Using Musical Chords To Analyze And Illustrate Hydrogen Molecule's Response To Laser Pulses

Daily Science Journal (Feb. 10, 2008) — For Kansas State University physics professor Uwe Thumm, confirmation of a theory about the behavior of small molecules became music to his ears -- literally. He and colleagues in Heidelberg, Germany, have shown how a hydrogen molecule responds to laser pulses by using the changing musical chord created by the molecule's vibrational motion.

Researchers in Heidelberg visualized the development over time of molecular resonance. The distance between the two nuclei (R) in the heavy hydrogen (deuterium) ion D2+ is plotted against the time. After approximately 100 femtoseconds, the wave packet, i.e. the location of the nuclei, starts to become hazy, after 400 femtoseconds there is a "revival" and the wave packet is put back together again. (Credit: Max Planck Institute for Nuclear Physics)

Thumm is a member of K-State's J.R. Macdonald Laboratory, where he is among several researchers who work on the properties and behavior of atoms and small molecules.

For decades, researchers had used the Macdonald Laboratory to make atoms and molecules collide with particles. Thumm said much of what scientists know about atoms and molecules is based on such collision experiments. To predict and explain what happens in these collisions, a large group of experimental physicists works closely with Thumm and two other theorists. The theorists use computers, make models and crunch numbers with the hope of producing results that are compatible with what experiments show.

Thanks to improvements in laser technology, around 1999 the Macdonald Laboratory researchers realized that they could transfer a lot of their expertise in atomic collisions to study in detail what happens when atoms and molecules get irradiated by very intense laser light. The new laser systems in the laboratory offer some advantages over the big particle accelerators, Thumm said. The laser pulses offer more control and can be made so short that the researchers now routinely observe the motion of nuclei inside small molecules in time. In addition, the laser pulses' peak intensity is enormous and would equal all of the sun's light focused onto a small spot of the size of a postage stamp or smaller.

Motivated by these opportunities, Thumm and his colleagues became curious about figuring out what would happen if the smallest and simplest molecule, hydrogen, were exposed to such ultra short and intense laser pulses. Together with his postdoctoral collaborator Bernold Feuerstein, Thumm developed a model and did calculations to determine how laser pulses influence the motion of the two protons in the hydrogen molecule.

"The short answer is that the laser pulse either makes the molecules vibrate more violently or blows them apart," Thumm said. He said this wasn't surprising because in the hydrogen molecule, two protons are connected by two electrons that function like a spring. When hit with the laser pulses, the protons oscillate back and forth.

Although this model may be easy to imagine on a large scale, Thumm said particles behave differently at the quantum level. This means that determining the locations of these oscillating protons isn't easy. Thumm described determining the protons' movements after being hit with the laser like what happens if you drop a marble in a bathtub. Looking at the circular ripples of water in the center of the tub, it's pretty easy to tell where the marble was dropped in. But when those ripples bounce off the sides of the tub, the wave pattern changes shape, and it becomes harder to tell where the marble was dropped. The wave gets delocalized. Thumm said the same thing happens to the protons not in a matter of seconds, but in a matter of femtoseconds -- that's a billionth of a millionth of a second. After about 60 femtoseconds, it's impossible to tell where the protons are.

"You quickly loose track of what the distance between the two protons is," Thumm said." All you can say is that they have a certain likelihood of being at a certain distance. This is in agreement with the bathtub experiment: Seconds after the marble was dropped, you can't tell where exactly it plunged in."

But things work differently at the quantum level, and the researchers were surprised that about 600 femtoseconds after being hit with the laser, the distance between the protons again becomes well defined. "We call this a revival of the original motion of the protons," Thumm said. "It's not going to happen in the bathtub, but it happens at the quantum level."

Thumm and Feuerstein published their theoretical prediction in 2003. Thumm said that they were pleasantly surprised when experiments at the Max-Planck Institute in Heidelberg, Germany, in 2006 confirmed the revival described in their model. "The agreement between the new experiments and our model was almost perfect and exceeded our expectations," Thumm said.

