SURF-IT Research Projects  


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2005 SURF-IT Research Projects

The SURF-IT program is committed to offering students challenging and unique research opportunities that explore the diverse, multidisciplinary nature of telecommunications and information technology, and ultimately focus on furthering the development of the Internet. Students will be fully immersed in the research laboratory, collaborating with their faculty mentors and teams, and using state-of-the-art equipment. These projects will fully engage the student and provide the opportunity to see how telecommunication and information technology developments are applied in real life to produce significant and tangible final results.

Calit2 faculty, students and research professionals with leading California technology companies conduct research in “living laboratories” focused on the scientific, technological, and social components related to information technologies.

The following faculty-mentored research projects are available during the 2005 SURF-IT Program. They are divided into their own unique areas of research. Select a link for an overview of the project, associated faculty mentors, project prerequisites, and related publications.

Undergraduate Research Projects Mentored by Calit2 Faculty

    1) Axon Guidance Using Microfluidic Devices 

    2) Biomemetic Modular Design for Advanced Biomaterials 

    3) Can Computer Games Encourage the Empathic Involvement That Fosters Moral Treatment of Others? 

    4) Cell Migration in Microfluidic Devices 

    5) Coordinated Monitoring in Large-scale and Dynamic Sensor Networks 

    6) Design and Implementation of an Identification Layer for an Interactive Digital Workspace 

    7) Dielectrophoretic Separation Systems 

    8) Distributed Data Reduction Techniques Applied to California Climate Change Simulations 

    9) Earth and Planetary System Science Game Engine (EPSS-GE) 

    10) Fingerprint Data Collection and Analysis 

    11) Hermetic Packages for Transmissive Optical Components 

    12) Implementation of Jakes Channel Simulator for Multiple-Input-Multiple-Output Wireless Systems 

    13) IrOx Derived Biosensors 

    14) Nanoelectronic Circuits for Chemical and Bio-sensors 

    15) Nanoscale Communication: System Design 

    16) Semiconducting Nanowires as Nanoelectronic Building Blocks 

    17) Supersize Me: Visualizing Parallel Workspace Activities on a Next-Generation, Massively-Tiled Display System 

    18) The EcoRaft Project 

    19) Ultra-Low-Power Wireless Communication for Neural Micro Implants 

    20) VirtualCalit2 

 Undergraduate Research Projects Mentored by Calit2 Faculty 

Project #1: Axon Guidance Using Microfluidic Devices
Faculty Mentor: Professor Noo Li JeonBiomedical Engineering
Description: The goal of this project is to develop a new microfluidic device to culture Xenopus neurons and use it to study the effect of various chemicals in guiding growth cone navigation. You will learn to fabricate microfluidic devices as well as isolate and culture Xenopus retinal ganglion cells.

Prerequisites: This project is appropriate for students who have finished their sophomore level of an engineering curriculum. Students should have completed general chemistry and physics.

Recommended Web sites and publications: 
   Jeon Lab Web site:

Project #2: Biomemetic Modular Design for Advanced Biomaterials
Faculty Mentor: Professor Zhibin GuanChemistry
Description: This research explores a biomimetic modular polymer design as a new strategy to achieve advanced biomaterials. By mimicking Nature, the broad, long-term objective of this research is to develop rational design of biomaterials having well-defined, high order structures for advanced properties. A specific challenge in biomaterials research is to design a polymer that has a combination of mechanical strength, fracture toughness, and elasticity - three fundamental mechanical properties that are highly desired but are usually exclusive to each other in polymeric materials. Many structural biopolymers, such as the muscle protein titin, employs modular domain structures to achieve the combination of these three fundamental mechanical properties in one system. A major research effort in the Guan laboratory is to mimic the modular domain design in synthetic biomaterials. Specifically, we are synthesizing and investigating biomimetic modular polymers having the following modules: (1) quadruple hydrogen bonding modules, (2) peptidomimetic B-sheet modules, and (3) small protein modules. The hypothesis for this research is that the introduction of well-defined modular domain structures into synthetic biopolymers should lead to biomaterials having a combination of mechanical strength, toughness, and elasticity. Whereas numerous biomedical applications can be envisioned for this type of ideal biomaterials, this proposal is focused on developing model polymers having modular domain structures with which to study fundamental structure-property correlation in synthetic biomaterials.

We currently have four graduate students and one post-doc working on this project, which is supported by NIH and DOE grants. The Guan laboratory has approximately 2,000 square feet of laboratory and instrument space available for this research program with state-of-the-art hoods and air handling capability to provide a safe environment for the practice of synthetic chemistry. The research group is equipped with routine tools for modern organic and polymer synthesis, a dry-box for handling air-sensitive compounds, analytical and preparative chromatographic capability (GC, flash chromatography). More specialized instrumentation for the characterization of polymers includes TGA, DSC, and GPC equipped with a multi-angle light scattering detector. We are collaborating with Professor Albert Yee’s group at Calit2 on characterization of our special biomimetic polymers at both single molecule level using atomic force microscopy (AFM) and macroscopic scale using bulk mechanical testers.

Students will be working on the synthesis and studies of organic multiple hydrogen bonding modular polymers or the synthesis and studies of peptide-based and peptidomemetic modular polymers. Working on these projects will provide excellent training opportunities for undergraduate students on both chemistry and materials sciences.

Collaborating Mentor: Albert Yee

Prerequisites: The applicants should have completed the majority of sophomore organic chemistry and related laboratory courses, and have excellent academic standing.

Recommended Web sites and publications: 
   “Synthesis and Single-Molecule Studies of a Well-Defined Biomimetic Modular Multidomain Polymer Using a Peptidomimetic B-Sheet Module” Roland, Jason T. and Guan, Zhibin. J. Am. Chem. Soc. 2004, 126, 14328.: -
   “Modular Domain Structure - A Biomimetic Strategy for Advanced Polymer Materials” Guan, Zhibin; Roland, J. T.; Bai, J.; Ma, S.; McIntire, T.; Nguyen, M. J. Am. Chem. Soc. 2004, 126, 2058.: -

Project #3: Can Computer Games Encourage the Empathic Involvement That Fosters Moral Treatment of Others?
Faculty Mentor: Professor Kristen R. MonroePolitical Science
Description: Questions Addressed: What causes moral action? Do scholars have scientific answers to this question? If so, can scholarly findings be used to develop a curriculum to foster and encourage more ethical behavior in students? These questions take on a poignant immediacy when we read news reports of continuing prejudice, discrimination, on-going sectarian violence -- even genocidal activities and war -- and increasing polarization over issues of race, religion, and ethnicity, at home and abroad.

