2011 REU Projects
This paper introduces a test method that collects force and video data for the Climbing Autonomous Sprawled Hexapod (CLASH) robotic platform placed in a controlled climbing simulation. The collected data are used to inform successive iterations of foot and leg designs that are intended to expand CLASHâ€™s climbing ability beyond penetrable cloth surfaces to smooth surfaces. The full-body reaction forces that CLASH generates as it runs in the climbing simulation indicate how effective different designs are in facilitating adhesion and upward mobility. This test method will be an asset in developing CLASH as innovative materials and mechanisms for effective climbing are created and implemented.
Faculty Mentor: Prof. Ron Fearing; Graduate Mentor: Paul Birkmeyer; UC Berkeley Department of Electrical Engineering & Computer Science
Trichloroethylene (TCE) is a widely used industrial solvent and degreaser, and is the most frequently reported groundwater contaminant. It has been implicated in various cancers including renal cancer. The mechanisms of toxicity are poorly understood; however, a specific metabolite of TCE, dichlorovinylcysteine (DCVC) has been associated with renal cancer in rodents. This study investigates the genes and pathways involved in response to DCVC exposure, using parallel deletion analysis in yeast. Yeast is highly annotated with a large deletion library and many mechanisms in yeast are conserved in humans. A deletion pool of 4600 non-Ââ€essential genes was exposed to both acute and chronic exposures of DCVC to identify sensitive genes. Strains that exhibit sensitivity underwent enrichment analysis to identify biological pathways represented by these genes. Enrichment showed several genes associated with DNA repair processes. Further growth analysis confirmed these genes to be sensitive to DCVC, inferring DCVC is causing some type of DNA damage. The data also suggests that the primary pathway involved in response to DCVC exposure is error prone translesion syntheseis.
Faulty Mentor: Chris Vulpe; Graduate Mentor: Vanessa de la Rosa; UC Berkeley Department of Toxicology
Biomimetic structures use the inherent properties of biology to create new devices that mimic the functions of naturally found materials.Â Nature provides a vast array of monomers and organisms which all use the same basic building blocks to perform very different functions and obtain a wide range of appearances. Here, we present an effective way of generating biomimetic films using M13 phages.Â The films are created using phages which can self-replicate, self-assemble, and evolve to mimic the behaviors of monomers found in nature.Â The films are made on substrates by drawing the substrate up and out of a solution of modified M13 phages. The film bands created with faster pulling speeds are associated with lower surface roughness and thinner film thickness.Â The films created on substrates with surface property modifications show controlled assembly within the hydrophilic regions.Â By adjusting, fine-tuning, and controlling the parameters used to create phage films, a variety of different devices can be created to perform useful functions within the fields of tissue engineering or regenerative medicine.
Faculty Mentor: Seung-Wuk Lee; Post Doc Mentor: Byung Yang Lee; UC Berkeley Department of Bioengineering
In this project, a computational algorithm was developed to rank different RNA transcriptome assemblies. Such a tool is desirable because it is possible to generate many different RNA assemblies from high-throughput sequencing data. Applying the algorithm will yield information that can be used as a comparative base for ranking assemblies. The advent of this algorithm will facilitate better usage of said assemblies in analyzing gene expression; better analysis of gene expression will assist testing the environment for toxins.
Faculty Mentor: Chris Vulpe; Graduate Mentor: Leona Scanlon; UC Berkeley Department of Toxicology
Having been characterized six years ago, graphene is known to be highly electrical conductive so that it is an ideal material for electrical sensing devices. Many scientists have used graphene in working electrode modification and successfully improved the sensitivity and lowered the detection limit of many different types of electrochemical sensors. In our project, a glassy carbon electrode (GCE) was modified with graphene and described as a hydrogen peroxide (H2O2) sensor. Graphene deposited on copper through chemical vapor deposition (CVD). The modified electrode showed a significant improvement in sensing hydrogen peroxide concentration in solutions, comparing to a glassy carbon electrode alone. The sensor with graphene and Pt is currently being studied. Pt nanoparticles grew on graphene through galvanic displacement (GD). A further study will be done by depositing glucose oxidase and Nafion on the surface of the sensor to create a glucose biosensor, which would be significant to medical studies and clinical applications.
Faculty Mentor: Roya Maboudian; Post Doc Mentor: Albert Gutes; Graduate Mentor: Ben Hsia; UC Berkeley Department of Chemical Engineering
Ge nanocrystals were grown in silica using ion beam synthesis (IBS) at various implanting conditions. These samples were examined by grazing incidence small angle X-ray scattering (GISAXS), and the resulting intensity plots were analyzed to gain information about the average particle radius to compare with results from Transmission Electron Microscopy (TEM) and Atomic Force Microscopy (AFM). GISAXS analysis is significant because it is relatively fast to complete, and does not physically alter the sample. The average radii from samples with an implanting temperature of 650ËšC ranged from 2.29 to 2.83 nm. The radii for the free-standing particle samples and the Pulse Laser Melted samples at 650ËšC were larger, ranging from 4.13 to 4.39 nm, and 3.28 to 4.09 nm, respectively. The average radii from samples with a room temperature (RT) implant ranged from 1.20 to 2.01 nm. The radii for the free-standing particle samples at RT and the Pulse Laser Melted samples were larger as well, ranging from 2.60 to 2.80 nm, and 2.43 to 2.90 nm. These values are in good agreement with a different form of analysis performed on the same samples.
