Researchers create living human gut-on-a-chip

Building on the Wyss Institute's breakthrough "Organ-on-Chip" technology that uses microfabrication techniques to build living organ mimics, the gut-on-a-chip is a silicon polymer device about the size of a computer memory stick. Wyss Founding Director, Donald Ingber, M.D., Ph.D., led the research team, which included Postdoctoral Fellow, Hyun Jung Kim, Ph.D; Technology Development Fellow, Dan Huh, Ph.D.; and Senior Staff Scientist, Geraldine Hamilton, Ph.D. Ingber is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and the Vascular Biology Program at Children's Hospital Boston, and Professor of Bioengineering at Harvard's School of Engineering and Applied Sciences.

The new device mimics complex 3D features of the intestine in a miniaturized form. Inside a central chamber, a single layer of human intestinal epithelial cells grows on a flexible, porous membrane, recreating the intestinal barrier. The membrane attaches to side walls that stretch and recoil with the aid of an attached vacuum controller. This cyclic mechanical deformation mimics the wave-like peristaltic motions that move food along the digestive tract. The design also recapitulates the intestinal tissue-tissue interface, which allows fluids to flow above and below the intestinal cell layer, mimicking the luminal microenvironment on one side of the device and the flow of blood through capillary vessels on the other.

In addition, the researchers were able to grow and sustain common intestinal microbes on the surface of the cultured intestinal cells, thereby simulating some of the physiological features important to understanding many diseases. These combined capabilities suggest that gut-on-a-chip has the potential to become a valuable in vitro diagnostic tool to better understand the cause and progression of a variety of intestinal disorders and to help develop safe and effective new therapeutics, as well as probiotics. The gut-on-a-chip could also be used to test the metabolism and oral absorption of drugs and nutrients.

"Because the models most often available to us today do not recapitulate human disease, we can't fully understand the mechanisms behind many intestinal disorders, which means that the drugs and therapies we validate in animal models often fail to be effective when tested in humans," said Ingber. "Having better, more accurate in vitro disease models, such as the gut-on-a-chip, can therefore significantly accelerate our ability to develop effective new drugs that will help people who suffer from these disorders."

Gut-on-a-chip represents the most recent advance in the Wyss Institute's portfolio of engineered organ models. The platform technology was first reported on in Science in June 2010, where a living, breathing, human lung-on-a-chip was described. That same year, the Wyss received funding from the National Institutes of Health and the U.S. Food and Drug Administration to develop a heart-lung micromachine to test the safety and efficacy of inhaled drugs on the integrated heart and lung function. In September 2011, the Wyss was awarded a four-year grant from the Defense Advanced Research Projects Agency to develop a spleen-on-a-chip to treat sepsis, a commonly fatal bloodstream infection.

Provided by Harvard University (news : web)

Researchers discover a new path for light through metal

Helping bridge the gap between photonics and electronics, researchers from Purdue University have coaxed a thin film of titanium nitride into transporting plasmons, tiny electron excitations coupled to light that can direct and manipulate optical signals on the nanoscale. Titanium nitride's addition to the short list of surface-plasmon-supporting materials, formerly composed only of metals, could point the way to a new class of optoelectronic devices with unprecedented speed and efficiency.

"We have found that titanium nitride is a promising candidate for an entirely new class of technologies based on plasmonics and metamaterials," said Alexandra Boltasseva, a researcher at Purdue and an author on a paper published March 27 in the Optical Society's (OSA) open-access journal Optical Materials Express. "This is particularly compelling because surface plasmons resolve a basic mismatch between wavelength-scale optical devices and the much smaller components of integrated electronic circuits."

Value of Plasmons

Metals carry electricity with ease, but normally do nothing to transmit light waves. Surface plasmons, unusual light-coupled oscillations that form on the surface of metallic materials, are the exception to that rule. When excited on the surface of metals by light waves of specific frequencies, plasmons are able to retain that same frequency, but with wavelengths that are orders-of-magnitude smaller, cramming visible and near-infrared light into the realm of the nanoscale.

In the world of electronics and optics, that 100-fold contraction is a boon. Circuits that direct the paths of electrons operate on a much smaller scale than optical light waves, so engineers must either rely on small but relatively sluggish electrons for information processing or bulk up to accommodate the zippy photons. Plasmons represent the best of both worlds and are already at the heart of a number of optoelectronic devices. They have not had widespread use, however, due to the dearth of materials that readily generate them and the fact that metals, in most cases, cannot be integrated with semiconductor devices.

Plasmonic Materials

Until now, the best candidates for plasmonic materials were gold and silver. These noble metals, however, are not compatible with standard silicon manufacturing technologies, limiting their use in commercial products. Silver is the metal with the best optical and surface plasmon properties, but it forms grainy, or semi-continuous, thin films. Silver also easily degrades in air, which causes loss of optical signal, making it a less-attractive material in plasmon technologies.

In an effort to overcome these drawbacks, Boltasseva and her team chose to study titanium nitride- a ceramic material that is commonly used as a barrier metal in microelectronics and to coat metal surfaces such as medical implants or machine tooling parts- because they could manipulate its properties in the manufacturing process. It also could be easily integrated into silicon products, and grown crystal-by-crystal, forming highly uniform, ultrathin films- properties that metals do not share.

To test its plasmonic capabilities, the researchers deposited a very thin, very even film of titanium nitride on a sapphire surface. They were able to confirm that titanium nitride supported the propagation of surface plasmons almost as efficiently as gold. Silver, under perfect conditions, was still more efficient for plasmonic applications, but its acknowledged signal loss limited its practical applications.

To further improve the performance of titanium nitride, the researchers are now looking into a manufacturing method known as molecular beam epitaxy, which would enable them to grow the films and layered structures known as superlattices crystal-by-crystal.

Technologies and Potential Applications

In addition to plasmonics, the researchers also speculate that titanium nitride may have applications in metamaterials, which are engineered materials that can be tailored for almost any application because of their extraordinary response to electromagnetic, acoustic, and thermal waves. Recently proposed applications of metamaterials include invisibility cloaks, optical black holes, nanoscale optics, data storage, and quantum information processing.

The search for alternatives to noble metals with improved optical properties, easier fabrication and integration capabilities could ultimately lead to real-life applications for plasmonics and metamaterials.

"Plasmonics is an important technology for nanoscale optical circuits, sensing, and data storage because it can focus light down to nanoscale," notes Boltasseva. "Titanium nitride is a promising candidate in the near-infrared and visible wavelength ranges. Unlike gold and silver, titanium nitride is compatible with standard semiconductor manufacturing technology and provides many advantages in its nanofabrication and integration."

According to the researchers, titanium nitride-based devices could provide nearly the same performance for some plasmonic applications. While noble metals like silver would still be the best choice for specific applications like negative index metamaterials, titanium nitride could outperform noble metals in other metamaterial and transformation optics devices, such as those based on hyperbolic metamaterials.