Broad Program- To respond to this challenge, the faculty of the UCI Interdisciplinary Center for the Scientific Study of Ethics and Morality (CEM) have developed a program to bring together the scientific findings on the drive toward moral behavior and then to develop a curriculum to instruct at diverse levels, from school children and the general public to college and graduate students. The intense inter-disciplinary program will involve students in biological sciences, computer science, engineering, humanities, social ecology, and social sciences. Students are encouraged to think deeply about their own attitudes toward people judged “different”, whether these differences are associated with race, ethnicity, and religion or with age, disability, sexual preference, weight, etc. Students are asked to measure their own self-awareness of prejudice toward different groups, using both quantitative and qualitative measures. They also take a series of implicit assumption tests (IAT) designed to measure the difference between conscious and subconscious attitudes toward prejudice. Students then participate in a program designed to heighten their empathic involvement with members of groups judged different. In some years, this empathic involvement is induced by student interviews with members of these groups, such as an elderly person or a member of a different ethnic group. In other years, students participate in role-playing games, both in class and via computer and video games especially designed by students in computer science at UCI.

At the end of the project, students will take the same tests for tolerance, to determine whether the program altered their underlying prejudice toward members of different groups. The assumption is that classes designed to involve students in empathic involvement actually can influence the students’ cognitive frameworks significantly and that this empathic involvement is fostered as effectively using computerized simulations of interaction as it is via the more traditional narrative interviews and face-to-face role playing. The program thus (1) provides information on how research on ethics can most effectively be taught and (2) tests a major empirical finding on ethics, suggesting that a critical influence behind ethics is the empathic involvement with others, an involvement that helps us see the world from another’s perspective, thereby heightening the sympathy for the other that fosters a sense of responsibility and concern for the other’s suffering.

Summer 2005 Program, Specific Focus and Duties- The call for proposals from Calit2 would involve that part of the program which involves computer students. In particular, we will ask computer science students to develop computer and video games to create role playing games that can teach tolerance. Students will be exposed to critical experiments in social and political psychology. They then will work with Professor Monroe to create computerized versions of these games. (Goals 1, 5, 7, 8, 11, and 12, below.) Faculty in Social Ecology (Peter Ditto) and in Computer Science (Gloria Mark) will also participate in the program.

Overall Goals:
[1] foster increased ethical sensitivity to underrepresented groups by sensitizing students to ethical implications of cognitive classification of others, with special focus on differences associated with age, physically disabilities, women in science and engineering professions, religion, ethnicity, race, and sexual preference
[2] sensitize students to ethical issues involved when interviewing human subjects
[3] determine the role of face-to-face involvement in fostering empathy
[4] contrast effectiveness of empathic involvement when instilled by (a) in-depth interviewing, (b) role-playing in class experiments and (c) role-playing in computerized games
[5] determine if/how computer games can encourage empathic involvement
[6] increase sensitivity to the situation of women in science and engineering, as an underrepresented group
[7] help computer science students develop web tools to circulate results to a larger audience, thereby both disseminating information and increasing ethical sensitivity of the computer science students creating these tools and websites
[8] post on the CEM website curricula for graduate courses on empathic involvement
[9] work with the International Society of Political Psychology’s Caucus of Concerned Scholars, Committee on Ethics and Morality to evaluate existing tests of tolerance and ethical sensitivity
[10] evaluate alternative methods of measuring tolerance and ethical sensitivity using both qualitative and quantitative tests measuring self-awareness of prejudice and the implicit assumption test (IAT) measuring divergence between unconscious and conscious attitudes
[11] disseminate information to political psychologists via the CEM and the ISPP websites
[12] disseminate information about our program to the broader community via a program of public outreach to local community colleges in the Southern California area

Broader Impact of the Project- The UCI program is part of a broader effort between the CEM and the Caucus of Concerned Scientists, Committee on Altruism and Ethics, established by the International Society of Political Psychology (hereafter ISPP). To disseminate results, we have established ties with appropriate human rights’ organizations, such as the International Committee of the Red Cross and the Detroit Holocaust Museum, and will work to develop further projects to expand and broaden our work to include students other than UCI students.

Research Facilities- UCI Interdisciplinary Center for the Scientific Study of Ethics and Morality, UCI Computer facilities.

Collaborating Mentors: Peter Ditto and Gloria Mark

Prerequisites: Computer skills, willingness to do independent work in an internship program.

Recommended Web sites and publications: 
   Relevant publications for students to consult to learn about Monroe’s work: The Hand of Compassion (Princeton UP 2004) or The Heart of Altruism (Princeton UP, 1996).: -
   Interdisciplinary Center for the Scientific Study of Ethics and Morality :
   International Society of Political Psychology, Caucus of Concerned Scholars, Committee on Ethics and Morality:

Project #4: Cell Migration in Microfluidic Devices
Faculty Mentor: Professor Noo Li JeonBiomedical Engineering
Description: The goal of this project is to use microfluidic chip technologies to study the behavior of cancer cells in various anti-cancer drugs. The student will learn to fabricate microfluidic devices and culture breast cancer cells. The student will also learn and use a combination of microtechnology and biology tools such as cell culture, and will perform time-lapse experiments and analyze the migration data.

Prerequisites: This project is appropriate for students who have finished their sophomore year engineering classes including a year equivalent of general chemistry and physics.

Recommended Web sites and publications: 
   Jeon Lab Web site:

Project #5: Coordinated Monitoring in Large-scale and Dynamic Sensor Networks
Faculty Mentor: Professor Tatsuya SudaComputer Science
Description: In the proposed project, we consider a highly dynamic sensor network containing a large number of sensors and multiple mobile targets (i.e., objects that are being monitored). Sensors may have various capabilities (e.g., mobility, distance-awareness, direction-awareness, and location-awareness); the network may dynamically change due to sensor movement, sensor failure, and communication link failure; target status (e.g., movement speed, movement direction, temperature) may dynamically change; and the environment around targets may change due to target movement and different environmental conditions (e.g., obstacles, humidity, and temperature) at different locations.

