh (Department of Biology)

Thao Yang (Department of Chemistry)

Affiliation:

University of Wisconsin, PO Box 4004, Eau Claire, Wisconsin 54702 USA

ABSTRACT:

The efficacy in growth inhibition of Staphylococcus aureus and Escherichia coli of the IonatorEXP™ activated tap water was compared to plain tap water, Quatsyl™, and Butchers Neutral Disinfectant™. Treatment with Quatsyl™ or Butchers Morning Mist™ Neutral Disinfectant resulted in complete inhibition of growth for both S. aureus and E.coli. Treatments with IonatorEXP™ activated tap water, performed as directed by the manufacturer, or plain tap water, resulted in no observable inhibition of growth for either of the bacterial strains tested. This observation is not unexpected given that analysis of pH, conductivity and H2O2 on IonatorEXP™ activated tap water were statistically the same values as those determined for plain tap water that was not activated by the IonatorEXP™.

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A Multi-Objective, Linked-Simulation-Optimization of Henry’s Saltwater Intrusion Problem using HST3D and Box’s Method

https://doi.org/10.33697/ajur.2012.005

Author(s):

Emily Curtis and Robert Willis

Affiliation:

Department of Environmental Resources Engineering, Humboldt State University, Arcata, California 95521 USA

ABSTRACT:

A multi-objective linked simulation and optimization (LSO) model for a three dimensional saltwater intrusion problem has been developed. The LSO employs HST3D and Box’s algorithm. The weighting method of multi-objective optimization solves the multi-objective planning problem. The model is capable of determining the optimal pumping rates that minimize the saline concentration at the well sites, as well as, the cost associated with pumping, while satisfying an exogenous water demand. The model is valid for a wide range of applications as explicitly defined by the simulation model. The application of the model was limited to a modified version of Henry’s saltwater intrusion problem. Henry’s problem was modified to include a third spatial dimension and well sites. The multi-objective optimization yielded explicit tradeoff information between the two objectives.

https://doi.org/10.33697/ajur.2011.016

Editorial: The Lessons of Pittsburgh

https://doi.org/10.33697/ajur.2011.017

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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The ERC Mechanism and the Formation of Abnormal Product in the Stevens Rearrangement

https://doi.org/10.33697/ajur.2011.018

Author(s):

Soumendranath Bhakat

Affiliation:

Nutanpalli, P.O. Suri, Dist. Birbhum, West Bengal, Pin: 731101 INDIA

ABSTRACT:

To explain the new abnormal product of the Stevens Rearrangement which is not explainable by different existing mechanisms like “radical pair mechanism”; “ionic pair mechanism”, I proposed a new mechanism scheme entitled the ERC (Elimination Recombination Coupling) mechanism and a new abnormal product of the Stevens Rearrangement. This mechanism also maintains parity between the “radical pair mechanism” and the “ionic pair mechanism.

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Physiological Versus Perceived Foot Temperature, and Perceived Comfort, during Treadmill Running in Shoes and Socks of Various Constructions

https://doi.org/10.33697/ajur.2011.019

Author(s):

Rachel M. Barkley, Mike R. Bumgarner, and Erin M. Poss (Biochemistry, Cell and Molecular Biology Program)

David S. Senchina (Biology Department)

Affiliation:

Drake University, Des Moines, Iowa 50311 USA

ABSTRACT:

The purpose of this investigation was to determine whether people could accurately perceive physiological foot temperature during brief bouts of treadmill running in different combinations of shoe and sock models, and also how perception of comfort was influenced. Sixteen young adult males (21.3  0.8 years, 181.8  1 cm, 74.6  1.5 kg) participated in two separate studies where they alternated running and resting for 10 min each with temperature probes attached at two sites on the lateral dorsal aspect of the right foot. Subjects reported perceptions of foot comfort and temperature after each run using 10 cm visual analogue scales. In the first experiment, different sock models were tested with the same shoe model; in the second experiment, different shoe models were tested with the same sock model. Foot temperature did not differ statistically as a function of shoe or sock model in either experiment. Subjects did not perceive any difference in foot temperature in the shoe experiment, but perceived their foot as being cooler when wearing either a polyester sock or a calf compression sleeve and more comfortable when wearing shoes with less mass. Taken together, the results suggest that subjects’ perceptions of foot temperature may not coincide with physiological foot temperature and are more strongly influenced by sock characteristics than shoe characteristics. Further, shoe mass (but not sock fiber weave or composition) may impact comfort perception by subjects.

