2015

Community College Participants and Projects: 2015

Undergraduate Researcher: Jorge Avila
Intended Major: Electrical Engineering and Computer Science
Home Institution: East Los Angeles College
Research Project: Balance Estimation of Human Exercise Using Kinect
Faculty Advisor: Prof. Ruzena Bajcsy
Postdoctoral Mentor: Dr. Qifei Wang
UC Berkeley Department: Electrical Engineering and Computer Science
Project Abstract: Rehabilitation and exercise programs for the elderly can be greatly improved with real-time feedback on exercise execution. The Kinect camera offers a low-cost sensor for developing such applications. In this project, we investigated the use of pose information detected by the Kinect camera to estimate force dynamics of the human body. Particularly, the torques that gravity forces apply to body segments with respect to ground contact points. The chief application of this research is to evaluate balance to prevent injuries and counterproductive movements. The results showed that this model was not able to properly evaluate balance due to noise in the Kinect data. Filtering methods would need to be researched and implemented in order to compensate for noise. Project poster

Undergraduate Researcher: Alyssa Barbosa
Intended Major: Biology
Home Institution: Santa Barbara City College
Research Project: Investigating Effects of Shell Proteins on Molecular Transport in Bacterial Microcompartments
Faculty Advisor: Prof. Danielle Tullman-Ercek
Graduate Student Mentor: Mary Slininger
UC Berkeley Department: Chemical and Biomolecular Engineering
Project Abstract: Microcompartments are organelle-like structures that house metabolic reactions within bacteria, functioning to localize enzymes and prevent toxic intermediates from escaping into the cell. The 1,2-propanediol utilization microcompartment (MCP) in Salmonella enterica converts 1,2-propanediol into carbon and energy. The MCP is constructed of shell proteins with pores that let metabolites in and out. Pdu genes control the structure and function of these shell proteins. This research investigates shell protein structure effects on metabolite transport. Previously, mutations to the Pdu A shell protein gene were made by replacing with the Eut M and K26A genes, through the process of recombination. Eut M displayed a superior growth phenotype to WT. I optimized the growth curve assay of Eut M by determining the optimum position in a shaking incubator to decrease margin of error while achieving optimal growth. It was found that Eut M growth was optimized with low light and evenly distributed heat. Project poster

Undergraduate Researcher: Shany Ben Artsy
Intended Major: Civil and Environmental Engineering
Home Institution: Los Angeles Pierce College
Research Project: Short-Term Response of Oak Ridge Groundwater Microbes to Different Carbon Sources
Research Advisor: Dr. Romy Chakraborty
Postdoctoral Mentor: Dr. Xiaoqin Wu
UC Berkeley Department: Earth Sciences Division, Lawrence Berkeley Lab
Project Abstract: The purpose of this study is to explore the effects of different carbon sources on the growth of microbial communities present in groundwater from well FW305 at the Oak-Ridge Field Research Center, Tennessee. Six different carbon sources were chosen: acetate, glucose, benzoate, casamino acids, cell lysate, and FW305 sediment extracts. Microbes were isolated using two dilutions of three different media. Isolated colonies were identified using 16S rDNA gene sequencing. The results illustrated that different microbial species were enriched, highly influenced by specific carbon sources available to them. Each carbon source enriched different bacteria and this was confirmed by the 16S sequencing. Some novel strains of bacteria were isolated, and further work needs to be done to characterize these strains. Project poster

Undergraduate Researcher: Michael Estrada
Intended Major: Mechanical Engineering
Home Institution: Consumnes River College and Sacramento City College
Research Project: Estimation of Forces Acting on Human Joints via the Kinect Camera
Faculty Advisor: Prof. Ruzena Bajcsy
Postdoctoral Mentor: Dr. Qifei Wang
UC Berkeley Department: Electrical Engineering and Computer Science
Project Abstract: The Microsoft Kinect camera has been studied extensively in recent years for its ability to capture human motion. This study explored the use of the Kinect camera to evaluate the forces acting on a person’s joints while exercising. The motion trajectories recorded with the Kinect camera, in conjunction with a set of anthropometric parameters are applied to a dynamic model to calculate the forces affecting the human’s joints. Since these forces are created, dampened, or counteracted by the muscles, the analysis of these data can be used to quantify muscular performance and provide recommendations for appropriate exercises. Project poster

