A Grid Database: protein sequences

Oxford e-science projects

About BioSimGrid
Biomolecular simulations: a Grid Database (BioSim)


Modern biology requires new approaches to biomolecular simulation. With nearly 200 000 protein sequences in the genomic databases, and over 33 000 structures deposited in the Protein Data Bank, single simulations of a single protein do not address the needs of contemporary biology. We are developing tools that will enable biomolecular simulations to provide an essential link between structural genomics and systems biology. In particular, the simulation community has to addressing three key areas of simulation technology: high-throughput simulations for high-performance computing, a grid-enabled database for comparative analysis of simulation data, and multi-scale biomolecular simulations ranging from the quantum-mechanical to the meso-scale. That is, we need to be ready to provide both the computational infrastructure and pharmaceutically relevant test cases to demonstrate the validity of this new approach. BioSimGrid, as a distributed database for biomolecular simulations, provides the keystone in the endeavour.

http://e-science.ox.ac.uk/oesc/projects/index.xml.ID=body.1_div.1








Helium ions for microscope technology

Reaserchers ....are probing the newest microscope technology to further improve measurement accuracy at the nanoscale. Better nanoscale measurements are critical for setting standards and improving production in the semiconductor and nanomanufacturing industries.

This new microscope technology uses helium ions to generate the signal used to image extremely small objects, a technique analogous to the scanning electron microscope, which was first introduced commercially in the 1960s. Paradoxically, although helium ions are far larger than electrons, they can provide higher resolution images with higher contrast. The depth of field is much better with the new technology too, so more of the image is in focus. “It is the physics,” explains Andras Vladar, SEM project leader in NIST’s Nanoscale-Metrology Group. “Ions have larger mass and shorter wavelength than electrons, so they can be better for imaging.” The images, he says, appear almost three-dimensional, revealing details smaller than a nanometer—the distance spanned by only three atoms in the silicon crystal.

...The clearest advantage of the helium ion microscope is that the images show the actual edge of a sample better than the SEM, which is critical in precision manufacturing. “Meeting critical dimensions by knowing where an edge is in high-tech manufacturing can mean the difference of hundreds of dollars per piece,” explains Michael Postek.




An image of gold atoms on tin from a state-of-the-art scanning electron microscope (left) has relatively poor depth of field–only parts of the image are in sharp focus. By contrast, the entire image from a helium ion microscope image (right) is sharp and clear. NIST researchers are studying helium ion microscopes to improve measurements at the nanoscale that are important to the semiconductor and nanomanufacturing industries.

NIST Studies How New Helium Ion Microscope Measures Up
http://www.mrs.org/s_mrs/sec.asp?CID=1920&DID=84063#aug08_1a