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Determination of Cadmium and Lead in Northern Pike from the Missouri River

https://doi.org/10.33697/ajur.2011.020

Author(s):

Jennifer Even and Shahrokh Ghaffari

Affiliation:

Ohio University-Zanesville, Zanesville, Ohio 43701 USA

ABSTRACT:

Lead and cadmium are trace metals which accumulate in the body and are extremely toxic in living organisms. The purpose of this study was to find organ(s) with the greatest concentrations of these elements. In this study liver, gill, intestines, and kidney of five samples of Northern Pikes were analyzed. After the organs were dried and digested using nitric acid the anodic stripping voltammetry method was employed to analyze this samples. This method was used for its low detection limit of 10-9 to 10-10 M. However, no trace of either lead or cadmium was found in all 60 samples analyzed. Lack of detectable amount of both lead and cadmium is attribute to; first, Northern Pikes are not bottom dweller and thus would not be highly exposed to sediments that most commonly contain trace metals, second, the absence of a major industry which typically produces these contaminates in this area.

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Conic Sections in the Double-Slit Experiment

https://doi.org/10.33697/ajur.2011.021

Author(s):

Joe Hughes and Frederic Liebrand

Affiliation:

Walla Walla University, 204 S. College Avenue, College Place, Washington 99324 USA

ABSTRACT:

The use of conic sections in obtaining the locations of double-slit maxima is absent in many undergraduate treatments [1-3]. However, their inclusion is not conceptually difficult and increases the understanding not only of interference phenomena, but also of the underlying geometry. This paper illustrates how elliptic and hyperbolic conic sections arise naturally in a conceptual analysis of the double slit.

https://doi.org/10.33697/ajur.2011.011

Editorial: A Lack of Sustained Focus on STEM Education in the US

https://doi.org/10.33697/ajur.2011.012

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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Algorithms for Collective Construction of 2D Block Structures with Holes

https://doi.org/10.33697/ajur.2011.013

Author(s):

Zachary Fitzsimmons and Robin Flatland

Affiliation:

Department of Computer Science, Siena College, Loudonville, New York 12211 USA

ABSTRACT:

In this paper we present algorithms for collective construction systems in which a large number of autonomous mobile robots transport modular building elements to construct a desired structure. We focus on building block structures subject to some physical constraints that restrict the order in which the blocks may be attached to the structure. Specifically, we determine a partial ordering on the blocks such that if they are attached in accordance with this ordering, then (i) the structure is a single, connected piece at all intermediate stages of construction, and (ii) no block is attached between two other previously attached blocks, since such a space is too narrow for a robot to maneuver a block into it. Previous work has consider this problem for building 2D structures without holes. Here we consider 2D structures with holes. We model the problem as a graph orientation problem and describe an O(n2) algorithm for solving it. We also describe how this partial ordering may be used in a distributed fashion by the robots to coordinate their actions during the building process.

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A deterministic model for (n = 2) competitive products in a market system

https://doi.org/10.33697/ajur.2011.014

Author(s):

M. C. Kekana and O. D. Makinde

Affiliation:

Tshwane University of Technology, Private Bag X680, Pretoria 0001, Staatsartillerie Road, Pretoria West, Republic of South Africa

ABSTRACT:

We proposed a new deterministic model for the dynamics of two competitive products in a given market system. The model was analyzed qualitatively to determine the stability of its equilibrium under the influence of factors such as advertisement, personal interaction, immigration and emigration. Numerical verification of the analytical results is performed and presented graphically.

