| BioEngineering |
Fall 2006 |
Spring 2007 |
Adam Arkin : Bacterial morphology and genomic organization
Project Description:
The project involves looking at bacterial morphology. With the increasing focus on genomic information about organisms, systematic analysis of phenotypical information characterizing microorganisms has lagged behind. For example, no presently available database provides comprehensive information about physical properties of bacteria.
During the course of the project the student will systematically collect and analyze such data. The results of the analysis will then be compared with the genomic information about the organisms, which will serve to establish the relationship between their gene regulatory network organization and physiological properties.
The student will learn about properties of various classes of bacteria and their natural environments as well as genomic characteristics. The project will accommodate as much time commitment as the student is willing to make, but at least 2-4 hours/week. The project will be deemed successfully completed if the student is able to compile and encode a systematic list of extensive morphologies for 50 bacterial species. Additional work analyzing complied data and comparing it to organisms genomic characteristics may lead to publication. |
Adeeti Ullal |
Adeeti Ullal |
James Casey : Biomechanics of Plant Growth
Significant changes occur in the physical and mechanical properties of plants during the growth phase. Some of these are driven by biological forces, others by environmental conditions. Of particular interest in this new project is the dramatic stiffening that takes place in the stalk of the African Lily (Agapanthus Africanus) just prior to flowering. These blue or white lilies are very common in the Berkeley area. The project will involve a literature search and possibly experimental design and some modeling. |
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Harry Ching |
Steven Holbrook: Computational
Studies of RNA Structure, Function and Genetics; Protein machines
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Aaron Levitan
Akhil Dhar
Kunal Patel
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Sanjay Kumar:The effect of extracellular matrix mechanics on tumor cell structure and physiology
We seek an undergraduate to study the effect of the mechanical properties of the extracellular matrix on various aspects of the structure and physiology of tumors of the neural origin. The student will be responsible for fabricating cell culture substrates, culturing cells, and characterizing cell strucutre and function through immunfluorescence, live-cell imaging, and traditional biochemical and cell biological modalities. Previous tissue culture laboratory experience is required.
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Lizhi Cao |
| Luke Lee: Biomedical Devices for Quantitative Molecular Diagnostics and Systems Biology |
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Ryan Cooper |
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Professor Sharmila Majumdar/Dr. Galateia Kazakia: Bone Quality in the Proximal Femur: a MicroCT and MicroFTIR Study
Our research group focuses on advanced imaging techniques for the study of musculoskeletal structure and function (for details please see http://mqir.ucsf.edu/). For this project, we plan to use two recently developed imaging tools to investigate the structure and composition of trabecular bone in the human hip. State of the art micro computed tomography (microCT) will be used to create three-dimensional high-resolution images of bone structure and density. Fourier transform infrared (FTIR) microspectroscopy will be used to investigate the composition of bone. Utilizing these methods we will investigate relationships between bone quality and anatomical location, loading state, and disease in the proximal femur. This clinically relevant research will be performed in collaboration with UCSF orthopaedic surgeons.