Faculty Mentor: Daryl Chrzan; Graduate Mentor: Matt Sherburne; UC Berkeley Department of Materials Science & Engineering
This paper presents a modeling toolbox, written in MATLABÂ®, for use in degas-driven microfluidic device design.Â This model yields temporal velocity profiles of fluid movement, pressure gradients within the microchannels, and gaseous concentration profiles within the polymeric microfluidic device.Â Additional information such as shear stress can also be inferred from these simulations.Â The user has the option to input different channel geometries, such as channel shape, size, length, and permeability (diffusion coefficient), which allows for material selection and determination of optimal parameters such as the thickness of the chip.Â This model will allow the user total control over the design of the device with results that are valid and predictable.Â The results demonstrated by the model validate its functionality and affirm applicability for the future use in the design of microfluidic based chips.
Faculty Mentor: Luke Lee; Graduate Mentor: John Waldeisen; UC Berkeley Department of Bioengineering
Organic photovoltaic cells are an effective means of harvesting copious amounts of incoming solar energy. Significant previous research has shown the effectiveness of bulk heterojunction organic photovoltaic devices made with various polymers and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). Thus, fabrication conditions were optimized for a poly(3-(2â€™-ethyl)hexyl-thiophene) (P3EHT) and PCBM system. Solvent choice, weight ratio of P3EHT to PCBM, concentration of spin-coating solution and annealing duration conditions were independently tested. The optimal conditions were chlorobenzene as the solvent with a composition of 20 wt% P3EHT and 80 wt% PCBM and a concentration of 30 mg/mL. Lastly, annealing at 50ÂºC for various time periods showed a decrease in efficiency.
Faculty Mentor: Rachel Segalman; Graduate Student: Victor Ho; UC Berkeley Department of Chemical Engineering
It is believed that the cooling rate within the graphene growth process is an important factor in synthesizing uniform graphene films. The effects of cooling rate on graphene uniformity and quality are explored by testing various cooling rates. Graphene is grown on a nickel substrate using the micro chemical vapor deposition system, taking advantage of its exceptionally wide, adjustable cooling rate The optimal cooling rate for graphene growth is determined to produce the best combination of uniformity and quality. Raman spectroscopy is used to analyze the graphene films.
Faculty Mentor: Liwei Lin; Graduate Mentor: Qin Zhou; UC Berkeley Department of Mechanical Engineering
The goal of this study is to establish correlations between structural and electrical properties of ferroelectric materials. Ferroelectrics have recently found interesting applications in non-volatile information storage technologies and field effect transistors (FET). For these applications, precise control of electronic properties is required. Here it is shown that by using pulsed laser deposition (PLD) to grow films of different thicknesses, the tetragonality of ferroelectric PbZr0.2Ti0.8O3 (PZT) can be tailored and thus the dielectric constant controlled.
Faculty Mentor: Sayeef Salahuddin; Graduate Mentor: Asif Khan; UC Berkeley Department of Electrical Engineering & Computer Science
Microfluidic devices have many applications involving diagnostics and point-of-care devices. One such devise uses a trapping mechanism based on the hydraulic jump phenomena. Hydraulic jump is a result of a sharp decrease in velocity which produces a vertical change in a solution. This mechanism has been implemented in trapping cells in microfluidic devices for further study and analysis. To improve upon future design it is important to characterize pathlines of cells as they travel through trap regions. Â Â We visualized the traps of a â€˜trap and releaseâ€™ microfluidic device using a traditional non-inverted microscope which is converted to view laterally. Cross-sectional images and video are taken while running samples through the device which is then used to obtain data of cellular height and distance. Cellular pathlines were constructed and compared to previous theoretical and computational results showing that this phenomenon maintains its prevalence in the scales used by microfluidic devices.
Faculty Mentor: Luke Lee; Research Scientist Mentor: Paul Lum; Graduate Mentor: Debkishore Mitra; UC Berkeley Department of Bioengineering
Faculty Mentor: Seung-Wuk Lee; Post Doc Mentor: Jin-Woo Oh; UC Berkeley Department of Bioengineering
We observe the effects of reversible doping in PbSe quantum dot (QD) field-effect transistors (FETs) exposed alternately to air and ethanethiol (EtSH). The process of doping via oxidation and reduction leads to large conductance modulation while majority carrier mobilities remain relatively unchanged. While the EtSH-treated PbSe QD films exhibit ambipolar transport, the oxidized films illustrate the p-type unipolar behavior. By soaking the oxidized films to EtSH solution to remove the oxygen from the surface, the FETs were able to return to ambipolar behavior. This work demonstrates that the effective carrier concentration in quantum dot films can be controlled and modulated through manipulation of surface oxide species.
Faculty Mentor: Paul Alivisatos; Graduate Mentors: Jesse Engel & Matt Lucas; Department of Chemistry