TeraGrid Roundtable Update

SDSC

03-12-09

Data, Visualization

• Lustre-WAN–PSC Research Collaborations

•Created a local instance of a Lustre-WAN object storage target (OST) on the SDSC SUN-based Lustre test cluster seen by the PSC (JWAN) Lustre-WAN filesystem (this is entry into creating a Lustre-WAN DSS)

–IU Collaboration•Created an IA-64 testbed

•Mounted the IU Lustre-WAN filesystem (Data Capacitor)

•Did performance tests and got 100MB/sec on a 1Gb/sec link (essentially line speed)

• File transfer (GridFTP options)–Directly to/from GPFS-WAN using IBM P5 system

•500MB/sec – 1GB/sec rates achieved

–Directly to/from HPSS–Directly to/from 12 IA-64 servers

Software, Scheduling

• The Grid Universal Remote (GUR) co-scheduler is now available as an optional CTSS component in the Application Development and Runtime Support kit.

• The Master Control Program (MCP) automatic resource selection tool has been checked into repo as a CTSS component. Addition to an appropriate kit is planned.

Advanced User Support• SDSC involved in the following collaborative ASTA projects jointly with AUS

staff from other RP sites:1. Direct Numerical and Large-eddy Simulation of Complex Turbulent Flows. PI: M.

Krishnan, University of Minnesota.

2. SCEC PetaSHA: An Earthquake System Science Approach to Physics-Based Seismic Hazard Research. PI: T. Jordan, University of Southern California and SCEC PIs

3. Network for Earthquake Engineering Simulation (NEES). PI: S. Krishnan, UCSD and multiple other NEES PIs

4. Molecular Dynamics. – QM/MM and AMBER simulations. PI: Adrian Roitberg, U. Florida

5. DNS of Spatially Developing Turbulent Layers. PI: A. Ferrante, U. Washington

6. Multiscale anlysis of size dependence of deformation and fracture of Hierarchy Protein Materials. PI: M. Buehler, MIT

7. Global Kinetics Simulation of the Magnetoshpere. PI: H. Karimabadi, UCSD

8. Insight into Biomolecular Structure, Dynamics, Interactions and Energetics from Simulation. PI: T. Cheatham, U. Utah

9. Few other unofficial ASTA type work in progress with potential to be official ASTA

• SDSC AUS staff participating in the Molecular Dynamics advanced project along with multiple other staff from other RP sites

SDSC EOT Highlight

SMART Teams: (Students Modeling A Research Topic)

– Collaboration with Milwaukee School of Engineering

– SDSC is one of four national partnership sites, with:

• Rockefeller University

• UC San Francisco

• University of Maryland

– Teachers and local researchers serve as team mentors

Program Content

SDSC, in partnership with The Scripps Research Institute (TSRI), is currently hosting four high school teams from underserved areas of San Diego County in its first year of the program (23 students)

Local researchers in the field of drug discovery serve as team coaches, guiding student research

Teachers receive training in molecular modeling prior to student team research project launch so they work in partnership with the local researcher, integrating the research into the students’ school activities and leading additional enrichment activities

Students learn:

protein structures

protein visualization software

design a physical model

write abstracts

Student share their research with peers and with the community at the San Diego High Tech Fair and the San Diego Science Festival.

Influenza hemagglutinin (HA)

What’s it all about?           The Influenza virus is an avian (bird) virus that can infect humans. Occasionally, a virus can mutate to where it can be transferred from human to human, like the common flu.  In 1918, the virus was extremely deadly due to a specific type of binding agent known as hemagglutinin.  Hemagglutinin allows the virus to fuse with human cells and inject its viral RNA. By contrast, neuraminidase allows the influenza virus to detach from the cell and spread into the bloodstream.            Hemagglutinin is the key to the virus’s entrance into the cells that line the human airway. It is a glycoprotein on the outside of the influenza membrane, which is composed of three identical monomers that work together as a single unit.  One part of the protein has a binding site for sialic acid, sugar, on the host cell membrane in order to anchor to the host cell.  The host cell then takes in the virus during endocytosis; the drop in pH level caused by the proton pumps triggers the metamorphosis of hemagglutinin.  A hydrophobic peptide on hemagglutinin is inserted into the endosome membrane, and then folds back, fusing the two membranes. Antibodies can neutralize the receptor binding sites by attaching to hemagglutinin where the sialic acid would.             Without hemagglutinin, the influenza virus would not be able to bind to any host cells, rendering it unable to spread.  By studying hemagglutinin, researchers can learn about the spread of influenza.  New antibodies that bind to hemagglutinin may help prevent a pandemic like the 1918 influenza.            In the model the sialic acid bounding sites to are emphasized with a space-filling atom representation.  The space-filled sugars would normally be on the end of the carbohydrate chains on the host cell.  The rest of the molecule is represented by a thick backbone.

How does it work?(HA) or hemagglutinin is found on the surface of the influenza virus. It is responsible for binding the virus to the cells that are being infected. After HA binds to sugars of the cells membranes, endocytosis begins and the virus is folded into the host cell. HA’s reaction to an acidic environment within the endosome is what drives the fusion of the endosomal and virus’ membranes. This allows for the releasing of the viral RNA, which then goes on the take over the cells machinery producing more HA containing viruses. HA is responsible for the widespread success of viruses like the deadly 1918 pandemic. This research is important in the development of immunization against viruses.

Dark Grey: monitor linesGrey: backbone Orange: hydrogen bonds Red: oxygenBlue: hydrogen receptor sitesCyan: carbons

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Breaking news: Vaccine Protects Against 1918 Influenza StrainScience Daily (Feb. 25, 2009) — Researchers have developed a vaccine that appears to protect against the 1918 "Spanish" influenza virus. Using a mammalian expression system they created a virus-like particle (VLP) that mimics the 1918 influenza virus, prompting the immune system to develop protective antibodies.This research was presented February 24, 2009 at the ASM Biodefense and Emerging Diseases research Meeting in Baltimore, MD.

Authors: Wade Edwards, Luisa Lee, Patrick Lucero, Annette Ramirez, Luis Rios, Marianna Zapanta

Teacher: Sandra Galea-MartinezEl Capitan High School 10410 Ashwood

Street, Lakeside, California 92040

Mentor: Damian Ekiert, Graduate Student-The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, California 92037

Future Plans

Based on San Diego's success, UCSD and the Scripps Research Institute will host the national SMART Team’s first west coast summer training from July 20-24, 2009 to recruit additional  teacher mentors for 2009- 2010

Goal for 2009-2010 is ten new SMART teams

San Diego’s Miramar Community College has joined the San Diego area partnership for 2009, helping to strengthen regional leadership for independently replicating the program more broadly

Participating teacher/mentors will submit a proposal to present at TG-09’s EOT track