Nanotechnology
DNA In Another Dimension
3-D construction technique creates a wealth of structures
Bethany Halford

USING DNA as a basic chemical building block rather than a genetic molecule, scientists have devised a method for creating complex three-dimensional nanostructures with precisely controlled dimensions that range from 10 to 100 nm (Nature 2009, 459, 414). The strategy of self-assembly could provide a general route for manufacturing sophisticated devices with nanoscale features, the researchers say.

The technique, developed by William M. Shih of Boston's Dana-Farber Cancer Institute and colleagues, is an extension of DNA origami, in which hundreds of short oligonucleotides fasten to a long single strand of DNA in such a way that it folds into a predetermined shape (C&EN, March 20, 2006, page 10). Researchers have already used the technique to create 2-D snowflakes and smiley faces, as well as a 3-D DNA box (C&EN, May 11, page 30). Shih's strategy allows nanotechnologists to build a vast diversity of 3-D DNA structures, a capability his group demonstrated by constructing a tiny railed bridge, a genie bottle, and an icosahedron.

Shih's team designs the structures by computationally "carving" them out of a honeycomb lattice made of a DNA double helix. Using computer-aided design, they arrange a single strand of DNA so that it winds around that carved structure and then determine what short oligonucleotides are required to hold it in place.

"The challenge was actually getting it to work," Shih tells C&EN, because DNA is negatively charged, and repulsive forces tend to keep it from packing into the compact sculptures. "We didn't know what kind of tricks we would need to get it to fold correctly," he says. Ultimately, patience proved to be one of the tricks. Although most 2-D DNA origami structures fold within an hour, Shih's 3-D sculptures take about a week to fold.

"This successful move into three dimensions heralds a new era for the field of structural DNA technology," writes Duke University chemistry professor Thomas H. LaBean in a commentary that accompanies the paper. "Through the ages, some of the most iconic and lasting artifacts of human ingenuity have been sculptures and carvings, created from a wide variety of materials. But until now, a general purpose material from which nanometer-scale, three-dimensional shapes could be made has been lacking."


Source :http://pubs.acs.org/cen/news/87/i21/8721notw6.html

Quantum Dots That Don't Blink
Core structure suppresses blinking and leads to unusual spectral behavior
Celia Henry Arnaud

A team of scientists has synthesized semiconductor nanocrystals, or quantum dots, that are "nonblinking," in that they emit light steadily. Such behavior has long been a goal of scientists working with quantum dots and should improve the usefulness of the nanocrystals for biological labeling applications by increasing the number of photons the particles emit.


Ted Palwicki
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NO BLINKING Quantum dots with a gradient core emit continuously and at multiple wavelengths.Blinking is a hallmark of fluorescent single molecules and nanometer-scale crystals; it occurs because the luminescence intermittently turns off even with continuous excitation. Excited quantum dots get rid of their extra energy through radiative processes—by emitting light—or nonradiative processes. "When the dot blinks off, nonradiative processes are winning," says team leader Todd D. Krauss, associate professor of chemistry at the University of Rochester. In quantum dots, this blinking is thought to be the result of extra charges that enhance nonradiative decay.

Krauss's team eliminates the blinking by making quantum dots whose compositions gradually change from the center to the shell (Nature, DOI: 10.1038/nature08072). They layer ZnSe on top of a CdSe core, anneal the layers, and deposit additional ZnSe around it. The process generates a ternary core with a radial composition gradient that smooths the particle's potential energy function and makes nonradiative processes less efficient.

However, the nonblinking comes with unusual spectral behavior. Quantum dots usually have a single, sharp emission peak. The new quantum dots, in contrast, have multiple peaks in their emission spectra. Multiple peaks might mean emission spectra of different quantum dots will overlap, which could complicate their use as biological sensors. The extra peaks come from part of the quantum dots' excitation energy being emitted as photons at longer wavelengths. In addition, the time the unblinking quantum dots stay in their excited state before emitting a photon is much shorter than that of traditional CdSe nanocrystals.