The proposed project aims to develop distributed algorithms to allow sensors to autonomously form monitoring structures around mobile targets in order to monitor the targets and to detect intruders approaching the targets. The algorithms allow the monitoring structures to adjust based on the required quality of monitoring (i.e., satisfactory detail of the target’s status information or satisfactory level of detecting intruders). The algorithms are also fully distributed with sensors only relying on locally available information and adaptive to dynamically changing networks and environmental conditions. In the proposed project, we investigate how well the algorithms satisfy the requirements of scalability, adaptability, robustness, efficiency and ability to provide the required quality of monitoring through simulations and through empirical experiments.

We are looking for students to implement empirical experiments in the proposed project. Students will be in charge of implementing wireless communication (e.g. 802.11b) module and constructing a visualization tool to visualize the collected data from the experiments. Students with a background in computer networks are preferred.

Prerequisites: ICS153 and C++ programming

Project #6: Design and Implementation of an Identification Layer for an Interactive Digital Workspace
Faculty Mentor: Professor Falko KuesterElectrical Engineering & Computer Science
Description: Over the past fifteen years a huge number of multimedia devices have emerged, including laptops, personal digital assistants, smart phones and game consoles that feature high-performance embedded processors and a wide range of display capabilities. General development followed the vision of enhanced and pervasive communication capabilities and adequate tools to handle, store, exchange, and manipulate digital data contents. In addition, vast amounts of next-generation prototype systems can be found at universities, research centers, and in industry that are still too expensive for the personal device market. Among these are visualization systems and large-area displays, high capacity, throughput and bandwidth computational resources, as well as a broad range of human-computer interfaces. Many of these components are designed for a very specific purpose and use in dedicated research settings. Recent efforts are now focusing on harnessing these capabilities for the design of fully integrated digital, collaborative research environments. These environments have emerged as a prime testbed for pervasive communications and computing research. VizClass, our digital collaborative workspace, is one of these
systems. Testbed verification of VizClass is targeted towards numerical methods education using visual paradigms.

The goal of the VizClass project is to develop a reconfigurable, highly-interactive classroom environment, which promotes active learning. Students, instructors and researchers entering VizClass will be able to spontaneously connect and use their own devices, further extending the capabilities of the system. Real-time student-teacher interaction on digital contents and collaborative work between student teams using
networked devices will be possible, while users will have access to all networked resources.

The underlying middleware system providing the required services for this highly heterogeneous environment is part of the VisClass core application layer called VizION. This communication and data exchange layer has been developed during the first project phase and is now ready to serve as the backbone of the system.

Task Description- The primary task is to design and implement a login manager based on the VizION communication middleware. This important component of VizClass will allow access permissions to be established and enable users of VizClass to transparently access the full set of resources available.

Modules (called nodes) can be implemented independently from each other, which will allow students to work in parallel on separate components. Each student working on the project will be assigned a specific research/development task and work closely with all team members to guarantee successful system integration. The following four system components will be targeted:

* VizClass GUI/Main GUI Controller- The VizClass GUI Node will be designed with Qt designer and implemented in PyQt. The interface will run on a 15-inch touch display, which means that the interactive control buttons for the interface have to be laid out according to touch display standards. A method must be developed to include child GUIs from different VizClass control modules, which will be added in later versions; initial Login and Profiler interfaces must be developed which will serve as the first child GUIs to simulate this functionality. In addition, a system output window must be included which displays the state of the system, warnings and error messages. The functionality of the GUI must be implemented in the underlying Main GUI Control Node to ensure the separation of GUI interface and controlling instance. This Node will directly interact with the Profiler and Login Node and broadcast setup information to all VizClass Nodes attached to the system.

* GateKeeper- The gatekeeper component verifies user credentials and returns a valid user id, or an error code if the credentials are invalid. Authentication mechanisms can be diverse, ranging from passwords to USB keys to associations of Rorschach blobs. This system is the key component of the security infrastructure in VizClass.

* ProfileAgent- The task of the ProfileAgent is to store and retrieve a list of user profiles, where each user may have multiple profiles for different uses of the classroom. Presented with a valid user ID, the ProfileAgent returns a list of profiles in a sensible order based on the history of profiles used in the past.

* VizCam- Implement and test the idea of VizCam within VizClass, supporting a set of remotely controllable cameras
for real-time teleconferencing and lecture recording. The available hardware components are a Sony pan/tilt/zoom camera and a Toshiba pan/tilt/zoom web camera. The two cameras will be connected to the VizClass PC cluster and mounted in the front and back of VizClass respectively, to provide a view of the instructor as well as the audience. A camera-independent VizION control module must be developed. Finally, video client and server modules must be designed and implemented so that users can watch video feeds in real-time from a remote location.

Research Facilities- The available research facilities for this project will be the Calit2 Visualization Lab and VizClass. All facilities are equipped with wireless networks and the required computer hardware.

Questions Being Addressed- This project will investigate and answer questions focused on design strategies for middleware that will have to provide flexibility, scalability, failure tolerance and ease of use. In highly dynamic ubiquitous environments such as VizClass, in which arbitrary devices may join or exit the space at any given time, the middleware system will have to automatically adapt to intended as well as unexpected changes to the environment. Therefore, one important aspect of this research project will be the design of a new automatic device and service discovery process that will facilitate versatile device management.

Duties Assigned to Students- Each student will be responsible for one specific system component. All students will closely collaborate and continuously interface with all of the team members.

Overall Values/Skills Required and Acquired-
The students will learn how to collaboratively work on complex research and development projects. All team members should be able to conceptualize, formulate and articulate research problems.

Throughout the project, students will acquire specific knowledge in software development, pervasive and network centric computing, and the design and implementation of graphical user interfaces (GUIs). To succeed with these projects, potential candidates will need a strong background in programming.

