About
the program | Program Calendar | Research
Projects | Student Applications | Faculty
Applications | Past
Years
Projects - Summer 2008
Please note: We have expanded to include bioengineering faculty at UC San Francisco! This is an exciting opportunity to work with faculty not usually accessible to Berkeley undergrads. However, students working with UCSF faculty must be able to commute to San Francisco 5 days per week during the summer. UCSF campuses are accessible by public transit, and by a network of free UCSF shuttles, but there may be significant commute time.
Seung-Wuk LeeResearch Area: Biomaterials
Campus: UC Berkeley
Department: Bioengineering
leesw@berkeley.edu, phone: 510-486-4628
Lab Description: We investigate the molecular level properties of the model bone surfaces using single crystal hydroxyapatite. Using in situ atomic force microscopy techniques, we will study the morphology changes of the model bone surfaces in the simulated body conditions.
Desired student knowledge or qualifications: We want a student who has good mathematic and computational skills with solid state physics and chemistry background.
Optional project description: Student will synthesize the hydroxyapatite crystals with the guidance of a postdoctoral fellow and analyze the atomic force microscopy images.
Valerie Weaver
Research Area: Biomechanics
Campus: UCSF Parnassus
Department: Department of Surgery
weaverv@surgery.ucsf.edu, phone: 415 476-3826
Lab Description: The Weaver Laboratory is studying the role of matrix composition, topology and mechanical properties in tumor progression and metastatsis and in human embryonic stem cell fate. Approaches involve the use of whole animal models and real time imaging, generation of 2D and 3D hydrogels with defined mechanical and topological features, examination of biochemical mechanisms by which cells sense and respond to force to alter cell fate and clinical specimen analysis.
Desired student knowledge or qualifications: Strong interest in tissue mechanics, biomaterials manipulation experience, some familiarity with mechanics. Cell culture experience considered highly desirable.
Optional project description: Projects are available to study the role of matrix stiffness and mechanical force in breast tumor progression and metastasis. Another project is also available to use a force reactor to establish the role of force in human embryonic cell differentiation.
Jenni Buckley
Research Area: biomechanics
Campus: UCSF General Hospital
Department: UC San Francisco, Dept. Orthopaedic Surgery, Industrial Research Center
buckleyj@orthosurg.ucsf.edu, phone: 415-206-8892
Lab Description: Our laboratory, the UCSF/SFGH Industrial Research Center (IRC), is essentially a cooperative research environment for clinical faculty members in the UCSF Department of Orthopaedic Surgery to conduct objective, scientifically-based industry-sponsored research projects. These projects are all related to interproduct comparisons of orthopaedic implants or surgical techniques, e.g., total intervertebral disc replacement systems or arthroscopic suture repair protocols. All studies conducted at the IRC involve mechanically testing human cadaveric tissue with the ultimate aim of improving product clinical safety and efficacy.
Desired student knowledge or qualifications: Applicants should have a strong mechanics background, and familiarity with electronic systems, materials testing systems, and mechanical design/machining is a plus. Students MUST be comfortable working with and around heavy machinery and must be willing and capable of handling human cadaveric material.
Optional project description: Students will work as part of a multidisciplinary team of academicians, surgeons, medical students and residents, and staff engineers to investigate the feasibility of new orthopaedic technologies. Current projects for this summer include acetabular fracture repair, elbow joint laxity, lumbar total disc replacements, and upper cervical spine fixation systems.
Clifton Schor
Research Area: Biomechanics
Campus: UC Berkeley
Department: Optometry
schor@berkeley.edu, phone: 642-1130
Lab Description: We study the human ocular focusing mechanism and its loss with aging. We are currently evaluating a prosthetic ocular lens that is intended to restore ocular focusing ability in older patients. The analysis is of the optical wave front using the Shack-Hartman wave front sensor. We can sample the wave front at 50HZ to follow dynamic changes in the wave front.
Desired student knowledge or qualifications: Someone interested in wave-front optics and human vision and prosthetic devices.
Optional project description: We will conduct wavefront analysis using a dynamic aberrometer of retinal image quality in patients who have a new accommodating intraocular lens that is intended to restore ocular focusing in older eyes. The wave front analysis is intended to learn how the implant works by analyzing the wave front to discriminate between adding aberrations and by changing focus.
David Rempel
Research Area: Biomechanics
Campus: UCB Richmond Field Station
Department: Bioengineering
david.rempel@ucsf.edu, phone: 510-665-3403
Lab Description: Rempel Lab studies hand, shoulder and neck biomechanics related to performing work. Past studies have focused on the design of keyboards, computer mice, chairs and assembly work. The lab has 4 PhD students, a postdoctoral fellow, and an engineer and is equipped with a motion analysis system, video processing equipment, machine shop and electronics shop.