Feuerstein had since moved to Heidelberg, where he and his group of researchers continued to collaborate with Thumm's group at K-State. Excited about the success of their model, they began to analyze the molecule's vibrational motion by breaking it down into its various frequencies. Each frequency being like a note in a chord, the frequencies told researchers how the protons were behaving. However, the frequency of these molecular vibrations is way above the audible range. The two researchers share an interest in music and had collaborated musically before. So when it came time to illustrate the revival, they decided the best way to do it was to scale the frequencies down to 1,000 Hertz, which is in the range at which the human ear hears best. "This way you can listen to the vibrations and hear the revival. In the same way sound is analyzed and decomposed, we decomposed the vibration with regard to the frequencies," Thumm said. Their result, a changing musical chord coupled with a movie illustrating the protons' vibrations can be heard and viewed at http://www.mpg.de/video/FilmundoAudio-KdM.wmv

Thumm said researchers hope to be able to do the same thing for more complex molecules like water or methane. Just as a C Major chord sounds different from a d minor chord, Thumm said other molecules also would have their own unique sound. Thumm and Feuerstein's most recent work was first published last fall in the Physical Review Letters. Their research was supported by the National Science Foundation, the U.S. Department of Energy and the Max-Planck Society. Thumm said such basic research supports the long-term goal of applying lasers to steer chemical reactions. The hope is to largely increase the efficiency of chemical reactions by enhancing desired reaction pathways with lasers, he said.

Adapted from materials provided by Kansas State University.

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DNA Is Blueprint, Contractor And Construction Worker For New Structures

Daily Science Journal (Feb. 4, 2008) — DNA is the blueprint of all life, giving instruction and function to organisms ranging from simple one-celled bacteria to complex human beings. Now Northwestern University researchers report they have used DNA as the blueprint, contractor and construction worker to build a three-dimensional structure out of gold, a lifeless material.

Computer rendition of a structure created by using DNA to assemble nanoparticles into well-defined crystal lattices. (Credit: Northwestern University)

Using just one kind of nanoparticle (gold) the researchers built two common but very different crystalline structures by merely changing one thing -- the strands of synthesized DNA attached to the tiny gold spheres. A different DNA sequence in the strand resulted in the formation of a different crystal.

The technique, to be published in the journal Nature, and reflecting more than a decade of work, is a major and fundamental step toward building functional "designer" materials using programmable self-assembly. This "bottom-up" approach will allow scientists to take inorganic materials and build structures with specific properties for a given application, such as therapeutics, biodiagnostics, optics, electronics or catalysis

Most gems, such as diamonds, rubies and sapphires, are crystalline inorganic materials. Within each crystal structure, the atoms have precise locations, which give each material its unique properties. Diamond's renowned hardness and refractive properties are due to its structure -- the precise location of its carbon atoms.

In the Northwestern study, gold nanoparticles take the place of atoms. The novel part of the work is that the researchers use DNA to drive the assembly of the crystal. Changing the DNA strand's sequence of As, Ts, Gs and Cs changes the blueprint, and thus the shape, of the crystalline structure. The two crystals reported in Nature, both made of gold, have different properties because the particles are arranged differently.

"We are now closer to the dream of learning, as nanoscientists, how to break everything down into fundamental building blocks, which for us are nanoparticles, and reassembling them into whatever structure we want that gives us the properties needed for certain applications," said Chad A. Mirkin, one of the paper's senior authors and George B. Rathmann Professor of Chemistry in the Weinberg College of Arts and Sciences, professor of medicine and professor of materials science and engineering. In addition to Mirkin, George C. Schatz, Morrison Professor of Chemistry, directed the work.

By changing the type of DNA on the surface of the particles, the Northwestern team can get the particles to arrange differently in space. The structures that finally form are the ones that maximize DNA hybridization. DNA is the stabilizing force, the glue that holds the structure together. "These structures are a new form of matter," said Mirkin, "that would be difficult, if not impossible, to make any other way."

He likens the process to building a house. Starting with basic materials such as bricks, wood, siding, stone and shingles, a construction team can build many different types of houses out of the same building blocks. In the Northwestern work, the DNA controls where the building blocks (the gold nanoparticles) are positioned in the final crystal structure, arranging the particles in a functional way. The DNA does all the heavy lifting so the researchers don't have to.

Mirkin, Schatz and their team just used one building block, gold spheres, but as the method is further developed, a multitude of building blocks of different sizes can be used -- with different composition (gold, silver and fluorescent particles, for example) and different shapes (spheres, rods, cubes and triangles). Controlling the distance between the nanoparticles is also key to the structure's function.

"Once you get good at this you can build anything you want," said Mirkin, director of Northwestern's International Institute for Nanotechnology.

"The rules that govern self-assembly are not known, however," said Schatz, "and determining how to combine nanoparticles into interesting structures is one of the big challenges of the field."

The Northwestern researchers started with gold nanoparticles (15 nanometers in diameter) and attached double-stranded DNA to each particle with one of the strands significantly longer than the other. The single-stranded portion of this DNA serves as the "linker DNA," which seeks out a complementary single strand of DNA attached to another gold nanoparticle. The binding of the two single strands of linker DNA to each other completes the double helix, tightly binding the particles to each other.