Collaborating Mentor: Tara Hutchinson

Prerequisites: Programming skills in C/C++/Python; Grasp of basic networking concepts; Computer Graphics or animation background desired

Recommended Web sites and publications: 

Project #7: Dielectrophoretic Separation Systems
Faculty Mentor: Professor Marc MadouMechanical & Aerospace Engineering
Description: The student will get hands-on practical experience in designing and implementing a dielectrophoretic separation system. Dielectrophoretic force is applied to particles within a fluid through application of nonuniform AC or DC electric fields. Dielectrophoresis is one of the few methods of exerting a significant force onto uncharged microscale and submicron particles without moving the fluid medium. There is a great need for high-throughput separation systems, especially for separation of micro and nanoscale particles. Possible uses for this technology include separation of carbon nanotubes (All current methods of creating carbon nanotubes create a mixture of semiconducting and metallic nanotubes.), separation of cells for improved assay performance, and separation of contaminants from fluids.

Research area: interdisciplinary research (fluidics, electrical, electrokinetics)

Prerequisites: Basic engineering and science training

Project #8: Distributed Data Reduction Techniques Applied to California Climate Change Simulations
Faculty Mentor: Professor Charles S. ZenderEarth System Science
Description: Climate simulations prepared for the Fourth Assessment Report (AR4) of the Intergovernmental Panel on Climate Change (IPCC) reside on a distributed network of storage archives known as the Earth System Grid (ESG). This project will use new Distributed Data Reduction and Analysis (DDRA) techniques to characterize the envelop of future Californian climate contained within these datasets. Our goals are two-fold: 1. To quantify the Californian climate expected under a variety of IPCC forcing scenarios. 2. To benchmark, characterize, and reduce bottlenecks encountered in DDRA of geophysical datasets.

Recent Californian climate assessments are based on data from incomplete ranges of climate scenarios, and on simulations from out-of-date models because the storage to hold all the relevant simulations from state-of-the-art models does not exist at any one facility. Hence the DDRA techniques being developed as part of our NCO/SCO project will improve our understanding California's climate pathways. These DDRA techniques have never been applied to terascale ESG data. During this novel application, we will identify, characterize, and try to reduce DDRA bottlenecks encountered.

We seek an upper division undergraduate to use the computer resources of the Earth System Modeling Facility (ESMF) to perform this research. The student will gain skills and understanding of high-performance computing, data analysis, and climate change.

Collaborating Mentor: Steve Jenks

Prerequisites: The student will work in a UNIX/Linux research environment and should have prior experience with data analysis, and environmental science.

Recommended Web sites and publications: 
   NCO→SDO Project:

Project #9: Earth and Planetary System Science Game Engine (EPSS-GE)
Faculty Mentor: Professor Falko KuesterElectrical Engineering & Computer Science
Description: This Calit2 Center of GRAVITY project is an interdisciplinary project between researchers from the departments of Electrical Engineering and Computer Science, Earth System Science and Studio Art.

The objective of the Earth and Planetary System Science Game Engine project (EPSS-GE) is to build an infrastructure that will support the exploration of environmental systems using gaming technology as a means for very large groups of individuals to collectively interact with scientifically accurate geophysical simulations. The EPSS-GE project work for this summer is focused on interacting with a reduced model of geophysical forcing using the National Center for Atmospheric Research (NCAR) Community Atmospheric Model (CAM). The team is actively researching simulation and data exchange between the Earth System Modeling Facility (ESMF), the game grid, and client applications. The client application will include a limited set of interactive user experience functions. The project Post-Doc and Graduate Researcher are currently developing a working EPSS-GE prototype for which the SURF-IT students will extend the functionality by completing a series of focused short term projects.

Approximately seventy percent of the student’s time will be devoted to integrating Earth system science data into existing client game engines as well as designing and testing prototype visualization techniques. The students will also analyze and modify geophysical model boundary conditions to explore how Earth systems are altered through model “forcing” and develop concepts for intuitive feedback and interaction mechanisms. In order to help deepen the SURF-IT student’s knowledge of the research, the students will participate in regular weekly project meetings and discussions of scenarios, models, underlying geophysics, simulations, parameters or observations, and interaction mechanisms driving the game research and its scientifically anchored visualization.

Summer undergraduate research positions are available for exceptional SURF-IT students to be “paid to play.” A portion of the student’s time will be focused on studying computer games such as Black and White, SimEarth and Spore; popular culture movies such as Twister, A Perfect Storm and The Day After Tomorrow; and experimenting with displays such as Ambient Device’s “Orb.” These experiences will help foster creativity and a rich research context in which the students will use scientific visualization to explore notions of geophysical scale (temporal and spatial); model interpretation and data exchange mechanisms for the EPSS-GE system.

The SURF-IT student’s day-to-day experience will be in a laboratory “team type” environment using state-of-the-art research facilities. Their primary work place will be the Visualization Laboratory and the VizClass. The HIPerWall will be used for prototyping. The students will have their own workstations and desks.

Collaborating Mentors: Charlie Zender, Robert Nideffer, Christopher Knox and So Yamaoko.

Prerequisites: Strong programming skills in C/C++, computer graphics or animation background; other desirable, but not required, skills are a knowledge of Unix and a game engine such as Torque.

Recommended Web sites and publications: 
   Calit2 Center of GRAVITY :
   Earth Science Modeling Facility :
   Community Atmospheric Model (CAM):
   Climate Prediction Net :
   Johnson, Andrew, Moher, Thomas, Ohlsson, Stellan, and Mark Gillingham. “The Round Earth Project – Collaborative VR for Conceptual Learning.” IEEE Computer Graphics and Applications. November/December (1999):60-69. : -
   McPherson, Allen, Painter, James, McCormick, Partick, Ahrens, James, and Catherine Ragsdale. “Visualizing Simulation Data.” Computer Graphics. February (1999):11-15. : -
   The EdGCM Cooperative :

Project #10: Fingerprint Data Collection and Analysis
Faculty Mentor: Professor Simon A. ColeCriminology, Law & Society
Description: This project will continue an ongoing data collection and analysis effort. The project is not fully funded at this time. However, a grant proposal, co-sponsored by Calit2, is currently pending at the National Institute of Justice. The project has also drawn in UROP funds, some funds from the PI’s National Science Foundation CAREER award, and the PI’s startup funds.