Desired student knowledge or qualifications: No summer school enrollment, work regular hours, attention to details, ability to work well with others (subjects and colleagues), knowledge of excel.
Optional project description: Head and Torso Biomechanics during Computer Work Student will assist with study of the effect of computer monitor positioning on head and torso postures and geometry. Will recruit subjects, collect data with subjects, use a motion analysis system, calculate joint centers of rotation and body segment moments, and assist with statistical analysis and preparation of manuscript. Research will be carried out at the UC Berkeley Richmond Field Station.
Roger Cooke
Research Area: Biomechanics
Campus: UCSF Mission Bay
Department: Biochemistry/Biophysics
cooke@cgl.ucsf.edu, phone: 476-4836
Lab Description: The laboratory works on the biophysics of the motor proteins and on muscle physiology.
Desired student knowledge or qualifications: Some knowledge of physics desirable; expect 10 weeks at 40hrs/week; schedule negotiable.
Optional project description: Project will be chosen according to student's interests. One possibility is the use of electron magnetic resonance spectroscopy to probe the mechanism of force generation by the motor proteins. A second possibility is measurement of single muscle fiber mechanics to understand muscle fatigue.
Mohammad Mofrad
Research Area: Biomechanics
Campus: UC Berkeley
Department: Bioengineering
mofrad@berkeley.edu, phone: 3-8165
Lab Description: Our research is focused around two goals: (1) To understand the principles underlying cellular mechanics and mechanotransduction, (2) To understand the multi-scale processes involved in cardiovascular tissue biomechanics and mechanotransduction underlying diseases like aortic valve calcification and arterial atherosclerosis.
Desired student knowledge or qualifications: Minimum GPA 3.5; interested in computational projects.
Optional project description: Molecular Cell Biomechanics
Amy E. Herr
Research Area: BioMEMS and Nanotechnology
Campus: UC Berkeley
Department: Bioengineering
aeh@berkeley.edu, phone: (510) 666-3396
Lab Description: A major focus of our lab is engineering innovation for analysis of complex biological systems -- as is required to address questions important to both fundamental biological systems and applied clinical research. We employ a combination of approaches drawn from chemical engineering, mechanical engineering, and electrical engineering with strong foundations in biology, materials science, and analytical chemistry. In essence, we strive to advance the "mathematization" of biology & medicine. (see herrlab.berkeley.edu for more details)
Desired student knowledge or qualifications: Junior or Senior; independent, inquisitive, with keen observational and documentation skills; knowledge of protein assays (e.g., ELISA, microarray, immunoassays) and microfabrication is helpful. Outstanding references are required.
Optional project description: Protein analysis in microfluidic devices -- specifically electrophoresis under non-uniform chemical conditions.
Dan Fletcher
Research Area: BioMEMS and nanotechnology
Campus: UC Berkeley
Department: Bioengineering
fletch@berkeley.edu, phone: 643-5624
Lab Description: The Fletcher Lab studies the mechanics and dynamics of cell movements and shape changes involved in tissue development and repair. For these studies, we develop new instrumentation and measurement technologies to quantify cell and molecular mechanics. Our tools include optical microscopy, atomic force microscopy (AFM), optical trapping, and microfabrication, as well as biophysical modeling and simulation. Based on our understanding of cell and molecular mechanics, we are developing medical devices that aid in clinical diagnosis and treatment of disease.
Desired student knowledge or qualifications: Full time, experience or interest in microfluidics, optical microscopy, and image processing.
Optional project description:
Colin Studholme
Research Area: Computational Biology
Campus: UCSF Parnassus
Department: Department of Radiology
colin.studholme@ucsf.edu, phone: 1 415 221 4810 x2824
Lab Description: Our research is on the development and application of novel computational techniques to study brain anatomy from in-vivo medical imaging. Our lab web page is at: http://www.radiology.ucsf.edu/bicg
Desired student knowledge or qualifications: Students should be interested in computing and/or mathematics and research into their application to Biomedical or clinical research. Some experience in programming and an interest in image processing would be good.
Optional project description: The student project would be based around the reconstruction and analysis of images of the human fetal brain acquired from clinical MRI studies. The project would involve collaborations between computer scientists, physicists and clinicians to relate clinical measures to structural models of the brain.