Krauss and coworkers, including Alexander L. Efros of the Naval Research Laboratory, posit that both the suppressed blinking and the unusual spectral characteristics can be explained by the lower efficiency nonradiative processes caused by the composition gradient. "Nonradiative processes become efficient only when you have very sharply defined potential barriers," Krauss says, and the gradient rounds off the corners of the potential energy function. Krauss plans to test their model of quantum dot behavior by varying the materials and sizes of nonblinking quantum dots.

Jennifer Hollingsworth, a chemist at Los Alamos National Laboratory who also is developing nonblinking quantum dots, comments that the work by Krauss and coworkers is "certainly an interesting addition" to earlier studies by two groups, including hers, that reported having significantly suppressed but not completely eliminated blinking in semiconductor nanocrystals. "It will be important to see whether they will be able to extend this approach to other systems and whether this thin-shell motif will hold up to processing."

Source: http://pubs.acs.org/cen/news/87/i20/8720news4.html

The Kilogram Isn't What It Used to Be—It's Lighter

by Dava Sobel
From the March 2009 issue, published online March 8, 2009


iStockphoto
Sèvres Cedex, France—What I love best about the kilogram is its tangibility, its solid, sculpted form of shiny platinum and iridium. I’m referring to not just any kilogram but the quintessential one that resides here—the actual International Prototype Kilogram, or IPK, created in 1879 as the official standard of mass. It’s a smooth cylinder of alloy, only an inch and a half high and an inch and a half in diameter. Though petite, the IPK is necessarily dense; it weighs 2.2046 pounds. If you went to pick it up, you might think someone had cemented it to the tabletop for a prank. Even if you knew what to expect, its compact heft would still boggle your senses.

Of course, they won’t let you pick it up. They won’t even let you anywhere near it. If you touched it—if you so much as breathed on it—you would change its mass, and then where would we be? That’s why the IPK leads such a sheltered life. It is kept under a triple bell jar inside a temperature- and humidity-controlled vault in a secure room within the Parc de Saint-Cloud enclave of the International Bureau of Weights and Measures, or BIPM (Bureau International des Poids et Mesures). Thus protected, it reigns over a world’s worth of measurement. Every hill of beans, every lump of coal, every milligram of medication—in short, every quantity of any substance that can be weighed—must be gauged against this object.

The IPK is, in and of itself, the International System of Units’ definition of mass. Through a complex dissemination protocol, the essence of the kilogram is transferred from the IPK to its counterparts at standards laboratories around the world, and from there to centers of industry and scientific research, ending up in grocery stores, post offices, and bathrooms everywhere.


Although I have come to pay my re-spects to the IPK, I am denied even a glimpse of the thing. Nor can I see one of its six official copies, for these reside alongside the prototype in guarded seclusion. I must content myself with replicas —with the working standards that fill the ultraclean laboratory of Richard Davis, an American physicist in Paris who for the past 15 years has headed the Mass Section at the BIPM.

Gloved for work, Davis wears a lab coat over his street clothes, blue paper bootees over his shoes, and a net over his hair. Around him kilogram weights of various shapes and materials sit on colored plates under glass bell jars, like an assortment of fine cheeses. They have been delivered here from other countries to be reckoned in comparison with the IPK.

“That one belongs to Ireland,” Davis says, indicating a stainless-steel kilogram on a red dish. Member states—signatories to the Meter Convention—pay dues to the BIPM that cover the cost of periodic checks on their national reference standards.

It takes a minimum of four days to calibrate a single kilogram according to the BIPM’s cautious regimen of repeated comparison weighings. Visiting kilograms could theoretically go home after a week, but they typically stay in the lab for months, allowing the time it takes them to become thermally stable in their new surroundings, undergo cleaning by the BIPM method, and prove themselves, through repeated trials, to be worthy ambassadors of mass. Given the uncertainty, however minuscule, in every measurement, such repetitions are essential before these national standards can leave with a calibration certificate stating how they compare with the IPK, along with a precise correction factor.

