Draft Project Descriptions

Draft Project Descriptions STEP project AY 2012-2013 May 9, 2012

Research Sponsor STEM Discipline Dr. Jen Forbey Biology Dr. Kristen Mitchell Biology Dr. Henry Charlier Chemistry Dr. Liljana Babinkostova Mathematics Dr. Jaechoul Lee Mathematics Dr. Marion Scheepers Mathematics Dr. Zach Teitler Mathematics Dr. Arvin Farid Civil Engineering Dr. Sondra Miller Civil Engineering Dr. Alark Joshi Computer Science Dr. Jim Browning Electrical and Computer Engineering Dr. Vishal Saxena Electrical and Computer Engineering Dr. Will Hughes Materials Science and Engineering Dr. Don Plumlee Mechanical Engineering Dr. Stephen Tennyson Mechanical Engineering

Help design the next generation of computers

Dr. Vishal Saxena, Electrical and Computer Engineering

The Mixed-Signal and Photonic Integrated Circuit laboratory has students working on design of high-speed electronic circuits for analog-to-digital conversion (ADCs), and next-generation silicon photonic ICs. The latter is a novel area of research whereby, laser (photons) is introduced into conventional electronic chips, to enable terabit speed data communication and signal processing. Our group is looking for motivated undergraduate students to assist graduate students with instrumentation and testing and learn about this exciting area of research.

Visit our website: http://www.lumerink.com/siphotonics/index.htm ------Create a more efficient mathematical model to help understand the world around us!

Dr. Jaechoul Lee, Mathematics

The regression model with autocorrelated errors is frequently fitted in many econometric, environmental, and engineering practices whose objective is to determine if the effect of covariates on the model responses is significant over time. This study aims to develop an efficient computing algorithm for generalized least squares. This algorithm will be developed in some popular periodic regression models with autocorrelated errors. Use of this algorithm will greatly reduce the dimension of the matrix to be inverted regardless of the sample size n. Some appealing examples where the computing time is drastically reduced will be provided. Create supergraphs using chip-firing game theory!

Dr. Zach Teitler, Mathematics

Chip-firing games describe how objects (such as bits of information) disperse across a network. This project will study chip-firing games, including games on unusual networks such as aperiodic tilings of the plane, mostly through an experimental approach --- trying different networks and initial configurations of chips to understand the general behavior. You will learn the basics of the area of math known as graph theory, as well as some more advanced topics such as chip-firing games and aperiodic tilings; and over the course of the project you'll also learn about prior work done in this area, including applications to physics and to other areas of math.

Use DNA to build computers of the future!

Dr. Will Hughes, Materials Science and Engineering

From a biological perspective, DNA is the language for life. But what may be less widely known is DNA’s potential as a programmable building block at the nanoscale. Combining the elegance and mass-parallelism of self-assembly with the exquisite information density and spatial control of DNA, programmable self-assembly for device applications is being investigated. Studies include the design, synthesis, and characterization of DNA-based: 1) origami for opto-electronic applications, 2) chemical reaction networks for diagnostic applications, and 3) molecular machines for biomedical applications. As one example, DNA is to catalytic amplifiers as silicon is to transistors. As modular components, DNA amplifiers can be interconnected to perform complex calculations chemically much the same way that transistors can be combined to perform calculations electronically. By harnessing this computational power, DNA amplifiers can detect specific miRNAs, amplify the signal, perform calculations on the amplified signal, and generate an observable output for diagnosis. As a second example, DNA is also a structural material that can be folded into biological substrates (nano-breadboards) onto which DNA, RNA, miRNA, proteins, nanomaterials, and electronic circuits with molecular-scale components can be assembled. As an inexpensive alternative to semiconductor manufacturing, DNA origami has shown promise for the fabrication of opto-electronic components. In summary, DNA nanotechnology is the rational design and spontaneous assembly of DNA into complex nano- structures, networks, and machines. It has been adopted/adapted as a manufacturing tool because of the simplicity and specificity of programmable self- assembly. Programmable self-assembly provides the unique ability to systematically design DNA to fold, perform logic, and interact with its environment in predefined ways.

Design electron-based devices to help satellites communicate!

Dr. Jim Browning This project involves experimental research in the use of miniature vacuum field emission electron sources in microwave amplifiers. These amplifiers are used in radar and satellite communication systems. The research involves operation of the amplifier test system in a vacuum chamber while measuring the microwave power input and output.

Harness plasma to create thrusters for satellites!

Dr. Don Plumlee, Mechanical Engineering

This project involves the design, fabrication and testing of micro-plasma thrusters for pointing/station-keeping operations of satellites in low-earth orbit. The devices generate a plasma using an Inductively-coupled antenna inside of a containment cylinder. The plasma is then accelerated electrostatically out of the device using two charged grids mounted on the containment tube. The research involves design and fabrication in low temperature co-fired ceramics (LTCC), testing and measuring the plasma devices in a vacuum chamber. The fabrication process involves the processing of devices using the current C-MEMS methodology including CO2 laser for routing, screen printing/direct write of circuits, then lamination and firing.

