SAN DIEGO — After only 15 months, researchers using the Triton Resource, a medium-scale high performance computing system at the University of California San Diego’s San Diego Supercomputer Center (SDSC), are giving the system high marks for accelerating research across a wide variety of disciplines.

Designed primarily to support UC San Diego and UC researchers, Triton Resource currently has a roster of more than 600 users across campus and the UC system. Research projects range from cancer research and molecular dynamics, to global climate forecasting, earthquake simulations and nanoengineering activities.  

“For both SDSC and a research campus such as UC San Diego, the strong level of interest among researchers in tapping into the Triton Resource underscores the fact that high-performance computing is now an essential part of scientific discovery,” said Michael Norman, SDSC’s director. “This system is perfect for the researcher who requires a small- to medium-scale computing capability and ample amounts of storage without needing to access a large, remote national system.”

Featuring a 2,000-processor computing cluster, a unique “large-memory” cluster for data-intensive computing and a high capacity, high performance data storage system, the Triton Resource is also available on a space-available basis to researchers throughout the larger academic community, as well as private industry and government-funded organizations.

Recent research projects that have leveraged the capability of SDSC’s Triton Resource include:

Drug Discovery: Repurposing an AIDS Drug
Philip Bourne, a professor with the Skaggs School of Pharmacy and Pharmaceutical Sciences at UC San Diego and a distinguished scientist with SDSC, used the Triton Resource in a recent research project to create molecular dynamics simulations which indicate that a drug used to fight AIDS may be an effective treatment for some forms of solid tumors.

Bourne and his team, which includes Li Xie and Lei Xie, senior scientists with Bourne’s laboratory, and graduate research student Thomas Evangelidis, currently have a paper under review on how the weak inhibition of multiple kinases may contribute to the anti-cancer effect of Nelfinavir, a potent HIV-protease inhibitor with multiple effects in cancer cells. The team’s results suggest that Nelfinavir is able to inhibit multiple members of the protein kinase-like superfamily, which are involved in the regulation of cellular processes vital for carcinogenesis and metastasis.

“Using the Triton Resource, we were able to develop computational predictions that are supported by kinase activity assays and are consistent with existing experimental and clinical evidence,” according to Bourne. “This finding provides a molecular basis to explain the broad-spectrum anti-cancer effect of Nelfinavir, and presents opportunities to optimize the drug as a targeted polypharmacology agent.”

Nanoengineering: Developing Advanced Lithium-ion Batteries at the Nanoscale Level
UC San Diego researchers at the university’s Jacobs School of Engineering have been using the Triton Resource to develop new types of lithium-ion (Li-ion) batteries that could be used in a variety of NASA space exploration projects as well as a wide range of transportation and consumer applications.

NEI Corporation is the prime contractor on a NASA contract, which includes Shirley Meng, a professor in the Department of NanoEngineering at the Jacobs School of Engineering, as a subcontractor. The program is focused on modeling new nanocomposite structures for next-generation electrode materials to develop advanced Li-ion battery systems with high energy and power densities, and the ability to operate at low temperatures, as required for NASA’s exploration missions.

Such advanced battery packs could also be used in hybrid electric vehicles, consumer electronics, medical devices, electric scooters, and a variety of military applications.

“With Triton’s state of the art computation facility, we are able to build up a ‘virtual lab’ where computational modeling is used to predict relevant properties of new materials used in lithium- ion batteries, helping to guide the experimental investigation,” said Meng, who leads the Laboratory for Energy Storage and Conversion in the Department of NanoEngineering at the Jacobs School of Engineering.

Meng’s research group is also using the Triton Resource on several other projects, including one of 43 leading-edge projects funded with $92 million from the American Recovery and Reinvestment Act through the Department of Energy’s Advanced Research Projects Agency-Energy (ARPA-E). Working with General Atomics, the award is for development of a novel flow battery technology that pumps chemicals through the battery cell when electricity is needed, by using new materials that greatly increase power while resisting the corrosion that limits the cycle life of conventional lead-acid batteries, a century-old technology. The goal is to develop a battery that can be scaled for grid-scale energy storage, but which costs less and performs far longer than today’s technologies.

“We need to go beyond conventional ways to build batteries more economically viable for large scale storage, and safe and robust for day to day operations,” added Meng. “As interest in large-scale consumer technologies such as electric cars spreads, we also need to be mindful of our environment by making batteries last 10 years or more, instead of three years.”

Computational Biophysics: Electrostatic Steering in Molecular Motor-track Interactions
Using the Triton Resource to develop computational simulations of protein-to-protein associations, researchers at UC San Diego’s Department of Chemistry and Biochemistry have developed a new picture of how kinesin molecules move along microtubules. These proteins form a kind of molecular-scale railway, with kinesin engines hauling cargo along microtubule rails within cells. This new work shows that electrostatic attraction between the engine and the rail is critically important in making the railway work.  

“This research has shown us that computational methods can be used to rationally design mutant molecular motors, with altered electrostatic properties, that can regulate the speed of the railway,” said researcher Barry Grant, a member of the research lab headed by J. Andrew McCammon, Joseph Mayer Chair of Theoretical Chemistry and professor of Pharmacology at UC San Diego and a Howard Hughes Medical Institute Investigator.

In keeping with the train analogy, speeding up means having a more efficient transport of cargo, perhaps a drug. Slowing the speed provides researchers with a good test of the general operational constraints for producing directed motion on the molecular scale, which is informative for future nanoengineering projects. Moreover, defects in motor-dependent processes, such as slowing down or stopping altogether, are associated with a large range of diseases, including neurodegeneration, tumorigenesis and developmental defects.

“The Triton Resource helped us map the interactions of kinesin with microtubules, and allowed us to better understand how they work,” said Grant, noting that each simulation in the project consumed large amounts of memory (about 7GB ram/core) with subsequent analysis of data sets measuring about 1.8 terabytes in size. “Ultimately, construction of molecular motors to arbitrary specifications will provide a powerful toolkit for therapeutic delivery and nanotechnology applications.” 

The Triton Affiliates and Partners Program (TAPP) offers various mechanisms for accessing SDSC’s Triton Resource. Research inquiries may be directed to Ron Hawkins, Triton Affiliates program manager, at (858) 534-5045 or rhawkins@sdsc.edu.