Undergraduate Researcher: Kimberley Fountain
Intended Major: Mechanical Engineering
Home Institution: Berkeley City College and College of Alameda
Research Project: Impact-Testing the Integrity of 6-Strut Tensegrities
Faculty Advisor: Prof. Alice M. Agogino
Graduate Student Mentor: Lee-Huang Chen
UC Berkeley Department: Mechanical Engineering
Project Abstract: Tensegrity robots are a revolutionary generation of soft robotics, designed to operate safely and effectively alongside humans. For space exploration purposes, these robots have a much better chance at confident landing than traditional robots. Due to the natural compliance and structural force distribution properties of tensegrity structures1, these robots are able to absorb significant forces upon impact2, making them an effective replacement for traditional space rovers. Designing the first controlled drop test for tensegrity robots will further improve the framework of these structures and develop an optimized means of observation of their behavior upon impact, allowing for recognition of opportunities for improvements for subsequent versions of the robot. The current design focus of this study is on testing 6-rod tensegrity structures, but the design will be modular for developing and testing other tensegrity structures. Video analysis and motion tracking tools were used to perform detailed falling and impact analyses of the structure deformation and center of gravity during drop tests. By observing the results of the structural deformation per height drop upon different surfaces, scientists and engineers will be able to build a superior 6-strut tensegrity robot for planetary exploration. Project poster

Undergraduate Researcher: Irving Garduno
Intended Major: Mechanical Engineering
Home Institution: Los Angeles Trade Technical College
Research Project: Optimization of Patterned Thin Films of Photoresist for Plasma Etching Applications
Faculty Advisor & Mentor: Dr. Jeffrey Clarkson
UC Berkeley Organization: Marvell NanoFabrication Laboratory
Project Abstract: The process performance of photoresist coatings on SiO2 coated substrates and how it relates to plasma etching in the Marvell Nanofabrication Laboratory is reported. Process specification (PS) sheets and statistical process control (SPC) charts were used to monitor the thickness and uniformity of photoresist films as-coated, post-developed, and post-UV stabilized. The photoresist stabilization process highly influences the characteristics of patterned photoresist films and plays an important role in determining SiO2 plasma etch selectivity. Finally, the most robust photolithography process input parameters for plasma etching are defined. It was found that a standard oven hard bake at 120 C for 30 min. yielded the most vertical resist sidewalls and superior etch robustness. By using optimized photoresist coatings, the etch selectivity was increased ~ 15% and ~ 20% for DUV and i-line resist respectively. This research provides the Marvell Nanofabrication Laboratory with a better understanding of how photolithography affects etching applications and enhances on-going research throughout the lab. Project poster

Undergraduate Researcher: Kamaria Ashley Kermah
Intended Major: Bioengineering
Home Institution: El Camino College
Research Project: Engineering Signal Sequences for the 1,2-Propanediol Utilization Microcompartment
Faculty Advisor: Prof. Danielle Tullman-Ercek
Postdoctoral Mentor: Dr. Chris Jakobson
UC Berkeley Department: Chemical and Biomolecular Engineering

