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The main purpose of the wulffnet cluster is to support synchrotron related research programs that are conducted at Sector 5 of the Advanced Photon Source. These include programs from biological sciences to x-ray tomography. To support these programs LAM/MPI as well as PVM are available on the cluster. FFTW has also been installed on the cluster. In addition, serial jobs can be submitted using the Portable Batch System.

Computational Materials Science and X-ray Diffuse Scattering Calculations

The primary purpose of this project is to understand the two dimensional structure of two dimensional surface alloys using a variety of techniques. These techniques include measuring the x-ray diffuse scattering. The diffuse program written by Dr. Brent Butler as well as the discus program written by Dr. R.B. Neder and Dr. Th Proffen are being evaluated for use on the cluster. This work is being funded by the National Science Foundation DMR-0076063 and is a collaboration between Dr. Mark Asta , his group at Northwestern, Dr. Denis Keane, and Dr. John Quintana.

The cluster is also being used to run an ab initio molecular dynamics program to model the Pb/Ge interface system.

Ab Initio Crystal Structure Determination from Powder Diffraction Data

Dr. Richard Harlow (DuPont) has been collaborating with Dr. Armel Le Bail's group on a MPI based version of the ESPOIR program for performing ab initio structure determinations. A version of this code is currently being tested on the Wulffnet cluster.

X-ray Tomography

DND-CAT has a dedicated x-ray tomography station in the rear of one of its bending magnet enclosures. By collecting x-ray radiographs of a sample as it is rotated through 180 degrees, the three dimensional structure of the sample interior can be reconstructed inside of computer memory. Currently, the CCD used to collect data contains 1300 x 1340 pixels and replaces an older 1K x 1K system. The cluster is used to reconstruct the data from the various images.

DuPont works with tire companies to develop their 'Engineered Elastomer' products for various end uses. A continuing challenge has been to define the distribution of reinforcing fibers in rubber to be able to relate this structural feature to process variables and end-use performance. Using X-ray microtomography, DuPont has successfully produced 3D images of individual Kevlar pulp fibers in rubber. Heretofore, the only way to look at pulp distribution has been via microscopy and this only produces 2D pictures. Fibers have typical diameters of 1 to 12 microns and lengths of 0.5 mm. A three dimensional movie of a "master batch" containg 23% fiber pulp in elastomer is available for download.

Genetic modifications in plants can lead to structural modifications within a plants seeds. DuPont has been investigating changed in arabidopsis seeds since its genetic code is completely known. Wild type seeds with no genetic alterations are compared with seeds that have genetic alterations made. A three dimensional movie of three arabidopsis seeds mounted on a glass fiber is available for download. The images were provided by Dr. Randy Barton of DuPont and were prepared by David E. Jones of DuPont Scientific Computing.

File Compression

In some sense, this is mostly associated with the Tomography project, but other applications can use it as well. Large data sets can be transferred onto or created on the Wulffnet Cluster so they can be backed up to CD-R using the Plasmon CD Robot. In order to fit the most data on the CD's they can be compressed using bzip2 . The root of this is a simple script which creates a series of PBS jobs to compress individual files on the clusters disks.

Structural Genomics

Wulffnet is currently being used as a test cluster for the Midwest Center for Structural Genomics through collaborations with Dr. Steve Weigand. Local users can learn more about the user of the cluster for DND Macromolecular Crystallography research.
John Quintana (jpq@northwestern.edu) / May 2001