En route to or from Paris, the visiting kilograms disdain ordinary transport. Zeina Jabbour, group leader of Mass & Force at the National Institute of Standards and Technology in Gaithersburg, Maryland, recently brought two of the four U.S. kilograms here for calibration. She carried one herself in a specially designed case inside a padded camera bag that was all but handcuffed to her wrist, and she entrusted the other to a colleague who flew on a different plane. (“That way, if something happened to one of us.”) Soon after her flight touched down at Charles de Gaulle, she grabbed a taxi straight to the BIPM on the other side of the city for a handover directly to Davis.

Before picking up a kilogram with a pair of widemouthed forceps called lifters, Davis flicks off suspected specks of dust with a fine-tipped brush. (“My wife paints.”) He has modified the artist’s brush for his purposes by degreasing its fibers and covering its metal ferrule with plastic, “so if you accidentally hit the kilogram, you won’t scratch it.” On a balance precise to 10 decimal places, a scratch counts.

Davis tests the Irish kilogram in a sealed chamber against three BIPM working standards that are also made of stainless steel. He doesn’t weigh it against the platinum-iridium standard, since stainless weights are only one-third as dense, and therefore three times as large, displacing a much greater quantity of air. “You’d have to make an air buoyancy correction that would amount to almost a tenth of a gram,” he explains. “That is huge.”

Although Davis serves as the IPK’s official guardian, even he rarely sees the original prototype, which is too precious and vulnerable to damage to remain in constant use. Over the course of its century-plus lifetime, the IPK has emerged only three times to serve “campaigns” of active duty, most recently in 1988–1992, when it participated in a formal verification of all kilogram prototypes belonging to the 51 Meter Convention member states. On that occasion, however, the IPK itself was found wanting. Despite all the protective protocols and delicate procedures, it had mysteriously changed. No one can say whether the IPK has lost weight (perhaps by the gradual escape of gases trapped inside it from the start) or if most of the prototypes have gained (possibly by accumulating atmospheric contaminants). The difference is approximately 30 micrograms —30 billionths of a kilogram—in a hundred years. (Imagine 30 cents out of a $10 million stack of pennies.)


Source: http://discovermagazine.com/2009/mar/08-kilogram-isn.t-what-it-used-to-be-it.s-lighter

WHAT IS WEB 2.0?
by Daniel Lewis

Web 2.0 is what the Web is turning into. It is a revolutionary step forward, including not just what Web sites look like, but methods of interaction, styles of development, and sources of content. This article discusses the Web 2.0 concept and characteristics.

One of the main ideas behind Web 2.0 is usability. Web 2.0 applications tend to look more like desktop applications than Web pages: they have simple interfaces with plain colors and no busy patterns, logos, or animation. Moreover, they provide a richness of interaction previously found only in desktop applications. How is this possible? It's not just talented graphic artists, but perhaps how the applications are developed...

Web 2.0 systems are developed by creative programmers using development frameworks such as Ruby On Rails (for the Ruby programming language) and Django (for the Python programming language), or families of technologies like AJAX. The developers favor dynamic languages because they enable fast development, debugging, and deployment. Compare this to compiled, static languages, which tend to require more time to develop and are more complex to deploy. Dynamic programming languages also allow data and information to flow through the Web system easily, providing dynamic content.

Dynamic content is another important force behind Web 2.0. Information can be gathered from multiple sources in real time and assembled on a single Web page. But where does the information come from? Often users of a site create the content themselves. This comes in many forms, including:

Blogging, or Web logging, which is like an online diary or news feed.
Syndication, a concept similar to blogging except that information does not need to be viewed on a Web page.
Resource sharing, which allows users to share their favorite Web links and other resources using descriptive words called tags. Example systems include del.icio.us and bibsonomy.org.
Similarly, topical information sharing is an open, collaborative approach to content generation that is typical of Web 2.0. The quintessential example of a topical information sharing system is the wiki (pronounced "wick-ee"). Wikis at first glance look like standard Web pages, but if you look carefully, you see that it is possible for any user to edit these pages. The most famous wiki is Wikipedia, an online encyclopedia that anyone can edit or add to.