Undergraduate Researcher: Divyashish Kumar
Intended Major: Mechanical and/or Chemical Engineering
Home Institution: College of San Mateo
Research Project: Ultrafast Magnetization Switching of Ferromagnetic Alloys through Optically Generated Spin Current
Research Advisor: Dr. Jeffrey Bokor
Postdoctoral Mentor: Dr. Richard Wilson
UC Berkeley Department: Electrical Engineering and Computer Science
Project Abstract: Current methods of controlling the magnetization dynamics of a ferromagnetic metal to store information have substantial limitations, especially in regards to processing speed and data storage density. Magnetization switching by spin-transfer-torque is a promising phenomenon for the operation of ultrafast nanoscale devices. In our study, we investigated the possibility of using optically generated spin current to manipulate the magnetization of a 0.5 nm ferromagnetic layer. The spin current is generated by the rapid demagnetization of a ferromagnetic metal with the use of an ultrashort laser pulse. To understand the experimental limitations, we developed numerical simulations that compare the measured temperature dependence of the remnant magnetization with the optically generated temperature rises in order to calculate the spin currents in four different ferromagnetic metals: Fe, Ni, Co50Fe50, and Ni43Fe57. From this model, we predict that Ni43Fe57 excited with a 100 fs laser pulse with a fluence of 25 Jm-2 can generate a net spin current of approximately 1010 A/s for ~ 0.5 ps. The model also suggests that 1010 A/s is the spin current threshold for switching the spin of a 0.5 nm layer of Co50Fe50B. This investigation allows us to explore new outlets of generating spin currents to flip the magnetization of a ferromagnetic film on the timescale of a few picoseconds. Project poster

Undergraduate Researcher: Danielle Naiman
Intended Major: Civil and Environmental Engineering
Home Institution: Santa Monica College
Research Project: The Effects of Different Insoluble Phosphate Media on Phosphate Solubilizing Bacteria from Mendocino Terrace Soil
Faculty Advisor and Mentor: Dr. Romy Chakraborty
UC Berkeley Department: Earth Sciences Division, Lawrence Berkeley Lab
Project Abstract: The goal of this project is to test isolated Phosphate Solubilizing Bacteria (PSB) from Mendocino Ecological Staircase soil samples and screen them for their ability to solubilize different insoluble phosphates in growth media: FePO4, AlPO4, and phytic acid. Almost one hundred strains were grown on an LB broth initially for robust growth, and then transferred to FePO4, AlPO4, and phytic acid containing basal media until the bacteria reached the stationary phase. A colorimetric assay using malachite green was used to detect soluble phosphate in the filtrate for each culture. Isolate E3, initially taken from the phytic acid plate, was found to be the quickest grower and produced the most solubilized phosphate on phytic acid. E3 was identified as Burkholderia sediminicola using 16s rDNA sequencing. B. sediminicola was then inoculated and grown in triplicate in AlPO4 and phytic acid containing basal medium as the sole source of phosphorus. Optical density measurements at 600 nm and the colorimetric assay were used at regular time points to determine growth and solubilized phosphate. It can be concluded B. sediminicola grows best in phytic acid containing media when compared to AlPO4 containing media and is efficient at solubilizing phosphate from phytic acid. Further research can be implemented into characterizing this particular strain and the mechanism, for phosphate solubilization. Project poster

Undergraduate Researcher: Robert Nguyen
Intended Major: Electrical Engineering and Computer Science
Home Institution: Chabot College
Research Project: Germanium Vertical Field Effect Transistor
Faculty Advisor: Prof. Tsu-Jae King Liu
Postdoctoral Mentor: Dr. Kimihiko Kato
UC Berkeley Department: Electrical Engineering and Computer Science
Project Abstract: To increase the density of transistors on an integrated-circuit “chip” without further scaling down the transistor gate length, a vertically oriented germanium-channel field-effect transistor (Ge-vFET) design is proposed. Technology computer-aided design (TCAD) simulations of Ge-vFET devices indicate that a high on-off current ratio, up to 7 orders of magnitude, can be achieved if the gate-length (Lg) to channel width (Wchannel) ratio is sufficiently large. The optimal dopant concentration for this junctionless FET design is found to be ~1017 cm-3. Project poster

Undergraduate Researcher: Tiffany Pan
Intended Major: Computer Science
Home Institution: Norco Community College
Research Project: Investigations on Techniques for Rapid Extraction of Topology Information for the Circle of Willis
Faculty Advisor: Prof. Shawn Shadden
Postdoctoral Mentor: Dr. Debanjan Mukherjee
UC Berkeley Department: Mechanical Engineering
Project Abstract: The Circle of Willis is a network of the major cerebral arteries in the brain, playing a key role in cerebral circulation. Considerable anatomical variations exist in its topology, with the complete network being observed in only about one-third of human population. Such topology variations are likely to influence cerebral hemodynamics and distribution of embolic particles that cause ischemic stroke. The correlation between these aspects has not been clearly established. Extraction of topology from medical image data is essential for such an effort. The objective Project poster is to develop tools to enable rapid extraction of topology of the Circle of Willis vasculature from medical image data. Project poster