Story Source:

The above story is reprinted from materials provided by Optical Society of America.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Gururaj V. Naik, Jeremy L. Schroeder, Xingjie Ni, Alexander V. Kildishev, Timothy D. Sands, Alexandra Boltasseva. Titanium nitride as a plasmonic material for visible and near-infrared wavelengths. Optical Materials Express, 2012; 2 (4): 478 DOI: 10.1364/OME.2.000478

Researchers create more efficient hydrogen fuel cells

 Hydrogen fuel cells, like those found in some "green" vehicles, have a lot of promise as an alternative fuel source, but making them practical on a large scale requires them to be more efficient and cost effective.

A research team from the University of Central Florida may have found a way around both hurdles.

The majority of hydrogen fuel cells use catalysts made of a rare and expensive metal -- platinum. There are few alternatives because most elements can't endure the fuel cell's highly acidic solvents present in the reaction that converts hydrogen's chemical energy into electrical power. Only four elements can resist the corrosive process -- platinum, iridium, gold and palladium. The first two are rare and expensive, which makes them impractical for large-scale use. The other two don't do well with the chemical reaction.

UCF Professor Sergey Stolbov and postdoctoral research associate Marisol Alcántara Ortigoza focused on making gold and palladium better suited for the reaction.

They created a sandwich-like structure that layers cheaper and more abundant elements with gold and palladium and other elements to make it more effective.

The outer monoatomic layer (the top of the sandwich) is either palladium or gold. Below it is a layer that works to enhance the energy conversion rate but also acts to protect the catalyst from the acidic environment. These two layers reside on the bottom slice of the sandwich -- an inexpensive substrate (tungsten), which also plays a role in the stability of the catalyst.

"We are very encouraged by our first attempts that suggest that we can create two cost-effective and highly active palladium- and gold-based catalysts -for hydrogen fuel cells, a clean and renewable energy source," Stolbov said.

Stolbov's work was recently published in The Journal of Physical Chemistry Letters.

By creating these structures, more energy is converted, and because the more expensive and rare metals are not used, the cost could be significantly less.

Stolbov said experiments are needed to test their predictions, but he says the approach is quite reliable. He's already working with a group within the U.S. Department of Energy to determine whether the results can be duplicated and have potential for large-scale application.

If a way could be found to make hydrogen fuel cells practical and cost effective, vehicles that run on gasoline and contribute to the destruction of the ozone layer could become a thing of the past.

Story Source:

The above story is reprinted from materials provided by University of Central Florida.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Sergey Stolbov, Marisol Alcántara Ortigoza. Rational Design of Competitive Electrocatalysts for Hydrogen Fuel Cells. The Journal of Physical Chemistry Letters, 2012; 3 (4): 463 DOI: 10.1021/jz201551e

Researchers create more efficient hydrogen fuel cells

A research team from the University of Central Florida may have found a way around both hurdles.

The majority of hydrogen fuel cells use catalysts made of a rare and expensive metal – platinum. There are few alternatives because most elements can't endure the fuel cell's highly acidic solvents present in the reaction that converts hydrogen's chemical energy into electrical power. Only four elements can resist the corrosive process – platinum, iridium, gold and palladium. The first two are rare and expensive, which makes them impractical for large-scale use. The other two don't do well with the chemical reaction.

UCF Professor Sergey Stolbov and postdoctoral research associate Marisol Alcántara Ortigoza focused on making gold and palladium better suited for the reaction.

They created a sandwich-like structure that layers cheaper and more abundant elements with gold and palladium and other elements to make it more effective.

The outer monoatomic layer (the top of the sandwich) is either palladium or gold. Below it is a layer that works to enhance the energy conversion rate but also acts to protect the catalyst from the acidic environment. These two layers reside on the bottom slice of the sandwich -- an inexpensive substrate (tungsten), which also plays a role in the stability of the catalyst.

"We are very encouraged by our first attempts that suggest that we can create two cost-effective and highly active palladium- and gold-based catalysts –for hydrogen fuel cells, a clean and renewable energy source," Stolbov said.

Stolbov's work was recently published in the Journal of Physical Chemistry Letters.

By creating these structures, more energy is converted, and because the more expensive and rare metals are not used, the cost could be significantly less.

Stolbov said experiments are needed to test their predictions, but he says the approach is quite reliable. He's already working with a group within the U.S. Department of Energy to determine whether the results can be duplicated and have potential for large-scale application.

If a way could be found to make hydrogen fuel cells practical and cost effective, vehicles that run on gasoline and contribute to the destruction of the ozone layer could become a thing of the past.

Stolbov joined UCF's physics department in 2006. Before that he was a research assistant professor at Kansas State University. He earned multiple degrees in physics from Rostov State University in Russia and was a Postdoctoral Fellow at the Carnegie Institution of Washington, D.C. He is a frequent international speaker and has written dozens of articles on physics.

Provided by University of Central Florida (news : web)

Researchers devise simple, inexpensive approach to making soft magnetic films for microwave applications

Developers tend to use thin films of soft magnetic materials, as opposed to their bulk form, in mobile applications, such as cell phones and laptops, as well as military applications, such as stealth aircrafts. However, the conventional approach to making soft magnetic films requires a high vacuum environment, which is expensive and time-consuming. Moreover, the usual fabrication system is not suitable for the preparation of large sheet films, thereby limiting its application in manufacturing the soft magnetic materials for microwave absorption.

Bao-Yu Zong at the A*STAR Data Storage Institute and co-workers have now demonstrated the viability of fabricating soft magnetic thin films through electrodeposition, a plating technique that is scalable and can be performed at room temperature. The approach is not only simpler and cheaper to operate, but also versatile enough for making a wide range of soft magnetic materials for microwave applications.

The researchers chose to work with iron–cobalt–nickel alloy, a soft magnetic material with low permeability, high coercivity and other less-than-ideal properties. They added small amounts of organic compounds, including dimethylamine borane and sodium dodecyl sulfate, to the plating solution prior to deposition. The resulting thin films had much higher permeability and lower coercivity, which make them more desirable for microwave applications. The researchers suggest that the additives might have prevented iron from oxidizing during electrodeposition, thereby improving the quality of thin films obtained.

Zong and his team also explored the effect of adding inorganic compounds, such as aluminum potassium sulfate, to the plating solution. They detected an increased resistivity in the thin films — a result that is likely to be a consequence of the change in morphology of the material; that is, the shape of the nanoparticles changed from common granular to columnar (see image), as revealed by atomic force microscopy. The iron–cobalt–nickel thin films also exhibit strong microwave absorption in comparison to ordinary magnetic films. These unique properties are perfect for high-frequency microwave applications, including magnetic data storage, portable wireless and biotechnology devices.

The researchers have high hopes that their approach is applicable to the fabrication of a wide range of soft magnetic materials. "Our technique is cost-effective and scalable. We can create soft magnetic thin films on different size and type of substrates," says Zong. "In a subsequent step, we hope to transfer this methodology to related industrial companies."

More information: Research article in Journal of Materials Chemistry

Provided by Agency for Science, Technology and Research (A*STAR)

Researchers capture first-ever image of two atoms forming a molecule

 Researchers have recorded the first-ever image of two atoms bonding together to form a molecule.

Key to the experiment, which appears in the journal Nature, is the researchers' use of the energy of a single electron as a kind of "flash bulb" to illuminate the reaction.