Xiaojuan Li
Research Area: Imaging
Campus: UCSF China Basin
Department: Radiology, UCSF
xiaojuan.li@radiology.ucsf.edu, phone: 415-353-4909
Lab Description: The research in my lab is focused on developing advanced magnetic resonance imaging (MRI) and MR spectroscopic imaging (MRSI) techniques to improve early diagnosis and treatment follow-up for osteoarthritis (OA) and other knee injuries (such as anterior cruciate ligament tears). OA is the most common type of arthritis, affecting over 20 million people in the United States. It is a disease characterized primarily by cartilage degeneration. Current clinical imaging methods are limited to providing primarily morphologic changes of cartilage that happen at late stages of OA. We aim at developing imaging techniques that can probe biochemical changes in the collagen-proteoglycan (PG) matrix that occurs during early OA. The imaging parameters will also be correlated with biochemical and biomechanical measurements and gene expression evaluation, using specimens from patients with total knee replacement. The students will be involved in MRI and HRMAS (high resolution magic angle spinning) spectrometer acquisition and processing, obtaining specimens from orthopaedic surgery room, biochemical measurements, biomechanical measurements, and gene expression analysis in the lab, as well as statistical analysis and data interpretation.
Desired student knowledge or qualifications: Working full time and no summer school enrollment. No class year limitation. Preferred experience: matlab or C coding, previous lab research experience.
Optional project description:
Martin Banks
Research Area: Imaging
Campus: UC Berkeley
Department: Optometry, Vision Science
martybanks@berkeley.edu, phone: 510-642-9341
Lab Description: We study human vision. The student would be working on a few projects involving the development of 3D displays for use in medical imaging, scientific visualization, and other virtual reality applications.
Desired student knowledge or qualifications: Experience with MATLAB and data analysis. Would expect at least 20 hours/week in the lab. Time of day the student would work is flexible.
Optional project description:
Stanley Klein
Research Area: imaging
Campus: UC Berkeley
Department: Vision Science & Bioengineering
sklein@berkeley.edu, phone: 6438670
Lab Description: We do signal processing on electric and magnetic fields (EEG and MEG) generated by the brain to figure out how multiple brain areas communicate with each other. In order to separate activity from multiple areas we make use of the cortical folding patterns revealed by MRI and fMRI. Another way to say it is that we are hooking up the exquisite temporal information of EEG/MEG with the spatial resolution of fMRI/MRI.
Desired student knowledge or qualifications: Main skill is good facility with Matlab and comfort with some mathematics like signal processing. We are flexible with hours.
Optional project description: There are several possible projects. Our DARPA funded project involves machine learning of EEG and eye movement patterns to speed up object detection.It is like a brain-computer interface project. We also have a variety of other projects to choose from involving: separation and identification of cortical sources processing of MRI and fMRI signals nonlinear dynamics of brain activity and more.
Jean Pouliot
Research Area: Imaging
Campus: UCSF Mount Zion
Department: Radiation Oncology
jpouliot@radonc.ucsf.edu, phone: 415 353-7190
Lab Description: Image-guided brachytherapy. see www.ucsf.edu/jpouliot and click on Inverse Planning IPSA for more details.
Desired student knowledge or qualifications: Student with a physics or scientific background, self motivated, computer savvy, with an interest in the medical field and applications of scientific concepts to radiation therapy. Good writing skill would be a plus. Typically 40 hour week, but flexible schedule.
Optional project description: Research Projects A new brachytherapy suite recently completed in our department offers real time imaging (Fluoroscopy, Conebeam CT, 3D ultrasound), needle navigation system and inverse planning (IPSA) for High Dose Rate (HDR) and Permanent Prostate Implant (PPI) brachytherapy. This provides the platform for the development of a wide range of clinical scenarios of Image-Guided Brachytherapy with quasi real-time planning. In particular we currently investigate dose distributions achievable with novel spatial arrangements of needles and catheters that can reduce patient trauma and side effects. Preliminary studies suggest that new catheter and needle arrangements can dramatically improve treatment effectiveness by reducing side effects. New catheter and needle arrangements can also allow physicians to treat patients previously considered unsuited for brachytherapy treatment (pubic arch interference). During the Summer, the student will become familiar with: - Physics concepts of radiation therapy - Clinical workflow of radiation treatment - Basic principle of Brachytherapy - Conebeam CT imaging - Inverse Planning - Concepts of IGBT The role of the student The student will join the group in its ongoing effort to further develop the IGBT process and define new clinical applications. In particular, the student will 1- test and validate the transfer, registration and fusion of images from the different imaging modalities and 2- use our inverse planning IPSA to explore the dosimetric impact of non-standard catheter patterns. The student will work in a clinical environment with a multi-disciplinary team of physicists (Mentor, postdoctoral fellow, graduate students, summer students), research engineers and clinicians (radiation oncologists and medical residents), and understand how the technology can and should be developed to improve the efficiency of cure and benefit health in general.
