Community College Participants and Projects: 2012
Undergraduate Researcher: Hen Su Choi Ortiz
Intended Major: Computer Science
Home Institution: Santa Monica College
Research Project: Using Brain-Computer Interfaces
to Analyze EEG Data for Safety Improvement
Faculty Advisor: Prof. S. Shankar Sastry
Research Mentor: Dr. Galina Schwartz
UC Berkeley Department: Electrical Engineering & Computer Sciences Department
Project Abstract: Brain-computer interfaces (BCIs) deliver commands using electroencephalographic (EEG) activity or other electro-physiological measures of brain function. In this paper, we use EEG signals to collect important information about the states of a subject. Vigilance states are particularly important in this project. Drowsiness is a well-known safety issue for operators who must stay alert consistently for long periods of time. The objective of the present work was to record EEG data of individuals using a single-channel active dry electrode system. The hardware used in this work is the NeuroSky Mindwave, Mindset and Myndplay, three commercially available noninvasive BCI headsets. Raw data are presented and compared among the devices. Project poster
Undergraduate Researcher: Michael Coe
Intended Major: Mathematics
Home Institution: City College of San Francisco
Research Project: Programming Module to Facilitate the Implementation of Virtual Sensors in Teleoperated Robots
Faculty Advisor: Prof. Ronald S. Fearing
Postdoc Mentors: Andrew Pullin & Paul Birkmeyer
UC Berkeley Department: Electrical Engineering and Computer Science
Project Abstract: Implementing a graphic user interface offers a way to simplify the experiment processes, decrease experiment times, and provides a means for real time computer feedback when operating teleoperated robots. The programming language Python was chosen for this task due to built in multithreading and queue libraries, which means that multiple streams of commands can be issued and resulting data can be read at the same time. Multithreading assists in the implementation of virtual sensors using the OptiTrak motion capture positioning system currently used. By simulating a virtual sensor of a hazardous material within the OptiTrak and utilizing a real-time command scheme, it is possible to lead a robot to the center of a hazardous source. Project poster
Undergraduate Researcher: Efrain Carlos Cuellar
Intended Major: Bioengineering
Home Institution: Reedley College
Research Project: Characterizing the Microbial Communities Associated with the Coffee Berry Borer (Hypothenemus Hampei)
Advisor & Mentor: Dr. Javier Ceja-Navarro
Hosting Institution: Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory
Undergraduate Researcher: Gabriel Denham
Intended Major: Physics and Applied Mathematics
Home Institution: College of San Mateo
Research Project: Strain Calculation and Modeling of Graphene Nanobubbles on a Deformable Polymer
Faculty Advisor: Prof. Michael Crommie
Graduate Student Mentor: Kacey Meake
UC Berkeley Department: Department of Physics
Project Abstract: The process of straining graphene in particular ways has been shown to produce graphene nanobubbles containing strong pseudo-magnetic fields. A new technique involving light reactive polymers may provide greater control over nanobubble production. This new technique requires graphene to be accurately strained to a specific percentage by the deformable polymer underneath. Calculation and detailed modeling of the polymer’s expansion, and the resulting strain on the graphene, can clue us in to the ideal conditions for the creation of nanobubbles in graphene. Finite element analysis of the elastic strain on the graphene sheet at and around the nanobubbles will allow us to create the previously established ideal strain parameters and control nanobubble production with great accuracy.