The team used ultrafast laser pulses to knock one electron out of its natural orbit in one of the atoms, just as the two atoms were bonding together. When the electron fell back into place, it emitted an energy signal that scattered around the newly forming molecule as a flash of light would scatter around an object, or ripples would scatter in a pond.

Principal investigator Louis DiMauro of Ohio State University said that the feat marks a first step toward not only observing chemical reactions, but also controlling them on an atomic scale.

"Through these experiments, we realized that we can control the trajectory of the electron when it comes back to the molecule, by adjusting the orientation of the laser that launches it," said DiMauro, who is a professor of physics at Ohio State. "The next step will be to see if we can hit the electron in just the right way to actually control a chemical reaction."

A more common imaging technique involves shooting a molecule with an electron beam, bombarding it with millions of electrons per second. The researchers deemed the new single-electron approach more reliable, based on theoretical developments by the paper's coauthors at Kansas State University.

"If we shot an electron beam from outside the molecule, there would only be a certain probability that one of the electrons would scatter off the molecule," explained Ohio State postdoctoral researcher Cosmin Blaga. "But in this case, when we use a laser to launch an electron from inside the molecule we are studying, we have a 100 percent probability that it will fall back into the molecule and scatter."

The technique, called laser induced electron diffraction (LIED), is commonly used in surface science to study solid materials. This is the first time anyone has used LIED to study a single molecule as it formed.

The molecules the researchers chose to study were simple ones: they brought two nitrogen atoms together to form molecular nitrogen, or N2, then repeated the experiment with two oxygen atoms forming molecular oxygen, or O2. N2 and O2 are common atmospheric gases, and scientists already know every detail of how they form, so these two very basic reactions made good test cases for the LIED technique.

In each case, the researchers hit the forming molecule with laser light pulses of 50 femtoseconds, or quadrillionths of a second. They were able to knock a single electron out of the outer shell of one of the constituent atoms and detect the energy signal of the electron as it fell back into the molecule.

DiMauro and Blaga likened the electron signal to the diffraction pattern that light forms when it passes through slits. Given only the diffraction pattern, scientists can reconstruct the size and shape of the slits. In this case, given the diffraction pattern of the electron, the physicists reconstructed the size and shape of the molecule -- that is, the locations of the constituent atoms' nuclei and the electron shells orbiting them.

The resulting 3D image marks the first image ever recorded of bonds forming in a molecule.

Beyond its potential for controlling chemical reactions, the technique offers a new tool to study the structure and dynamics of matter, Blaga said. "Ultimately, we want to really understand how chemical reactions take place. So, long-term, there would be applications in materials science and even chemical manufacture."

"You could use this to study individual atoms," DiMauro added, "but it's safe to say that we won't learn anything new from an atomic physics standpoint. The greater impact to science will come when we can study reactions between more complex molecules. Looking at two atoms -- that's a long way from studying a more interesting molecule like a protein."

Coauthors on the paper included Anthony DiChiara, Emily Sistrunk, Kaikai Zhang, Pierre Agostini, and Terry A. Miller of Ohio State; and C.D. Lin of Kansas State. Coauthor Junliang Xu pursued the theoretical side of this research to earn his doctorate at Kansas State, and will soon join DiMauro's lab as a postdoctoral researcher.

Funding came from the U.S. Department of Energy Basic Energy Sciences Program.

Story Source:

The above story is reprinted from materials provided by Ohio State University, via Newswise.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Cosmin I. Blaga, Junliang Xu, Anthony D. DiChiara, Emily Sistrunk, Kaikai Zhang, Pierre Agostini, Terry A. Miller, Louis F. DiMauro, C. D. Lin. Imaging ultrafast molecular dynamics with laser-induced electron diffraction. Nature, 2012; 483 (7388): 194 DOI: 10.1038/nature10820

The secret life of proteins: Researchers discover dual role of key player in immune system

That protein, STIM1, was previously known to sense a change in calcium within immune cells, a process that occurs when the body confronts a pathogen. Upon sensing this change, STIM1 opens a type of pore in the cell membrane, called a CRAC channel, to allow the flow of calcium ions — a vital step in activating the immune system.

The Feinberg team, led by Murali Prakriya, assistant professor of molecular pharmacology and biological chemistry, discovered that STIM1 not only opens these pores but is responsible for determining the exquisite selectivity for calcium ions within the CRAC channels, a critical factor in kick starting the body's immune system. These findings were recently reported in the journal Nature.

"People have generally thought that selectivity of ion channels is fixed and that selectivity and opening are separate processes; this is a fundamental shift in the way scientists believe ion channels operate," says Prakriya, referring to the 'pores' that STIM1 regulates. "CRAC channels and STIM1 are absolutely vital to activating the immune system. As is observed in some human patients, you can block key parts of the system by blocking these molecules in immune cells. These finding reveal not only a novel mechanism by which CRAC channels operate, but also new ways in which it encodes biological information. This represents exciting new possibilities to develop therapeutics to treat a broad range of conditions."

To determine that STIM1 is responsible for selectivity and opening, the researchers created a mutated CRAC channel designed to keep the pore open without the assistance of STIM1. When the channel was opened without STIM1, multiple types of ions were passed through the pore, including sodium and potassium. When STIM1 was added back in, the channel became very selective for calcium ions again, like the normal channel. Even at low doses of STIM1, the unmutated channel lost its normally high calcium selectivity, allowing the entry of multiple types of ions.

Conditions that might benefit from immune suppression are likely targets for future CRAC channel targeted therapy, including autoimmune diseases and many types of allergies. Additionally, targeting CRAC channels could provide improvements for existing immune suppression therapies such as those used during transplantation.

"The CRAC channel is emerging to be incredibly important for the immune system," says Prakriya. "But we have been solely focused on its calcium conducting mode that occurs in response to STIM1. It is certainly possible that there could be other players in the cell that open the CRAC channel pore to permit the flux of other ions to stimulate different cell functions. That's the next question."

Also in the Nature article, Prakriya's team identified the location of the barrier, or gate, within the CRAC channel that controls its opening and closing.

"The identification of the molecular and structural regions of the pore that controls opening and closing is highly valuable for facilitating drug design targeting CRAC channels for the treatment of immune disorders," he adds.

Provided by Northwestern University (news : web)

Researchers discover the processes leading to acute myeloid leukemia

The UCSB research team described how a certain mutation in DNA disrupts cellular function in patients with acute myeloid leukemia (AML). The researchers were prompted to study this process by another research team's discovery that AML patients have a mutation in a certain enzyme, which was reported in the New England Journal of Medicine. The enzyme is a protein called DNMT3A, which leads to changes in how the DNA of AML patients is methylated, or "tagged." Norbert Reich, professor in the Department of Chemistry and Biochemistry at UCSB, was already studying that particular enzyme with his research group, so they began to study the disease process of AML at the cellular level.

Reich explained that tagging is a way of reading DNA at the cellular level. This falls within an area of study called epigenetics, a process that occurs "on top" of genetics. Each person has approximately 200 types of cells, all with the same DNA, and these must be controlled in different ways. "There is an enzyme –– a protein –– that tags DNA and controls which of the genes in your cells, your DNA, gets turned on and off," said Reich. "So you have 20,000 genes, and you have to control them differently in your brain than in your liver."