Each gold nanoparticle has multiple strands of DNA attached to its surface so the nanoparticle is binding in many directions, resulting in a three-dimensional structure -- a crystal. One sequence of linker DNA, programmed by the researchers, results in one type of crystal structure while a different sequence of linker DNA results in a different structure.

"We even found a case where the same linker could give different structures, depending on the temperatures at which the particles were mixed," said Schatz.

Using the extremely brilliant X-rays produced by the Advanced Photon Source synchrotron at Argonne National Laboratory in combination with computational simulations, the research team imaged the crystals to determine the exact location of the particles throughout the structure. The final crystals have approximately 1 million nanoparticles.

"It took scientists decades of work to learn how to synthesize DNA," said Mirkin. "Now we've learned how to use the synthesized form outside the body to arrange lifeless matter into things that are useful, which is really quite spectacular."

The Nature paper, entitled "DNA-programmable nanoparticle crystallization" is to be published January 31, 2008. In addition to Mirkin and Schatz, other authors are Sung Yong Park, a former postdoctoral fellow in Schatz's lab and now at the University of Rochester (lead author); graduate student Abigail K. R. Lytton-Jean, Northwestern University; Byeongdu Lee, Advanced Photon Source, Argonne National Laboratory; and Steven Weigand, Northwestern's DND-CAT Synchrotron Research Center at Argonne's Advanced Photon Source.

Adapted from materials provided by Northwestern University, via EurekAlert!, a service of AAAS.

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New Nanotube Findings Give Boost To Potential Biomedical Applications

Daily Science Journal (Feb. 4, 2008) — Carbon nanotubes-cylinders so tiny that it takes 50,000 lying side by side to equal the width of a human hair-are packed with the potential to be highly accurate vehicles for administering medicines and other therapeutic agents to patients. But a dearth of data about what happens to the tubes after they discharge their medical payloads has been a major stumbling block to progress.

A representation of a carbon nanotube accessorized with a coating of branched PEG. (Credit: Courtesy of Hongjie Dai)

Now, Stanford researchers, who spent months tracking the tiny tubes inside mice, have found some answers.

Studies in mice already had shown that most nanomaterials tend to accumulate in organs such as the liver and spleen, which was a concern because no one knew how long they could linger. But fears that the tiny tubes might be piling up in vital organs, like discarded refrigerators at the bottom of a rural ravine, can now be put to rest, said Hongjie Dai, the J. G. Jackson and C. J. Wood Professor of Chemistry at Stanford, whose research team has demonstrated that the nanotubes exit the organs.

Dai and his group found that the carbon nanotubes leave the body primarily through the feces, with some by way of the urine. ''That's nice to know,'' Dai said. ''This now proves that they do get out of the system.''

The full extent of the news, which is scheduled to be published the week of Jan. 28 in Proceedings of the National Academy of Sciences Online Early Edition (PNAS), is even better than that: The three-month-long study also allays worries that the nanotubes, by simply remaining in the organs for a long time, would prove toxic to the mouse.

''None of the mice died or showed any anomaly in the blood chemistry or in the main organs,'' said Dai, senior author on the PNAS paper. ''They appear very healthy, and they are gaining weight, just like normal mice. There's no obvious toxicity observed.'' The lack of toxicity of nanotubes in mice is consistent with a previous pilot study done by Sanjiv Gambhir, a professor of radiology at Stanford, and his research group in collaboration with Dai's group.

''This is the first time anyone has done a systematic circulation and excretion study like this for nanotubes, and data on other nano particles is also scarce,'' Dai said. ''The excretion pathway may apply to other nano materials and may need to be looked at closely like this also.''

Previous research published by Dai's group has demonstrated the potential for using nanotubes in treating cancerous cells and targeting tumors in mice.

His group used Raman spectroscopy, a method of applying light from a laser beam that effectively ''illuminates'' the presence of the target molecules in the organs of the mice.

Being hit with light from the beam causes a detectable change in the state of a molecule's energy. Carbon nanotubes, composed entirely of carbon atoms that are mostly arranged in linked hexagonal rings, give off a strong signal in response to the beam. This allowed the researchers to pinpoint the position of the chosen molecules, as well as ascertain their abundance in the blood or organs.

Previous detection methods that relied on attaching fluorescent labels or spectroscopic tags to the nanotubes had yielded unreliable results. The attachments tended to either come loose from the tubes or decay over time spans ranging from a few days to only a few hours-far too short to reveal the ultimate fate of the nanotubes.

