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July 13, 2005

  In This Issue:
bullet JILA Study of RNA Dynamics May Help in Drug Design

Temperature Control Improves NIST X-ray Detector

bullet New Infrared Tool Measures Silicon Wafer Thickness
bullet NIST Finds Rough Spot in Surface Measurement
bullet Predicting the Lifetime of Extreme UV Optics

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JILA Study of RNA Dynamics May Help in Drug Design

30 to 40 single RNA molecules

These false-color images show the behavior of about 30 to 40 single RNA molecules tagged with fluorescent dyes in the absence of magnesium (left) and with high magnesium concentrations (right). Green indicates that the tagged molecules are farther apart (undocked) whereas red indicates they are closer together (docked), showing that magnesium promotes docking.

Click here for a high-resolution version of this image.

Biophysicists have developed a method for studying, in real time, a nanoscale “docking and undocking” interaction between small pieces of ribonucleic acid (RNA), a technique that may be broadly useful in studying structural changes in RNA that affect its function. The research at JILA, a joint institute of the National Institute of Standards and Technology (NIST) and University of Colorado at Boulder, may have applications in the design of effective new drugs based on small RNA strands.

RNA is a chain-like molecule that contains genetic information, makes proteins and catalyzes biological reactions. Scientists at JILA are studying RNA using methods that reveal how individual chemical units of RNA dock, or lightly and temporarily bond, to form special three-dimensional shapes that exhibit biochemical activity. The latest work, to be published the week of July 11 in the Proceedings of the National Academy of Sciences,* adds to understanding of the intramolecular “stickiness” between specific loops and sequences in the RNA that help stabilize this folding. This type of information is crucial to understanding RNA structure and, ultimately, how it affects function.

The JILA group developed a simple model system for studying the reversible docking of a small piece of RNA at a receptor site in the same molecule. They used a technique called fluorescence resonance energy transfer, in which the two pieces of RNA are labeled with different dyes that have overlapping emission bands. One dye emits light of the same color that the other dye absorbs; the second dye then emits light of a different color. One piece of RNA is excited by a laser and, when the two pieces are close enough together to dock, passes energy to the other one, which then fluoresces. This method was used to measure the distance between the two pieces of RNA as it varied from less than 4 nanometers in the docked state to about 7 nm in the undocked state.

The scientists used ultrasensitive laser-based microscopy methods to image many isolated RNA molecules simultaneously, in effect generating a “movie” of single molecule docking kinetics in real time. They used this method to study thousands of pieces of RNA over time scales of 10 to 30 seconds, and observed about two-thirds of them rapidly docking and undocking. The rates of docking and undocking were measured as a function of the concentration of magnesium ions in the surrounding fluid, revealing a complex dependence on metal ions, as is typical for RNA. The docking rate rose 12-fold as magnesium concentrations increased. A significant number of molecules still docked in the absence of magnesium—the first time this phenomenon has been observed, according to the paper.

The research is supported by NIST, the National Science Foundation, National Institutes of Health, and the W.M. Keck Foundation initiative in RNA science at CU-Boulder.

*J.H. Hodak, C.D. Downey, J.L. Fiore, A. Pardi and D.J. Nesbitt 2005. Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single molecule fluorescence resonance energy transfer. Proceedings of the National Academy of Sciences. Week of July 11.

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



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Temperature Control Improves NIST X-ray Detector

Research physicist Terrence Jach prepares to analyze a sample with the NIST X-ray microcalorimeter.

Research physicist Terrence Jach prepares to analyze a sample with the NIST X-ray microcalorimeter. Improved temperature sensing and control systems allow the instrument within the gold chamber to the right to detect X-rays characteristic of specific elements over a broad range of energies with higher resolution.

Photo credit: Gail Porter/NIST

Click here for a high-resolution version of this image.

Researchers at the National Institute of Standards and Technology (NIST) have developed an improved experimental X-ray detector that could pave the way to a new generation of wide-range, high-resolution trace chemical analysis instruments. In a recently published technical paper*, the researchers described how they used improved temperature-sensing and control systems to detect X-rays across a very broad range of energies (6 keV or more), with pinpoint energy resolution (an uncertainty of only 2 eV).

The detector’s ability to distinguish between X-rays with very similar energies should be especially useful to the semiconductor industry for chemical analysis of microscopic circuit features or contaminants. Many types of high-resolution microscopes routinely used in the industry and throughout science produce detailed chemical maps by scanning a surface with electrons and then analyzing the X-rays emitted, which are characteristic of specific elements.