– Click Project poster
Undergraduate Researcher: Mohamed Elamin
Intended Major: Electrical Engineering
Home Institution: Laney College
Research Project: FPGA-Based Multiplexer for Quantum Information Processing Based on Ion Traps
Faculty Advisor: Prof. Hartmut Haffner
Graduate Student Mentor: Erick Ulin-Avila
UC Berkeley Department: Department of Physics
Project Abstract: Quantum computers make use of the principles of quantum mechanics, and thus offer greater processing capabilities than conventional computers. One of the methods used to develop Quantum computers is through the use of RF Ion traps. In an RF Ion trap, ions are confined by manipulating electrostatic potential by using varying voltages of several control electrodes (Metodi et al.,2005). The different voltages required to trap the ions will be produced by a digital analog convertor (DAC) that is connected to a pulsar which provides digital signals. The DAC will convert the digital signals from the pulsar into analog signals to be sent to The Amplifier Board which will send the voltages to the trap. These voltages will be measured by an FPGA controlled Multiplexer in order to precisely monitor the voltage sent to the electrodes. Project poster
Undergraduate Researcher: Qijun (Daniel) Hu
Intended Major: Bioengineering
Home Institution: Chabot College
Research Project: Understanding the Complexity of Synthetic Protein Scaffolds
Faculty Advisor: Prof. John Dueber
Undergraduate Mentor: Jacinto Chen
UC Berkeley Department: Bioengineering
Project Abstract: Synthetic scaffold has shown to be beneficial in increasing the metabolic flux while reducing metabolic load in engineered microbes. In John Dueber’s nature biotechnology paper “Synthetic Protein Scaffolds Provide Modular Control Over Metabolic Flux”, optimize stoichiometry of three mevalonate biosynthetic enzymes recruited to a synthetic scaffolds improved mevalonate production by 77-fold. However, understanding how the scaffold can produce higher titer is extremely complex. For instance, recent discoveries have suggested that internal ribosome binding site (iRBS) is problematic since truncated scaffold is being expressed at higher level than full-length scaffold. Through reconstructing the scaffold DNA without any internal RBS which produces the full-length scaffold and retesting the new scaffold construct would explain how the scaffold function. Additionally, enzyme tagged with PDZ peptide leads to shorter half-life. Additionally, enzyme tagged with PDZ peptide can be regulated and tProject posterby reducing activity of off-scaffold enzymes. Project poster
Undergraduate Researcher: Sara Marie Komenan
Intended Major: Biology
Home Institution: Los Angeles Valley College
Research Project: Synthetic Spike-In Standards for 16S rRNA Gene iTags
Research Host & Advisor: Dr. Ulisses Nunes da Rocha
Hosting Institution: Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory,
Project Abstract: Microbial communities are very complex both in their abundance and composition. As most microbes are yet-to-be cultured, most of the knowledge of the microbial diversity was produced through PCR amplification, cloning and Sanger sequencing of conserved molecules, usually the 16S ribosomal RNA gene. Those traditional methods can be laborious and costly and may not be sufficient to fully characterize all these existing complex communities. Next-generation sequencing platforms such as the Illumina 16S amplicon analysis (iTags) overcome previous limitations such as the number of samples and sequences generated. One limitation for iTags is the fact that results are given as relative abundances. The production of synthetic spike-in standards for the 16S rRNA gene iTags will allow us to determine the actual copy number and sequence of the 16 S in our samples which will allow us to better analyze changes in 16S rRNA gene expression and better understand the biodiversity in environmental samples. This work describes the design and validation of these internal controls.  - Click Project poster
Undergraduate Researcher: Cindy Lei
Intended Major: Chemical Engineering
Home Institution: LA Trade-Technical College
Research Project: Analysis of the Mevalonate and Non-mevalonate Pathway Intermediates
Advisor: Dr. Edward Baidoo
Hosting Institution: Joint BioEnergy Institute
Project Abstract: The mevalonate and non-mevalonate pathway to isoprenoid production are essential in many types of plant, bacteria, and living organisms. Isoprenoids (terpenes), the largest group of natural products, are organic compounds that consist of at least two specific patterns of hydrocarbon units. Many applications have been aimed at isoprenoid production, given their wide range of functions from primary and secondary metabolism. Such areas have included carotenoids, vitamins, plant defense, and communication. In addition, commercial and industrial uses involving isoprenoids have accounted for the expansion of corporate enterprise, from the production of perfumes to natural rubber or flavorings. TProject posterfore, the immense amount of uses that isoprenoids possess is paramount and dynamic in many aspects of life. However, microbial extraction of isoprenoids poses major challenges. Such can be contributed to bottlenecks through the accumulation of metabolic intermediates. To identify these potential bottlenecks in the mevalonate and non-mevalonate pathway, the use of Liquid Chromatography (LC) and Mass Spectrometry (MS) was utilized to measure these metabolic intermediates in both biosynthetic pathways. Hydrophilic Liquid Interaction Chromatography was used to separate metabolic intermediates of the two-biochemical pathways, and the time-of-flight mass spectrometry was used for detection. Both instrument setups were coupled via an electrospray ionization interface. Since this method was recently developed, it requires validation in order to be applied to biological experiments.  - Click Project poster
Undergraduate Researcher: Shyh-Herng Lo
Intended Major: Chemical Biology
Home Institution: El Camino College
Research Project: Investigating the Role of AntB and AntO in Antimycin Biosynthesis