While knowing the carbon nanotubes will move through the digestive system at a healthy pace is critical to future practical applications, it is also crucial that the nanotubes not enter the digestive system too soon after being injected; they need to spend enough time in the circulatory system to find their way to their target location.

The key to fine-tuning the carbon nanotubes' speed of circulation turns on how the basic, bare-bones floor model is chemically accessorized.

''You can make the nanotubes circulate a very long time in the blood, if the chemistry is done right,'' Dai said. The researchers found that coating their carbon nanotubes with polyethylene glycol (PEG), a common ingredient in cosmetics, worked best.

They used a form of PEG with three little limbs sprouting off a central trunk. ''Those provide better shielding to the nanotube than just a single branch. Therefore, they interact less with the biological molecules around them,'' Dai said.

The team stuffed the PEG liberally into the linked hexagonal rings that compose the nanotubes, prompting Dai to describe the end result as resembling rolled-up chicken wire with feathers sticking out all over.

Though they may sound less than gorgeous visually, the feathery nanotubes turned in a beautiful performance in practical terms, Dai said. The coating of PEG made the nanotubes highly water soluble, which helped them to stay in the blood instead of being absorbed.

''They circulate in the blood for about 10 hours or so in mice, which seems to be a good length of time,'' Dai said.

The right chemical coating on nanotubes also can help ease them out of the mouse in a timely fashion, and the three-branched PEG was effective there, too.

Dai's earlier research demonstrated that nanotubes have promise for treating cancer with two different approaches. Once they have zeroed in on the target cells, shining light on the nanotubes causes them to generate heat, which can kill cancer cells. The other method is to rig the nanotubes to accumulate at targeted sites, where they can deliver medication from within the tubes.

''[Carbon nanotubes] seem to be promising for biomedical applications and for potentially treating cancer, either using drugs or using the physical properties,'' Dai said. ''This is the reason we carried out the study of the fate of nanotubes in mice. I think this is really a very fundamental issue.''

The research was funded by the Cancer Center for Nanotechnology Excellence, which is funded by the National Institutes of Health and the National Cancer Institute. The first author of the PNAS paper is Zhuang Liu, graduate student in chemistry. The paper's other authors, all affiliated with Stanford University, are Xiaoyuan ''Shawn'' Chen, assistant professor in radiology; Dr. Corrine Davis of the Veterinary Service Center in the Department of Comparative Medicine; Weibo Cai, postdoctoral scholar in radiology; and Lina He, formerly a technician in Chen's research group.

Adapted from materials provided by Stanford University.

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Swarm Approach To Photography Improves Contrast And Detail In Digital Photos

Daily Science Journal (Feb. 3, 2008) — A new approach to cleaning up digital photos and other images has been developed by researchers in the UK and Jordan. The method uses a computer algorithm known as a PSO (Particle Swarm Optimization) to intelligently boost contrast and detail in an image without distorting the underlying features.

Malik Braik and Alaa Sheta of the Department of Information Technology, at Al-Balqa Applied University, in Salt, Jordan, working with Aladdin Ayesh in the Division of Computer Engineering, at De Montfort University, Leicester, UK, explain that the Particle Swarm Optimization (PSO) algorithm represents an entirely new approach to solving all kinds of optimization problems. PSO has recently been used in computer science and electrical engineering.

The roots of the PSO algorithms lie in Swarm Intelligence paradigm which is inspired by models of living systems, artificial life (A-life) in general, and by theories of how and why birds flock, why schools of fish behave the way they do and in particular what controls swarming insects. Despite its potential it relies on only simple mathematics and does not need powerful computers to run, which means software applications based on PSO would not be limited only to academic researchers and those with access to supercomputers.

There have been several approaches to image enhancement developed by image manipulation software companies and others. However, none comes up to the standards of the kind of image enhancement often seen in fiction, where a blurry distorted image on a screen is rendered pin-sharp at the click of a mouse. PSO, however, takes image enhancement a step closer to this ideal.

PSO is based on a mathematical model of the social interactions of swarms. The algorithm treats each version of an image as an individual member of the swarm and makes a single, small adjustment to contrast levels, edge sharpness, and other image parameters. The algorithm then determines whether the new members of the swarm are better or worse than the original according to an objective fitness criterion.

"The objective of the algorithm is to maximize the total number of pixels in the edges, thus being able to visualize more details in the images," explain the researchers. Such enhancement might be useful in improving snapshots of CCTV quality for identification of individuals or vehicle number plates, it might also have application in improving images produced with lower quality cameras, such as camera phones, that are required for use in publishing or TV where image quality standards are usually higher.