The overall goal of the research is to measure (1) the inherent variability of human friction ridge skin (finger and palm “prints”), and (2) the accuracy of source attributions of “latent” (crime-scene) prints. Due to the difficulty of measuring variability as perceived by the human eye and accuracy among human analysts, the focus of the present research at this time is to measure variability as perceived by machine systems and machine matching accuracy.

The SURF-IT project will involve four tasks:
1. Continuing an ongoing project of searching prints against a database provided by the National Institute of Standards and Technology (NIST). The database contains approximately 27,000 mated pairs of fingerprints, of which we have thus far searched approximately 6,000. This initial search took approximately four months, and required supervision of the automated searching process.
2. Data analysis of the initial search project described in (1).
3. Analysis of a data set of fingerprints collected from Human Subjects volunteers during Winter quarter 2005. Approximately 600 individuals’ fingerprints were sampled. We intend to measure the machine’s ability to make correct matches searching latent print derived from the volunteers against this database.
4. Exploration of the usefulness to the overall project of a set of tools distributed by NIST for the measurement of fingerprint quality.

Two undergraduate student researchers will be needed. Students will gain familiarity with automated pattern recognition searching systems, computer applications in criminal justice, and methods for evaluating the reliability and accuracy of biometric technologies.

Collaborating Mentor: Max Welling

Prerequisites: Familiarity with biometric identification, pattern recognition, and information technology in general are desired.

Recommended Web sites and publications: 
   Forensic Science Resources:
   Simon A. Cole, “Grandfathering Evidence: Fingerprint Admissibility Rulings from Jennings to Llera Plaza and Back Again,” American Criminal Law Review, Volume 41, Number 3, pp. 1189-1276.: -

Project #11: Hermetic Packages for Transmissive Optical Components
Faculty Mentor: Professor Andrei M. ShkelMechanical & Aerospace Engineering
Description: A new optical package will be developed to facilitate the use of interchangeable drop-in components for optical fiber networks. Such a package is needed where the optical path is aligned with and through the individual optical components. The student will design such a package using 3D computer aided design (CAD) software, including parts and assembly drawings. The student will assemble the package using a combination of off-the-shelf and custom optical and packaging components. Finally, a prototype component will be packaged and aligned by the student and tested in a simple optical network test bed to demonstrate the merits and drawbacks of the design.

Prerequisites: Experience with computer aided design (CAD), especially SolidWorks, and computer aided engineering (CAE) packages.

Recommended Web sites and publications: 
   Research Paper: Perez, M. and Shkel A.M. "Conceptual Design of a Serial Array of High-resolution MEMS Accelerometers with Embedded Optical Detection". Smart Structures and Systems. Vol.1, No 1. January 2005. (invited): -
   UCI Engineering Mems :

Project #12: Implementation of Jakes Channel Simulator for Multiple-Input-Multiple-Output Wireless Systems
Faculty Mentor: Professor Hamid JafarkhaniElectrical Engineering & Computer Science
Description: The goal is to implement a software package that is capable of generating a set of data representing the time-varying wireless channels based on the Jakes’ fading model.

Data transmission in mobile wireless communication systems is very different from data transmission in wire-line communication systems. This is because the wireless link between two communication terminals – what is called a channel – is relatively unprotected and vulnerable to environmental factors. Among the phenomena that affect the wireless channels are noise, attenuation, delay, Doppler effect, reflection, and interference. Thus, the strength of the received signal can be a function of many, or practically infinite factors. Each of the above-mentioned factors is a function of location and time. Hence, a moving receiver will have time-varying signal levels – an effect called fading. The resulting channel is called a fading channel.

Due to the complexity of the environment of a fading channel, it is practically impossible to predict the signal strength and the signal-to-noise ratio at any given location and time. Therefore, statistical methods are widely adopted to model the fading channels. One of the most commonly used models is the Jakes’ fading model [1], developed by William Jakes in 1970’s. In general, Jakes’ model predicts that the channel path gains will follow a Gaussian distribution with the following auto-correlation: , where h(t) denotes the channel path gain, and t and τ denote the time and delay, respectively. E(●) and R(●) denote the expectation operator and auto correlation function, respectively. J0(●) is the zero-order Bessel function of the first kind, and fD is the Doppler frequency.

The Jakes’ simulators are widely used in the evaluation of different wireless systems. In addition, implementation of the Jakes’ channel simulator is still an active research topic. In the recent years, new methods have been proposed [2], [3], [4], [5], and [6]. The focus of this research is to improve the numerical accuracy and reduce the computational complexity of the Jakes’ simulator in a multiple-input-multiple-output (MIMO) wireless system.

Our main goal is to develop a software package that will produce sets of data representing the time varying MIMO channel perceived at the receiver. The software platform should be flexible enough to work for any Doppler frequency, any number of antennas, and any block length. As mentioned above, there are various algorithms for implementing the Jakes’ simulator. Therefore, the focus of this project is the analysis and comparison of the various existing algorithms. Overall, we aim to combine the advantages of the different methods and develop a universal software platform. The new software platform should be more flexible than most of the existing schemes. In general, the project should be carried out in the following phases:

1. Implementation of different algorithms- In this phase of the project, the student should investigate the latest progress made on the Jakes’ simulator. The mentor faculty member should also help the student to understand the underlying principle of various algorithms. Finally, the student will implement several promising candidate algorithms.
2. Development of a testing platform- In this stage, we will implement a universal testing tool. This tool will have the capability of collecting data from the various Jakes’ simulators, and will compute and compare the performance of the targeted algorithm in the following aspects:
* Accuracy of the algorithm. Basically, the testing tool should examine whether the output channel path gains follow a Complex Gaussian distribution, and whether the output auto-correlation functions follow a zero-order Bessel function of the first kind.
* Correlation between different antennas. Ideally, the different data streams should be uncorrelated.
* Randomness of each block of data. Ideally, the channel data in different blocks should be uncorrelated.
* Speed and memory requirement. The testing tool should also quantify the MIPS and memory requirement for the different algorithms.
3. Analysis / Comparison- At this stage, the student applies the testing tool developed in phase two on each of the Jakes’ simulators implemented in phase one. As a result, the student will submit a thorough performance report. With help from the faculty mentor, the student shall be able to classify the different Jakes’ simulator algorithms based on their speed, accuracy, and the targeted Doppler frequency. Basically, each group of algorithms is most suitable for one particular case of the wireless channel.
4. Implementation of a universal Jakes’ simulator -The final phase will involve using the knowledge gained in the third phase to implement an optimal Jakes’ simulator. This tool will choose the best algorithm based on the input parameter sets. The final simulation tool should be flexible enough for any wireless communication system. Furthermore, the usage of the new simulator tool should be transparent to the users.

