Oct 09, 2009 - Claremont, Calif. - A $279,758 grant to the Harvey Mudd College (HMC) Department of Computer Science from the National Science Foundation (NSF) is one of several grants recently announced that will fund research, teaching and learning resources.

The three-year funding will underwrite a new Computer Science Department program, “CPATH-2: Modular CS1 from the Inside Out: Computational Thinking for all STEM Students,” which seeks to establish a curriculum suitable for any student intending to major in science, mathematics or engineering, including computer science students.
 
The project is based on HMC’s successful “CS for Scientists” curriculum. However, recognizing that CS for Scientists is tailored to HMC’s students, the researchers plan to expand CS for Scientists into a series of modules that present core computer technology (CT) and computer science (CS) topics in a manner relevant and exciting to a variety of students.

Christine Alvarado, assistant professor of computer science is one of four principal investigators, including computer science professors Geoffrey Kuenning, Ran Libeskind-Hadas and Zachary Dodds.
 
“In the years since we introduced CS for Scientists, we’ve seen a number of improvements to the curriculum, including better performance in subsequent courses in computation; significant increases in the sophistication with which students use and consider computation; as well as significant increases in the number of women who choose to continue taking computing courses,” Alvarado said.

The researchers aim to transfer the CS for Scientists success by working with several partner institutions to adapt and pilot different CT courses composed of the CPATH-2 modules. The project’s partner institutions include the University of California – Riverside, the Hong Kong University of Science and Technology and Claremont High School.

In addition to the CS for Scientists project award, Kuenning received NSF funds this fall for two other projects. He is collaborating with Erez Zadok of Stonybrook University to study how to reduce the power consumption of storage systems—commonly called “disk farms”—in high-end computing installations. A $100,000 grant entitled “CRI-CI-ADDO-EN: National File System Trace Repository” will allow Kuenning to continue running and enhancing a repository for scientific data used by file systems researchers (people who study how to store files efficiently, cheaply and reliably). He said, “We established the repository several years ago, and it has become the go-to place for getting this sort of data. The grant will allow us to continue running it, to add new features and to clean up some of the internal design."
 
The Next Generation of Biologists
A $157,489 grant from the NSF is contributing to the training of undergraduate HMC biologists with strong quantitative backgrounds. Additionally, through research opportunities and coursework, the project, entitled “RUI: Characterizing Context Dependent Biases iNucleotide Substitution,” will help introduce students to molecular evolution and computational biology.
 
“Nucleotide substitution is an important mechanism by which genomes change over time,” explained Eliot Bush, principal investigator and assistant professor of biology. “This project seeks to improve our understanding of nucleotide substitution by focusing on an aspect that is currently poorly characterized: how the context of neighboring nucleotides biases substitution.”
 
He noted that currently the best-described bias effects are those due to immediately adjacent nucleotides. However, more distant nucleotides also affect substitution. “The goal of the project is to develop and apply a method to systematically characterize more distant context effects.” The information gathered from Bush’s study can be used to further improve models of nucleotide substitution.
 
“Twenty-five percent of HMC’s graduates receive a Ph.D. within nine years of graduation,” noted Bush. “This project will contribute to the training of a new generation of biological researchers with exceptional quantitative skills. An additional benefit of the research grant is that the software we develop for this project will be available at no cost to a wide range of audiences via the Web.”

The Eyes Have It
HMC Professor of Engineering and Biology Elizabeth Orwin received a $192,900 grant from the National Institutes of Health to continue research on the pioneering “Controlling Cell Phenotype in a Tissue-Engineered Corneal Model” project.

Orwin—along with her multidisciplinary team of 14 HMC students and collaborating professors Richard Haskell and Dan Petersen in physics, and Shenda Baker in chemistry—is exploring the ability to design a tissue-engineered artificial cornea. The group’s focus has been on developing a collagen sponge scaffold material that supports corneal cell attachment and growth.

The goal is to make a new cornea out of cells and matrix material or biological polymer, similar to what is found in the skin or eye. “We put the cells and matrix together in a dish and then add mechanical and chemical signals by growing it in a bioreactor,” she said. “Then we can use the optical coherence microscope (OCM) to look at tissue structure, confocal techniques to assess the behavior of the cells, and materials testing to determine the mechanical properties of the matrix.”

One of the research team’s main areas of concentration is to try and create a model cornea that is transparent, just like a healthy cornea. This will allow greater study into controlling the cornea’s response to wounding, reduce the use of animal testing in corneal research, and ultimately create a cornea that can be implanted.