The process of enhancing step by step is repeated to create a swarm of images in computer memory which have been graded relative to each other, the fittest end up at the front of the swarm until a single individual that is the most effectively enhanced.

"The obtained results using grey scale images indicate that PSO is better than other approaches in terms of the computational time and both the objective evaluation and maximization of the number of pixels in the edges of the tested images," they add.

This research was published recently in Inderscience's International Journal of Innovative Computing and Applications.

Adapted from materials provided by Inderscience Publishers, via EurekAlert!, a service of AAAS.

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Using Carbon Nanotubes To Seek And Destroy Anthrax Toxin And Other Harmful Proteins

Daily Science Journal (Dec. 13, 2007) — Researchers at Rensselaer Polytechnic Institute have developed a new way to seek out specific proteins, including dangerous proteins such as anthrax toxin, and render them harmless using nothing but light. The technique lends itself to the creation of new antibacterial and antimicrobial films to help curb the spread of germs, and also holds promise for new methods of seeking out and killing tumors in the human body.

Transmission electron microscope images show carbon nanotubes conjugated with anthrax toxin before (a, b) and after (c, d) exposure to ultraviolet light. This light caused the adsorbed toxin to deactivate and fall off the nanotube, which is why the structures in pictures c and d are smaller in diameter than those in pictures a and b. (Credit: Rensselaer/Ravi Kane)

Scientists have long been interested in wrapping proteins around carbon nanotubes, and the process is used for various applications in imaging, biosensing, and cellular delivery. But this new study at Rensselaer is the first to remotely control the activity of these conjugated nanotubes.

A team of Rensselaer researchers led by Ravi S. Kane, professor of chemical and biological engineering, has worked for nearly a year to develop a means to remotely deactivate protein-wrapped carbon nanotubes by exposing them to invisible and near-infrared light. The group demonstrated this method by successfully deactivating anthrax toxin and other proteins.

"By attaching peptides to carbon nanotubes, we gave them the ability to selectively recognize a protein of interest -- in this case anthrax toxin -- from a mixture of different proteins," Kane said. "Then, by exposing the mixture to light, we could selectively deactivate this protein without disturbing the other proteins in the mixture."

By conjugating carbon nanotubes with different peptides, this process can be easily tailored to work on other harmful proteins, Kane said. Also, employing different wavelengths of light that can pass harmlessly through the human body, the remote control process will also be able to target and deactivate specific proteins or toxins in the human body. Shining light on the conjugated carbon nanotubes creates free radicals, called reactive oxygen species. It was the presence of radicals, Kane said, that deactivated the proteins.

Kane's new method for selective nanotube-assisted protein deactivation could be used in defense, homeland security, and laboratory settings to destroy harmful toxins and pathogens. The method could also offer a new method for the targeted destruction of tumor cells. By conjugating carbon nanotubes with peptides engineered to seek out specific cancer cells, and then releasing those nanotubes into a patient, doctors may be able to use this remote protein deactivation technology as a powerful tool to prevent the spread of cancer.

Kane's team also developed a thin, clear film made of carbon nanotubes that employs this technology. This self-cleaning film may be fashioned into a coating that -- at the flip of a light switch -- could help prevent the spread of harmful bacteria, toxins, and microbes.

"The ability of these coatings to generate reactive oxygen species upon exposure to light might allow these coatings to kill any bacteria that have attached to them," Kane said. "You could use these transparent coatings on countertops, doorknobs, in hospitals or airplanes -- essentially any surface, inside or outside, that might be exposed to harmful contaminants."

Kane said he and his team will continue to hone this new technology and further explore its potential applications.

Details of the project are outlined in the article "Nanotube-Assisted Protein Deactivation" in the December issue of Nature Nanotechnology.

Co-authors of the paper include Department of Chemical and Biological Engineering graduate students Amit Joshi and Shyam Sundhar Bale; postdoctoral researcher Supriya Punyani; Rensselaer Nanotechnology Center Laboratory Manager Hoichang Yang; and professor Theodorian Borca-Tasciuc of the Department of Mechanical, Aerospace, and Nuclear Engineering.

The group has filed a patent disclosure for their new selective nanotube-assisted protein deactivation technology. The research project was funded by the U.S. National Institutes of Health and the National Science Foundation.

Adapted from materials provided by Rensselaer Polytechnic Institute, via EurekAlert!, a service of AAAS.

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