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Quantum computing? Progress in the fight against quantum dissipation

Scientists at Yale have confirmed a 50-year-old, previously untested theoretical prediction in physics and improved the energy storage time of a quantum switch by several orders of magnitude. They report their results in the April 17 issue of the journal Nature.

High-quality quantum switches are essential for the development of quantum computers and the quantum internet -- innovations that would offer vastly greater information processing power and speed than classical (digital) computers, as well as more secure information transmission.

"Fighting dissipation is one of the main goals in the development of quantum hardware," said Ioan Pop, a postdoctoral researcher in applied physics at Yale and lead author of the paper. "A quantum switch needs to act reversibly without losing any energy. Our result is very encouraging for the development of superconducting quantum bits acting as switches."

Superconducting quantum bits, or qubits, are artificial atoms that represent information in quantum systems. They also manipulate that information as they switch among states -- such as "0," "1," or both simultaneously -- under the influence of other qubits. But in switching states, they tend to lose energy, resulting in information loss.

In the Yale experiment, researchers demonstrated that a type of superconducting quantum bit can be immune to dissipation in presence of a quasiparticle -- a microscopic entity that normally saps the energy of the qubit.

"We can engineer a system that is immune to quasiparticle dissipation," Pop said.

The researchers used an artificial fluxonium atom as their qubit.

The experiment confirms by direct measurement a theoretical prediction made by Nobel Prize-winning British physicist Brian Josephson in the 1960s, namely that quasiparticle dissipation should vanish under certain conditions. Josephson junctions are superconducting devices with properties well suited for building quantum processing systems.

The results open new frontiers in areas related to quantum information and quantum measurements, the researchers said, providing both a strategy for building dissipation-immune quantum systems and a specific new device that could be adapted for better measuring properties of quasiparticles and understanding their origin and dynamics.

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The above story is based on materials provided by Yale University. The original article was written by Eric Gershon. Note: Materials may be edited for content and length.

 

Computational method dramatically speeds up estimates of gene expression

With gene expression analysis growing in importance for both basic researchers and medical practitioners, researchers at Carnegie Mellon University and the University of Maryland have developed a new computational method that dramatically speeds up estimates of gene activity from RNA sequencing (RNA-seq) data.

With the new method, dubbed Sailfish after the famously speedy fish, estimates of gene expression that previously took many hours can be completed in a few minutes, with accuracy that equals or exceeds previous methods. The researchers' report on their new method is being published online April 20 by the journal Nature Biotechnology.

Gigantic repositories of RNA-seq data now exist, making it possible to re-analyze experiments in light of new discoveries. "But 15 hours a pop really starts to add up, particularly if you want to look at 100 experiments," said Carl Kingsford, an associate professor in CMU's Lane Center for Computational Biology. "With Sailfish, we can give researchers everything they got from previous methods, but faster."

Though an organism's genetic makeup is static, the activity of individual genes varies greatly over time, making gene expression an important factor in understanding how organisms work and what occurs during disease processes. Gene activity can't be measured directly, but can be inferred by monitoring RNA, the molecules that carry information from the genes for producing proteins and other cellular activities. RNA-seq is a leading method for producing these snapshots of gene expression; in genomic medicine, it has proven particularly useful in analyzing certain cancers.

The RNA-seq process results in short sequences of RNA, called "reads." In previous methods, the RNA molecules from which they originated could be identified and measured only by painstakingly mapping these reads to their original positions in the larger molecules.

But Kingsford, working with Rob Patro, a post-doctoral researcher in the Lane Center, and Stephen M. Mount, an associate professor in Maryland's Department of Cell Biology and Molecular Genetics and its Center for Bioinformatics and Computational Biology, found that the time-consuming mapping step could be eliminated. Instead, they found they could allocate parts of the reads to different types of RNA molecules, much as if each read acted as several votes for one molecule or another.

Without the mapping step, Sailfish can complete its RNA analysis 20-30 times faster than previous methods.

This numerical approach might not be as intuitive as a map to a biologist, but it makes perfect sense to a computer scientist, Kingsford said. Moreover, the Sailfish method is more robust -- better able to tolerate errors in the reads or differences between individuals' genomes. These errors can prevent some reads from being mapped, he explained, but the Sailfish method can make use of all the RNA read "votes," which improves the method's accuracy.

