Computer Science Clinic
The Aerospace Corporation
Grid-Enabling the VISPERS Application
Liaisons: Joseph Betser, Robert Davis ’91, Matthew Presley ’89, Jorge Seidel
Advisor: Robert Keller
Students: Brian Bentow (PM), Jon Dodge, Aaron Homer, Chris Moore
The Clinic team designed and implemented a version of waveform analysis tool, VAIL, based on the “grid” highly-parallel computing paradigm, using the Globus toolkit. VAIL is part of a larger system that analyzes realtime sensor data to characterize the vibroacoustic shock environment of launch vehicles. We conducted a performance analysis of the grid-enabled tool, measured speedup, and analyzed communication bottlenecks. We also researched and surveyed the current state-of-the-art in grid computing tools and provided a study to facilitate future grid implementations by The AerospaceCorporation.
Polymerase Chain Reaction Net Software Version 2
Liaison: Andrew Byshenk
Advisor: Belinda Thom
Students: Jacob Seene (PM), Timothy Chew (CMC), Krislin Lee, Paul Scott
Polymerase Chain Reaction (PCR) Net is a piece of software used to monitor and control GeneAmp PCR 9700 instruments. These instruments, in turn, are used to amplify DNA samples. Amplified DNA samples can be analyzed and then used in forensic analysis, gene sequencing, and genetic defect determination. Our team is enhancing PCRNet by improving the user interface, extending the error logging capabilities, and enabling core features of the application to be run across a local network.
The Boeing Company GPS IIF Control Segment
Modeling and Simulation of GPS
Liaisons: Darryl Nakata ’86, Ryan Ripken
Advisor: Michael Erlinger
Students: Victoria Krafft (PM), Tarun Abhichandani (CGU), Brian Merdian, Trudi Miller (CGU), Sonya Zhang (CGU)
The current United States Air Force’s Global Positioning System (GPS) consists of earthorbiting satellites and a world-wide network of monitoring stations. The Clinic team has developed a simulation model representing the GPS network using the OPNET network modeling platform. The model has been verified via data provided by Boeing and other sources. The team has created a set of“what if” scenarios and applied them to the GPS model to evaluate possible modifications to the GPS infrastructure.
Fair Isaac Corporation
Constrained Optimization in Convex Programming
Liaison: Frank Elliott
Advisor: Ran Libeskind-Hadas
Students: Brian Tagiku (PM), Dave Buchfuhrer, Dan Halperin, Brad Tennis, Chris Weisiger
Fair Isaac Corporation provides companies with mathematically-based solutions for a variety of business problems. Many of these problems can be modeled using quadratic programs with large numbers of variables and linear constraints. The Clinic team has taken on the task of developing a prototypical software package that solves linear and quadratic programs. A number of algorithms have been incorporated into this package to accurately solve these types of problems.
Differential Test Coverage Analysis in the Context of the Wine Project
Liaison: Dan Kegel
Advisor: Elizabeth Sweedyk
Students: Cal Pierog (PM), Aaron Arvey (CMC), Edward Kim, Evan Parry
This project will help ensure that Google’s Windows applications run properly under Wine, which is a program that allows Windows programs to run under Linux. The team improved coverage tools to identify areas of untested code used by an application. The team also used these new tools to identify bugs in Wine that affect Google applications, focusing on the Picasa application.
Distributing Search in a Document Database
Liaisons: Kurt Rapelje, Karl Chan ’89
Advisor: Zachary Dodds
Students: Adam Kangas (PM), Janna DeVries, Joseph Walker, Kamil Wnuk
As organizations make the shift from paper documents to electronic document imaging systems, the size of electronic document repositories is constantly growing. This team has researched distributed methods for reducing the amount of time required to perform full-text searching in large document databases.
Sandia National Laboratories
Mesh Optimization Algorithms for Parallel Computing with MESQUITE
Liaison: Patrick Knupp
Advisor: Melissa O’Neill
Students: Dominik Slusarczyk (PM), Elisa Celis, John Hicks, Yu-Min Kim
This Clinic project extended the MESQUITE mesh smoothing toolkit developed by Sandia National Laboratories to operate on a distributed processing cluster. Parallel smoothing requires efficient partitioning of meshes into subparts, correct smoothing of those subparts, and effective cross-cluster synchronization during and after computation. The project drew on existing research in the field of distributed mesh smoothing and on established tools, including MESQUITE itself, the Zoltan partitioning toolkit, and the MPI toolkit for distributed computing. Distributed computation would be pointless without speedup over ordinary single-CPU computation, so the team has also developed and deployed performance analysis methods which have inspired further optimizations to the code.