Reich explained that there is current interest in this broader field of epigenetics as a direction for the treatment of cancer. "There's definitely the idea that this may be a new way of developing therapeutics, because you don't have to kill the cancer cell," said Reich. "Almost every cancer therapy that's out there works on the principle that a cancer cell needs to be killed."

In this artist's conception, the four-protein complex called DNMT3A is shown in its normal configuration (top left). The complex reads or "tags" the cell's DNA. In the upper right side of the image, several of these tags are shown on top of the double helix of DNA. The tags control which genes in a cell get turned on and off. In the bottom left image, the complex of four proteins is disrupted. This disruption is caused by the mutation found in patients with acute myeloid leukemia. In the right side of the bottom image, the protein leaves only one tag on the DNA and then moves on. Credit: Norbert Reich, UCSB

With epigenetics, instead of only having DNA sequence coding for certain genes, there is an epigenetic process, with another layer of information on top of the genetic process. In this case, that information is the tagging by the methyl groups.

"If you really think about it, this is part of the answer as to how your cells can be so different and yet they all have the same DNA," said Reich. "You have the same genome in every one of your cells, but you do not have the same epigenome, which is basically the methylation pattern, the tagging pattern. That is different in every type of your cells. And the way this relates back to cancer, with leukemia, in those patients, the tagging is messed up. The patterns are not correct. Our big contribution to that is we've explained how the mutations in the enzyme could lead to that disruption of the tagging pattern."

The UCSB group developed a test to demonstrate that the mutant enzymes in AML can only work on DNA for short distances. As a result, the precise methylation patterns of a healthy cell are disturbed, resulting in genes being turned on at the wrong place and time, which in turn can initiate the growth of cancerous cells.

The team found that the mutation AML patients have causes a certain complex of four proteins to be disrupted. "The surprise was that the disruption doesn't stop the enzyme from being active; it doesn't stop the enzyme from tagging the DNA," said Reich. "Instead, it stops the way it can do it. Instead of going to your DNA and tagging an entire region of chromosome, it goes there, does one thing, and leaves. That process, that change, is what we see in the AML patients. So we think we have a molecular explanation for this disease."

Reich said that the currently prescribed drug Vidaza works by affecting the same enzyme that is mutated in AML. There is interest in the pharmaceutical industry in developing other therapeutics to target the enzymes responsible for tagging the DNA. These epigenetic inhibitors would reprogram rather than kill the cell.

Traditional cancer therapies use radiation and chemotherapy to remove or kill cancer cells. "The problem with that is that cancer cells are often very subtly different from normal cells," said Reich. "So you have one of the most difficult therapeutic challenges known to man, which is to distinguish between two human cells –– one that's cancerous and one that's not. Instead of killing the cell, the notion is that if you could just reprogram the cell, then it goes back to being normal. You intercept the cancer development. This is still an aspiration; it hasn't been achieved really, but that's what attracts people to the field of epigenetic-based therapies, because of the prospect of not having to kill cells."

Provided by University of California - Santa Barbara (news : web)

Researchers model potential of toxic algae photoreceptors

Massimo Olivucci, Ph.D., a research professor of chemistry at Bowling Green State University (BGSU), is focusing on Anabaena sensory rhodopsin (ASR) bacteria, which has served as a model for studies of most cyanobacteria since its genome was fully mapped in 1999.

"An in-depth understanding of light sensing, harvesting and energy conversion in Anabaena may allow us to engineer this and related organisms to thrive in diverse illumination conditions," said Olivucci. "Such new properties would contribute to the field of alternative energy via the microbial conversion of light energy into biomasses, oxygen and hydrogen. Biophysical studies of the bacterial photoreceptor and its underlying molecular mechanisms can help us to understand its biotechnological potentials and the associated environmental implications."

Using sunlight as an energy source, a sensory protein within ASR detects light of two different colors and behaves like the "eye" of Anabaena, using its green-light sensitivity to activate a cascade of reactions. In sophisticated computer simulations Olivucci created at the Ohio Supercomputer Center (OSC), he found that a short fragment of the long retinal chromophore backbone of ASR undergoes a complete clockwise rotation powered by the energy carried by two photons of light.

"We are constructing quantum-mechanical and molecular-mechanical models on Ohio Supercomputer Center systems," Olivucci explained. "Past simulations have revealed that light induces a molecular-level rotary motion in the protein interior.

"Now, the same computer models will be used to engineer hundreds of mutants that display programmed spectroscopic, photochemical and photobiological properties and identify which mutants should be prepared in the laboratory. This new approach constitutes a unique opportunity for developing computational tools useful for understanding the molecular factors that control the spectra of proteins and their photo-responsive properties in general."

Olivucci's research is expected to lead to an unprecedented tool by which hundreds to thousands of mutant models can be screened for wanted properties, such as color, excited state lifetime or photochemical transformations. This will provide tailored genetic materials for generating organisms that, for instance, can thrive under alternative light conditions and modulate biomass production or be used in engineering applications.

"Ohio is an international player in the biosciences and energy/environmental issues, which is why OSC focuses many of its resources and services on those areas to support important research like this cyanobacteria study," said Ashok Krishnamurthy, Ph.D., interim co-executive director of OSC. "Dr. Olivucci's computational investigations into the potential uses of Anabaena are a great example of how modeling, simulation and analysis can advance research into subjects only imagined just a few short years ago."

More information: Olivucci's research project, "Computational engineering and predictions of excited state properties of bacterial photoreceptor mutants," is supported by the Ohio Board of Regents and BGSU. Initial computational work relating to the project was published in the prestigious Proceedings of the National Academy of Sciences in 2010.

Provided by Ohio Supercomputer Center

Researchers discover method to unravel malaria's genetic secrets

"The malarial genome has been a black box. Our technique allows us to open that box, so that we can learn what genes in the most lethal human parasite actually do," said Dennis Voelker, PhD, Professor of Medicine at National Jewish Health and senior author on the paper that appeared in the January 2, 2012 , issue of the Journal of Biological Chemistry. "This could prove tremendously valuable in the fight against a disease that has become increasingly drug-resistant."

The genome of P. falciparum was sequenced in 2002, but the actual functions of many of the organism's genes have remained elusive. One of the primary methods for discovering gene function is to copy a specific gene, insert it into a model organism that is easy to grow, often the yeast Saccharomyces cerevisiae, then draw on the incredible knowledge base about yeast and its abundant genetic variants to discover how that inserted gene changes the organism's biology.

DNA is composed of building blocks with the shorthand designations A,T,C and G. The genome of P. falciparum is odd because it is particularly rich in A's and T's. Because of this A-T-rich nature, P. falciparum genes generally do not function when they are inserted into other organisms. As a result, scientists have been largely stymied when trying to understand the functions of P. falciparum's genes.