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Using Web 2.0 Data to Estimate Alcohol-Related Travel

https://doi.org/10.33697/ajur.2011.015

Author(s):

William Conroy and Duncan Smith

Affiliation:

Department of Geography, University of Washington, Box 353550, Smith Hall 408, Seattle, Washington 98195 USA

ABSTRACT:

Using ArcGIS, the locations of pubs, clubs, and bars were geocoded onto the street network of Seattle. Upon calculating the density of these drinking establishments throughout the city, the six densest areas, representing nightlife districts, were converted to polygons. Using publicly available check-in data from Gowalla, user check in data within these six polygons was obtained. After cross referencing the Gowalla users’ legal names with the Washington State Voter Registration Database, straight line distances between their legal addresses and bars patronized were calculated. As a result, distance traveled profiles were calculated for each nightlife district.

https://doi.org/10.33697/ajur.2011.006

Editorial: “The World Festival of Science — Could this go viral?”

https://doi.org/10.33697/ajur.2011.007

Author(s):

C. C. Chancey

Affiliation:

American Journal of Undergraduate Research, University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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Sizing Up Outer Billiard Tables

https://doi.org/10.33697/ajur.2011.008

Authors and Affiliations:

Filiz Doǧru
Department of Mathematics, Grand Valley State University, 1 Campus Drive. Allendale, Michigan 49401 USA

Samuel Otten
Division of Science & Mathematics Education, Michigan State University, 116 North Kedzie Hall, East Lansing, Michigan 48824 USA

ABSTRACT:

The outer billiard dynamical system models the motion of a particle around a compact domain, such as a planet orbiting a star. When considering outer billiards in hyperbolic space, an interesting problem is to determine precisely the conditions in which an orbiting particle breaks orbit and escapes to infinity. Past work has classified triangular and Penrose kite billiard tables according to whether or not their orbiting particles escape. This article presents a classification of regular polygonal tables.

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Using Ohm’s Law to Calibrate a Picoammeter to 0.4 Pico-ampere Precision

https://doi.org/10.33697/ajur.2011.009

Author(s):

Joseph Hashem, Tiankuan Liu, Zhihua Liang, and Jingbo Ye

Affiliation:

Department of Physics, Southern Methodist University, Dallas, Texas 75275 USA

ABSTRACT:

We present an experimental method based on Ohm’s Law to calibrate the Keithley 6485 picoammeter with the calibration error less than 0.4 pico-ampere (pA), which is specified as the highest sensitivity of this instrument. The maximum calibration difference between the measurement current and the calibration current in the picoammeter’s 2 nano-ampere (nA) range is 0.25 pA. This difference is far less than the highest accuracy, 0.4 pA, specified by the instrument. Measurement errors are estimated and discussed.

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Designing and Constructing a Controlled-Flow Apparatus to Study the Effect of Surface Flow Velocity on the Quality of Electropolishing of Niobium

https://doi.org/10.33697/ajur.2011.010

Authors and Affiliations:

Tina Wang
Chemical and Biological Engineering Department, Princeton University, Princeton, New Jersey 08544 USA

Michael J. Kelley
Applied Science, Thomas Jefferson National Accelerator Facility, Newport News, VA 23606 USA

ABSTRACT:

