UC San Diego Undergrads Embark on Summer of International Collaborative Science

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UC San Diego Undergrads
Embark on Summer of
International Collaborative Science

By Maureen Curran

June 29, 2009

The largest group ever of UC San Diego undergraduates in the Pacific Rim Undergraduate Experiences (PRIME) program -- 33 -- has embarked on a nine-week summer adventure: working as researchers in laboratories across the Pacific Rim and India. They left for their destinations last week.

Calit2's Alex Matthews (left) shows Michael Nekrasov the underwater housing for an HD video camera. Nekrasov will be working on a project of the Scripps Institution of Oceanography and Calit2. He will be part of the team that is setting up a remote monitoring system for the coral reef at Kenting, Taiwan, using florescence to detect coral health. Two video cameras will be circulating among the students at several of the host locations to capture the research and cultural aspects of their summer.

PRIME is a unique program which provides undergraduates with hands-on, full-time research experiences in internationally collaborative settings. Against the backdrop of living abroad in another culture, the students will work as full-time researchers in one of 13 host institutions in Australia, China, India, Japan, Malaysia, New Zealand, or Taiwan, working closely with mentors at both their host institution and back at UC San Diego.

"I really want to experience everything, culturally and especially the lab aspect of the summer, because I've only traveled abroad on vacation, never stayed and worked," enthused Anna Pham. "Just to be integrated into the environment, I'm really excited about that." Pham is at Osaka University in Japan.

PRIME gives students a wider view of the world and their place in it. This is the sixth year of the highly successful program and the first to have a sibling following (almost) in his brother's footsteps. Two summers ago, Samson Hang (PRIME 2007) went to Hsinchu, Taiwan and worked on a multi-walled carbon nanotube and polyethylene oxide composite computer visualization model. This summer, Jefferson Hang is going to New Zealand. "My brother told me his stories when he was abroad, and his experience working with professors from another country," Jefferson recounted. "His experience definitely made me more interested in PRIME. But, I also wanted to apply because I could both travel and do research."

"We are immersing the students in both scientific research and a new culture in order to provide them with experiential training in both the conduct of research and the international global workplace," said Gabriele Wienhausen, PRIME's principal investigator and co-founder. Wienhausen is the associate dean of education for the UC San Diego Division of Biological Sciences.

2009 PRIME student before they embarked for Asia, Australia and New Zealand.

PRIME leverages the scientific community and cyberinfrastructure built by the Pacific Rim Applications and Grid Middleware Assembly (PRAGMA) project.

PRAGMA is a group of leading Pacific Rim research organizations collaborating on advancing grid technology applications. The majority of the PRIME host institutions are members of PRAGMA. A listing of the host institutions and mentors can be found below, as well as information on each student's research plans.

"PRIME gives undergraduates experience with the increasingly collaborative and international scientific workplace of today," said Peter Arzberger, co-founder of PRIME. Arzberger is also the founding chair of PRAGMA's Steering Committee.

A pre-departure dinner was held recently at which the PRIME 2009 students were joined by many PRIME alums who came to provide first-hand information and offer their support, as well as celebrate and recount their experiences.
"I came to support and answer any questions that the upcoming PRIME students want to know," said Phillip Pham (PRIME 2008, Osaka University), "from basic things, like everyday living in Japan, or maybe what did you do in Japan, as far as research goes."

PRIME 2009 students enjoyed getting together and learning about each other's projects.

Also there: Marshall Levesque (PRIME 2006), who was just a sophomore when he went to Osaka University. "PRIME was the beginning of my research career, and it really opened up a lot of doors," he said. For the last two summers and again this summer, Levesque has helped mentor the new PRIME researchers going to Osaka, including Phillip Pham, who was able to publish a paper in conference proceedings on his summer's work.

Simon Han (PRIME 2008) was another alum providing guidance. "Last year all the PRIME Japan students sat at that table and chatted for a long time," he explained. "We were the last group to leave, so I wanted to be here for this year's students, just as last year's were for me."

Jim Galvin of the Programs Abroad Office at UC San Diego works closely with PRIME to help students with the cultural-adjustment aspect of their international experience. "We do a variety of things to prepare students to really learn about cultures as an ongoing process, not just during their nine weeks for PRIME, but during the rest of their academic career and their lives beyond," said Galvin, who directs Opportunities Abroad in Faculty-led programs.

"I had the opportunity to sit in on many of the interviews for PRIME this year, and I was so impressed with all the students," Galvin continued. "It was particularly interesting that many of the applicants were either born abroad then came to the U.S. in grade school, or have lived or spent significant time overseas. So they already have some understanding of crossing cultures.

Many PRIME alums joined the 2009 group at the departure dinner to share their experiences and answer questions. Among them: (l-r) Phillip Pham, Marshall Levesque and Simon Han.