It turns out, however, that P. falciparum has a close cousin, P. knowlesi, which shares almost all its genes with P. falciparum, but with fewer A's and T's. As a result, P. knowlesi genes function well when inserted into yeast. Scientists can now insert P. knowlesi genes into yeast, discover their function, and then match them to corresponding genes in P. falciparum, which reveals the function of the malarial parasite's genes.

"This technique could lead to an explosion in knowledge about malaria and the parasite that causes it." said Dr. Voelker.

The researchers used the technique to discover a new gene involved in the synthesis of lipids in cell membranes of P. falciparum. The gene, phosphatidylserine decarboxylase, directs the formation of a protein unique to malarial parasites and is a potential therapeutic target. For example, selective disruption of lipid synthesis in P. falciparum, would prevent the organism from making new cell membranes, growing and reproducing in human hosts.

Provided by National Jewish Health

Researchers seek to beat 'molecular obesity'

Professor Andrew Hopkins and his team from the University's College of Life Sciences have developed a mathematical formula that they believe has the potential to more effectively identify compounds that have the best chance of being successfully developed into drugs to treat and protect against disease.

In order to succeed as a drug, a compound has to have the right balance of properties. Those compounds that are too large or too greasy - said to be molecularly obese - tend not to be well absorbed by the body when taken orally as pills and have been blamed for increasing rates of failure and rising costs in the drug development process.

This is why the most commonly used and effective orally dosed drugs that are available on the market tend to be relatively small and lean. Compounds sharing these properties are said to be "drug-like" and assessment of "drug-likeness" is a key consideration when selecting compounds for further development.

Until now this assessment has been made according to a widely used set of rules that determine whether or not compounds are suitable for further development as orally absorbed pills.

However, the evaluation of drug-likeness in black and white terms does not adequately reflect the whole spectrum of compound quality as many successful drugs apparently 'break the rules' so the Dundee team set about developing an alternative model.

They have pioneered a measure of drug-likeness based on the concept of desirability called Quantitative Estimate of Druglikeness (QED) which rates a compound between 0-1 based on its molecular properties, with 1 indicating an ideal candidate.

Once the scores have been calculated any set of compounds can be easily ranked by their relative merit. Importantly, the formula is derived entirely from historical data on the observed properties of successful drugs. This approach is more flexible than simply attributing a pass or fail to a compound, and offers several advantages to researchers looking to develop new drugs, according to Professor Hopkins.

"We think this may be a better way of appraising compounds in drug discovery," he said. "What we are trying to overcome is a problem of judging which compounds have the lowest risk of failure before synthesizing or buying them. This is important because the cost of drugs is in part driven by the high failure rate in developing new therapies.

"Compounds that don't have the correct properties or features make them particularly unsuitable, but this doesn't tell the whole story. Scientists judge them according to the rules, which might suggest a particular compound will work, but not that they will only work to a certain extent and that there are more effective alternatives available.

"Over the past two decades the compounds made by the pharmaceutical industry have tended to get larger and greasier. This trend has been called molecular obesity, and while these "obese" compounds may pass the rules they are far from the ideal.

"Some experts in the industry argue that the increasing failure rate and increasing cost in developing new drugs may be due to the rise in molecular obesity of new compounds. QED gives us a new tool to guide drug design toward leaner, fitter, more attractive compounds, with hopefully a greater overall chance of success.

"The rules which chemists use are useful, but only as far as telling us that it does or doesn't work. We are trying to get away from the concept of using hard and fast rules and looking instead at the shades of grey, which reflect the reality of the situation. What we are trying to do is increase the odds of identifying a successful compound."

The Dundee team's work is published in the most recent edition of the Nature Chemistry journal. The paper, entitled 'Quantifying the chemical beauty of drugs', is co-authored by colleagues in England and Sweden.

After attributing values to several thousand compounds, the researchers asked around 80 chemists to evaluate them based on their own knowledge and scientific methods. This showed that the Dundee method was an effective way of identifying attractive candidates which agreed very well with the chemists' intuition.

Professor Hopkins continued, "Chemists often refer to compounds as looking "good, bad or ugly" according to their suitability, and we asked the chemists who took part in this survey whether a drug was attractive or not, and found their tacit knowledge fitted well with our calculation.

"The whole idea is to use statistics, data, and underlying probability distributions which has been gathered on drugs over the years to help us more quickly and effectively identify attractive compounds in the future.

"The formula encodes the properties that seem to determine a compound's attractiveness, and reflects the knowledge required in drug discovery. What we found exciting is the idea of a mathematical formula that reflects the chemists experience and intuition of what they consider an "attractive" compound to synthesise.

"From here we can develop a more nuanced approach to identifying lower risk compounds for drug discovery."

Provided by University of Dundee

Researchers develop new drug release mechanism utilizing 3-D superhydrophobic materials

The study was electronically published on January 16, 2012 in the Journal of the American Chemical Society.

Boston University (BU) graduate student Stefan Yohe, under the mentorship of Mark Grinstaff , PhD, BU professor of biomedical engineering and chemistry, and Yolonda Colson, MD, PhD, director of the Dana-Farber Cancer Institute/Brigham and Women's Hospital (BWH) Cancer Center, prepared drug-loaded superhydrophobic meshes from biocompatible polymers using an electrospinning fabrication method.

By monitoring drug release in aqueous solution and mesh performance in cytotoxicity assays, the team demonstrated that the rate of drug release correlates with the removal of the air pocket within the material, and that the rate of drug release can be maintained over an extended period.

"The ability to control drug release over a 2-3 month period is of significant clinical interest in thoracic surgery with applications in pain management and in the prevention of tumor recurrence after surgical resection," said Colson. Colson is also a thoracic surgeon at BWH with an active practice focused on the treatment of lung cancer patients.

This approach along with the design requirements for creating 3D superhydrophobic drug-loaded materials, the authors write, should facilitate further exploration and evaluation of these drug delivery materials in a variety of cancer and non-cancer applications.

Provided by Brigham and Women's Hospital

Researchers seek high-pressure materials without high-pressure processes

The Defense Advanced Research Projects Agency's (DARPA's) Extended Solids program seeks to identify processes that enable stabilization and production of high pressure phase materials, without the limitations of scale introduced by current high-pressure processes, that exhibit properties far superior to those currently available for DoD applications.

"We seek the ability to access these ultrahigh pressure phases without having to use the ultrahigh pressures currently required to achieve them," said Judah Goldwasser, DARPA's program manager for this effort. "In the thermochemical world, the ability to synthesize the vast array of materials available both biochemically and synthetically is predicated on exploitation of multistep synthesis and stabilization strategies, so target materials can be produced through intermediates using methods and conditions mild enough to be viable."

Through this program, DARPA seeks the development of analogous strategies that can be applied to the barochemistry, or ultrahigh pressure regime. This technology could fundamentally change the way high-pressure polymorphs/phases are synthesized, potentially opening a vast new material design space for exploitation.

Goldwasser stressed that the complex nature of this research effort requires diverse sets of skills and expertise to meet program objectives and milestones, and encouraged potential researchers to team with others to help ensure success.

Provided by Defense Advanced Research Projects Agency

Researchers figure out how to outperform nature's photosynthesis

Says io9: “They frankensteined together proteins from Synechococcus sp. with those from Clostridium acetobutylicum using molecular wire to create a 'hybrid biological/organic nanoconstruct' that was more efficient than either on their own.”

