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Jacobs School Undergrads Go International this Summer with PRIME

PRIME 2009 students
2009 PRIME students from UC San Diego: 24 of the 33 PRIME students are from the Jacobs School of Engineering.

San Diego, CA, July 07, 2009 -- Twenty four Jacobs School undergraduates are among the 33 University of California, San Diego undergraduates working as researchers in laboratories across the Pacific Rim and India this summer.

The Pacific Rim Undergraduate Experiences (PRIME) program 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 scientific institutions in Australia, China, India, Japan, Malaysia, New Zealand, or Taiwan. The students will collaborate with mentors at both their host institution and back at UC San Diego.

In its 6th year, PRIME gives students a wider view of the world and their place in it. "PRIME gives undergraduates experience with the increasingly collaborative and international scientific workplace of today," said Peter Arzberger, co-founder of PRIME.

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

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, a bioengineering-biotechnology major working in Australia; Brian McMahon, a computer science major working in India; Michael Nekrasov, a computer engineering major working in Taiwan; and Jade Kwan, a cognitive science/human computer interaction major working in Japan.

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 and National Center for High-performance Computing (NCHC) Taichung, 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 and National Center for High-performance Computing (NCHC) Taichung, 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, K.V. Subbarao and Rajeev Wankar
UCSD: Tony Fountain and Sameer Tilak

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 and National Center for High-performance Computing (NCHC) Taichung, 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 and National Center for High-performance Computing (NCHC) Taichung, 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.

PRIME is funded by the National Science Foundation (NSF) (including supplemental support from NSF's program for India and supplemental NSF funding via PRAGMA for three students), 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.

This is an abridged version of a story written by Calit2's Maureen Curran.

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