Specific duties for the UROP student will include preparation of specimens from cadaver bones, microCT and FTIR imaging, and analysis of the results. All training will be provided. Prerequisites include coursework in anatomy. ME C176 recommended but not required. The student must be independently motivated and posses the ability to work in a team. The lab is situated in a new building on the UCSF Mission Bay campus. The campus is BART accessible - work schedule is flexible and can be adjusted to accommodate the commute from Berkeley. This is a great chance to learn about bioengineering research in a clinically important project. |
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Katrina Lin |
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David Rempel: Hand biomechanics and keyboard design
The student will work with a graduate student evaluating the effects of keyboard designs on wrist and forearm postures of computer users. Will use a 3D motion analysis system. Project will lead to a publication. Work is done at the Richmond Field Station - bus runs from campus to RFS every hour. Student should have at least 10 hours per week time to devote to this project. |
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| Chemical Engineering |
Fall 2006 |
Spring 2007 |
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No projects |
TBD |
| Civil and Environmental Engineering |
Fall 2006 |
Spring 2007 |
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Slav Hermanowicz: Membrane Filtration for water reclamation
Research assistant wanted to work on the fundamentals of the cutting edge technology to reclaim water. Project involves understanding of ultrafiltration mechanisms. Position will involve performing routine laboratory analysis, reactor operation and data entry. Qualified applicant must have an interest in environmental engineering, be able to work up to 20 hours per week. Previous experience in a water,wastewater, chemical or biological lab highly desirable. |
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David Leung |
Claudia Ostertag Project #1: Effect of confinement on crystal growth
The student will investigate the effect of confinement on crystal growth in cement based materials. The student will use X-ray diffraction and scanning electron microscopes to investigate the effect of confinement on crystal growth and resulting crystal morphology. |
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Joanna Chang |
Claudia Ostertag Project #2: Rapid Hardening Fiber Reinforced Concrete
Project Description:
Bridge repair requires a concrete to be not only durable but also to harden and develop strength in less than 6 hours. The student will be involved in designing concrete mixes for rapid hardening. In addition the student will be conducting mechanical testing and characterization of the concrete mixes for bridge applications. |
Xiu Li |
Xiu Li |
Jasenka Rakas : Project #1 Airport Layout Analysis and Modeling
The design and layout of airside airport elements, such as runways, taxiways, and parking stands has a large effect on the efficiency of ground operations. For example, at LAX, the terminals are located midfield between two sets of parallel runways. The situation is much the same at Atlanta, however, at LAX, the terminals are pier-shaped, and are arranged around a central circulation ring. At Atlanta, the terminals are of the satellite type, allowing planes to easily access either the north or south runway complex from any gate. This is not the case at LAX, where there are only two taxiways that allow planes to move from the north field to the south field and vice versa. It is believed that this impacts operation efficiency on the ground and in the air in several ways. First, a plane may be forced to land in a runway complex that is appropriate to its origin/direction of travel (i.e. a plane with a gate at the north complex approaching from the southwest, and therefore nee!
ding to get into the north field landing pattern). On the ground, the lack of mobility can be a problem when gates are reassigned, or when a plane may need to access a different runway complex with appropriate runways.
Another similar problem occurs at OAK airport where executive jets often seek a permission to take off from northern runways, which are closer to their gates. However, the noise issues force these aircraft to take off from RW 29, located in the southern part of OAK airport. As a result, increased taxi time, fuel consumption, emission and aircraft ground traffic become increasingly important issues at this airport.
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Ian Nicolson |
Open |
Jasenka Rakas : Project #2 Airport Planning and Design:
Searching for the Weakest Links among Airport Elements
Project Description:
In this research we will explore the interactions and compatibilities of Airport components in support of a good Airport Master Plan. Because each Airport Mater Plan, and in particular the Airport Layout, should always have all airport components well connected and balanced, we will explore the bottlenecks, weak links and insufficiencies commonly present in airport designs.
In particular, this research will explore the following issues:
1) Runway Directions and New Large Aircraft
2) Environmental Issues
3) Airside Ground Operations
4) Airport Terminal Design
Case studies that include analytic and simulation analyses will be considered as a part of the research project. A list of problematic links in the design of an airport will be provided as well as potential solutions.
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Daniel Guzmen
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Renard Gamaliel
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Francisco J.Martin
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Aleksandr Prodan |
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| Electrical Engineering and Computer Sciences |
Fall 2006 |
Spring 2007 |
Ruzena Bajscy: TEEVE (tele-immersive environment for every man and woman)
We have build a laboratory composeed of 48 cameras and stereo display, we are looking for people who are interested in real time graphics and Computer vision tasks. |
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Open |
Jose Carmena: BMI Software Platform
Brain-machine interface (BMI) systems require neuronal data to be translated into mechanical arm positions through hardware and software. The student will write a C/C++ program that can interface between the neuronal data acquisition hardware and the mechanical arm hardware through TCP/IP networking. |
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Michael Clancy:UC-WISE II design and development
The UC-WISE project aims to develop useful technologies for university course curricula. Our main focus to date has been to rework CS 3 and CS 61B with highly interactive web-based instruction. These efforts have been quite successful; we are looking to continue and extend our accomplishments inside and outside Berkeley. We are in the beginning stages of creating a new UC-WISE system (UC-WISE II) that incorporates a new Java-based infrastructure. The proposed URO projects address different aspects of the system design and development.
Michael Clancy: Project #1 -
Design and implement the core features of UC-WISE II.