These researchers have created a tiny solar-powered device that works twice as fast as nature to produce hydrogen biofuel. In describing their research they say that although solar biohydrogen systems using photosystem I (PSI) have been developed, few attain the electron transfer throughput of oxygenic photosynthesis.

They say they optimized a nanoconstruct that tethers FB, the terminal [4Fe-4S] cluster of PSI from Synechococcus sp. PCC 7002, to the distal [4Fe-4S] cluster of the [FeFe]-hydrogenase (H2ase) from Clostridium acetobutylicum.

“On illumination, the PSI-[FeFe]-H2ase nanoconstruct evolves H2 at a rate of 2,200 ± 460 µmol mg chlorophyll-1 h-1, which is equivalent to 105 ± 22 e-PSI-1 s-1. Cyanobacteria evolve O2 at a rate of approximately 400 µmol mg chlorophyll-1 h-1, which is equivalent to 47 e-PSI-1 s-1, given a PSI to photosystem II ratio of 1.8.

“The greater than twofold electron throughput by this hybrid biological/organic nanoconstruct over in vivo oxygenic photosynthesis validates the concept of tethering proteins through their redox cofactors to overcome diffusion-based rate limitations on electron transfer.”

The researchers are among scientists in general who are looking at photosynthesis to invent materials and design new processes that can help save our planet. Associate Professor John Stride, of the University of New South Wales, commented to the ABC that “nature has had millennia to solve problems, and photosynthesis is very efficient.”

In turning to biomimicry, scientists are designing devices based on photosynthesis. As for the study authors, in making their biofuel device they replaced the FNR enzyme with hydrogenase.

One of the co-authors, Penn State Professor Donald Bryant, said there are good prospects for using some of these biological photosynthesis systems to produce biofuels for the future.

More information: Solar hydrogen-producing bionanodevice outperforms natural photosynthesis, PNAS, Published online before print December 12, 2011, doi: 10.1073/pnas.1114660108

Abstract
Although a number of solar biohydrogen systems employing photosystem I (PSI) have been developed, few attain the electron transfer throughput of oxygenic photosynthesis. We have optimized a biological/organic nanoconstruct that directly tethers FB, the terminal [4Fe-4S] cluster of PSI from Synechococcus sp. PCC 7002, to the distal [4Fe-4S] cluster of the [FeFe]-hydrogenase (H2ase) from Clostridium acetobutylicum. On illumination, the PSI–[FeFe]-H2ase nanoconstruct evolves H2 at a rate of 2,200 ± 460 µmol mg chlorophyll-1 h-1, which is equivalent to 105 ± 22 e-PSI-1 s-1. Cyanobacteria evolve O2 at a rate of approximately 400 µmol mg chlorophyll-1 h-1, which is equivalent to 47 e-PSI-1 s-1, given a PSI to photosystem II ratio of 1.8. The greater than twofold electron throughput by this hybrid biological/organic nanoconstruct over in vivo oxygenic photosynthesis validates the concept of tethering proteins through their redox cofactors to overcome diffusion-based rate limitations on electron transfer.

? 2011 PhysOrg.com

Researchers identify lipid profile characteristic of newly diagnosed type 1 diabetes

The Editors-in-Chief of Clinical Biochemistry and Clinica Chimica Acta selected the paper for the distinction and included it in a booklet distributed at international meetings sponsored by the International Federation of Clinical Chemistry.

T1DM affects more than 1 million individuals in the United States alone. Currently, the best approach for predicting those at risk for developing T1DM before symptoms appear is by measuring autoantibodies to islet cell antigens in the pancreas.
Lipids 101
Lipids are one of the four major molecular components of biological organisms, along with proteins, sugars, and nucleic acids. They store energy, make up the structures of cells, and participate in cell signaling.  The "lipidome" refers to all lipids in cells and "lipidomics" to the measurement thereof. Autoantibodies cause many autoimmune diseases. Multiple autoantibody positives and their persistence are unequivocally related to the risk of progression to T1DM. However, autoantibodies are difficult to measure with consistent sensitivity and specificity, and assay performance varies considerably among laboratories. Sound methods are needed to identify new biomarkers that predict T1DM development and can also be transferred to other laboratories.

To improve and standardize measurement of autoantibodies associated with T1DM and identify novel protein biomarkers, the Centers for Disease Control and Prevention (CDC) and the Immunology of Diabetes Society created the Diabetes Antibody Standardization Program (DASP). Scientists at PNNL and the CDC previously conducted a global proteomics analysis of plasma and serum samples from the DASP and identified five candidates in a sample subset (Metz et al. 2008).

The role of ZAG: Scientists found that one protein in particular, zinc alpha-2-glycoprotein (ZAG), was strongly upregulated, or increased, in individuals with T1DM. ZAG, a member of the immunoglobulin superfamily, is responsible for lipid mobilization. This means that increased levels of ZAG in patients may indicate a system-wide mobilization of lipids for energy production, particularly because these individuals lack endogenous insulin and cannot rely on blood glucose (sugar) for their energy needs. The scientists hypothesized that perturbations, or changes, may be present in the blood lipidome of individuals with newly diagnosed T1DM.

To test their hypothesis, they performed lipidomics analyses on the same DASP samples to identify perturbations in the lipids of individuals with recently diagnosed T1DM and to potentially identify a lipid profile that could predict or diagnose the disease.

"When discussing lipids in the context of personal health, most people think of total cholesterol, HDL, LDL, and triglycerides, which are the lipids typically measured in a blood lipid panel at clinics and hospitals," said PNNL chemist Dr. Thomas Metz. "They don't realize that there is a broad diversity of lipids in blood and tissues—thousands of individual lipid molecular species comprising about a dozen or so major classes.

"For example, HDL and LDL themselves are comprised of hundreds of molecular species of cholesterol esters and triglycerides. So, while the typical clinic blood lipid panel may not indicate differences in total cholesterol, HDL, LDL, and triglycerides, there may be dramatic changes at the level of lipid molecular species. These are the changes that only mass spectrometry can identify with sufficient sensitivity and throughput."

The scientists used capillary liquid chromatography (LC) coupled with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) and the accurate mass and time (AMT) tag approach developed at PNNL to identify and quantify lipids present in healthy and diabetic individuals. The AMT tag approach relies on initial, low-throughput shotgun LC-MS/MS analyses to populate a database of identified molecules followed by higher throughput and more quantitative LC-MS analyses.

They identified more than 559 lipids that were significantly different (q < 0.05) between control and patient samples, of which 55 were structurally identified by matching to entries in a blood plasma lipid AMT tag database. These lipids may represent a profile characteristic of newly diagnosed T1DM.

"The patients in our study had well-controlled blood glucose levels, so their blood lipid panels showed no differences in total cholesterol, HDL, LDL, and triglycerides compared to the controls," Metz said. "In that respect, it is very exciting that we identified so many lipid molecular species that showed statistically significant differences between the patients and controls. It really highlights an area worth further study in the context of T1DM."