The focus of this project was to design and construct a model controlled-flow apparatus to study electropolishing of one cm2 niobium coupons at surface flow rates typical of cavity processing. A simulation of the apparatus was constructed using CFDesign, a flow and thermal simulation software, to ensure that the selected dimensions may be expected to provide steady-state, laminar flow across the surface of the niobium coupon. Based on these dimensions, a sample system and apparatus was produced to determine the correct reservoir elevation heights for the desired flow rates for fluid viscosities represented in the mixed acid electrolyte. From the CFDesign simulations, it was found that the flow channel supplied laminar flow rates when the center of the niobium coupon was located 40 mm downstream from the inlet stream. The corresponding system, based on the CFDesign simulations, showed that the reservoir elevation heights for flow rates of 0 cm/s to 5 cm/s ranged from 0 to 1.27 cm. The correlation between pressure heads and flow rates has been analyzed and an equation for flow rate was determined using experimental results. The detailed dimensions regarding the flow channel and information regarding the respective pressure heads serve as resources to finding the optimal flow rate for electropolishing the niobium cavities. Although previous research has found a correlation between the quality of electropolishing and internal surface flow rates, research facilities, including Jefferson Lab, did not have the equipment to pursue further analysis. Each nine-cell niobium cavity costs over $50,000, so it is cost prohibitive to use real cavities to conduct early stage research. The prototype built through this research work provides a cost effective alternative. It can be used to validate some of the theoretical results obtained through simulation. In addition, the device allows for easy variable measurements that are either difficult or impractical with an enclosed niobium cavity, as sensors can be embedded into the device in the construction stage. Moreover, the data collected through our experiment furthers superconducting radiofrequency (SRF) technology by allowing Jefferson Lab to design a more effective electropolishing process. 

https://doi.org/10.33697/ajur.2011.001

Editorial: “The Most Terrifying Problem in American University Education…”

https://doi.org/10.33697/ajur.2011.002

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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Investigation of the Effect of Concentration on Molecular Aggregation of Cyanine Dyes in Aqueous Solution

https://doi.org/10.33697/ajur.2011.003

Author(s):

John Kunzler, Leen Samha, Renwu Zhang, and Hussein Samha

Affiliation:

Department of Physical Science, Southern Utah University, Cedar City, Utah 84720 USA

ABSTRACT:

The aggregation of the cyanine dye, 3,3’-disulfobutyl-5,5’-dichloro thiacarbocyanine triethylamine, (NK-3796) in aqueous solution was investigated using absorption and emission spectroscopy. The equilibrium, n(monomer) ⇆ n(dimer) ⇆ (H-aggregate)n , was observed over a series of dye concentrations ranging from 10-4 mM to 0.1mM. At concentrations <10-3 mM, the dye exists in solution mostly in the monomeric form. However, dimers become more significant when the concentration of the dye exceeds 10-2 mM. Unlike the substituted dye in the 9th position, the NK-3796 dye tends to form H-aggregates at higher concentration (>10-1 mM). Monomers and dimers exhibit strong emission in the visible region. Also notable, is that the emission from the H-aggregates was very weak due to self quenching.

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An Interruption in the Highway: New Approach to Modeling Car Traffic

https://doi.org/10.33697/ajur.2011.004

Author(s):

Amin Rezaeezadeh

Affiliation:

Physics Department, Sharif University of Technology, Tehran, Iran

ABSTRACT:

A very common phenomenon in car traffic is investigated in this article. The problem is one-dimensional. We find the wave equation of the traffic, and illustrate a simulation using Matlab 7.6

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Design Optimization for DNA Nanostructures

https://doi.org/10.33697/ajur.2011.005

Author(s):

Jacob Girard, Andrew Gilbert, Daniel Lewis, and Mary Spuches

Affiliation:

Department of Mathematics, Saint Michael’s College, One Winooski Park, Colchester, Vermont 05439 USA

ABSTRACT:

This paper is concerned with minimizing the cost of self-assembling DNA nanostructures by minimizing the number of different components used in the construction. We first describe the nanostructures, then give a combinatorial formalization of the assembly process and demonstrate that the octet truss provides an accurate geometric framework for current branched junction molecule assembly. We choose the octet truss because it is highly symmetric and has an appropriate number of edges for the application. We develop a method of differentiating among branched junction molecules, the basic building blocks of the nanostructures, within this structure. In the mathematical model, we represent the branched junction molecules graphically with „tiles‟. We use this approach to find the minimum number of tiles necessary to construct Platonic and Archimedean solids naturally occurring within the octet truss. This will be useful and cost efficient for the chemists and biologists who actually build these branched junction molecules because once a branched junction molecule is created, a lab can make many copies of it.