"In fact, several students said that they hope the PRIME experience would allow them to reconnect with the culture of their birth country, or their family's country," Galvin added. "We're really excited by that, because that's another dimension of culture."

Some PRIME students are again serving as "foreign correspondents" throughout the summer, briefing the wider UC San Diego community on their experiences. The Dispatches from the Field series written by UCSD students working abroad will appear in This Week@ UCSD, an e-zine published by the University Communications and Public Affairs Office. Reporting on their adventures will be Ramya Chitters (Australia), Jade Kwan (Japan), Brian McMahon (India) and Michael Nekrasov (Taiwan).

PRIME is funded by the National Science Foundation (NSF) (including supplemental support from NSF's program for India), with additional support from the UC San Diego division of the California Institute for Telecommunications and Information Technology (Calit2), the National Biomedical Computation Resource (NBCR), the Gordon and Betty Moore Foundation, the bioengineering department of UCSD's Jacobs School of Engineering, additional partners and the host institutions, including additional support at USM, NiCT and Doshisha University. Five of this year's PRIME students received outside scholarships to participate. Teri Simas is the program manager for PRIME, based in Calit2's Atkinson Hall.

The PRIME students will be working on a wide variety of projects across a broad range of areas including engineering, biological, physical, social and computer sciences, art history, and others. A brief summary of each of their projects follows.