The NIST device, an improved version of its previous microcalorimeter X-ray detector, uses a quantum-level, transition edge sensor (TES). NIST has led development of these sensors for several years. A TES works by measuring the current across a thin metal film that is held just at the knife-edge transition temperature between a superconducting state and normal conductance. A single X-ray photon striking the detector raises the temperature enough to alter the current proportional to the energy of the photon.

TES microcalorimeters offer an unequaled combination of high resolution with detection of a broad energy range, allowing identification of many different chemical elements simultaneously. The two kinds of detectors conventionally used in X-ray microanalysis typically have a resolution of no better than 130 eV, or have a high resolution but only for a very narrow range of energies. TES sensors, however, must be kept at very low temperatures (about 97 millikelvin) for hours at a stretch to collect trace-level data. Tiny changes in temperature would cause previous versions of the instrument to “drift” over time, requiring constant recalibrations. The improved temperature control system for the new detector eliminates this problem, making the system much more practical for a broad range of applications.

*T. Jach, J.A. Small and D.E. Newbury. Improving energy stability in the National Institute of Standards and Technology microcalorimeter X-ray detector. Powder Diffraction v. 20, No. 2, June 2005.

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


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New Infrared Tool Measures Silicon Wafer Thickness

A new NIST calibration system under development used infrared laser light to precisely measure the thickness of 300 millimeter silicon wafers.

A new NIST calibration system under development used infrared laser light to precisely measure the thickness of 300 millimeter silicon wafers. Changes in color within the spatial map above represent changes in wafer thickness. Green represents the average wafer thickness, while red, orange and yellow areas are thicker, and turquoise and blue areas are thinner.

Credit: Q. Wang, U. Griesmann/NIST

Click here for a high-resolution version of this image.

In the last few years, semiconductor circuit features have shrunk to sub-100 nanometer (nm) dimensions, while the size of the thin silicon wafers that these circuits are constructed on has grown from 200 millimeters (mm) to 300 mm (about 12 inches). The payoff is a higher yield of finished devices from fewer wafers.

The tough part, however, is to make wafers substantially larger while simultaneously meeting higher quality control specifications. The optics and materials for “printing” nanoscale circuit lines require that the wafers used are perfectly flat and of uniform thickness. To help the semiconductor industry meet its 2010 quality control roadmap goals, researchers at the National Institute of Standards and Technology (NIST) recently developed a new instrument that accurately measures differences in thickness across a 300 mm wafer with an excellent repeatability of 5 nm. The researchers hope the tool, with further refinements, will allow them to establish a new calibration service for “master wafers” used in the industry to measure wafer thickness.

The NIST researchers will describe the instrument, the Improved Infrared Interferometer, or IR3 for short, at a technical conference* in late July. Like all interferometers, the IR3 uses intersecting waves of light to create interference patterns, which in turn can be used as a ruler to measure nanoscale dimensions. While most interferometers use red laser light, the IR3 uses infrared laser light. And unlike visible light, these much longer wavelengths pass right through a silicon wafer. This means that IR3 can illuminate the top and bottom on a 300 mm wafer and produce a detailed spatial map of differences in thickness in one pass. Conventional tools require spinning the wafer and measuring at multiple locations.

The NIST researchers make precision measurements of the wafer’s index of refraction—the amount that light is “bent” as it passes through the silicon—as a critical step in correctly interpreting the interference patterns. Increased precision in the refractive index measurement will be necessary before “absolute” measurements of thickness rather than relative differences will be possible with the new instrument.

*Q. Wang, U. Griesmann and R. Polvani. Interferometric thickness calibration of 300 mm silicon wafers. ASPE Summer Topical Meeting on Precision Interferometric Metrology (July 20-22, 2005).

Media Contact:
Gail Porter,, (301) 975-3392


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NIST Finds Rough Spot in Surface Measurement

For makers of computers, disk drives and other sophisticated technologies, a guiding principle is the smoother the surfaces of chips and other components, the better these devices and the products, themselves, will function.

So, some manufacturers might be surprised to learn that a fast and increasingly popular method for measuring surface texture can yield misleading results. As reported at recent conferences and in an upcoming issue of Applied Optics,* a team of National Institute of Standards and Technology researchers has found that roughness measurements made with white light interferometric microscopes, introduced in the early 1990s, differed by as much as 80 percent from those obtained with two other surface-profiling methods.