Faculty Advisor: Prof. Wenjun Zhang
Graduate Student Mentor: Moriah Sandy
UC Berkeley Department: Bioengineering
Project Abstract: Antimycins are natural products produced by different Streptomyces species. The biosynthesis of antimycins can be studied from the already known biosynthetic gene cluster of Streptomyces. In Streptomyces albus, tProject poster are sixteen genes of DNA encoding enzymes for this biosynthetic pathway. The goal of this project is to examine the function of the enzymes produced by genes antB, and antO. Project posterin, we report the progress towards determining the functions of AntB and AntO in antimycin biosynthesis. Our results indicate that AntB is responsible for addition of R1 group in the antimycin biosynthesis. Project poster
Undergraduate Researcher: Omotayo Olukoya
Intended Major: Electrical Engineering and Materials Science
Home Institution: Chabot College
Research Project: Characterization of Layered Gallium Telluride (GaTe)
Faculty Advisor: Prof. Oscar Dubon
Graduate Student Mentor: Jose Fonseca
UC Berkeley Department: Material Science and Engineering Department
Project Abstract: In recent years, the interest in two-dimensional (2D) semiconductors has increased, as they might play an important role in the future of electronic materials because it is relatively easy to produce complex structures from them. Gallium (II) telluride (GaTe) is a layered-monochalcogenide semiconductor. Unlike other layered-chalcogenides, GaTe has not been fully investigated, even though its 1.7 eV energy gap makes it a promising material for electronic applications. Few-layers GaTe crystals were obtained by mechanical exfoliation on a SiO2/Si substrate. The transferred flakes were characterized by atomic force microscope (AFM) in order to determine the thickness and amount of layers, while Raman spectroscopy was performed to corroborate the presence of GaTe, and to determine the spectrum dependency on the number of layers. The flakes were further tested for variation on their energy band at different thickness by photoluminescence spectroscopy. Knowing and being able to control some key properties such as the band gap of this compound from bulk to 2D layers could open doors to many key applications for electronic and optical devices. Project poster
Undergraduate Researcher: Kevin Pease
Intended Major: Chemical Engineering and Material Science Engineering
Home Institution: Contra Costa College
Research Project: Printed and Ultrathin Films of Peptoids
Faculty Advisor: Prof. Ana Claudia Arias
Postdoc Mentor: Dr. Felippe Pavinatto
UC Berkeley Department: Electrical Engineering and Computer Science
Project Abstract: Peptoids are sequence-specific oligomers of N-substituted glycine with a similar structure to proteins. Their versatile structure and tunable characteristics make peptoids a fascinating material with many applications. In this work we studied the deposition of Langmuir-Blodgett (LB) films of an anionic peptoid. Film growth was primarily followed by surface pressure versus time curves, and then confirmed by AFM. A peptoid-based ink was prepared, characterized and tested in gravure printing. Both gravure and LB films are currently being tested in electrical measurements. We aim to assess the viability of applying such films in electronic devices as capacitors or transistors. Project poster
Undergraduate Researcher: Emily Sarwas
Intended Major: Mechanical Engineering
Home Institution: College of Siskiyous
Research Project: Investigating the Robustness of MEM Relay Beams
Faculty Advisor: Prof. Tsu-Jae King Liu
Graduate Student Mentors: Philip Chen
UC Berkeley Department: Electrical Engineering & Computer Sciences Department
Project Abstract: Transistors currently used in integrated circuits (IC) have high off-state current leakage, hindering the efficiency of devices with IC. Because of the poor efficiency of these highly ubiquitous IC, tProject poster is a need for the development of more efficient electronics. One solution to the problem of off-state leakage in common transistors is the use of micro-electromechanical (MEM) relays in IC. While MEM relays are electrically efficient, they are prone to failing over time due to mechanical fatigue. The robustness of MEM relays needs to be better understood to fully know their ability and know how MEM relays can be improved. This paper looks at 4 terminal (4T) MEM relays, which were tested for robustness over time at varying temperatures. With the findings presented in this paper, MEM relays can be improved upon in the future for longer usage and a greater degree of reliability. Project poster
Undergraduate Researcher: John Smail
Major: Mechanical Engineeering
Home Institution: Sacramento City College
Research Project: Characterization of Transport Properties of VO2 Thin Films Across the Metal-Insulator Transition
Faculty Advisor: Prof. Junqiao Wu
Postdoc Mentor: Dr. Deyi Fu
UC Berkeley Department: Materials Science and Engineering
Project Abstract: Vanadium dioxide is a unique semiconductor material that undergoes a first-order metal-insulator transition at ~68 °C from a low-temperature insulating (monoclinic) phase to a high-temperature metallic (rutile) phase. It is being actively investigated due to its potential in switching devices as well as fundamental scientific interest in understanding correlated electron systems. Understanding the transport characteristics such as carrier density, mobility and other electrical properties are of critical importance for its application and implementation. Project poster we present a detailed study of the electrical properties and characteristic across the MIT of high-quality vanadium dioxide thin-films grown by pulsed laser deposition on sapphire (0001) substrate. Our results show >3 orders of magnitude increase in conductivity as well as electron concentration across the metal-insulator transition, while the electron mobility changes little and remains around 0.09 to 0.15 cm2/Vs. The results will be helpful for both future device applications and continued scientific research based on this material system. Project poster