Host Institution Mentor/s: Host UCSD Mentor	*PRIME student, major* and project summary**
Monash University, Melbourne, Australia Mentors: David Abramson UCSD: Kim Baldridge	Elisa Abate, bioengineering: premedical This project involves enhancement and use of a framework being designed for ligand-protein investigations. Using computational chemistry software of Prof. Baldridge and the workflow tools of Prof. Abramson, the goal will be to do several parametric experiments to investigate changes in structure, environment, and methodology, and record the results for further analysis.
University of Hyderabad, India Mentors: Arun Agarwal and Anand K. Kondapi UCSD: Jason Haga	Dee Chen, bioengineering My goal is to screen other members of the DSP family that ensure the inhibitors found from the SSH-2 screen are specific for SSH-2, using DOCK6 installed on the PRAMA grid sites.
National Museum of Marine Biology and Aquarium (NMMBA), Kenting, Taiwan Mentors: Tony Fan and Fang-Pang Lin UCSD: Ryan Kastner	Robert Chen, computer engineering My project will involve the application of various image processing techniques for the purpose of characterizing coral larvae blooms. Image and video processing will utilize parallel computing while the processed data will be streamed into the DataTurbine middleware.
University of Waikato, Hamilton, New Zealand Mentors: David Hamilton UCSD: Jane Teranes	Jacqueline Chin, environmental engineering Analysis and modeling of the effects of non-photochemical quenching on chlorophyll fluorescence to better analyze algal biomass growth in the lakes of Lake Rotorua because of the abundance of accurate chlorophyll fluorescence data (except for cases of quenching).
Monash University, Melbourne, Australia Mentors: David Abramson UCSD: Anushka Michailova	Ramya Chitters, bioengineering-biotechnology The goal of my project is to use NIMROD/E to perform parameter sensitive analysis in cardiac electrophysiological models.
National Taiwan University (NTU), Taipei, Taiwan Mentors: Jung-Hsin Lin UCSD: Wilfred Li	Jennifer Choy, biochemistry and cell biology The goal of this research project is to utilize virtual screening, docking, and off-target analysis to design inhibitors that will preclude the Non-Structural Protein 1 (NS1) from binding to the double-stranded RNA (dsRNA) to utilize the host cell’s mechanisms to replicate and distribute its own genetic material; ultimately terminating the host immune system. A second goal of this project is to develop small molecule drugs to ameliorate the human influenza A H5N1 virus infection.
Cybermedia Center, Osaka University, Osaka, Japan Mentors: Susumu Date UCSD: Jason Haga	Allyson Clark, bioengineering This research project involves verifying SSH-2 inhibitor specificity through virtual screening experiments on the grid.
Monash University, Melbourne, Australia Mentors: David Abramson UCSD: Jürgen Schulze	Nicholas Echols, computer science, interdisciplinary computing and the arts (ICAM) The goal of my project will be to create a viewing interface on the tiled-display wall for both 2-D images and 3-D image stacks acquired from the confocal microscope at Monash University. This interface will visually act as a two dimensional plane along which the images can be moved, rotated, and scaled. The interface will also provide interaction with multiple users, each being able to independently manipulate the images on the plane. The users will ideally use wiiremotes to carry out interaction, but the software should facilitate use with any pointing device.
National Institute for Information and Communications Technology (NiCT), Tokyo, Japan Mentors: Kaori Fukunaga and Shinji Shimojo UCSD: Maurizio Seracini	Isabelle Fanchiu, interdisciplinary computing and the arts (ICAM) Under Professor Maurizio Seracini's supervision, I will be building panels painted with different colors and types of paint as a standard measurement. I will bring the panels to Tokyo to begin the analysis of colors and materials with the THz scanning technology, compile the data, and document digitally at Dr. Kaori Fukunaga's lab at NiCT in Japan.
Doshisha University, Kyoto, Japan Mentors: Nozomu Inoue UCSD: Robert Sah	Utsav Gupta, bioengineering: biotechnology The goal of this project is to develop digital image processing methods to determine synovial fluid volume of the knee using 3-D imaging data. This has implications for diagnosis of osteoarthritis and monitoring after therapeutic intervention.
University of Auckland, New Zealand Mentors: Jason Ingham and Liam Wotherspoon UCSD: Lelli Van Den Einde	Jefferson Hang, structural engineering I will be helping the University of Auckland set up a network infrastructure that will allow them to collect data during experiments, upload it to their server, provide real-time stream to other researchers. All of this will be done through their network, LabView, NEESdaq, Data Turbine, and RDV.
Universiti Sains Malaysia (USM), Penang, Malaysia Mentors: Habibah Wahab UCSD: Wilfred Li	Jessica Hsieh, bioengineering: biotechnology My proposed PRIME project is to optimize the design of small interfering RNAs (siRNAs) test probes targeting the nucleocapsid protein (NP) in the influenza virus.
National Center for Research on Earthquake Engineering (NCREE), Taipei, Taiwan Mentors: Keh-Chyuan Tsai UCSD: Lelli Van Den Einde	Lori Jue, structural engineering I will be helping with research and testing of Specially Concentric Braced Frames at the National Center for Research on Earthquake Engineering.
Cybermedia Center, Osaka University, Osaka, Japan Mentors: Susumu Date UCSD: Jürgen Schulze	Sasha Koruga, mathematics-computer science To use Osaka University’s laser and camera system to capture a human subject in motion, and then to render such subject realistically in Calit2's pentagon-shaped virtual reality room (dubbed the StarCave) in real time with high-quality textures and detail.
National Institute for Information and Communications Technology (NiCT), Tokyo, Japan Mentors: Shinji Shimojo and Taku Morinobu UCSD: Jürgen Schulze	Jade Kwan, cognitive science: human computer interaction I will be working on data visualization taking scientific datasets to create an artistic 3-dimensional mapping. I will use software called Autodesk Maya to model and script these mappings to then present them on high resolution tiled-display walls.
Cybermedia Center, Osaka University, Osaka, Japan Mentors: Susumu Date UCSD: Jason Haga	Christopher Lau, bioengineering My project is to incorporate various computer programs to visualize the results of virtual protein screening on a tiled-display wall. Because individuals need to compare hundreds of receptor-ligand interactions, multiple side by side comparisons using a tiled-display wall would lead to more effective and less time consuming analysis.
National Museum of Marine Biology and Aquarium (NMMBA), Kenting, Taiwan Mentors: Tony Fan and Fang-Pang Lin UCSD: Doug Palmer	Tsung Han Lin, computer science Monitoring plankton is important in understanding current marine ecosystems. I will be developing a Plankton Automatic Recognition System to improve the efficiency of the plankton monitoring.