More information: Sorensen CM, J Ding, Q Zhang, T Alquier, R Zhao, PW Mueller, RD Smith, and TO Metz. 2010. "Perturbations in the lipid profile of individuals with newly diagnosed type 1 diabetes mellitus: lipidomics analysis of a Diabetes Antibody Standardization Program sample subset." Clinical Biochemistry 43(12):948-956.

Metz TO, W-J Qian, JM Jacobs, MA Gritsenko, RJ Moore, AD Polpitiya, ME Monroe, DG Camp II, PW Mueller, and RD Smith. 2008. "Application of Proteomics in the Discovery of Candidate Protein Biomarkers in a Diabetes Autoantibody Standardization Program Sample Subset." Journal of Proteome Research 7(2):698-707.

Provided by Pacific Northwest National Laboratory (news : web)

Researchers discover one of the most porous materials to date

Working with metal-organic frameworks—crystalline compounds comprising metal- cluster vertices linked together by organic molecules to form one-, two-, or three-dimensional porous structures—researchers addressed changing the size of the vertex (the metal cluster) rather than the length of the organic molecule links, which resulted in the largest metal organic framework pore volume reported to date.

"Think of this the way you imagine Tinkertoys®," said Nathaniel Rosi, principal investigator and assistant professor in Pitt's Department of Chemistry in the Dietrich School. "The metal clusters are your joints, and the organic molecules are your linkers. In order to build a highly open structure with lots of empty space, you can increase the linker length or you can increase the size of the joint. We developed chemistry to make large joints, or vertices, and showed that we could link these together to build a material with extraordinarily large pores for this class of materials.

"Essentially, we're like architects. We first make a blueprint for a target material, and we then select our building blocks for construction," added Rosi. "We develop methods for designing structures and controlling the assembly of these structures on a molecule-by- molecule basis."

Rosi and Jihyun An, who graduated with a PhD degree in chemistry from Pitt in 2011 and is lead author of the paper, said this new approach could have an impact on storing large quantities of gas such as carbon dioxide or methane, an important development for alternative energy, or large amounts of drug molecules, which could impact the drug-delivery field. Since joining Pitt five years ago, Rosi has developed a lab that includes students and postdoctoral researchers from various chemistry-related disciplines and focuses on new methods for materials' design and discovery.

Provided by University of Pittsburgh

Swiss researchers create unscratchable gold

By combining a gold alloy with boron carbide, an extremely hard ceramic that’s used in bulletproof vests, a team of EPFL researchers has succeeded in making the world’s toughest 18-karat gold (75% gold). With a Vickers hardness number of 1000, it’s harder than most tempered steels (600 Vickers) and thus almost impossible to scratch, except with a diamond. This discovery is the result of a three-year collaboration between the Mechanical Metallurgy Laboratory in EPFL’s Institute of Materials, under the leadership of Professor Andreas Mortensen, and the Swiss watchmaking company Hublot.

The process for developing this material is relatively complicated. Powdered boron carbide is heated to almost 2000°C, where it forms a rigid, porous structure by a process called sintering. A liquid molten alloy of gold is infiltrated under very high pressure into the pores of this structure, and then solidified, yielding a pore-free composite material. The final material is thus made up of two kinds of crystals that are intimately interconnected in space, like two three-dimensional labyrinths. Because the molten gold used is a previously-made alloy based on 24-karat gold and aluminum (3%) for strength, the final gold is thus 3% aluminum, 75% gold and 22% boron carbide
.
By definition, gold is very soft. Managing to harden it to this degree while still maintaining 18-karat purity was a real challenge for the EPFL scientists. They overcame the obstacle by taking the ceramic-metal composite approach. Composite materials are created by artificially combining several materials that conserve their individual characteristics even after they’re assembled. In this they are different from alloys, in which atoms mix together to form a new, homogeneous, material.

The EPFL researchers aren’t the first to play around with different materials in an effort to make more resistant gold. They are, however, the first to have attained this degree of hardness in 18-karat gold. The first watches made using this new gold will be presented in 2012 at BaselWorld, the world watch and jewelry show.

Provided by Ecole Polytechnique Federale de Lausanne

Mock atoms prove attractive: Researchers added first pseudo atoms to electronegativity scale

Electron attraction and repulsion determine how atoms and pseudo-atoms behave in different environments. This study provides scientists with the information they need to better predict, manipulate and control those behaviors, whether in batteries for solar farms or catalysts for bio-fuel production.

This study began when Alexander Whiteside, a student at Heriot-Watt University, came to PNNL as part of the 2008 Summer Research Institute for Interfacial and Condensed Phase Physics. During that summer visit, Whiteside, his advisor Maciej Gutowski, and Laboratory Fellow Sotiris Xantheas started to determine the electronegativity of the ammonium radical.

The team calculated the electronic structure of the neutral ammonium molecule, NH4, and its positive and negative ions. Next, they computed the properties of ammonium complexes, specifically combining ammonium with astatine or selected borohydrides; the latter are promising materials for hydrogen storage.

"These results clarified the properties of NH4 and placed it in the proper scale compared to the alkali metals," said Xantheas. "In comparison with alkali atoms, ammonium's electronegativity punches above its effective cationic radius. Nobody had really put it into the scale yet. This study did just that."

The results graced the cover of Chemistry: A European Journal and were highlighted in the Royal Society of Chemistry's Chemistry World.

"Past generations of physical and theoretical chemists were intrigued by the properties ammonium. Alex was standing on the shoulders of giants—Berzelius, Pauling, Mulliken, Herzberg—whose pictures are highlighted in the cover of the journal, while Sotiris and I helped him to keep his balance," joked Gutowski.

"This work opens up the opportunity to developing a comprehensive view on other pseudo-alkali metal species, pseudo-halogens and other pseudo-atoms" says Alexander Boldyrev of Utah State University.

Indeed, the team is expanding their study to the properties of the nearly ubiquitous hydronium and methyl groups, which contain a single oxygen or carbon atom and three hydrogen atoms. In addition, they are examining cyanide, a carbon and nitrogen atom combination that could provide new insights into that pseudo-atom's behavior.

More information: Whiteside A, SS Xantheas, and M Gutowski. 2011. "Is Electronegativity a Useful Descriptor for the Pseudo-Alkali Metal NH4?" Chemistry: A European Journal 17:13197-13205. DOI:10.1002/chem.201101949

Provided by Pacific Northwest National Laboratory (news : web)

Researchers discover secret of weevil diamond-like coat

Researchers and various other people have been puzzled for years as to how the diamond weevil manages to produce a coat that sparkles as well as any real diamond, but until recently, lacked the technology necessary to uncover the secret.

Now, using electron microscopy, this team discovered that the diamond-like material is actually made of nothing more than chitin, a long polymer derivative of glucose. Its most commonly found in anthropoids, mollusks and crustaceans as well as in a variety of insects. In this case, the diamond weevil.