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The above story is based on materials provided by Carnegie Mellon University. Note: Materials may be edited for content and length.

 

Information storage for the next generation of plastic computers: Efficient conversion from magnetic storage to light is key

Inexpensive computers, cell phones and other systems that substitute flexible plastic for silicon chips may be one step closer to reality, thanks to research published on April 16 in the journal Nature Communications.

The paper describes a new proposal by University of Iowa researchers and their colleagues at New York University for overcoming a major obstacle to the development of such plastic devices -- the large amount of energy required to read stored information.

Although it is relatively cheap and easy to encode information in light for fiber optic transmission, storing information is most efficiently done using magnetism, which ensures information will survive for years without any additional power.

"So a critical issue is how to convert information from one type to another," says Michael Flatté, professor of physics and astronomy in the College of Liberal Arts and Sciences (CLAS) and director of the UI Optical Science and Technology Center.

"Although it does not cost a lot of energy to convert one to the other in ordinary, silicon-chip-based computers, the energy cost is very high for flexible, plastic computing devices that are hoped to be used for inexpensive "throwaway" information processors.

"Here we show an efficient means of converting information encoded in magnetic storage to light in a flexible plastic device," says Flatté, who also serves as professor in the UI College of Engineering's Department of Electrical and Computer Engineering.

What Flatté and his colleagues did was to successfully accomplish information transduction (or transfer and conversion) between a magnet and an organic light-emitting diode at room temperature and without electrical current flow between the magnet and the organic device.

"The magnetic fields from the magnetic storage device directly modify the light emission from the device. This could help solve problems of storage and communication for new types of inexpensive, low-power computers based on conducting plastics," says professor Markus Wohlgenannt, also of the Department of Physics and Astronomy and the Optical Science and Technology Center.

Professor Andrew Kent of New York University notes that while these studies were conducted on relatively large devices, miniaturized devices would operate on the same principles and enable new types of high capacity storage technologies.

In addition to Flatté, Wohlgenannt and Kent, co-authors of the Nature Communications paper are Fujian Wang and Nicolas J. Harmon of the UI Department of Physics and Astronomy and Optical Science and Technology Center, and Ferran Macià of the NYU Department of Physics. The complete title of the paper is "Organic Magnetoelectroluminescence for Room Temperature Transduction between Magnetic and Optical Information."

The research was funded by the U.S. Army Research Office (ARO) Multidisciplinary University Research Initiative (MURI) grant #W911NF-08-1-0317 and F. Macià also by EC-MC grant IOF-253214.

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The above story is based on materials provided by University of Iowa. The original article was written by Gary Galluzzo. Note: Materials may be edited for content and length.

   

Computer simulations help predict effective drug candidates

Using computer simulations to predict which drug candidates offer the greatest potential has thus far not been very reliable, because both small drug-like molecules and the amino acids of proteins vary so much in their chemistry. Uppsala researchers have now cunningly managed to develop a method that has proven to be precise, reliable and general.

The largest class of human target proteins for drugs are the so-called G-protein-coupled receptors. They are targets for about 40 per cent of all drugs on the market. These receptors are found in the cell membrane and handle the communication between the outside and the inside. When they react to external stimuli, by binding molecules, for example, a structural transformation takes place on the inside that triggers a signalling cascade (see 2012 Nobel Prize in Chemistry).

"In this way these receptors regulate our senses of smell, taste and vision as well as a number of other conditions and feelings," explains Professor Johan Åqvist, who directed the study, which is now being published in the journal PLoS Computational Biology.

Of the roughly 900 G-linked-protein receptors in humans, today we know the three-dimensional molecular structure of only about twenty. It is important to know this molecular structure when drugs are developed.

The method used today to understand how the receptors function is complicated and time-consuming. First the binding strength of series of molecules is measured (the binding of so-called agonists and antagonists). Then mutations are induced in the receptors in order to see how the binding properties are affected.

"This is both time-consuming and often difficult, because the genetically modified receptors have to be expressed in living cells. With our computational method, the mutation can be created in the computer, and the effect on receptor binding can be calculated with great precision," says Johan Åqvist.

