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Holland Computing Center

Research

A team of scientists led by University of Nebraska-Lincoln biochemist Vadim Gladyshev has developed a new way to rapidly identify amino acids in proteins that have redox function. The work is published in the current issue of Science magazine.

The process developed by Gladyshev and Dmitri Fomenko, a research assistant professor in Gladyshev's laboratory, focuses on cysteines, amino acids found in most proteins.

In some proteins, cysteines have no critical function, while in others they play roles such as binding metals, regulating certain protein functions, or targeting proteins to a particular location in cells. In still other proteins, cysteines are key players in redox regulation, which is a basic biological process used by all organisms.

The team's work, which used Prairiefire, UNL's renowned supercomputer, developed a simple, accurate way to determine which cysteines are redox amino acids found in most proteins. In some proteins, cysteines have no critical function, while active.

Following this bioinformatics procedure, the researchers then verified their technique by characterizing a protein involved in arsenic detoxification, one of many proteins the team has found to contain a redox cysteine.

University of Nebraska-Lincoln (UNL) chemistry professor Xiao Cheng Zeng and colleagues recently reported in the Proceedings of the National Academy of Sciences' online edition that they have found evidence of the first free-standing hollow cage structure composed of clusters of pure metal atoms, which they've dubbed golden hollow cages.

Zeng's team was the first to combine quantum chemistry calculations with a powerful computerized search technique to identify previously unknown nanoscale structures and substances.

Using UNL's PrairieFire supercomputer together with computers in the chemistry department, they applied their combined technique to generate many theoretical fingerprints of the gold clusters' structure.

*12/11 update on Zeng's group Nano-ice

University of Nebraska-Lincoln scientists and facilities are playing a key role in one of the world's largest physics experiments. David Swanson (Director, RCF), and Ken Bloom and Aaron Dominguez (Assistant Professors, Physics) have received a $2 million grant from the National Science Foundation to support those efforts.

'It makes us an important center for CMS data analysis,and puts UNL in the forefront of research involving Grid computing, which is the coordinated use of computers that are spread around the world,' said Swanson.

'Particle physicists study the questions: what is the world made of and what are its rules?' explains Dominguez.

'Amazingly, 95 percent of the universe seems to be made of unknown stuff. With CMS, we are poised on the threshold of an incredibly exciting time of potential discovery.'

The experiment is the international particle-physics project known as the Compact Muon Solenoid, or CMS, an experiment for the Large Hadron Collider, the world's largest particle accelerator, at the European Organization for Nuclear Research (CERN). Scheduled to begin in 2007, the experiment will explore the frontiers of energy, matter, space and time. But the experiment will create so much data that dozens of supercomputers crunching 24/7 will take years to analyze all the information. To solve that problem, a 'tiered' hierarchy of computing facilities is being created; UNL is a member of that hierarchy. UNL will host a subset of the data that is anticipated to be on the order of half a petabyte, and the Holland Computing Center's computing power is anticipated to approach 10 teraflops, which is more than 10 times the power of the current Prairiefire supercomputer at UNL.