Educational Benefits to the Student- After the completion of this project, the student will acquire a high level of understanding about the field of wireless communications. This project provides the student valuable experience for the problems in the design of a wireless system. Also the student will be exposed to a high level of mathematical knowledge used in the field. Application of the software tools during the implementation of the simulator will be a good experience that is useful for further work in this area. Also, the general research experience is very beneficial for the student’s long-term career development.

Prerequisites: * Knowledge of probability theory and random processes (EECS 140) * Knowledge of signals and systems (EECS 150 series) * Skills in C++ and MATLAB

Recommended Web sites and publications: 
   [1] W. C. Jakes, Jr. Microwave Mobile Communications. John Wiley & Sons, NY, 1974.: -
   [2] A. Jamoos, “Uncorrelated Rayleigh fading channels":
   [3] A. Kandangath, “Simulation of Frequency-flat Fading Channels":
   [4] R. Safaya, “A Multipath Channel Estimation Using the Kalman Filter” :
   [5] M. Yan, “Doppler Frequency and Rayleigh Fading Process" :
   [6] C. Komninakis, “A Fast and Accurate Rayleigh Fading Simulator” :
   [7] Simeon Furrer, “Multiple-Antenna Signaling over Fading Channels with Estimated Channel-State-Information: Performance and Capacity Analysis":

Project #13: IrOx Derived Biosensors
Faculty Mentor: Professor Marc MadouMechanical & Aerospace Engineering
Description: Using melt-oxidized Ir wires, a series of sensors will be demonstrated: pH, CO2, and urea. The first two will be combined in one sensor for use in fermentors and intended to perform as well or better than commercial devices while being much smaller and more durable. The urea sensor will be used in dialysis to stop the treatment once all urea has been washed from a patient's blood. The students will be exposed to the science of miniaturization as applied to a series of simple electrochemical sensors. They will learn how to fabricate and test their own sensors.

Research area: interdisciplinary research (sensors, materials, biomedical)

Prerequisites: Basic engineering and science training

Project #14: Nanoelectronic Circuits for Chemical and Bio-sensors
Faculty Mentor: Professor Philip CollinsPhysics & Astronomy
Description: Students will be given the opportunity to work in this exciting nanoscience collaboration. Various proteins and peptides are currently being connected into molecular-sized circuits made using carbon nanotubes. Students may choose to pursue projects involving chemical functionalization, microfluidic delivery, or electronic characterization of these circuits. In any project, students will also be trained in atomic force microscopy, scanning electron microscopy, and nanocircuit preparation, handling and characterization. These projects could lead to suitable Senior Honors Theses for students continuing research in the academic year.

Collaborating Mentors: R. Penner, G. Weiss, N. Allbritton

Prerequisites: Minimum requirements include completion of Physics 52AB or Chemistry 51ABC. Preference will be given to students specializing in a relevant related field through courses such as BME 130/140, Chem 153, BioSci 114/116L.

Recommended Web sites and publications: 
   Collins Research Group Web site:
   Penner Group:
   The Weiss Lab:

Project #15: Nanoscale Communication: System Design
Faculty Mentor: Professor Tatsuya SudaComputer Science
Description: Molecular Communication is a new and interdisciplinary research area that spans the nanotechnology, biotechnology, and communication technology. Molecular communication allows nanomachines to communicate using nano-scale particles. Molecular communication is inspired by the observation that communication in biological systems such as inter/intra cell signaling is done through molecules. Current research focuses on observing and understanding existing biological systems such as how communication is done within a cell or between cells. Molecular communication would work towards the actual design and control of nano-scale communication systems. Molecular communication is a completely new paradigm and would potentially enable new applications in bionanotechnology such as communication between nano-scale devices and molecular computing. We are currently designing potential molecular communication systems and investigating the characteristics of the designed systems through simulation studies.

Research facilities: High-speed computers available

Research issues (Questions being addressed):
*Design and characterization of molecular communication systems

Duties assigned to student(s):
* System design of molecular communication systems in collaboration with other students and mentors who have different backgrounds including engineering, chemistry, biology and biochemistry.
* System evaluation and characterization through the use of simulation software

Overall educational value/skills student(s) will acquire or learn:
* Interdisciplinary approach to a network system design
* Collaboration and communication skills
* Advanced programming and computer simulation techniques
* Basic knowledge of biology and biotechnology
* Basic knowledge of mathematical modeling for biochemical networks
* Basic knowledge of simulation algorithms for biochemical networks

Collaborating Mentor: Tadashi Nakano

Prerequisites: * Programming experience (in any programming language) preferred * Basic knowledge in two or more of the following areas preferred: biology, chemistry, physics, computer science, and engineering.

Recommended Web sites and publications: 
   S. Hiyama, Y. Moritani, T. Suda, R. Egashira, A. Enomoto, M. Moore and T. Nakano, “Molecular Communication,” Proc. of the 2005 NSTI Nanotechnology Conference, 2005.: -
   T. Suda, A. Enomoto, R. Egashira, T. Nakano, M. Moore, S. Hiyama, and Y. Moritani, “Exploratory Research on Molecular Based Nano Scale Communication,” poster presentation, IEEE INFOCOM 2005, U.S.A., March 2005.: -
   Y. Moritani, S. Hiyama, T. Suda, R. Egashira, A. Enomoto, M. Moore, and T. Nakano, “Molecular Communication between Nanomachines,” poster presentation, IEEE INFOCOM 2005, U.S.A., March 2005.: -
   T. Suda, M. Moore, T. Nakano, R. Egashira, and A. Enomoto, “Exploratory Research in Molecular Communication between Nanomachines,” Technical Report, 05-3, School of Information and Computer Science, University of California, Irvine, 2005.: -