The new UC-WISE system will be based on the new Scalable Architecture for Interactive Learning (SAIL), being developed in the School of Education. Using this architecture, we will need to develop new features to handle the demands of UC-WISE courses.
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Ionas Porges-Kiriakou |
Ionas Porges-Kiriakou |
Richard Fateman: Handwriting and Voice Input of Mathematics to computers.
It seems plausible to make it possible to handwrite mathematics or speak mathematics into modern "multimedia" desktop computers. In fact it is rather challenging. Students interested in improving the programs, using Microsoft .NET, Java, Lisp, C#, and library packages for handwriting and speech, can learn more about the Math Speak and Write project at http://www.cs.berkeley.edu/~fateman/msw |
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| Brian Harvey: Extensions
to the Berkeley Logo Interpreter |
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Wei Shum Valerie Wong |
Scott Shenker: New Data-Oriented Internet Architectures
We are in the process of investigating alternative Internet architectures, including new addressing, naming, and protocol designs. We are particularly interested in our proposed data-oriented network architecture (DONA). There are still some design issues to resolve (particularly in the areas of how users will handle names and how enterprises will manage DONA-based networks). We are in the process of implementing our initial version of DONA and plan on a test deployment on Planetlab. We would welcome help from undergraduates in helping us design, build, and deploy DONA.
To see more about these proposals, see http://cs.shenker.net/files/ArchitecturePapers.zip for a collection of related papers by our group. Feel free to contact me (by email) if you have any questions.
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Kye Hyun Kim |
Vivek Subramanian: Software development for printing Technology for low-cost electronics
Printing is considered to be a promsing technology for realizing ultra-low cost electronics for such applications as roll-up flexible displays, etc. My research group is working on the development of novel printing techniqeues for fabrication of electronic circuits. We have developed and fabricated several printers for this application. We are looking for students to write control software to automate the printing processes involving the following tasks:
1) Development of control software to control custom printers using driver API's that will be provided
2) Development of routines for automated computer vision systems to achieve alignment of printers and distortion correction, etc.
3) Development of a user interface for the same.
A first generation of the software already exists as a guideline. We are currently pursuing a major re-write to improve functionality and automation. |
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Joshua Hunt |
Avideh Zakhor: Algorithms for 3D city modeling
This project deals with fast, automated modeling of urban environments. WE have build experimental apparatus made of laser scanners and cameras which are mounted on ground and airborne vehicles. Data is acquired while the vehicles are in motion in a continusous fashion, rather than in a stop and go fashion, resulting in extremely fast data acquisition times. This combined with a "no human in the loop" approach results in a fast, automated approach to urban modeling.
Our goal over the next year is to extend this technique so that it is scalable and can generate large models for large areas in a fast, efficient manner. |
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Steven Jian |
| Engineering Science |
Fall 2006 |
Spring 2007 |
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No projects |
TBD |
| Industrial Engineering and Operations Research |
Fall 2006 |
Spring 2007 |
Ken Goldberg: Networked Cameras and Robots
The Internet provides a low-cost and widely-available interface that can make robots accessible to anyone with a desktop computer and network access. In this project we're designing and developing "collaborative" networked cameras and robots for natural environments, see: http://www.c-o-n-e.org/
URO applicants should have a basic engineering background in either IEOR, EECS, or ME. A minimum of 6 hours per week is required. For examples of past and current projects, see http://goldberg.berkeley.edu/
I'm looking for highly creative and intelligent students seriously interested in research who are comfortable working independently. If you have strong programming or design skills, a GPA over 3.7, and can commit at least 6-8 hours per week for the entire semester, read on:
I need to get an idea about your skills and creativity. Please review
the research projects listed on my home page and come up with 2
creative suggestions about a research/programming project you can take
on to improve/enhance one of our current projects based on your skills
in programming/design/etc.
Email me a short summary goldberg@berkeley.edu of this in plain text (no attachments!) and include your name, major, expected graduation date, GPA, and relevantqualifications,n with "Student interested in URO position" on thesubject line. Alas, I may get many responses so check back if you don'thear back from me before the deadline. |
David Jaeger Nathanson |
David Jaeger Nathanson |
Lee Schruben: International biopharmaceutical regulation and its impact on production
Currently most nations have specific regulations for biopharmaceuticals. These rules govern both the end product as well as the processes used in production. Process regulations mean that manufacturers of this class of drugs have to decide how to make a drug before they know where it can be sold. Using a particular piece of equipment in production may preclude sales in a given market, even though the drug exceeds product standards for that market. This means that a biopharm company, when scheduling production, has to consider producing nearly a million different varieties of a product even though they are in essence making only a single drug.