The problem with this type of computer simulation has previously been that the amino acids of the proteins are so different, in terms of size, electrical charge, etc., which has presented problems in the calculations. But when the researchers divided the procedure into a long series of smaller computations, something happened -- suddenly they were getting exact and stable results.

The method has now been tested on a neuropeptide receptor and has been shown to be able to predict with great reliability both the effects of mutations and the receptor's ability to bind a series of different molecules. The method also makes it possible to determine whether a three-dimensional structural model of the molecules that are bound to each other is correct.

"The results are brilliant. We believe this has the potential to be extremely useful in drug research. It quite simply makes it easier and faster to find candidates for new drugs. The computational method is also so general that it can be used to study all sorts of other proteins bound to various types of functional molecules," says Johan Åqvist.

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The above story is based on materials provided by Uppsala University. The original article was written by Anneli Waara. Note: Materials may be edited for content and length.

 

Key to enjoying massive online photo files may be giving up some control

The ability of individuals to store and instantly access thousands of their photos online has become a commonplace luxury, but the sheer size of these archives can be intimidating. Researchers at Carnegie Mellon University and Microsoft Research Cambridge, UK, have found people might actually enjoy their collections more by giving up a bit of control and learning to wait.

Their 14-month study showed that people reflected more on past events and developed a renewed interest in their online photos when a device called Photobox would randomly print four or five of those photos at varying intervals each month. Though the study involved just a handful of households, the researchers said their findings suggest that, in a world where technology is always on, people sometimes find value in taking it slow.

"We have all these devices -- smartphones, touchpads, televisions -- that are always competing for our attention," said Will Odom, a Ph.D. student in Carnegie Mellon's Human-Computer Interaction Institute who interned at Microsoft Research, Cambridge. "People who had Photobox in their homes came to appreciate the usefulness of a technology that is in the background."

Odom and his collaborators, including researchers at the University of Nottingham and Newcastle University, will present their findings April 29 at the CHI Conference on Human Factors in Computing Systems in Toronto.

Thanks to ubiquitous cellphone cameras, people today take more photos than ever and online sites such as Flickr allow people to store photos without space constraints.

Consequently, many people have amassed gigantic collections. But Odom notes that the size of these collections and the fact that most photos are never made into physical prints often means that people interact very little with these photos. Out of sight, out of mind.

Photobox, which was developed by Microsoft Research Cambridge, is designed to re-engage people with their own photos.

"Rather than allowing these large collections of images to stay hidden away, this device explores the use of serendipity as one approach to delighting people, while also making their images a regular part of their everyday life," said Richard Banks, principal design manager at Microsoft Research Cambridge.

Photobox is a Bluetooth-enabled printer housed inside an antique oak chest. Four or five times each month, it makes 2x3-inch prints of an image randomly selected from the user's Flickr account. Users discover the photos by opening the chest's lid.

"Most technology is all about control," Odom noted. "But in this case, the owner never really knows what photo is going to print or when it is going to print."

A CMU research team -- including Jodi Forlizzi and John Zimmerman, both associate professors of human-computer interaction and of design -- installed Photoboxes in three households of varying sizes and makeup. For the first few months, most of the users encountered some frustration with this concept of slow technology and indicated they would prefer to speed up the printing process. But after a period of adjustment, "people tended to like it," Odom said.

In one household with several roommates, for instance, the photos became a subject of discussion. "We were all a little curious … wondering who might be in the next photo," one roommate remarked. "Sometimes we'd all be here and looking at the photos and asking (the Flickr account holder) about them. Like, why one of us was in one but someone else wasn't."

"Overall it's been an interesting experience," agreed the account holder. "We'd never be sitting around my tiny laptop laughing about my photos like we did."

The researchers were surprised to the extent that Photobox led the users to reconsider their relationships with other technology. One person, for instance, decided to take a break from Facebook after the slower pace of Photobox demonstrated that clicking through life was not necessarily the best way to live.

"By subverting people's control over technology and designing it to 'behave' in a much slower way, we opened them up to thinking about technology in their lives and what it might be doing to their relationships," Odom said.

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The above story is based on materials provided by Carnegie Mellon University. Note: Materials may be edited for content and length.

   

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