Tim O'Reilly, the originator of the Web 2.0 concept, gives examples of Web 1.0 systems and ideas versus Web 2.0 systems and ideas [3]:

Web 1.0 Web 2.0
DoubleClick Google AdSense
Ofoto Flickr
Akamai BitTorrent
mp3.com Napster
Britannica Online Wikipedia
personal websites blogging
Evite upcoming.org and EVDB
domain name speculation search engine optimization
page views cost per click
screen scraping Web services
publishing participation
content management systems wikis
directories (taxonomy) tagging ("folksonomy")
stickiness syndication

As Web 2.0 systems emerge and develop, they are bringing desktop programs to the Web, to the point that desktop applications may be replaced by the Internet browser . We can already replace Word with Writely.com and Excel with Google Spreadsheet. We may eventually be able to replace Photoshop or GIMP with Pixoh.com.

There are a few potential problems to look out for though, as Web 2.0 takes shape. Chief among these is the loss of structure that could occur if Web developers focus exclusively on presenting data in human-oriented formats. The data can become messy and unreadable for machine users, hiding important or interesting information and making automation of tasks difficult. But the sheer numbers of Web 2.0 services already available show that it is time to upgrade the system.

For further detail and discussion, Paul Graham presents an interesting review of the technology [2]. There is also a Web 2.0 site that checks to see if other websites could be claimed as Web 2.0 [1]. Or check out an alternative view of Web 2.0 and its possible successor in [4].


Source: http://www.acm.org/crossroads/xrds13-1/web20.html

New Molecules In Space
Discovery of two complex compounds hints at more chemical diversity lurking in space
Steve Ritter

AN INTERNATIONAL research team has peered into a gaseous cloud at the heart of the Milky Way galaxy and detected ethyl formate and n-propyl cyanide, two of the most complex organic molecules ever observed outside our solar system. On the basis of spectroscopic evidence and computer models of how the molecules were formed, the scientists believe that molecules with even greater chemical complexity are waiting to be discovered in space.

One of those molecules is glycine, the simplest amino acid, which has eluded detection thus far. Glycine is similar in size and complexity to the two new compounds, and its presence would help confirm suspicions that prebiotic chemistry exists beyond our solar system.

Team member Robin T. Garrod, an astrochemist at Cornell University, announced the discovery on behalf of the team on April 21 during the European Week of Astronomy & Space Science at the University of Hertfordshire, in England. The study is also being reported in the journal Astronomy & Astrophysics (DOI: 10.1051/0004-6361/200811550).

Commenting on the discovery, astrochemist Steven B. Charnley of NASA's Goddard Space Flight Center, in Greenbelt, Md., tells C&EN that detecting these compounds should help shed new light on how complex molecules are formed in space and "gives impetus to future searches for higher amino acids, as well as for nucleobases and their heterocyclic precursors."

The researchers used millimeter-wavelength spectroscopy to study a dense cloud of gas and icy dust particles in the star-forming region Sagittarius B2. This particular spot in the universe has been a treasure trove of many different types of small organic molecules (C&EN, June 16, 2008, page 58). Even so, detecting ethyl formate and n-propyl cyanide was difficult for the scientists because the 36 spectral lines they assigned to the two compounds were hidden in a forest of 3,700 overlapping spectral lines from the many molecules detected.

The study supports the idea that larger and more complex molecules like ethyl formate and n-propyl cyanide form stepwise on the surface of dust grains by tacking a functional group onto a building block formed from an existing molecule, rather than by adding atoms sequentially, Garrod says. This process appears to be limitless, "so there's good reason to expect even more complex organic molecules to be out there, if we can detect them," he adds


Source: http://pubs.acs.org/cen/news/87/i17/8717notw3.html