Computational Accelerator Physics
The advanced modeling tools developed in the Computational Accelerator Physics Grand Challenge are allowing particle accelerators to be designed with reduced cost and risk as well as improved reliability and efficiency. Three parallel application codes-IMPACT, Omega3P, and Tau3P-have been developed under the Grand Challenge.

These three codes have already made a significant impact on several important DOE projects such as the Next Linear Collider (NLC), Accelerator Production of Tritium (APT), and Spallation Neutron Source (SNS). The IMPACT simulation of a 500-million-particle beam helped to predict the maximum particle amplitude, and hence the required beam pipe aperture, in the SNS linac. IMPACT was also used in the first systematic study of halo formation due to longitudinal/transverse coupling in charged particle beams. Omega3P and Tau3P simulations were pivotal in realizing an improved NLC structure design with higher acceleration gradient that results in a $100 million savings in the cost of constructing the linac.

Computational Chemistry of Nuclear Waste Characterization and Processing
In this Grand Challenge, researchers are developing and applying the methods of relativistic quantum chemistry to assist in the understanding and prediction of the chemistry of actinide and lanthanide compounds. Modeling these heavy-element compounds is essential to modeling the fate and transport of nuclear wastes in the environment, as well as evaluating remediation alternatives. Existing codes have been parallelized for the T3E and extended to enable calculations on larger molecules at higher levels of accuracy.

In order to determine qualitatively correct electronic spectra for heavy metals, especially for actinides, the effects of both electron correlation and the spin-orbit interaction must be taken into account. A large component of the work on the T3E has been spin-orbit configuration interaction (CI) calculations upon various actinide ions. Much effort has been devoted to developing and understanding accurate descriptions of the electronic spectra of various actinide and lanthanide ions. This is very challenging and has required development of new relativistic effective core potentials. The theoretical and computational methodology being developed will supplement current, very expensive experimental studies of the actinides and lanthanides. This will allow limited experimental data to be extrapolated to many other regimes of interest.

Grand Challenge Application on High Energy and Nuclear Physics Data
The purpose of the Grand Challenge Application on HENP Data is to develop techniques and tools that will enable efficient access to the massive datasets generated by the Relativistic Heavy Ion Collider (RHIC) experiments in their search for the quark-gluon plasma. This project had several notable accomplishments. First, they successfully ported the CERNLIB physics software to a parallel architecture-a large and complex task that had been attempted several times before but never completed. Second, a cross-country data transfer experiment, from NERSC in Berkeley to Brookhaven National Laboratory on Long Island, achieved transfer rates of 800-900 kB/sec over brief periods, and sustained an average 200 kB/sec over several days.

Most importantly, over the past two years the project has generated a large set of simulated heavy ion collision data to be used as a testbed for developing data management and analysis tools and algorithms. In FY 1999 alone, approximately 250,000 PE-hours were used and over 6 terabytes of simulated data produced. These data were essential as input for two large-scale Mock Data Challenges at the RHIC Computing Facility at Brookhaven, where the primary RHIC data will be stored and first analyzed. Mechanisms were developed to efficiently transport large volumes of data over the network between computing facilities spread across the country, a capability that will be crucial for the distribution of real RHIC data. As a result of these efforts, the RHIC physicists are now confident that the first data can be reliably handled and efficiently processed to extract the physics.

High Performance Computational Engine for the Analysis of Genomes
Interpretation of the human genome represents the next grand challenge at the interface of computing and biology. The many genome sequencing projects soon will be producing data at a rate that exceeds current analysis capabilities. New methods and infrastructure need to be implemented for effective analysis and management of this data. The overall objective of this Grand Challenge has been to design and implement a distributed computational framework for the genome community that provides users with services, tools, and infrastructure for high-quality analysis and annotation of large amounts of genomic sequence data.

This collaboration has developed a web-based framework, The Genome Channel (now in its second version), which shows the current progress of the international genome sequencing effort and allows navigation through the data down to individual sequences and gene annotations. Work in progress also includes developing a CORBA-based analysis framework to facilitate automation of the genome annotation process, and developing specialized software and databases for genome analysis, such as the previously discussed Alternative Splicing Data Base.