https://doi.org/10.33697/ajur.2010.011

Editorial: Science makes the pie bigger

https://doi.org/10.33697/ajur.2010.012

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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Forensic Identification of Salvia divinorum and Salvinorin A

https://doi.org/10.33697/ajur.2010.013

Author(s):

Dana Nontell and Douglas Armstrong

Affiliation:

Department of Physical Sciences, Olivet Nazarene University, Bourbonnais, IL 6091

ABSTRACT:

Salvia divinorum is a member of the mint family that is growing in popularity in the United States and many other countries as a hallucinogenic drug. Because of this, numerous studies have been conducted in identifying the plant material. Some of the most common methods include UV/Vis, TLC, and GC/MS. This article discusses these methods, as well as two other common identification methods proven to be ineffective towards salvia. An extraction method is also discussed.

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Odor and the Effects of Schema Activation on Recognition Memory

https://doi.org/10.33697/ajur.2010.014

Authors and Affiliations:

Kelly Appino, Claire Svec, Brandon Tankard, Amy A. Overman
Department of Psychology, Elon University, Elon, North Carolina 27244, USA

Joseph D. W. Stephens
Department of Psychology, North Carolina A & T State University, Greensboro, North Carolina 27411 USA

ABSTRACT:

This study investigated whether schema-consistent odors affect recognition memory. Forty-two undergraduate students read a story about baking in the presence of an odor that was either baking-related (schema-consistent) or not (schema-inconsistent). Further, the story contained information that was both inconsistent, and consistent, with baking. Participants were then tested on recognition of information from the story. It was predicted that participants who smelled the schema-consistent odor would be more likely to falsely recognize new (i.e., not in the story) schema-consistent information than those who smelled the schema-inconsistent odor. The results indicated that all participants were more likely to falsely recognize new schema-consistent information than schema-inconsistent information. However, odor had no statistically significant effects on recognition.

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Longitudinal Light Clock and Zeno’s Paradox

https://doi.org/10.33697/ajur.2010.015

Author(s):

Joshua Fixelle and K. Austin Johnson

Affiliation:

Department of Physics, The Pennsylvania State University, Abington, 1600 Woodland Road, Abington, Pennsylvania 19001, USA

ABSTRACT:

Introductory college text books consider time dilation through the derivation of the transverse light clock. We consider the case of the longitudinal light clock and derive the time dilation formula of special relativity. Our methods yield the same result as derived by the transverse light clock, and help explain the concept of failure of simultaneity.

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Metal Ion Concentration within Algal Tissue of Species Growing in Proximity to Tioga River Outflows Affected by Acid Mine Drainage in Northern Pennsylvania

https://doi.org/10.33697/ajur.2010.016

Author(s):

Cheyenne McKibbin, Kyle Root, and Gregory Carson

Affiliation:

Department of Chemistry and Physics, Mansfield University, Mansfield, Pennsylvania 16933 USA

ABSTRACT:

In this study, two species of algae from two different areas impacted by acid mine drainage (AMD) were analyzed for metal ion accumulation. The two species of algae collected were Klebsormidium and Entransia. Both algal species are located in an area of high metal ion concentrations and low pH (ranging from 2.28 to 2.89). The study assessed the concentration of iron, manganese, zinc, copper and nickel in the algal tissue. Data shows that both Entransia and Klebsormidium are absorbing or adsorbing iron selectively.

