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Aug. 17, 2006

  In This Issue:
blue bullet Structure of Key Enzyme in Plague Bacterium Found
 ‘Atomic Switch’ Experiments Expand Nanoscale Toolkit
 Advanced Imaging Facility Watches Fuel Cells at Work
blue bullet

New Web Database Improves Access to Ionic Liquid Data

  Quick Links

Putting Search and Rescue Robots Through Their Paces

bluebullet Draft Guidance on Improving Security of Home Computers
bluebullet Correction for Tech Beat Issue of July 20, 2006

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Structure of Key Enzyme in Plague Bacterium Found


Ribbon rendering of the structure of AC-IV in Yersina pestis as determined at NIST. The enzyme is a dimer (two identical subunits around a vertical axis), and each of the two subunits forms a central barrel made of eight strands surrounded by short helices. The active site is believed to lie inside the barrel.

Credit: NIST
View hi-res image

Researchers at the National Institute of Standards and Technology (NIST) have solved the structure of a key enzyme from the bacterium responsible for plague, finding that it has a highly unusual configuration. The results may shed light both on how the bacterium kills and on fundamental cell signaling processes.

The NIST team determined the three-dimensional shape of class IV adenylyl cyclase (AC), an enzyme found in plague bacteria—Yersinia pestis—by purifying and crystallizing the protein and using X-ray crystallography at the Center for Advanced Research in Biotechnology to resolve its configuration. Adenylyl cyclase is a fundamental enzyme found in one form or another in organisms ranging from bacteria to mammals. It synthesizes cyclic AMP (cAMP*), an important signaling molecule that in turn triggers a variety of cellular processes. Six distinct classes of AC are known, playing a wide variety of roles. AC-II is part of the anthrax bacterium’s killing mechanism, for example, while AC-III triggers adrenaline release in humans.

Shape plays an essential role in determining the biological function of a protein, but it’s very difficult to determine for such large molecules. Three-dimensional structures are known for only two other forms of AC. The NIST experiments revealed that AC-IV has a shape completely different from the other two known shapes. AC-IV folds into a rare form of a barrel-like shape previously seen in only three other unrelated proteins.

The purpose of AC-IV in plague is not well understood, but it may play a role in disrupting cell processes in the infected host. Plague is not as common as it was in the Middle Ages, when it killed millions, but the World Health Organization still logs about 1,000 to 3,000 cases a year, an average of 10 to 15 in the United States. It is rated as a highest category biothreat agent by the Centers for Disease Control and Prevention and the National Institute of Allergy and Infectious Diseases. Fundamental molecular data on this enzyme and its various forms may be critical to the development of defenses against plague and other pathogens, including Bacillus anthracis (Anthrax) and Bordetella pertussis (Whooping cough). Beyond that, structural and functional studies of AC-IV, with its unusual shape, may lead to deeper understanding of the cAMP signaling mechanism and other fundamental cellular processes.

Details of the structure of AC-IV are published in: D.T. Gallagher, N. Smith, S-K Kim, A. Heroux, H. Robinson and P. Reddy. Structure of the class IV adenylyl cyclase reveals a novel fold. J. Mol. Biol., In Press, Corrected Proof, Available online 14 Aug. 2006.

*cyclic adenosine 3’, 5’- monophosphate

Media Contact:
Michael Baum,, (301) 975-2763



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‘Atomic Switch’ Experiments Expand Nanoscale Toolkit

atomic switch figure

NIST researchers used a scanning tunneling microscope (STM) to move a single cobalt atom (blue sphere) in a small molecule back and forth between two positions on a crystal surface (first two images). A computer-generated spatial map of the atom switching speed and probability shows that switching is most likely when the STM tip is positioned to the left of the cobalt atom (blue and white speckled area in the third image).

Credit: J.A. Stroscio, J.N. Crain and R.J. Celotta, NIST
View hi-res image (A and B)
View hi-res image (C)

Scientists at the National Institute of Standards and Technology (NIST) have used a beam of electrons to move a single atom in a small molecule back and forth between two positions on a crystal surface, a significant step toward learning how to build an “atomic switch” that turns electrical signals on and off in nanoscale devices.

