Meet the EnVision Arts and Engineering Maker Studio Coordinator

Meet Colin Zyskowski, a graduate student in computer music. Colin is Jesse’s right-hand man. We asked him, “What exactly do you do?”

I oversee the undergraduate staff, help maintain the equipment, assist classes with the tools, and I assist Jesse with his mountain of day to day tasks, including the website. We’ll have a new project demonstration and tutorial page up soon.

How did you end up in this position?

I worked with COSMOS over the summer teaching the music technology cluster in EnVision. That was my first exposure to the space. I had been looking for a place like that since I started my PhD at UC San Diego. I started volunteering the following quarter.

What is your goal?

I want to go into academia. I really like the atmosphere – being around a group of people on the cutting-edge of research.

Do you feel like your time at EnVision fits into that?

Oh absolutely. I like that it’s geared towards prototyping. I myself do a lot with hardware design.

What is your dissertation on?

Audio processing on mobile robotic networks - I'm researching various methods and applications for processing audio on groups of robots. These robots communicate with each other via wireless networks that I have built. The audio processing takes place on small computers or microcontrollers including the Raspberry Pi, Beaglebone Black, and a board that I designed and fabricated. The applications that I have focused on are musical performance, sound-source localization, dynamic audio spatialization, and positional determination. The network also has various functions, such as streaming audio, spatial mapping, group learning, and cooperative performance. I'm currently in my fifth year of the PhD program, and am planning to graduate in the spring of 2018. I work primarily with Miller Puckette (music) and Mauricio de Oliveira (mechanical engineering).

What else are you working on?

I also play music (guitar, drums, piano, bass), work as an audio engineer, build quirky electronic instruments, and do a lot of woodworking.    

You can see some of Colin’s projects here.

NanoEngineering meets chemical engineering meets electrical engineering for one grad student

Lindsay Freeman at Research Expo on Thursday, April 14, 2016

NanoEngineering meets chemical engineering meets electrical engineering for Lindsay Freeman, a graduate student at the University of California San Diego’s Jacobs School of Engineering. Freeman is getting a Ph.D. in chemical engineering, her home department is NanoEngineering, and she is doing her research in an electrical engineering lab.

Freeman presented a poster on the fusion between optical physics and chemistry at Research Expo on Thursday, April 14 (see abstract below and see all poster abstracts here).

“The nucleic acids in DNA strands functionalized to silver have been shown to have fluorescent properties, similar to a fluoroflore,” said Freeman. “This is due to the charge transfer effect; energy is given off as light when the electrons move between the orbitals of the atoms of the nucleic acids and those of silver. We want to understand why this works. It began as trying to understand nucleic acid-silver composites, but turned into, ‘Can we use this as a way to figure out how molecules bind to a surface?’”

Freeman, from South Carolina, knew she wanted to be an engineer. As a child, she loved to build computers, and pursued computer engineering as a result. However, she shifted away from it when she realized she really liked chemistry.

“My passion is in bio-detection,” said Freeman. “I like the fusion between electrical and chemical engineering – the interdisciplinary effect of looking at biosensors. There are two components: sensors are easily understood by science, but biology is difficult. I find this field to be challenging.”

Freeman says she chose UC San Diego because the school is dedicated to both engineering and medicine, and San Diego is a well-known hub for biotech. “I looked at the facilities offered, the collaboration opportunities.”

Freeman plans to complete a postdoc at UC San Diego before pursuing other job opportunities in the area.

Regarding Research Expo, Freeman says, “My goal is to get better communicating science. In addition to networking with industry professionals, I also love interacting with other students. We publish all this great research, and this is the one time we get to see all of our fellow graduate students in one place.”

See the best poster award winners here.

Want to meet more than 200 graduate students doing innovative engineering research, like Freeman? Don’t miss Research Expo in 2017!