The Aerospace Corporation
An Extended Range A/D Assmebly
Liaison: Samuel Osofsky ’85
Advisor: David Money Harris
Students: Henry Chen (TL), Keane Kaneakua (S), Shane Ouchi, Chris Prounh (F), Amanda Rainer (S), Alexander Utter
Certain traditional systems that enhance the dynamic range of an analog-to-digital (A/D) converter require a tradeoff between precision, dynamic range, and system complexity. Using a novel approach that simplifies and optimizes these systems, the team has designed, built, and tested a highspeed A/D converter assembly that enhanced the dynamic range of an 8-bit A/D converter while minimizing these drawbacks.
Bubble Formation in Microfluidic Chambers
Liaison: Umberto Ulmanella
Advisors: Mary Cardenas, Jon Jacobsen
Students: Jacob Pinheiro (TL), Angela Cho, Don Lee, James O’Grady (S), Michaela Reagan (F), Mele Sato
The study of microfluidics is a growing discipline in fluid engineering, with many applications in medical and pharmaceutical industries. In these applications, the formation of bubbles in microfluidic reaction chambers is a major problem. A parametric study of the factors influencing bubble formation was completed through extensive experimentation and analysis. Computer simulations were compared with experimental results, with a mathematical model of bubble formation as the objective.
Center for Integration of Medicine and Innovative Technology (CIMIT)
Design of a Prototype Cooling System to Prolong and Preserve Limb Viability
Liaison: Alex Pranger ’92/93
Advisor: Donald Remer
Students: Nicolas von Gersdorff (TL), Jay Chow, Mike Le (S), Robert Panish (S), Ajay Shah (F)
While combat armor advancements have increased soldiers’ survival rates, modern weaponry ravages warfighters’ extremities, causing massive trauma and tissue loss; 2/3 of the 10,000 combat injuries in Iraq and Afghanistan afflicted patients’ limbs. Inducing local hypothermia upon injury would prolong limb viability, lengthening the window for soldiers to obtain restorative and regenerative care and thereby avoid amputations. The team has developed a lightweight, easily deployable, evaporative cooling wrap to induce therapeutic hypothermia on the battlefield.
Defense Advanced Research Projects Agency (DARPA)
Proprioceptive Feedback System For Lower Limb Amputees
Liaisons: William Wiessman M.D., Geoffrey Ling M.D., Adrian Urias ’99/00
Advisor: Ziyad H. Duron ’81
Students: Sophia Huynh, Lisa Jacobs (TL), Atsushi Kobayashi, GeorgeKorir (S), Karen Shi (F), Chris Wottawa
The Defense Advanced Research Projects Agency (DARPA) is funding the development of a rehabilitation device which utilizes mechanical feedback to provide lower limb amputees proprioceptive information from their prosthesis and its interaction with the outside environment. The Clinic team has designed and developed a prototype unit which mimics proprioceptor functions and provides the patient sensory feedback regarding location of the prosthetic in time and space.
Federal Aviation Administration (LED)
Enhanced LED Airport Approach Lighting System
Liaison: Calvin Miles ’87
Advisor: Carl Baumgaertner
Students: Nicholas Carbone (TL), Ruben Betancourt (S), Mark Festini (F), OliverHou(S), Karen Hsin (S), Ko Ihara, Robert Sweney (F)
The FAA-LED team continues the development of a highly efficient LED airport approach lighting system to replace presently-used incandescent lamps. The improved system uses photodiodes and temperature sensors in a closed-loop system to compensate light levels for snow, rain, dirt and LED aging. Visual acquisition of the airport is improved with an innovative LED configuration and computer-controlled strobe sequences. Fuel cells are evaluated for use as backup power and a detailed economic analysis of the LED system is also performed.
Federal Aviation Administration VOR
An Integral Monitoring System for the Very-High-Frequency Omni-Directional Range (VOR) Aircraft Navigation System
Liaison: Nelson Spohnheimer
Advisors: John Molinder, Qimin Yang (F)
Students: Min Shim (TL), Brad Greer, Robert Little (F), Kawika Maunupau (F), Jessica Riley (S), Wayne Tanaka (S)
Design, build, and test a system for monitoring the voltage standing wave ratio (VSWR) on VOR antenna feed lines to augment the prototype integral monitoring system developed by the 2003-04 project teams and currently installed at the Drummond, Montana VOR site. Perform a parametric analysis to determine the effect of various VOR system failures on VSWR and demonstrate the monitor’s capability to detect some or all of these failures via computer simulation, use of the 535B VOR rack on loan to HMC from the FAA, and installation at the Drummond VOR site. Remotely collect and analyze data to verify the performance of the currently installed prototype. Suggest approaches for development of a production-ready design.