The results, described in the Aug. 18, 2006, issue of Science,* are the first to be published about work at NIST’s new Center for Nanoscale Science and Technology (


“It’s still futuristic to talk about a real atomic switch but we’re getting closer,” says physicist Joseph Stroscio, lead author of the paper. In addition, by applying the findings to nanoscale fabrication on semiconductors and insulating thin films, it may be possible to develop new classes of electronic and magnetic devices constructed atom by atom.


The NIST physicists used a custom-built, cryogenic scanning tunneling microscope (STM) to perform several different types of atomic scale measurements and manipulations. A molecular chain of one cobalt atom and several copper atoms was constructed, atom by atom, on a surface of copper atoms using the STM to move the atoms. Then the STM was used to shoot electrons at the molecular chain and its effect on the switching motion of the cobalt atom was measured. NIST theorists performed calculations of the atoms’ electronic structure, which confirmed the experimental results.


The team used a new technique called “tunneling noise spectroscopy"—based on their 2004 discovery that an atom emits a characteristic scratching sound when an STM is used to move the atom**—to determine how long the atom stays in one place. They found that a single electron boosts the molecule above a critical energy level, allowing a key bond to break so the cobalt atom can switch positions. The cobalt atom was less likely to switch as the molecular chain was extended in length from two to five copper atoms, demonstrating that the atom switching dynamics can be tuned through changes in the molecular architecture.


The researchers also found that the position of the STM tip is critical—switching is most likely when the STM tip is positioned to the left of the cobalt atom. “This insight raises the possibility that molecular orbital analysis may be used to guide the design and control of single atom manipulation in nanostructures,” the authors write.


The work was supported in part by the Office of Naval Research. For more details, see:


*J.A. Stroscio, F. Tavazza, J.N. Crain, R.J. Celotta and A.M. Chaka. Electronically induced atom motion in engineered CoCun nanostructures. Science. Aug. 18, 2006.


**J.A. Stroscio and R.J. Celotta. Controlling the dynamics of a single atom in lateral atom manipulation. Science Express, Sept. 9, 2004.

Media Contact:
Laura Ost,, (301) 975-4034




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Advanced Imaging Facility Watches Fuel Cells at Work
fuel cell research

NIST scientist David Jacobson prepares an experimental fuel cell for real-time imaging at the NIST Center for Neutron Research. A new research station at the center produces still images akin to CAT scans and movies recorded at a rate of up to 30 frames per second, or 30 times faster than a first-generation instrument.

© Robert Rathe

For high-resolution image contact

Thanks to a new and improved imaging instrument at the National Institute of Standards and Technology (NIST), scientists now can conduct detailed surveillance of water inside hydrogen fuel cells—a piece of intelligence key to making the technology practical for powering automobiles.

With visualization powers 10 times better than those achieved previously, researchers can watch water being produced and removed inside the maze-like solid housing of fuel cells under a range of simulated operating conditions, from arctic cold to desert heat. “This as-it-happens, inside view is essential because fuel-cell performance depends on a delicate balance,” explains NIST physicist Muhammad Arif, who leads the NIST team that developed the instrument. “Too little—or too much—water can shut it down.” A 2005 National Research Council (NRC) review described the imaging method as “one of the most significant analytical advances in the membrane fuel cell realm in decades.”


Better water management is fundamental to meeting targets for fuel cell performance, reliability and durability. Water is the by-product of the chemical process in fuel cells that strips electrons from hydrogen molecules to generate electricity. NIST’s newly commissioned Neutron Imaging Facility can image water quantities smaller than 1 microgram (millionth of a gram), and details as small as 0.02 millimeter can be discerned in images. Even better spatial resolution is expected. The facility produces still images akin to CAT scans and movies recorded at a rate of up to 30 frames per second, or 30 times faster than the first-generation instrument that NIST built to demonstrate the usefulness of neutron imaging for fuel cell research.


Located at the NIST Center for Neutron Research (NCNR), the Neutron Imaging Facility research station is operated as a national user facility, open to scientists from industry, universities and government agencies. It is jointly funded by NIST, the Department of Energy and General Motors. Although the new facility has been optimized for fuel cell research, it has many potential applications, from evaluations of metal-casting techniques to non-destructive analysis of archeological artifacts.


For more information, see and for technical details on the instrument, including how to apply to use it, see

Media Contact:
Mark Bello,, (301) 975-3776




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New Web Database Improves Access to Ionic Liquid Data

Chemical engineers and others designing “green” industrial processes using new ionic liquid solvents now have an important new resource, an on-line database of physical properties developed by the National Institute of Standards and Technology (NIST). 