Undergraduate Researcher: Melissa Roberts
Intended Major: Molecular and Cellular Biology
Home Institution: Diablo Valley College
Research Project: Understanding the Role of Lipid Modifications in ER Protein Quality Control
Faculty Advisor: Prof. James A. Olzmann
Graduate Student Mentor: Clark Peterson
UC Berkeley Department: Nutritional Sciences and Toxicology
Project Abstract: Endoplasmic reticulum (ER)-associated degradation (ERAD) is a cellular process responsible for the identification and degradation of misfolded proteins. Defining the mechanisms underlying this process is vital to understanding the pathogenesis of numerous human diseases that result from impaired ER protein quality control. Recent reports indicate that the inhibition of acyl-CoA synthetases with small molecule, triacsin c disrupts ERAD. However, it remains unknown why acyl-CoA synthetases are required for ERAD. Palmitoylation, the covalent addition of the fatty acid palmitate to a protein, requires acyl-CoA synthetase activity and can significantly impact protein localization, structure, and physical interactions. TProject posterfore, we hypothesized that palmitoylation of ERAD machinery regulates the identification and degradation of ERAD substrates. To test this hypothesis, we employed copper-catalyzed azide-alkyne cycloaddition to probe for palmitoylated ERAD proteins. Our results reveal palmitoylation of four prominent ERAD proteins: the E2-recruitment factor AUP1, the E3 ligase Hrd1, the rhomboid pseudoprotease Derlin1, and the mannosidase ERMan1, indicating that palmitoylation may regulate ERAD at multiple steps. Consistent with a functional role for palmitoylation in ERAD, we find that treatment the palmitoylation inhibitor 2-bromopalmitate significantly attenuated ERAD. Together, our results identify an unprecedented mechanism of ERAD regulation that will broadly impact our understanding of ERAD-associated diseases. Project poster

Undergraduate Researcher: Lakshika Ruwanpathirana
Intended Major: Chemical Engineering
Home Institution: Los Angeles Pierce College
Research Project: Optimization of Hexagonal Boron Nitride for 2D Electronics
Faculty Advisor: Prof. Alex Zettl
Graduate Student Mentor: Matt Gilbert
UC Berkeley Department: Department of Physics
Project Abstract: The 2D insulator hexagonal boron nitride (hBN) has been highly researched for its exceptional thermal conductivity, high tensile strength, and isostructural characteristics with graphene. However, the optimal parameters for its synthesis by chemical vapor deposition (CVD) have never been fully understood. This study investigated the relationship between precursor temperature and the growth of hBN for further synthesis. Raman spectroscopy and scanning electronic microscopy (SEM) were used to quantify the size, percent coverage, and number of layers of hBN. This research represents significant progress to optimize the precursor temperature for high-quality, large-scale hexagonal boron nitride for potential 2D nanoelectronics and other 2D nanodevices. Project poster

Undergraduate Researcher: Julius Tereck-Nojd
Intended Major: Electrical Engineering
Home Institution: San Francisco City College
Research Project: Optimizing Growth of Lead Zirconate Titanate Thin Films by Pulsed Laser Deposition
Research Advisor: Dr. Sayeef Salahuddin
Graduate Student Mentor: Claudy Serrao
UC Berkeley Department: Electrical Engineering and Computer Science
Project Abstract: Decreasing power consumption in transistors is of great interest to the electronics industry. A newly suggested architecture incorporating a ferroelectric film into the gate of the transistor has been shown to reduce the subthreshold slope and could lead to more efficient operation. To support these efforts, it is necessary to gain a better understanding of the factors affecting growth of ferroelectric materials. We investigated the effects of changing laser pulse frequency, laser energy, and substrate temperature to determine the optimal conditions for pulsed laser deposition of ultra-thin epitaxial lead zirconate titanate films. Project poster