Innovative Designs for Flushing Systems
Liaison: Chris Coppock
Advisor: Lori Bassman
Students: Joe Laubach (TL), Shawna Biddick, Rami Hindiyeh (S), Joey Kim, John Onuminya, Sarah Taliaferro (F)
Fluidmaster Inc. is a worldwide supplier of plumbing products. The company is determined to aid in the conservation of scarce fresh water resources as well as to enable people worldwide to enjoy the health benefits of safe and reliable sanitation. This requires a cost effective flushing system that uses a consistent low volume of water regardless of variations in supply water pressure and toilet resistance. The Harvey Mudd College Fluidmaster Clinic team has designed and prototyped two concepts that accomplish this task.
Determination of Duct Flow Characteristics Across Heat Exchanger Cores
Liaison: Steve White
Advisor: Anthony Bright
Students: Daniel Pederson (TL), Michael Bigelow (F), Daniel Lee, Emily Ross, Benson Tsai (S), Emily Vinding Nyden (S)
Honeywell has asked the team to explore the effects of various ducting configurations on the flow through a heat exchanger core to aid in the efficient design of future heat exchangers. The team designed, built, and tested a new experimental test setup to measure the flow distribution through the core of a compact fin heat exchangersupplied by Honeywell. Upon completion of the project, Honeywell will receive a full documentation and analysis of experimental results.
Irvine Ranch Water District
Alternative SCADA Backup Methods for Reservoir Monitoring
Liaisons: Carl Spangenberg, Dave Mazzarella
Advisor: Anthony Bright
Students: Sean Cramer (TL), Donya Frank (F), Abram Kim, Jed Harmsen (S), Vicky Luyapan (S), Elizabeth Winton (F)
The Irvine Ranch Water District (IRWD) clinic team researched, tested, and implemented telemetry solutions for a Supervisory Control And Data Acquisition (SCADA) backup system used to monitor potable and reclaimed water reservoir levels. The team tested the reliability of two potential solutions, recommended the best design, and prepared documentation and cost estimates for a full-scale backup system.
Jet Propulsion Laboratory/NASA
Antarctic Plateau Interferometer Concept Study
Liaisons: Mark Swain, Gautam Vasisht
Advisor: Pat Little
Students: Daniel Roche (TL), Kristina Knepper, Michel Guillon, Eph Lanford, Val Olsen (S)
The NASA JPL Polar Clinic team developed a design to “package” the Antarctic Plateau Interferometer in containers for transport to Dome C, Antarctica and support it during operation. To aid in this design, the team built and deployed an instrument package on the journey from Tasmania to Dome C this year which took measurements of acceleration loads. An isolation design for the optics truss and optical table system is proposed based on this data.
Lawrence Livermore National Laboratory
Hydrogen Embrittlement of Wires in a Neutron Time Projection Chamber
Liaisons: Adam Bernstein, Leslie J. Rosenberg
Advisor: Joseph King
Students: Tim Smith (TL), Zach Burstein, Jim Castelaz, Jamie Kunkle, Sarah Thomson (S)
The Lawrence Livermore National Laboratory has asked the team to evaluate the effects of a hydrogen environment on the strength and surface characteristics of wires used in a neutron Time Projection Chamber. The team designed a system to simulate the environment of an nTPC and characterized the effects of hydrogen embrittlement on very small diameter stainless steel, tungsten, and platinum wires.
Lockheed Martin Advanced Technology Center
Creating a Computer-Controlled Active Tracking Heliostat
Liaisons: Kenneth Lorell ’65, Mons Morrison ’85/87
Advisor: Erik Spjut
Students: Gabriel Takacs (TL), Lindsay Allen, Sheldon Logan (S), Peter Paras (F), Ruka Sakurai (S), Steven Santana (F), Josh Slater (S)
The Lockheed Martin Solar Astrophysics Lab develops space-borne instruments that must be tested prior to use. The testing is performed in the lab using a stationary image of the sun. The team has designed, built, and tested a computer-controlled, active-tracking heliostat that can stabilize an image of the sun to within one arc-second and allow controlled slewing and offset. Additionally, the team has designed an enclosure to protect the heliostat once it is installed.