There has been an explosion of interest in the last few years (including a near-exponential growth in journal articles) in the synthesis and use of ionic liquids—salts that melt below the boiling point of water. A large part of the interest is due to something ionic liquids don’t have: a measurable vapor pressure at room temperature. With typical vapor pressures in the range of  10-10 pascal (10-14 psi), ionic liquids have essentially no vapor emissions and so look like excellent candidates for “green solvents” to replace hazardous, air-polluting organic solvents like acetone and benzene. With dozens of anions and cations to choose from, they can be tailored to specific needs and may be particularly useful as solvents for biocatalysis.


One problem has been a lack of organized, reliable data on the basic physical properties of ionic liquids, critical information for designing industrial processes. NIST, in cooperation with the International Union of Pure & Applied Chemistry (IUPAC), has created ILThermo, the IUPAC Ionic Liquids Database. Launched at the end of July, ILThermo is a free, web-based research tool that allows users worldwide to access an up-to-date data collection of thermodynamic, thermochemical and transport properties of pure ionic liquids as well as binary and ternary mixtures.


Assembled from published data, ILThermo aims to include information on structure, thermodynamic and transport properties of pure ionic liquids and mixtures. The inaugural version of the database includes data for more than 200 ions and more than 300 ionic liquids. A particularly valuable feature, according to Michael Frenkel of NIST’s Thermodynamic Research Center, is the inclusion of uniformly calculated uncertainties (following guidelines adopted by the major scientific unions and NIST) for each data point in the collection, making it easier to compare the quality of different measurements.


The ILThermo portal on the web is at .


Media Contact:
Michael Baum,, (301) 975-2763




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Quick Links

Putting Search and Rescue Robots Through Their Paces

The National Institute of Standards and Technology (NIST), in cooperation with the U.S. Department of Homeland Security's Science and Technology Directorate, is sponsoring a workshop and a demonstration of urban search and rescue robots at the Montgomery County (Md.) Fire Rescue Training Academy in Rockville, Md., on Aug. 21, 2006.*

During the exercise, various types of sensor-laden robots, including small survey devices that can be thrown into a disaster site, unmanned systems that can cover rugged, uneven terrain, and small, rotary-winged aerial reconnaissance drones will attempt a number of activities, including detecting injured people and trace elements of radiation in simulated natural disaster or terrorist attack conditions.


The robot tests conclude a three-day workshop organized to give emergency responders an opportunity to deploy robots in realistic training scenarios and to help robot developers refine their designs, better understand robot and sensor performance requirements, and identify robots best suited for specific emergency situations. NIST will use the data collected during the exercise to develop standard test methods and usage guides. The outcomes of specific tests will not be published.


For more information on developing performance standards for urban search and rescue robots, visit


*Media planning to attend should call John Blair (301) 975-4261 by noon, Monday, Aug. 21, 2006.


Draft Guidance on Improving Security of Home Computers

The National Institute of Standards and Technology is looking for comments on new guidelines aimed at helping end-users, in particular telecommuting federal employees, improve the security of their personally owned desktop and laptop computers that run Windows XP Home Edition in a small office or home office environment. Like their larger office counterparts, home computers increasingly are the target of attackers looking to damage or disrupt files, steal identities or commit fraud. Guidance for Securing Microsoft Windows XP Home Edition: A NIST Security Configuration Checklist (Special Publication 800-69) contains detailed step-by-step directions for securing Windows XP Home Edition computers. It explains the need to use a combination of security protections, such as antivirus and antispyware software, a personal firewall, limited user accounts and automatic software updates. It also emphasizes the importance of performing regular backups to ensure that data are available after an attack against the computer, a hardware failure or human error. The draft publication is available at Comments should be submitted by Aug. 31, 2006, to with "Comments SP800-69/XPHome" in the subject line.


Correction for Tech Beat Issue of July 20, 2006

There is a calculation error in a figure reported in the Tech Beat article “Novel Nano-Etched Cavity Makes LEDs 7 Times Brighter” published on July 20. (See When originally published, the article said (of LEDs made with the new brightness-enhancing technique), "The brightest output was attained with 10 grooves, each about 240 nanometers (nm) wide ..." The correct value is 480 nanometers. We apologize for the error.


(Return to NIST News Page)

Editor: Michael Baum

Date created: 8/15/06
Date updated: 8/17/06