Project #16: Semiconducting Nanowires as Nanoelectronic Building Blocks
Faculty Mentor: Professor Jia Grace LuChemical Engineering & Materials Science
Description: This work focuses on the electrical, optical, magnetic and chemical sensing properties of individual single-crystal semiconducting nanowires, configured as field effect transistors. As an example, ZnO is a II-VI compound semiconductor with a wide and direct band gap of 3.4 eV. They demonstrate (i) enhanced transistor property with large on-off ratio; (ii) strong polarization dependent photoconductivity; and (iii) high sensitivity to toxic gases such as NO2, NH3, and CO. At present, we are working to obtain n-type and p-type metal-oxide nanowires with uniform electrical property, and fabricating vertically aligned field effect transistors and logic gates in order to fully utilize the scaling advantage of these nanomaterials. In addition, magnetic doping in the nanowires is being explored to study low-dimension ferromagnetic ordering and to develop efficient spin injectors and spin transistors. In summary, this project incorporates fundamental science and technological application of nanostructured materials, with the aim to build integrated nanoscale devices crucial for future information technology, fitting with the vision of Calit2.

Research facilities are adequate to carry out this project. My lab in the Engineering Tower is equipped with low pressure chemical vapor deposition setup, scanning probe microscope, high sensitivity and variable temperature electrical measurement system. In addition, the Material Characterization Facility and the Integrated Nanosystems Research Facility on campus will be used to facilitate the research project.

The student will be fully engaged in the research project, with the objectives:
* To understand the effect of reduced dimensionality on the electronic, optical and magnetic properties of semiconductors;
* To design, create, and characterize coupled nanostructures;
* To acquire valuable laboratory skills and knowledge concerning the synthesis, fabrication, and characterization of nanoscale materials.

Collaborating Mentors: Reg Penner, Frank Shi and Dan Mumm.

Prerequisites: Junior standing, completed core courses in Physics, Chemistry and Math.

Project #17: Supersize Me: Visualizing Parallel Workspace Activities on a Next-Generation, Massively-Tiled Display System
Faculty Mentor: Professor André van der Hoek Informatics
Description: We wish to develop Supersize Me: a visualization of parallel workspace activities on a next-generation, massively tiled display system. Large-scale visualizations have been effectively used in all kinds of disciplines, but have never been explored to advance the activity of software development itself. The goal of Supersize Me is to change exactly that by developing an experimental prototype that uses a 55 tile (11x5 tiles), 200 mega-pixel display (28,160 x 8,000 pixels) massively tiled display system to show, in real-time, which project files are being modified by whom, where, and by how much. The result will be the world’s first system ever to display, in a manner scalable to hundreds of developers worldwide, what is going in a software development project. This is critical to: (1) managers, who will be able to much better understand their ongoing projects and make effective and efficient task assignments as a result, (2) developers, who will understand their role in large-scale projects as well as the relationships of their work to that of others, and (3) projects, which, for the first time, we will be able to understand by peeking inside individual workspaces and combining all this data for a visualization of actual reality that is continuously updated.

Supersize Me brings together two strands of research: Palantír and HIPerWall. Palantír is a system for informing developers of which other developers are changing which files in parallel. This helps in coordination: if I know that another developer is changing a file that I want to modify as well, I probably should talk to that other developer. To date, Palantír has been built for small-scale project as an Eclipse plug-in. Its visualizations are small annotations in the Eclipse environment, with additional information being available as tool tips. Separate visualizations also exist, but they are still geared towards the individual developer and pack a moderate amount of information in a small space. They are effective for individuals, but are useless if we wish to understand the full state of a large ongoing software development project.

HIPerWall is a massively tiled display system consisting of a large number of individual display tiles. It is one of the world’s largest display systems in terms of available pixels, and is currently being assembled in the Calit2 Visualization Lab. HIPerWall is driven by a middleware system that distributes a single large picture over the multiple monitors. Different kinds of visualizations have been developed in the past, but these ran on smaller versions of the HIPerWall (i.e., fewer display tiles).

Supersize Me brings together Palantír and HIPerWall in a unique fashion to focus on project management: knowing what is going on in a project at any point in time. The implementation of Supersize Me will be able to leverage existing code in both Palantír and HIPerWall. From Palantír, we can reuse the workspace monitoring mechanism that sends events to the visualization. From HIPerWall, we can reuse the middleware to display the visualization. The project, thus, entails bringing those two technologies together, designing and implementing the visualization, and then testing, improving, and using the visualization to demonstrate the technology in use. Should time permit, we would like to simulate the visualization of an ongoing, well-known open source project of choice.

We have developed some prototype visualizations for Palantír that start addressing the “project wide” view. These can be used as input and inspiration, but will definitely require serious modifications and enhancements, and likely an entire reimplementation to make them suitable for the HIPerWall.

Research facilities: The research will be performed in the Calit2 Center for Gravity, where the setup of HIPerWall is currently being completed.

Questions being addressed:
Research questions include:
* Can these kinds of visualizations actually be developed in a scalable fashion?
* Can the visualizations effectively illustrate important project characteristics and if so, which ones?
* Can the visualizations provide developers with a better understanding of their project role and impact?
* Can the visualizations help managers to steer and guide their project in more effective ways?
* Can the visualizations illustrate interesting properties (evolution, dynamics, etc.) for the selected open
source projects?

Duties assigned to students:
Students will be responsible for all aspects of the research, from initial design of Supersize Me, to implementation,
incremental refinement, and actual evaluation of the tool using an example open-source project. Students will be responsible for learning the necessary technology, leveraging existing Palantír and HIPerWall code, and interacting with the faculty advisors and doctoral students (working on Palantír and HIPerWall) on a continuous basis to actively manage the project. The objective of this undergraduate research project is to pursue tangible research outcomes that will result in the publication of a collaborative research paper, and provide the foundation for long-term research that will support the retention and recruitment of the best students into our graduate programs. These kinds of visualizations are unique, as much of today’s software development still takes place in a low-tech environment.