92. SIMULATED RAMAN CORRELATION SPECTROSCOPY FOR NUCLEIC ACID-SILVER COMPOSITES BINDING ANALYSIS

Department: Electrical & Computer Engineering
Research Institute Affiliation: Graduate Program in Chemical Engineering
Faculty Advisor(s): Y. Shaya Fainman

Abstract
Plasmonic devices are of great interest due to their ability to confine light to the nanoscale level and dramatically increase the intensity of the electromagnetic field, functioning as high performance platforms for Raman signal enhancement. While Raman spectroscopy has been proposed as a tool to identify the preferential binding sites and adsorption configurations of molecules to nanoparticles, the results have been limited by the assumption that a single binding site is responsible for molecular adsorption. Here, we develop the simulated Raman correlation spectroscopy (SRCS) process to determine which binding sites of a molecule preferentially bind to a plasmonic material and in what capacity. We apply the method to the case of nucleic acids binding to silver, discovering that multiple atoms are responsible for adsorption kinetics. This method can be applied to future systems, such as to study the molecular orientation of adsorbates to films or protein conformation upon adsorption.

Industry Application Area(s)
Electronics/Photonics | Materials | Biosensing

Engineer demonstrates technique for targeting RNA inside living cells

Dave Nelles

When he’s not surfing in Mexico or listening to electronic music, Dave Nelles is busy tinkering – inside living cells!

Growing up, Nelles always knew he wanted to develop technology, but was intrigued by the complexity and diversity of processes in biology.

“Biology is on the verge of becoming a predictive and quantitative pursuit,” says Nelles. “Compared to fields like physics where we have many good models of natural phenomena, biology in general is less mature. One reason for this is a lack of tools to measure and alter specific components of living cells.”

Motivated by this gap, Nelles focused his graduate work in materials science and engineering on technologies to measure and alter a fundamental biological molecule: RNA. Inside cells, DNA is transcribed into messenger RNA (mRNA), which is subsequently translated into protein.

Proteins are the building blocks of life – many functions that take place inside of a cell are made possible by proteins.

“In many diseases, the processing of mRNA is dysfunctional, meaning that the protein that is encoded for by that RNA will not be made correctly, or at all,” said Nelles.

In molecular biology, there’s a technique called CRISPR-Cas9 that is used to modify DNA and has the potential to cure a range of genetic diseases. Nelles and his collaborators have been able to demonstrate that CRISPR-Cas9 can not only bind to DNA, but also to RNA.  This approach is described in a paper published on March 17^th in the journal Cell.

Nelles explains, “Just as CRISPR-Cas9 is making genetic engineering accessible to any scientist with access to basic equipment, RNA-targeted Cas9 may support countless other efforts for studying the role of RNA processing in disease or for identifying drugs that reverse defects in RNA processing.”

In collaboration with Mitchell O’Connell in the lab of Jennifer Doudna at the University of California, Berkeley, Nelles tagged Cas9 with a fluorescent protein and targeted various RNAs to track their movement inside living cells.

“This work is the first example, to our knowledge, of targeting RNA in living cells with CRISPR-Cas9,” said senior author Gene Yeo, PhD, associate professor of Cellular and Molecular Medicine. “Our current work focuses on tracking the movement of RNA inside the cell, but future developments could enable researchers to measure other RNA features or advance therapeutic approaches to correct disease-causing RNA behaviors.”

“For many experiments involving RNA tracking, the cells need to be dead or the targeted RNA must be genetically modified in order for the RNA to be detectable,” said Nelles. “Our experiments were done inside living cells with unmodified RNAs, which has many advantages – for example, we were able to observe RNA being transported to stress granules over time.“

Stress granules are accumulations of RNA and protein in a cell and their formation has been linked to neurodegenerative diseases. Nelles and his team hope that providing a way to track these RNAs will assist with new drug development.

After graduating this Spring, Nelles will be continuing his work as a postdoc at UC San Diego.

Want to learn more about other projects at the Jacobs School? Register to attend Research Expo on April 14, 2016.