Los Alamos National Laboratory
Variable Pulsed Laser Delay Line for Flash Photography of Mesoscopic Spatial Dynamics
Liaisons: Aaron Koskelo, Sam Clegg
Advisor: Lori Bassman
Students: Elliott Temkin (TL), Sara Al-Beaini (F), Dustin Brekke (F), Eric Flynn, Tyler Jank (S), Nate Yoder (S)
Los Alamos National Laboratory would like to use flash photography to study material fracture at a microscopic spatial and temporal scale. This project has developed part of the system that will be used to conduct this research. The team designed, built, and tested a variable optical delay line capable of splitting a laser pulse in two, delaying one portion of the beam a user-specified amount of time, and then exiting this delayed pulse collinearly with the undelayed pulse.
Occlusion Detection AlgorithmDevelopment in Insulin Pumps
Liaisons: Rick Bente ’04, Ian Hanson
Advisor: Joseph King
Students: Kevin Alley (TL), Robert Chambers (F), Galen Chui, Daniel Gruver, Faye Massen (S), Garry Newland (F)
Medtronic MiniMed produces insulin pumps for diabetics. This Clinic team is developing an algorithm to reduce the time it takes for the pump to detect a blockage in the delivery system. The Clinic team is also developing an analytical model of the pump system to aid Medtronic in developing future improvements to the pump.
Northrop Grumman Navigation Systems
External Fiber Optic Modulator
Liaison: David Hall
Advisor: Erik Spjut
Students: Nathan Mitchell (TL), Glenn Hudson, Kyle Kelley, Colin Marsh
Fiber optic acoustic systems at Northrop Grumman Navigation Systems utitilize a phase generated carrier architecture. The source laser needs to be modulated externally with a carrier frequency of 25 kHz. Northrop Grumman has fabricated a device consisting of a fiberwrapped piezoelectric cylinder. The team has produced a similar system and characterized its performance at 25 kHz.
Northrop Grumman Space Technology
Passive Millimeter Wave Lens Testing Automation
Liaisons: Larry Yujiri, Erin Englert
Advisor: Ruye Wang
Students: Jack F. Shepherd III (TL), Benjamin Howard (S), Eddie Huang, Steve Lin (F), Joshua Webb
The main goal of the project is to analyze millimeter wave imaging lenses delivered by Northrop Grumman Space Technologies (NGST). This analysis will focus on capturing the point spread function (PSF) of the lenses using radiation around 89GHz. Furthermore, the team is tasked with designing and implementing the automation for this lens characterization process.
Oregon Medical Laser Center
Optical Tumor Location Device
Liaison: Kenton Gregory M.D.
Advisor: Elizabeth Orwin ’95
Students: Mark Locascio (TL), Sara Adelman (F), Jeff Gabster, Teresa Pineda (F), Madineh Sedigh-Sarvestani, Philip Tam (S), Lily Tian (S)
The goal of this project is to design a minimally invasive illumination device and power system capable of emitting a detectable signal. The device would be used as a surgical aid to locate cancerous tissue in the breast. The device would be inserted into the tumor before surgery, and then used during the procedure to guide the surgeon to the cancer site.
ZigBee Digital Modem Suitable for Cellular Phone Platform
Liaison: Kenneth Easton
Advisor: Sarah Harris
Students: Karen Lee (TL), Nicole Kang, Gabriel Kwofie, Tommy Leung, Kenneth Maples (S), Jack Zheng (F)
ZigBee is an emerging wireless standard focused on lightweight, low cost, and low power networking of electronics. Integrating ZigBee into the cellular phone platform allows the phone to act as a Personal Environment Device, letting the owner control close range electronic items such as light switches, vacuum cleaners, and thermostats. The team designed and tested a Zigbee compliant baseband digital modem suitable for integration into QUALCOMM’s mobile cell phone ASIC designs.
Raytheon Space and Airborne Systems
Hyperspectral Image Data Processing Algorithms: Developing a Characterization Process
Liaison: Thomas G. Chrien
Advisor: Ruye Wang
Students: John Silny (TL), Mary Chen (F), Kevin Chu, Eugene Hsueh (F), Raymond Ryckman (S), Daniel Woo
Hyperspectral image data processing uses a wide-range of wavelength spectra to identify targets within an image. The goal of this project is to explore the characteristics of processing algorithms. The key components of the project are the development of a set of metrics to determine the success and failure rates of an algorithm, the creation of tools to optimize performance and the presentation of the results of applying the metrics and tools to a test process.