Overall educational value/skills students will acquire: Students will gain a strong appreciation of cutting-edge research and software development. Both Palantír and HIPerWall are at the forefront of research in the fields of software engineering and scientific visualization, respectively, and Supersize Me will not be trivial to develop. Students will learn critical team values, including skills fundamentally important to collaborative research, and – with some luck and determination – be involved in writing a scientific paper based on the work at the end of the internship. Students will also interact with the graduate and undergraduate students in both faculty mentor’s research groups, as well as visitors to Calit2 and the Informatics and EECS departments. Live demonstrations of the prototype technology will be a semi-regular occurrence.

Collaborating Mentor: Falko Kuester

Prerequisites: Experience: * Java and C/C++ programming * Graphics programming * Software design Interest / understanding / familiarity: * Middleware * Visualization * High-end computing * Software engineering

Project #18: The EcoRaft Project
Faculty Mentor: Professor Bill TomlinsonInformatics
Description: The goal of this project is to combine research in computer science, mobile computing, interactive animation and restoration ecology in order to develop a novel computational platform for environmental education. This platform will serve as the basis for regionally specific interactive exhibits that will be installed in science centers and museums around the United States. The interactive platform consists of a heterogeneous network of fixed and mobile computational systems, inhabited by autonomous animated agents (virtual species). This paradigm involves several stationary computer screens that serve as “virtual habitat patches” inhabited by small populations of the animated species, and several Tablet PCs that serve as “virtual rafts,” or dispersal mechanisms, with which people carry the species from patch to patch. This project has already been accepted to the Emerging Technologies venue at SIGGRAPH 2005; a major mid-summer milestone will be to present the group’s work at that conference.

Activities: Students will work as a group, in close contact with Professor Tomlinson and his graduate students, to develop an ecology-based version of the Virtual Raft Project. Each student will be primarily responsible for overseeing a subset of the project as a whole – computational implementation, biological research, animation and sound production, etc. Students will perform the bulk of their work in teams of 2-3 to create compelling and biologically-plausible virtual species to inhabit the computational world, and to build the interfaces to present these species in an appropriate setting for learning about ecological themes to take place.

Facilities: This project will take place in Calit2 Room 3100. Students will work on the computers maintained by Professor Tomlinson’s research group, and may draw on other campus resources as well.

Students are requested in the following areas: behavioral programming, mobile device programming, animation, sound design/programming, ecology, and education.

Questions being addressed include:
* How can we create animations that are believable and engaging while they move seamlessly between stationary and mobile devices?
* What are the most important ecological themes for children to learn?
* How can we create computational species that are both accurate and engaging?
* How do animation, sound, graphics and content combine to create effective interactive educational simulations?

* Behavioral programming – Write Java code to specify the behavior and interactions of the virtual animal and plant species.
* Mobile device programming – Write Java and/or C/C++ code to enable the species to move around on mobile devices.
* Animation – Create compelling models and animations of various animal and plant species, and oversee the integration.
Sound design/programming – Create interactive musical scores and sound effects to contribute to the engagement that participants feel with the system.
* Ecology – Conduct research and collaborate with rest of team to insure that the virtual species interact in plausible ways.
* Education- Perform background research, educational design and formative evaluations to examine the educational impact of the project.

Educational value/skills: The students will be performing original research in a collaborative, interdisciplinary project. In addition to conducting this research, they will also gain experience in working in an interdisciplinary team. There is the expectation that each member of the research team will be listed as an author on at least one scholarly publication as a result of his or her research over the summer.

Collaborating Mentor: Lynn Carpenter

Prerequisites: Each student is expected to have a background that is appropriate to the areas in which he or she will be working. However, we understand that this research will involve a very substantial learning component, and therefore students do not need to have an exhaustive knowledge of that area. For example, the animation student will be expected to have made animation of some kind, but not necessarily 3D computer animation, and the ecology student should have an understanding of ecology in general, but not necessarily of the ecosystems that we will be modeling.

Recommended Web sites and publications: 
   Virtual Raft Project:

Project #19: Ultra-Low-Power Wireless Communication for Neural Micro Implants
Faculty Mentor: Professor William C. TangBiomedical Engineering
Description: The project aims at developing the electronics, the communication protocols, and the power and signal transmission approaches for neural micro implants without onboard battery. The students will join ongoing collaborative research in both Dr. Tang’s and Dr. Heydari’s laboratories. Besides being mentored by Dr. Tang and Dr. Heydari, the students will work with graduate students as part of a research team, and therefore, will acquire teamwork skills as well. The research focuses on three aspects:

a) Circuit design strategies on achieving ultra-low-power consumption. The student will learn and research on state-of-the-art ultra-low-power circuit design strategies for analog signal processing and wireless communication. The proposed
circuits will be the core of the electronics integrated with a micro implants for signal transduction to and from the peripheral nerves or the central nervous system. The target power consumption is in the 10 to 100 µW range, necessitating novel circuit techniques to achieve such small power dissipation.

b) Ultra-low-power wireless communication protocols — The student will learn and research on state-of-the-art ultra-low-power wireless communication protocols for short-distance (2 cm maximum), low-signal-level, low bit-rate wireless communication protocols.

c) Wireless signal and power transmission — The student will learn and research on state-of-the-art inductive-coil coupling for signal and power transmissions over a short distance (2 cm maximum) through biological tissues. The secondary coil to be integrated with the micro implants needs to fit within a 1 mm3 volume, while the primary coil outside the body should be designed to maximize signal and power transfer to the secondary coil.

Prerequisites: EECS 170B and EECS 170C

Recommended Web sites and publications: 
   Dr. Heydari’s research group Web site:

Project #20: VirtualCalit2
Faculty Mentor: Professor Falko KuesterElectrical Engineering & Computer Science
Description: The VirtualCalit2 project is aimed at creating a photorealistic model of the institute in order to turn the entire building into a virtualized living laboratory. This model will serve as the foundation for research targeting areas such as emergency management and response, real-time structural monitoring, augmented reality and location-based games, to name a few.

The undergraduate student researcher(s) will work on modeling, animation and visualization tasks that will contribute towards the development of the initial 3D model.

Collaborating Mentor: Robert Nideffer

Prerequisites: Extensive modeling experience in 3D Studio Max and Maya is required. Scripting experience and familiarity with Torque are highly desirable.