This project is to explore this maze of international regulations and its impact on production decisions and develop strategies for dealing with these constraints. The goal is to help biopharm firms operate efficiently to produce high-quality drugs that are also affordable. |
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George Shanthikumar: Model Uncertainty, Operational Statistics and Operational Decision Theory
Much of the theory developed for the application of stochastic modeling and optimization assumes that all the parameters needed for the implementation of the theory will be known precisely at the time of implementation. In real applications though this is far from true. In this projects we will explore different approaches to overcome the ptifalls caused by this assumption in the current theoretical developments in industrial engineeriong, management science and operations research. |
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| Mechanical Engineering |
Fall 2006 |
Spring 2007 |
Michael Frenklach: Equilibrium-State Application for ME105
Project Description:
This project will involve writing a graphical user inteface (GUI) in Matlab, which will take as input certain properties of a system, and return as output the equilibrium state the system will eventually come to. It will compliment the existing Matlab software developed by Prof. Frenklach for undergraduate course in Thermodynamics (ME105). |
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Mike Langston |
A.K. Oppenheim: Combustion in piston engines
The intrinsic purpose of internal combustion engines is to create pressure that provides force for generation of their work output. The most appropriate way to assess engine performance is, therefore, by pressure diagnostics of its dynamometer test data - a procedure developed by Oppenheim. The objective of the project is to carry out such diagnostics for data provided by engine laboratories in a number of research institutions in Europe, America and Asia. To accomplish this task, numerical computations are performed by the use of EXCEL and MATLAB. Familiarity with these programs is therefore required. |
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Ralph Greif: Heat and Mass Transfer and Fluid Flow in a Micro Fuel Cell
Experimental and theoretical work with an emphasis in the reactor/reformer section. Variation of system perfomance with respect to temperature and flow rate will first be studied. |
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Masayoshi Tomizuka: Modeling and Control of Micropositioning System
This project is concerned with modeling and control of positioning at microscale. A challenge is that the system has multiple axes, the interaction of which must be taken into consideration. The work involves analysis, computer simulation and experimentation. |
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Benson Tongue: AWESOME: Designing an Engineering Knowledge Portal
This resarch project involves a continuation of AWESOME (A Web Enabled Study Of Mechanical Engineering), a web-based program that allows students to discover, on their own, the answers to a variety of questions. Questions such as: "What do Mechanical Engineers do?" "What do I learn in ME XX?" "Why kind of jobs use the material from ME YY?" The web page is multi-media and research will involve finding out and filling in some of the answers to the just mentioned questions, crafting effective web pages, etc. Ultimately the core material will be ported to other schools and to other disciplines but at this stage the target is ME here at Berkeley. |
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Aaron Chang |
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| Materials Science & Engineering |
Fall 2006 |
Spring 2007 |
Fiona Doyle: Project #1 - Chemical mechanical planarization of copper; atomic force microscopy measurements
Chemical mechanical planarization is used in the dual-damascene process for producing copper metallization during semiconductor manufacturing. As part of an interdisciplinary study of the synergistic interaction of mechanical and chemical effects, we plan to do scratch tests on copper in an environmental atomic force microscope (AFM). The work will involve removing well-defined areas of passive film in aqueous solutions representative of the chemistry of CMP slurries, and observing the transient electrochemical response, as the damaged film reforms. The effect of different slurry additives will be explored. Data obtained from these measurements will be incorporated into a mechanistic model for CMP that captures both mechanical and chemical contributions to material removal. The student working on this project would ideally be a junior or senior, and should have experience in preparing and handling chemical solutions. |
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Danny Wu |
Fiona Doyle: Project #2 - Development of microfluidic reactor for synthesizing semiconductor nanocrystals
We are developing a microfluidic reactor for synthesizing nanocrystals on an industrial scale, for point-of-use manufacture of nanocrystals. Numerous individual microreactors, including their reagent introduction systems and flow channels, could be contained in a single silicon-on-insulator wafer, allowing parallelization, and unprecedented control and scalability in synthesis and manufacturing. Two immiscible liquids will be used, with a channel geometry that induces spontaneous generation of droplets of one phase dispersed in the other. These droplets will then pass through the reactor with a tightly controlled residence time. Individual zones within the reactor will have well controlled temperatures, to promote chemical reactions leading to the nucleation of semiconducting nanocrystals, and growth of these nuclei. This project will involve either focused literature research or modeling on individual topics needed for the overall design. This could include fluid mechanic!