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The E3 Ubiquitin Ligase NARF Promotes Colony Formation in vitro and Exhibits Enhanced Expression Levels in Glioblastoma Multiforme in vivo

https://doi.org/10.33697/ajur.2010.017

Author(s):

Tucker W. Anderson, Christopher Wright, and William S. Brooks

Affiliation:

Department of Biology, Freed-Hardeman University, Henderson, Tennessee

ABSTRACT:

The ubiquitin ligase NARF is a newly identified protein belonging to a small family of structurally similar E3 proteins. NARF is a negative regulator of the canonical Wnt-β-catenin pathway, targeting TCF/LEF family members for proteolytic degradation through poly-ubiquitination. We examined the role that NARF plays in cell division and found that overexpression of NARF in a colony forming assay increases colony formation in a RING finger-dependent manner. Furthermore, we demonstrate that NARF transcripts are expressed at a higher level in the grade IV brain tumor glioblastoma multiforme as compared with low grade astrocytomas. Our data thus indicate that NARF is a positive regulator of cell growth and may be involved in the tumorigenic process.

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The Development of a Three-Dimensional Material Point Method Computer Simulation Algorithm for Bullet Impact Studies

https://doi.org/10.33697/ajur.2010.018

Author(s):

M.J. Connolly, E. Maldonado and M.W. Roth

Affiliation:

Department of Physics, University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

ABSTRACT:

The two-dimensional Material Point Method (MPM) algorithm outlined by Chen and Brannon has been extended to three dimensions. The development of the code is discussed as well as applications for simulating bullet impact on biological and non-biological systems.

https://doi.org/10.33697/ajur.2010.006

Editorial: Complexity in Our Everyday World

https://doi.org/10.33697/ajur.2010.007

Author(s):

C. C. Chancey

Affiliation:

American Journal of Undergraduate Research, University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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A Lesson Learned from Outer Billiard Derivatives

https://doi.org/10.33697/ajur.2010.008

Author(s):

Samuel Otten and Filiz Doğru

Affiliation:

Department of Mathematics Grand Valley State University, 1 Campus Drive Allendale, Michigan 49401-6495, USA

ABSTRACT:

As students move onward and upward through collegiate mathematics they are often impressed by the power of advanced techniques (aren’t they?), techniques allowing problems that were previously difficult or near-impossible to be solved with relative ease. For example, once students have learned the residue theorem in complex analysis they are able to elegantly evaluate integrals that were unwieldy in calculus. Among practicing mathematicians there is also a tendency to look to new or powerful results when trying to unlock a problem within one’s own research. This article presents a new theorem concerning derivatives within the outer billiard dynamical system, and in so doing serves as a reminder that higher-powered mathematics are not always needed and do not necessarily produce more satisfying proofs. Sometimes it is beneficial to keep elementary approaches in mind.

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The Applicability of the River Continuum Concept to the Upper Reaches of a Neotropical Lower Montane Stream

https://doi.org/10.33697/ajur.2010.009

Author(s):

Nicholas Skaff

Affiliation:

Department of Biology, Tufts University, Medford, Massachusetts 02155 USA

ABSTRACT:

The applicability of the River Continuum Concept (RCC) to the upper reaches of Quebrada Máquina, a lower montane stream in Monteverde, Costa Rica, was examined. Macroinvertebrate samples were taken from ten points along the stream from first through fourth order segments. The families of the collected individuals were then categorized based on functional feeding group. The similarity between the families found at each collection point was calculated, along with correlations between the functional groups and various stream characteristics. In most cases, RCC predictions did not apply to Quebrada Máquina. The first (first order) and last (fourth order) sample points were 92% similar despite RCC predictions of substantial divergence in relative functional group abundance. This digression from the RCC predictions may be caused by the relatively few differences in stream characteristics between first and fourth order sections. Specifically, the observed similarities and correlations may have been determined by local scale heterogeneity of the stream characteristics.

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On the Number of Rational Iterated Pre-Images of -1 under Quadratic Dynamical Systems

https://doi.org/10.33697/ajur.2010.010

Author(s):

Trevor Hyde

Affiliation:

Department of Mathematics, Amherst College, Amherst, Massachusetts 01002 USA

ABSTRACT:

For the class of functions fc(x)=x^2+c, we prove a conditional bound on the number of rational solutions to fc^N(x) =−1 and make computational conjectures for a bound on the number of rational solutions to  fc^N(x)=a fora in a specific subset of the rationals.