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

Research Expo 2016 Wrap-Up: And the poster awards go to…

Research Expo 2016 took place Thursday April 14, 2016 and featured a poster session, faculty talks, an awards ceremony and networking reception. The event was a success, thanks to our attendees, judges, sponsors and promotional partners, and the Jacobs School faculty, alumni, staff, and students. Students competed for a grand prize and the Rudee Outstanding Poster Award, as well as for the best poster award in each department. And the winners are…

Photo Credit: Erik Jepsen/UC San Diego Publications

The Rudee Outstanding Poster Award & NanoEngineering Best Poster

Timothy O'Connor, Rudee Outstanding Poster Award and Best Poster Award, NanoEngineering
Photo Credit: Erik Jepsen/UC San Diego Publications

180. STRETCHABLE AND ULTRA-FLEXIBLE ELECTRONICS: WEARABLE SOLAR CELLS

Student(s): Timothy Francis Oconnor

Professor(s): Darren J. Lipomi
Industry Application Area(s): Energy/Clean technology | Materials | Semiconductor

The winners of the Best Poster Awards for each department are:

Bioengineering Best Poster

Gaurav Agrawal, Best Poster, Bioengineering
Photo Credit: Erik Jepsen/UC San Diego Publications

60. ENGINEERED 3D SKELETAL MUSCLE-ON-A-CHIP AS AN IN VITRO TOOL

Student(s): Gaurav Agrawal 
Professor(s): Shyni Varghese 
Industry Application Area(s): Life Sciences/Medical Devices & Instruments

Computer Science and Engineering Best Poster

Ashish Kashinath, Debjit Roy and Justin Tee, Best Poster, Computer Science and Engineering
Photo Credit: Erik Jepsen/UC San Diego Publications

78. FIBBING TO ALLEVIATE CONGESTION IN WAN AND DATA CENTER NETWORKS

Student(s): Ashish Kashinath | Justin Tee | Debjit Roy 
Professor(s): George M. Porter 
Industry Application Area(s): Internet, Networking, Systems | Software, Analytics

Electrical and Computer Engineering Best Poster

Ashok Kodigala, Best Poster Award, Electrical and Computer Engineering
Photo Credit: Erik Jepsen/UC San Diego Publications

103. PLASMONIC NANOSTRUCTURES FOR NANO-SCALE SENSING: PATH TO AN ALL-OPTICAL INTEGRATED SENSOR

Student(s): Ashok Kodigala 
Professor(s): Boubacar Kante | Y. Shaya Fainman 
Industry Application Area(s): Electronics/Photonics | Materials | Semiconductor

Katie Osterday Best Poster Award Mechanical and Aerospace Engineering

Benjamin Levi Martins, Best Poster Award, Mechanical and Aerospace Engineering
Photo Credit: Erik Jepsen/UC San Diego Publications

137. EVALUATION OF FIBER OPTIC STRAIN SENSORS FOR APPLICATIONS IN STRUCTURAL HEALTH MONITORING

Student(s): Benjamin Levi Martins 
Professor(s): John B. Kosmatka 
Industry Application Area(s): Aerospace, Defense, Security | Civil/Structural Engineering | Energy/Clean technology

Structural Engineering Best Poster

Christine Wittich, Best Poster Award, Structural Engineering
Photo Credit: Erik Jepsen/UC San Diego Publications

199. EXPERIMENTAL AND NUMERICAL STUDIES OF FREESTANDING STRUCTURAL SYSTEMS

Student(s): Christine Wittich 
Professor(s): Tara C. Hutchinson 
Industry Application Area(s): Civil/Structural Engineering

Search all poster abstracts here.

Stay tuned for more photos from Research Expo 2016!

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.

Civil/Structural Engineer to Present Poster on Seismic Protection at Research Expo 2016

Born and raised in Italy, UC San Diego structural engineering graduate student Elide Pantoli knew she wanted to help people, but also knew didn’t want to be a doctor.

“I don’t like blood, so I knew I wouldn’t go into the medical field,” said Pantoli. “In Italy, there’s an association of doctors that was looking for civil engineers. That’s where I got the idea to study civil engineering.”

Pantoli chose to study civil engineering at the University of Bologna – the oldest university in the world. She knew she wanted to study abroad, and the university offered an exchange program with the University of California school system.

“I applied to study at UC San Diego, and came in 2007-2008,” said Pantoli. “After that, I wanted to stay abroad, so I applied to do research for a year at Columbia University.”

From there, Pantoli returned to start her Ph.D. at UC San Diego in 2010.  She started working on the Large High Performance Outdoor Shake Table (LHPOST) at UC San Diego – the largest outdoor shake table in the world – which provides the earthquake engineering community with a facility that allows the accurate reproduction of severe earthquake ground motions for the seismic testing of very large structures.

Pantoli tested a full-scale five-story building fully outfitted with nonstructural components. Her dissertation focuses on one of these – the precast concrete façade. This is what she will present at Research Expo 2016 (see abstract below).

“There have already been code changes due to this work,” said Pantoli. “All of my papers were published in partnership with industry. They say, here’s a problem, and we try to help them solving it.”

Pantoli is interested in both industry and academia – but her dream is to change engineering education.

“I’ve seen students in their third year that are so frustrated because they still don’t know what they are doing,” said Pantoli.

She is passionate about helping students master a subject.

Register today for Research Expo 2016 to hear more from Pantoli and 200+ engineering graduate students for the Jacobs School of Engineering.

Research Expo also features TED-style talks by faculty highlighting research from our agile research centers and a networking reception with faculty, students, industry partners and alumni.

200. SEISMIC DRIFT COMPATIBLE DESIGN OF ARCHITECTURAL PRECAST CONCRETE CLADDING: TIEBACK CONNECTIONS AND CORNER JOINTS

Department: Structural Engineering
Faculty Advisor(s): Tara C. Hutchinson

Primary Student
Name: Elide Pantoli

Abstract
Architectural precast concrete (APC) cladding is a nonstructural system sensitive to both seismic floor accelerations and story drifts. APC panels must be designed to resist forces in the out-of-plane direction of motion, while they must accommodate in-plane story drifts. This requirement presents specific challenges to engineers, namely the design and detailing of connections intended to allow in-plane drifts (termed ?tiebacks?) and corners of the system. Presently, these important issues are addressed rather broadly in design codes, leaving the details to the discretion and experience of the designer. With the goal of providing practical guidance to designers, system and component tests on representative APC cladding and tieback connections were performed. This poster summarizes key results obtained from these experiments and applies these findings to develop guidelines for drift-compatible design of tieback connections and corner systems.

Industry Application Area(s)
Civil/Structural Engineering

Related Links:

1.    http://bncs.ucsd.edu