s, heat transfer, reaction engineering, novel synthesis techniques, and nanotechnology, according to the interests and expertise of the student. |
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Jake Park |
Yuri Suzuki: Fucntional Oxide Thin Film Growth and Characterization
The family of complex oxide materials (that includes ternary and quaternary oxides) is of great interest fundamentally and technologically as it includes many materials with multiple functionalities. We focus on synthesizing so-called multi-functional materials in thin film form by physical vacuum deposition techniques and on characterizing their functional properties that include magnetic, electrical and optical properties. I have an opening for an undergraduate in my group to work with a graduate student to perform thin film synthesis as well as standard magnetic and electrical characterization. A minimum of 6 hours per week of research is expected in order to make reasonable progress during the semester. Student with coursework in electronic properties of materials or solid state physics is preferred. |
Douglas Chain |
Open |
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| Nuclear Engineering |
Fall 2006 |
Spring 2007 |
Joonhong Ahn: Reduction of environmental impact from geologic repositories for high-level wastes by application of advanced nuclear fuel cycle
In the current plan for Yucca Mountain Repository, commercial spent nuclear fuel will be disposed of in a deep geologic formation. For sustainable utilization of nuclear power, it is important to find technological solutions to expand repository capacity without increasing environmental impact. In the project, effects of various nuclear materials recycling schemes on the environmmental impacts will be investigated by developing mathematical models and computer codes. |
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Donald Olander: Compatibility of uranium-zirconium hydride fuel with high-temperature steam
This is an experimental project that will examine the reaction between the proposed new fuel for light-water reactors and high-temperature steam. This situation can arise in the event of a severe accident to the core of the reactor. The experiment uses a microbalance to follow the course of the reaction |
Michael Foxe |
Michael Foxe |
Per Peterson:High temperature heat transport for the efficient production of nuclear hydrogen and electricity
This project involves assisting in the analysis, design, construction and operation of experiments to simulate the use of high-temperature liquid salts for heat transport in fission and fusion energy systems. This project involves experience with machine-shop work, experiment construction, experiment data aquisition systems, data analysis, and the use of design and modeling tools including 3-D graphic design software. |
James An
Michael Toulouse
Chris Campen
James Franklin
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James An
Michael Toulouse
Chris Campen
James Franklin
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Brian Wirth: Project #1 - Computer simulations of helium diffusion in Fe alloys
The research project will investigate the mechanisms associated with the slowing down of energetic helium ions in Fe alloys, and the subsequent diffusion of helium. This research supports the development of advanced structural materials for fusion energy applications, in which the nucleation and growth of helium bubbles is a primary cause of dimensional instablity and changes in time-dependent deformation and fracture behavior. The research will involve computer simulations using molecular dynamics and kinetic Monte Carlo models. |
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Thien-Ahn Phan Nguyen |
Brian Wirth: Project #2 - Computer simulations of high energy displacement cascades in uranium dioxide
The research project will investigate the number and spatial distribution of defects formed by a recoiling heavy atom following radioactive alpha decay in uranium dioxide. This research supports understanding the degradation mechanisms of spent nuclear fuel, in assessing the potential for radiation enhanced diffusion of noble fission gas atoms that can degrade the structural integrity of the fuel. The research will involve computer simulations using molecular dynamics. |
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Minh Lu |
Brian Wirth: Project #3 - The behavior of coated particle fuels at high burnup
The research project will investigate the prior history of coated particle nuclear fuels operated in domestic and foreign high temperature gas reactors, to evaluate the potential for achieving high burnup in future reactors. The research will involve both literature studies which describe previous experience and the development of models to predict fuel performance and possible failure mechanisms at extended burnup. |
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Aaron Oaks |