Discover how plants defend themselves!

If you like getting out in the field as well as working in the lab, this project is perfect for you! This project will require your availability on some weekends.

Dr. Jen Forbey, Biology

I investigate the chemical co-evolutionary interactions between plants and herbivores. The main aim of my research is to evaluate 1) the qualitative and quantitative diversity of plant chemical defenses, 2) the mechanisms by which chemical defenses influence the behavior and physiology of herbivores; and 3) herbivore offenses that combat chemical defenses in the plants they consume. I have pursued these questions during my PhD work at the University of Utah, as a National Science Foundation International Research Fellow in Australia and New Zealand, as a Research Scientist in the pharmaceutical industry and currently as an Assistant Professor in the Department of Biological Sciences at Boise State University. I use a variety of study systems to pursue my research aims. These include interactions between sagebrush and sage grouse in Idaho; marine algae and herbivorous fish in New Zealand; marine algae and amphipods in Australia; birch and snowshoe hares in Alaska, Canada and Idaho. These projects may reveal the chemical mechanisms that drive plant-herbivore interactions and can also be applied to the conservation of species involved in these interactions.

Students will use a variety of analytical instruments to quantify and identify plant chemical defenses in sagebrush and the breakdown products (e.g. detoxification metabolites) of these chemicals in the animal that consume sagebrush. Specific activities may include collecting samples in the field, preparing samples for chemical analysis, and analyzing samples using gas chromatography, liquid chromatography and mass spectrometry. Students will enjoy this project best if they have an interest in wildlife and chemistry or pharmacology and can think analytically. Investigate mechanisms of liver regeneration and fibrosis!

Dr. Kristen Mitchell, Biology

This project is best suited for a student who is interested in cell biology and/or human physiology.

The student will work with a team of researchers to investigate mechanisms of liver disease, with emphasis placed on liver regeneration and fibrogenesis. He/she will have the opportunity to learn in vitro techniques such as mammalian cell culture, RT-PCR, western blotting, and ELISA. Our laboratory also uses two in vivo experimental models of liver disease: 70% partial hepatectomy to induce liver regeneration and bile duct ligation to induce fibrosis. We are interested in determining how liver cells become activated during injury/disease and understanding the molecular mechanisms that regulate liver cell activation and proliferation.

Use Rapid Prototyping to help inventors!

Dr. Stephen Tennyson, Mechanical Engineering

The student will be working with a team of professional and student engineers to assist in developing consumer products and research ideas. Their responsibilities will include the learning and operating of a Stereolithography Apparatus (SLA) and gaining experience with the accompanying tools and processes.

Help understand where our water comes from, and what’s in it!

Dr. Sondra Miller, Civil Engineering This study will result in a more robust assessment than any water quality research to date of the interrelated relationship between water supply and population growth and its effects. Studies have focused on atmospheric particulate matter deposition in snowpack at remote or high alpine locations. In contrast, the area under study in a population center, where both the local and regional influences affect water quality. This study will begin to offer new information to educate the general public and to guide policy makers and industry. This research will also offer powerful and precise data that policy makers have lacked about local and regional contaminant sources. The long-term goal of this study is to examine chemical signatures and air mass to identify individual contaminants like nitrogen and mercury, and follow atmospheric indicators to specify local and regional sources. The first step in achieving this long-term goal isunderstanding variations in atmospheric particulate matter under the influence of various local and regional conditions—such as urban versus rural environments. The 2012 NSF STEP student will: (1) will become trained in the fundamental principles and operation of air quality monitoring instrumentation (continuous ambient particulate monitor, TEOM; multiple orifice uniform deposition Impactor, MOUDI; laser particulate counter; precipitation collector) currently housed in the Environmental Research Building at Boise State University and remotely deployed in the Dry Creek Experimental Watershed; and (2) perform experiments simultaneously operating air quality instrumentation under varying conditions— sampling run-time, urban and rural environments, atmospheric stability.

Use computers to understand our aquifer!

Dr. Jairo Hernandez, Civil Engineering

It is known that the Treasure Valley Aquifer consists of shallow, intermediate, and deep aquifers that are interconnected but specific inter-relations on where and how these interconnections take place are unknown. There is also lack of knowledge on how water flows in both directions between the surface and the Treasure Valley Aquifer making the inter-relationship more complex. It is desirable to take a system approach due to the problem's complexity, added to the lack of certainty on parameters and the multiplicity of variables involved for managing the water resource. Information from past studies and aquifer models for the Treasure Valley will be collected for comparing the goals that each study pursued to the goal for this study.

The nature of this proposal is to perform descriptive basic research. This study will not require field work and office work will be computer based. The activities will be performed during one calendar year. This study will facilitate decision making and will help in avoiding water conflicts in the Treasure Valley.