Interferometric microscopes are used to measure surface heights, lengths and spaces by analyzing the interference patterns created by two light beams—one reflected by a reference specimen and the other by the object of interest.

To date, the team has evaluated a total of five white light instruments from three different vendors. They compared roughness measurements of gratings with both wavelike surfaces and random surfaces.

White light interferometers were compared with “phase shifting" interferometers, which use specialized single-color light sources, and with accurate, but sometimes destructive, stylus profiling instruments that trace a sharp probe over a surface. The latter two tools were in agreement across the spectrum of test samples within the expected measurement range of the phase shift interferometers. For measurements of relatively rough surfaces, white light interferometers also yielded results that corresponded closely. But for measurements of surfaces with an average roughness between 50 and 300 nanometers, results diverged significantly, peaking at about 100 nanometers.

“The discrepancy seems to be unrelated to the specific white light instrument used or to the randomness of the surface profile,” explains Ted Vorburger, head of NIST’s Surface and Microform Metrology Group.

The comparative study was carried out as part of an effort to develop international standards for three-dimensional measurements of surface texture. NIST researchers are now evaluating theoretical explanations for the observed discrepancies.

H.G. Rhee, T.V. Vorburger, J.W. Lee and J. Fu, Discrepancies between roughness measurements obtained with phase shifting interferometry and white-light interferometry. Applied Optics, 2005.

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

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Predicting the Lifetime of Extreme UV Optics

Extreme ultraviolet lithography (EUVL) may be the next-generation patterning technique used to produce smaller and faster microchips with feature sizes of 32 nanometers and below. However, durable projection optics must be developed before this laboratory technique can become commercially viable. As part of its long-standing effort to develop EUVL metrology and calibration services (summarized in a recent paper*), the National Institute of Standards and Technology (NIST) is creating a measurement system for accelerated lifetime testing of the mirrors used in EUVL.

The light to be used in EUVL has a wavelength of only 13 nm. It can only be efficiently reflected with mirrors consisting of 50 alternating bi-layers of molybdenum and silicon, each only 7 nm thick and deposited with near-atomic-scale precision. So although the EUVL mirrors will be very large, up to 35 centimeter (cm) in diameter, they are actually incredibly precise nanostructured devices. A single commercial lithography instrument may require six of these mirrors at a cost of more than $1 million each.

The mirrors are delicate, but the EUV radiation they must reflect is intense and damaging. The combination of this harsh radiation with the trace levels of water vapor and hydrocarbons typically found in the vacuum environment of EUV first-generation exposure tools can lead to rapid corruption of the EUVL mirror surfaces. And a loss of just 1 percent to 2 percent of a mirror’s reflectivity renders the optical system useless for efficient production of nanometer-resolution circuit features.

To help the semiconductor industry meet its goal of EUVL production by 2010, NIST has established a dedicated beamline at its Synchrotron Ultraviolet Radiation Facility for durability testing of multilayer mirrors. Initial tests established that standard mirrors topped with silicon would have lifetimes of just minutes to hours, while ruthenium-capped mirrors had lifetimes of a few tens of hours, still a thousand times less than industry’s requirement.

To determine how damage scales with various parameters, NIST researchers recently exposed EUVL mirrors (provided by SEMATECH from work it co-funded) to varying levels of light intensity, water and hydrocarbon concentrations.

Contrary to expectations, they found that increasing amounts of water vapor caused less mirror damage, which may be due to a simultaneous increase in the ambient hydrocarbon levels. Subsequent experiments have shown that deliberately introducing trace amounts of a simple hydrocarbon like methanol can mitigate significantly the water-induced damage. NIST scientists are commissioning a new beamline devoted to accelerated testing and will add a second branch to the existing beamline that will provide broadband illumination (wavelengths of approximately 11 nm to 50 nm) into a single spot at approximately 100 times the intensity of the current system.

For further information, see

*S. Grantham, S.B. Hill, C. Tarrio, R.E. Vest and T.B. Lucatorto.2005. EUV component and system characterization at NIST for the support of extreme-ultraviolet lithography. Proceedings of SPIE 5751, 1185-91.

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



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Editor: Gail Porter

Date created: 7/12/05
Date updated:7/13/05