Universiti Sains Malaysia (USM), Penang, Malaysia Mentors: Habibah Wahab UCSD: Wilfred Li	Jessica Liu, biochemistry and cell biology I will conduct research on neuraminidase through the usage of hierarchical screening to identify similar compounds which may also be active against neuraminidase. In addition, I will conduct off-target analysis to identify previously unknown targets in the human proteome which may be negatively affected by these neuraminidase hits.
University of Hyderabad, India Mentors: Arun Agarwal and Anand K. Kondapi UCSD: Tony Fountain	Brian McMahon, computer science I will be setting up a data streaming system for a sensor network in the Bay of Bengal. This system will be used to allow near real-time access to data for researchers to study, and possibly predict tsunami activity. To accomplish this task, I will be working with Dr. Tony Fountain of Calit2 and utilizing DataTurbine software.
University of Hyderabad, India Mentors: Arun Agarwal and Anand K. Kondapi UCSD: Jason Haga	Matthew Mui, bioengineering: premed The goal of the project is to find a specific inhibitor for a dual specificity phosphatase called SSH-2 using the Pragma Grid.
National Museum of Marine Biology and Aquarium (NMMBA), Kenting, Taiwan Mentors: Tony Fan and Fang-Pang Lin UCSD: Tony Fountain	Michael Nekrasov, computer engineering The goal of this project is to engineer a real-time system for studying coral, particularly focusing on coral larvae and the fluorescence of coral. Cameras capable of registering fluorescence will be integrated into DataTurbine, a computer system for environmental observing. The images captured will allow scientists to study coral health as well as capture interesting phenomena like coral blooms.
Cybermedia Center, Osaka University, Osaka, Japan Mentors: Susumu Date UCSD: Masahiko Hoshijima	Anna Pham, general biology Using computational tools, I will work to tailor the 3-D visualization of cardiac dynamic physiological events to make it more comprehensive.
National Center for Research on Earthquake Engineering (NCREE), Taipei, Taiwan Mentors: Keh-Chyuan Tsai UCSD: Lelli Van Den Einde	Sabina Piras, structural engineering I will be conducting research and applying instrumentation on Specially Concentric Braced Frames at the National Center for Research on Earthquake Engineering.
Monash University, Melbourne, Australia Mentors: David Abramson UCSD: Roy Kerckhoffs	Scott Revelli, bioengineering This summer I plan on analyzing a fully coupled electromechanic model of a healthy canine heart by using Nimrod to run parameter variations on the model. Through parameter variations I aim to be able to identify the distribution of myocardial cells, by comparing known characteristics of the different cells and the heart’s reactions to different strains.
University of Auckland, New Zealand Mentors: Poul Nielsen UCSD: Roy Kerckhoffs	Amir Shirkhani, computer engineering Continuity is a multi-scale modeling software written in Python. The project is to develop a module for the current version of Continuity that would allow users to import CellML models. The module needs to be developed in Python as well.
Monash University, Melbourne, Australia Mentors: David Abramson UCSD: Jürgen Schulze	Adi Singer, computer science My project will utilize the tiled-display walls at Monash University to create a 3-D geographic model allowing users to fly around and interact with existing city buildings and terrain. Useful for scientific research such as flood patterns, as well as fun to use. The OpenSceneGraph software I am developing to implement these virtual models will port the modeling algorithm currently being researched by Peter Serwylo, an IT student from Monash.
Computer Network Information Center, Chinese Academy of Sciences (CNIC CAS), Beijing, China Mentors: Kai Nan UCSD: Wilfred Li	Michael Siy, biology: physiology and neuroscience This summer I aim to evaluate the feasibility of the relaxed complex scheme for high affinity small molecule inhibitors for the hemagglutinin (HA) receptor-binding domain of the influenza virus. I would also like to develop a trimeric interface inhibitor against HA, through virtual screening using the relaxed-complex method, to stop conformational change of the trimers needed for membrane fusion.
Doshisha University, Kyoto, Japan Mentors: Nozomu Inoue UCSD: Koichi Masuda	Andrew Sou, microbiology The degeneration of facet joint cartilage is caused by opposing articular surface contact during flexion and extension; this can be systematically represented by the construction of a three-dimensional (3-D) computerized tomography (CT) model. The specific aims are to determine physiologic bending kinematics based on literature: intersegmental angles during flexion, stand, extension and to obtain CT data suitable for analysis and reconstruction of a 3-D computer model via the volume-merge method.
Cybermedia Center, Osaka University, Osaka, Japan Mentors: Susumu Date UCSD: Raj Singh	Cory Stevenson, bioengineering: biotechnology Developing software to effectively view very large images through SAGE on the tiled-display wall.
National Museum of Marine Biology and Aquarium (NMMBA), Kenting, Taiwan Mentors: Tony Fan and Fang-Pang Lin UCSD: Jennifer Smith	Winny Wen, environmental systems (ecology, behavior, & evolution) Using several different video recording devices, I hope to be able to capture different competition techniques between different corals themselves and those with other species native to their habitat.
Computer Network Information Center, Chinese Academy of Sciences (CNIC CAS), Beijing, China Mentors: Kai Nan UCSD: Wilfred Li	Chelsea Wong, human biology The first aim of my project is to characterize possible drug resistance by neuraminidase mutants and gain a better understanding of the mechanisms involved in the resistance emergence to a wide use of inhibitors of influenza virus neuraminidase. The second aim of my project is to do off-target analysis on drug candidates to see if they cause any toxicities or side effects, in particular, with focus on compounds that may inhibit all known viral neuraminidase and neuraminidase mutants.
Doshisha University, Kyoto, Japan Mentors: Nozomu Inoue UCSD: Koichi Masuda	Ling (Kelli) Xu, bioengineering: premedical Use nano CT to examine the 3-D microstructure of the endplate responsible for nutrient transport to the intervertebral disc and correlate its structural variations with differences in its fluid permeability to better understand how the change in the structure of the endplate contributes to the progression of osteoarthritis.
Cybermedia Center, Osaka University, Osaka, Japan Mentors: Susumu Date UCSD: Jason Haga	Wen-wai Yim, bioengineering To create a virtual layer on parallel processing computer clusters such that the molecular docking process (using the UCSF docking program Dock6) can be reliably and precisely performed on any computer cluster, regardless of local settings.

Media Contact: Maureen Curran, 858-822-4084, mcurran@ucsd.edu

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