Use a computer program to find solutions to a famous equation!

Dr. Marion Scheepers, Mathematics

Let k be a fixed positive integer. Consider the equation y2 = x3 + k in which x and y are unknown. This equation is known as Bachet’s equation. If k = 1, then the pair (x,y) = (3,2) gives a solution to this equation. Bachet, a sixteenth century mathematician, discovered a very interesting method to compute new solutions for this equation, given a known solution. The study of the solvability of this equation, as well as methods for finding solutions for it, has produced dramatic developments in mathematics and in cryptology.

In this project we will examine the solvability of this equation in finite simulations of the set of rational numbers. We are specifically interested, for fixed prime number p, when Bachet’s equation over the arithmetic system Zp will have exactly p-1 solutions. No formal background in number theory or algebra is required for this project. The students recruited for this project will learn in the course of working on the project what Zp is, how to count solutions to Bachet’s equation, and how to use the MAPLE program to collect data. Our objective is to identify those prime numbers p and the corresponding numbers k in Bachet’s equation for which there are in

Zp exactly p-1 solutions to Bachet’s equation. We will also explore possible applications of this work to other problems.

Design and understand codes and computer security!

Dr. Liljana Babinkostova, Mathematics The Data Encryption Standard (DES) is a block cipher standard published by the National Institute of Standards and Technology (NIST) in 1977. Block ciphers are a class of symmetric-key encryption algorithms that transform a fixed-length block of plaintext (unencrypted text) into a block of ciphertext (encrypted text) of the same length. This transformation takes place under the action of a user-provided secret key. Decryption is performed by applying the reverse transformation using the same secret key. Though the Data Encryption Standard was recently replaced by the Advanced Encryption Standard (AES), the DES algorithm is still of considerable importance.

The students will learn how to design pedagogically useful simplified versions of DES that has many features of DES. Then the students will start to analyze the security of these cryptosystems, investigating questions like whether the cryptosystem is pure or faithful and whether there is a possibility for installing a trapdoor.

Discover new ways to clean up oil spills!

Dr. Arvin Farid, Civil Engineering

Cleaning soils and groundwater of contaminant is a very important task for the entire nation. Oil spill in the Gulf of Mexico is an example. Airsparging is a popular method of soil and groundwater cleanup. Airflow in soil is a very uncontrolled and slow process. Enhancing airsparging requires improving airflow to a more controlled and relatively uniform distribution of air in soil/groundwater. The goal of this research is to enhance airsparging.

With the training, help, and supervision of graduate students, the undergraduate researcher will be performing an experiment (electromagnetic stimulation of dye diffusion) as well as, if time allows, preparation of another experimental setup to study EM stimulation of airsparging. In addition to the setup preparation, the experiment involves preparing the necessary setup to control and measure the injection of dye and air, collection of images of diffusion, learning how to use the series of equipment required to create the source of stimulation (EM waves) and measure emitted fields into the test medium at different points. Data processing and analysis is the next step. All of these require the training and supervision by the graduate student, which will be provided.

Help to create new ways to make cancer medication more effective!

Dr. Henry Charlier, Chemistry

Carbonyl reductase (CR) catalyzes the NADPH-dependent reduction of a wide range of carbonyls. CR has been connected to several important processes including but not limited to quinone detoxification, neuroprotection, prostaglandin metabolism, and, of clinical interest, anthracycline metabolism. CR reduction of anthracyclines significantly impacts their use in the treatment of cancer as it has been linked to both drug resistance and cardiotoxicity mechanisms. Therefore, inhibition of CR in conjunction with anthracycline therapy offers the potential both to increase the effectiveness of the drugs and to decrease the risk of the associated cardiotoxicity. The major emphasis of this work is to better understand how CR recognizes the molecules to which it binds, be they substrates or inhibitors. Equipped this information, drugs may be designed to control CR with the intention of reducing the risk of cardiotoxicity during anthracycline cancer treatment. Also, as the role of CR is other pathways is better understood such drugs may be used to treat other diseases as well.

Key to the success of this work is the development of a protein expression system in which human CR can be made in the bacteria, E. coli. Such work involves genetic engineering, protein chemistry, and enzyme kinetics. Once this system is constructed and optimized, a series of site-directed mutagenesis studies is planned. Students who work on this project will help to develop this protein expression system and time permits, will work on the site-directed mutagenesis work.

Make data come alive!

Dr. Alark Joshi, Computer Science

Multidimensional data is common in fields as diverse as weather, medicine, sports and so on. Exploring relationships between multiple variables in a dataset can be particularly hard. The aim of this project is to develop novel visualization techniques for interactively exploring multidimensional data. Interactive exploration has shown to be particularly useful in gaining insight into relationships between multiple variables. Students will get the opportunity to conduct application oriented research and work with real world data.