Materials, Methods, Microstructure and Magnetism
This Grand Challenge collaboration earned international acclaim in 1998 when their 1024-atom first-principles simulation of metallic magnetism in iron won the Gordon Bell Prize and was the first complete scientific application to break the teraflops barrier. Using their locally self-consistent multiple scattering (LSMS) code, the group studied quantum atomic interactions on a scale not previously accessible, and developed a new constrained local moment theory of non-equilibrium states in metallic magnets. This theory applies a separate magnetic field to each atom in a unit cell.

Developing a microscopic understanding of the dynamics of metallic magnets has been an abiding scientific challenge. An understanding of the relationship between magnetism and microstructure based on fundamental physical principles could result in breakthroughs in computer storage as well as power generation and storage, and could enable the design of magnetic materials with specific, well-defined properties.

This project uses a number of different first-principles techniques, including LSMS, tight-binding molecular dynamics (TMBD), and an iterative pseudopotential (IP) method, to perform fundamental studies of the atomistic, electronic, and magnetic structure of microstructural defects in metals and semiconductors that involve the interactions between large numbers of atoms (TBMD 20,000 atoms, IP >200, LSMS 250 to 1500 atoms). In addition, they are developing spin dynamics based on both model Hamilitonians and local spin density calculations as a fundamental theory of the magnetic properties of metals and alloys.

Numerical Tokamak Turbulence Project
Researchers in the Numerical Tokamak Turbulence Project (NTTP) reported a major advance in the computer modeling of fusion plasmas in the September 18, 1998 edition of Science magazine. Using NERSC's Cray T3E for three-dimensional nonlinear particle simulations of microturbulence in the plasma, they performed calculations involving 400 million plasma particles in 5000 time-steps-the first simulations realistic enough to compare with existing experiments. The Cyclone Project (an offshoot of NTTP), which compared various models for core transport in tokamaks, was also discussed in both Science and Nature in 1998.

The NTTP simulations are being used to produce linear and nonlinear calculations of drift-type instabilities in realistic tokamak equilibria, which are leading to a deeper understanding of anomalous transport in current experiments and to improving their performance. This simulation work is providing a basis for reduced transport models that fit current experimental databases and from which it is hoped that performance in future experiments can be reliably predicted and optimized. As controlling the energy transport has significant leverage on the performance, size, and cost of fusion experiments, reliable NTTP simulations can lead to significant cost savings and improved performance in future experiments.

Particle Physics Phenomenology from Lattice QCD
Detailed simulations of the Standard Model of particle physics, developed in this Grand Challenge, will help determine some of the fundamental constants of nature. As a field, lattice quantum chromodynamics (QCD) provides theoretical calculations of quantities which can be measured experimentally. This provides both cross-checks of the Standard Model of particle physics, and a determination of several of its fundamental parameters.

This research team successfully computed the decay amplitudes of kaons for the first time, and successfully reproduced the observed I = 1/2 effect. This is a longstanding puzzle of weak kaon decays, in which two seemingly similar decay processes (I = 0 and I =2) proceed at very different rates. They recently computed the weak matrix elements which are responsible for the I = 1/2 rule, and are working to help refine the theoretical calculation of the recently measured quantity . They also established a publicly available Gauge Connection archive, which provides unquenched lattice QCD configurations that include virtual quarks.

Protein Dynamics and Biocatalysis
In the Protein Dynamics and Biocatalysis Grand Challenge, researchers are working to understand the chemical mechanisms in enzyme catalysis, which are difficult to investigate experimentally. Computer simulations will eventually provide the necessary insights, at an atomic level of detail, for a complete understanding of the relationship between biomolecular dynamics, structure, and function. For example, while the class of enzymes known as beta-lactamases are largely responsible for the increasing resistance of bacteria to antibiotics, the precise chemical resistance mechanism used by this enzyme is still unknown. Simulations are critical for further study of this mechanism.

The focus of this research has been the development of a detailed understanding of the reaction mechanisms employed by beta-lactamases to hydrolyze b-lactam antibiotics. Researchers performed molecular dynamics simulations of the TEM-1 enzyme with a penicillin substrate to gain insights into accessible conformations of the enzyme/substrate (Michaelis) complex. They were interested in defining the roles of various active-site residues in binding and orienting the substrate into a conformation suitable for the catalytic reactions to proceed. The results of the simulations were consistent with two of three proposed mechanisms for the acylation step of the reaction. These simulations provide insights into the roles of several residues in binding and orienting the substrate in the active site. These insights may prove useful for the development of new antibacterial agents.