Sandia National Laboratories
Augmented HVAC Sensors for Near- Real-Time Modeling of Dispersed Airborne Materials in Buildings
Liaisons: Marvin Larsen, Richard Griffith
Advisor: Mary Cardenas
Students: Robert Krohn (TL), Alex Cohan, Justin Kauwale (F), Catherine Meyers (F), Jennifer Shockro (S), Jay Wright (S)
The threat of a contamination event in a building dispersing air through the heating and ventilation system has recently become a major concern to national security. The fate and transport of contaminants through a local building were modeled using CONTAM software. In order to accurately simulate contaminant flow, the standard HVAC system was augmented with additional flow sensors. The model was then validated through a series of on-site tracer gas releases.
Sierra Wireless America, Inc.
Ethernet – to – USB Bridge
Liaison: Jean Philippe Kielsznia
Advisor: David Money Harris
Students: Daniel Chan (TL), Kevin Lloyd, Daniel Rinzler, Rajdeep Roy (S), Max Yi
Sierra Wireless provides laptop cards for high speed Internet access over Verizon’s cellular network. These wireless cards require special driver software to be installed. The team has designed, built and demonstrated a small form factor bridge that connects any PC with Ethernet to the Verizon wireless network without special drivers.
Design and Vibration Characterization of a Passively Damped Satellite Bracket
Liaison: James Bockholt
Advisor: Ziyad Duron ’81
Students: David Lipke (TL), Mark Brenneman (S), Chad Foerster, Jeffrey Lin, Arran McNabb (F), Gwen Yoshinaga
An antenna bracket currently in use on Space Systems/Loral’s (SS/L) satellites is manufactured out of lightweight, but expensive carbon fiber composites. SS/L has charged the team with the redesign of the bracket in order to reduce the overall manufacturing and launch costs. The bracket must not exceed two pounds, and cannot exhibit a response greater than 25g’s at any frequency below 100Hz. Bracket and passive damping designs were numerically modeled and vibration tested to meet specifications.
Uniform Illumination for Fluorescent InVivo Imaging
Liaisons: Sean Gallagher, Darius Kelly, Colin Jemmott ’04
Advisors: Qimin Yang, Deb Chakravarti (KGI)
Students: Alyssa Caridis (TL), Stephanie Bohnert (S), Ekaterina Kniazeva, Erika Palmer (S), Laura Moyer (F), Jeremy Bolton (KGI), Linda Chen (KGI)
In order to improve the accuracy and effectiveness of live animal in vivo fluorescent imaging, UVP tasked a team of Harvey Mudd College and Keck Graduate Institute students to design, simulate, and test innovative imaging systems to achieve unparalleled illumination uniformity over five degrees of freedom. Uniform lighting is needed for quantitative analysis of in vivo images, which are used for cancer and disease research. Additionally, the team developed novel methodologies for measuring lighting uniformity.
Automated Analysis of Gene Expression Data
Liaisons: Kenneth Livak ’74, Mark Wechser
Advisor: Henry Krieger
Students: Kevin Krogh (PM), Jefferey Brenion, Theresa Poindexter, Ryan Riegel
Analysis of gene expression data can help identify genes that reliably classify patients into groups corresponding to disease variants. This analysis can be difficult for researchers not formally trained in statistics. We describe our work toward the development of an algorithm that automates this analysis. The team explored methods such as principal component analysis, discriminant analysis, and the use of ratios of gene expression levels.
Analyzing and Correcting Printer Drift
Liaisons: John Meyer, Gary Dispoto
Advisor: Weiqing Gu
Students: Jeffrey Hellrung (PM), Brianne Boatman, Durban Frazer, Katie Lewis
In color printing, a lookup table (LUT) is a mapping from a computer’s color space to the ink combinations required to print these colors. An LUT will drift over time due to a variety of factors including mechanical and environmental changes, resulting in an undesirable change in the printed results. Currently, constructing a new LUT is a time consuming process. This project focused on developing a quicker method to recalibrate a printer when drift occurs.
Sandia National Laboratories
Optical Characterization of Coated Soot Aerosols or Flames and Lasers
Liaisons: Hope Michelsen, Andrew McIlroy ’85
Advisor: Peter Saeta
Students: Patrick Hopper (PM), Brendan Haberle, Matt Johnson, Julie Wortman, Mark Dansson, Tavi Semonin
The optical properties of coated soot aerosols produce the greatest uncertainty in climate change models. This project aims to measure the scattering and absorption of light by sub-micron sized soot particles similar to those produced in diesel exhaust. Total absorption and scattering cross sections of 635-nm laser light are measured using cavityring down and angle-resolved scattering techniques. Soot particles are created in situ by partially combusting ethylene and coated with a volatile organic compound.