Scanning electron microscopy of single scales of E. imperialis. (a) A single, intact scale. The upper side of the scale consists of a set of more or less parallel furrows (scale bar: 20 ?m). (b) SEM image of a cross-section showing tilted sheets with hexagonal symmetry (scale bar: 2 ?m). Image (c) J. R. Soc. Interface, doi:10.1098/?rsif.2011.0730

In most other animals, chitin appears as a dull whitish material, and is used by those higher up the evolutionary chain as an ingredient in medical and industrial products. In diamond weevils, it’s the way the material that is arranged that is different. For some as yet to be discovered reason, the gems in their coats are crystal structured in the same way as real diamonds, i.e. as photonic crystals.

Turns out, each little “gem” has crystal scales on it, each of which reflect a different wavelength of light at a different angle, producing the sparkling effect.

Now that the little bug’s secret has been revealed, other researchers will no doubt be looking into whether such gems might be made artificially and if so, if there might be any good use for them.

More information: Hemispherical Brillouin zone imaging of a diamond-type biological photonic crystal, J. R. Soc. Interface, Published online before print December 21, 2011, doi: 10.1098/?rsif.2011.0730

Abstract
The brilliant structural body colours of many animals are created by three-dimensional biological photonic crystals that act as wavelength-specific reflectors. Here, we report a study on the vividly coloured scales of the diamond weevil, Entimus imperialis. Electron microscopy identified the chitin and air assemblies inside the scales as domains of a single-network diamond (Fd3m) photonic crystal. We visualized the topology of the first Brillouin zone (FBZ) by imaging scatterometry, and we reconstructed the complete photonic band structure diagram (PBSD) of the chitinous photonic crystal from reflectance spectra. Comparison with calculated PBSDs indeed showed a perfect overlap. The unique method of non-invasive hemispherical imaging of the FBZ provides key insights for the investigation of photonic crystals in the visible wavelength range. The characterized extremely large biophotonic nanostructures of E. imperialis are structurally optimized for high reflectance and may thus be well suited for use as a template for producing novel photonic devices, e.g. through biomimicry or direct infiltration from dielectric material.

via Wired

? 2011 PhysOrg.com

Trillion-frame-per-second video: Researchers have created an imaging system that makes light look slow

MIT researchers have created a new imaging system that can acquire visual data at a rate of one trillion exposures per second. That's fast enough to produce a slow-motion video of a burst of light traveling the length of a one-liter bottle, bouncing off the cap and reflecting back to the bottle's bottom.

Media Lab postdoc Andreas Velten, one of the system's developers, calls it the "ultimate" in slow motion: "There's nothing in the universe that looks fast to this camera," he says.

The system relies on a recent technology called a streak camera, deployed in a totally unexpected way. The aperture of the streak camera is a narrow slit. Particles of light -- photons -- enter the camera through the slit and pass through an electric field that deflects them in a direction perpendicular to the slit. Because the electric field is changing very rapidly, it deflects late-arriving photons more than it does early-arriving ones.

The image produced by the camera is thus two-dimensional, but only one of the dimensions -- the one corresponding to the direction of the slit -- is spatial. The other dimension, corresponding to the degree of deflection, is time. The image thus represents the time of arrival of photons passing through a one-dimensional slice of space.

The camera was intended for use in experiments where light passes through or is emitted by a chemical sample. Since chemists are chiefly interested in the wavelengths of light that a sample absorbs, or in how the intensity of the emitted light changes over time, the fact that the camera registers only one spatial dimension is irrelevant.

But it's a serious drawback in a video camera. To produce their super-slow-mo videos, Velten, Media Lab Associate Professor Ramesh Raskar and Moungi Bawendi, the Lester Wolfe Professor of Chemistry, must perform the same experiment -- such as passing a light pulse through a bottle -- over and over, continually repositioning the streak camera to gradually build up a two-dimensional image. Synchronizing the camera and the laser that generates the pulse, so that the timing of every exposure is the same, requires a battery of sophisticated optical equipment and exquisite mechanical control. It takes only a nanosecond -- a billionth of a second -- for light to scatter through a bottle, but it takes about an hour to collect all the data necessary for the final video. For that reason, Raskar calls the new system "the world's slowest fastest camera."

Doing the math

After an hour, the researchers accumulate hundreds of thousands of data sets, each of which plots the one-dimensional positions of photons against their times of arrival. Raskar, Velten and other members of Raskar's Camera Culture group at the Media Lab developed algorithms that can stitch that raw data into a set of sequential two-dimensional images.

The streak camera and the laser that generates the light pulses -- both cutting-edge devices with a cumulative price tag of $250,000 -- were provided by Bawendi, a pioneer in research on quantum dots: tiny, light-emitting clusters of semiconductor particles that have potential applications in quantum computing, video-display technology, biological imaging, solar cells and a host of other areas.

The trillion-frame-per-second imaging system, which the researchers have presented both at the Optical Society's Computational Optical Sensing and Imaging conference and at Siggraph, is a spinoff of another Camera Culture project, a camera that can see around corners. That camera works by bouncing light off a reflective surface -- say, the wall opposite a doorway -- and measuring the time it takes different photons to return. But while both systems use ultrashort bursts of laser light and streak cameras, the arrangement of their other optical components and their reconstruction algorithms are tailored to their disparate tasks.

Because the ultrafast-imaging system requires multiple passes to produce its videos, it can't record events that aren't exactly repeatable. Any practical applications will probably involve cases where the way in which light scatters -- or bounces around as it strikes different surfaces -- is itself a source of useful information. Those cases may, however, include analyses of the physical structure of both manufactured materials and biological tissues -- "like ultrasound with light," as Raskar puts it.

As a longtime camera researcher, Raskar also sees a potential application in the development of better camera flashes. "An ultimate dream is, how do you create studio-like lighting from a compact flash? How can I take a portable camera that has a tiny flash and create the illusion that I have all these umbrellas, and sport lights, and so on?" asks Raskar, the NEC Career Development Associate Professor of Media Arts and Sciences. "With our ultrafast imaging, we can actually analyze how the photons are traveling through the world. And then we can recreate a new photo by creating the illusion that the photons started somewhere else."

"It's very interesting work. I am very impressed," says Nils Abramson, a professor of applied holography at Sweden's Royal Institute of Technology. In the late 1970s, Abramson pioneered a technique called light-in-flight holography, which ultimately proved able to capture images of light waves at a rate of 100 billion frames per second.

But as Abramson points out, his technique requires so-called coherent light, meaning that the troughs and crests of the light waves that produce the image have to line up with each other. "If you happen to destroy the coherence when the light is passing through different objects, then it doesn't work," Abramson says. "So I think it's much better if you can use ordinary light, which Ramesh does."

Indeed, Velten says, "As photons bounce around in the scene or inside objects, they lose coherence. Only an incoherent detection method like ours can see those photons." And those photons, Velten says, could let researchers "learn more about the material properties of the objects, about what is under their surface and about the layout of the scene. Because we can see those photons, we could use them to look inside objects -- for example, for medical imaging, or to identify materials."

"I'm surprised that the method I've been using has not been more popular," Abramson adds. "I've felt rather alone. I'm very glad that someone else is doing something similar. Because I think there are many interesting things to find when you can do this sort of study of the light itself."

Story Source:

The above story is reprinted from materials provided by Massachusetts Institute of Technology. The original article was written by Larry Hardesty, MIT News Office.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.