Susan Noworolski
Research Area: Imaging
Campus: UCSF China Basin
Department: Radiology - UCSF
sue@radiology.ucsf.edu, phone: 415-353-9409
Lab Description: My research is on using MR imaging to evaluate diseases of the abdomen and pelvis. Dynamic contrast-enhanced MRI, MR spectroscopy, MR diffusion and MR anatomic images are tailored for the disease and evaluated as compared to pathology.
Desired student knowledge or qualifications: Much of this work will be performed on a unix workstation. The student should be comfortable on a computer and preferably has some programming background, ideally knowledgeable of UNIX, C, and perl.
Optional project description: The project will be on evaluating Dynamic Contrast-Enhanced MRI (DCE MRI) of prostate tissue to better identify and characterize prostate cancer. The DCE MRI will be correlated to other MR imaging and to pathology results. This will require image alignment and evaluation with the pathologist of the histopathology slides of the prostates.
Youngho Seo
Research Area: Imaging
Campus: UCSF China Basin
Department: Department of Radiology, UCSF & UCSF/UCB Joint Graduate Group in Bioengineering
youngho.seo@radiology.ucsf.edu, phone: 415-353-9464
Lab Description: We focus on how to quantify acquired images from nuclear medicine systems combined with x-ray computed tomography (SPECT/CT and PET/CT). The quantification heavily relies on physics of the imaging systems and how the images are reconstructed. The quantified data are correlated with independent results that share the same origin of the radionuclide imaging.
Desired student knowledge or qualifications: Basic understanding of modern physics (radioactive processes of particles). Basic understanding of modern biomedical diagnostic processes (why noninvasive imaging is a preferred choice of patient management). Basic understanding of physiology and anatomy. 20-40 hours per week, group meetings, and presentation/poster. Summer school enrollment is encouraged.
Optional project description: We will try to assign existing data sets (either from clinical or from preclinical (animal) imaging systems). The task for undergraduate students could vary depending on the qualification and experience of each individual.
Sharmila Majumdar
Research Area: Imaging
Campus: UCSF Mission Bay
Department: Radiology, UCSF and Bioengineering, UCB
sharmila.majumdar@radiology.ucsf.edu, phone: 415 476 6830
Lab Description: Our lab works on imaging the musculo-skeletal system, including bone, cartilage and other tissues. The goal is to combine imaging information with biochemistry, biomechanics and tissue engineering of musculo-skeletal tissues.
Desired student knowledge or qualifications: Motivation, quick learner, MATLAB experience preferred, computer experience preferred.
Optional project description: 1) Correlation of magnetic resonance imaging characteristics of cartilage with measures of local mechanics using nano-indentation. 2) High field (7 tesla) whole body magnetic resonance imaging of bone and relation to micro-computed tomography, a high-resolution imaging method.
Stefan Habelitz
Research Area: Tissue
Campus: UCSF Parnassus
Department: Preventive and Restorative Dental Sciences
stefan.habelitz@ucsf.edu, phone: 415-514-0818
Lab Description: My research focuses on the biomineralization process of calcified tissues in regards to 1.) the relationship between micro/nano-structure and properties, 2.) mechanisms of interactions between organic and inorganic molecules and phases, 3.) application of biomimetic approaches for the regeneration of dental hard tissues using recombinant proteins and/or dental stem cells.
Desired student knowledge or qualifications: At least two years in Bioengineering or Cell Biology Program. Must have taken Cell Biology course (MCB130L or BioE115 or equivalent) and experience with cell culture. 40 hours/week.
Optional project description: The student will investigate the suitability of dentin membranes for pulp-cell and dental stem cell growth. The effect of growth factors and amelogenins to encourage pre-odontoblast polarization in three-dimensional scaffolds will be studied as a first step towards tooth regeneration.
Patricia A. Leake
Research Area: Tissue
Campus: UCSF Parnassus
Department: Otolaryngology-Head and Neck Surgery, UCSF
pleake@ohns.ucsf.edu, phone: 415-465-5958
Lab Description: The project for which we are recruiting a student focuses on evaluating the effects of early deafness, electrical stimulation delivered by a cochlear implant, and potential neurotrophic agents such as brain derived neurotrophic factor (BDNF) upon the neurons of the inner ear and central auditory system.
Desired student knowledge or qualifications: Experience in using a light microscope; capturing and manipulating images is desirable but not absolutely essential. Hours flexible.
Optional project description: Light microscopy and morphometric/stereologic image analysis of spiral ganglion neuronal survival and somatic size in normal, early-deafened, and BDNF-treated cochleae (inner ear).
Announcements
2008 students have been selected.
2009 applications will be posted in Spring 09.
