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Using highly precise laser tweezers, chemists nudged two atoms to together to form a chemical bond

Using highly precise laser tweezers, chemists nudged two atoms to together to form a chemical bond | Amazing Science | Scoop.it

For the first time, researchers have played matchmaker between two specific atoms, joining them together to form a molecule. Typically, chemists make molecules by mixing up many constituent atoms, some of which stick to each other to form the desired compounds.

 

In the new, supercontrolled chemical reaction, researchers trapped a single sodium atom in one optical tweezer — a device that snares small particles in a laser beam — and a cesium atom in another tweezer. Both atoms were cooled to less than one ten-thousandth of a degree above absolute zero.

 

The researchers moved these tweezers closer together until the laser beams overlapped, allowing the sodium and cesium atoms to collide. A third laser shot a pulse of light at the atoms to provide a boost of energy that helped the atoms bond into a sodium cesium molecule, researchers report online April 12 in Science.

 

Fashioning individual molecules atom by atom could allow researchers to study atomic collisions in the most controlled environment possible, as well as to observe how molecules behave in isolation. Researchers could also use optical tweezers to construct molecules with specific quantum properties, says study coauthor Kang-Kuen Ni, a chemist at Harvard University. These designer molecules could store qubits of data in future quantum computers, she explains.

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'Chemical MP3 Player' Can 3D Print Pharmaceuticals On-Demand from Digital Code

'Chemical MP3 Player' Can 3D Print Pharmaceuticals On-Demand from Digital Code | Amazing Science | Scoop.it

Have you ever taken your old compact discs and converted them to MP3 files so you could listen to your favorite music on your laptop, or through a portable MP3 device that’s much smaller than an unwieldy portable CD player? Now, researchers from the University of Glasgow are working on a very similar process, but instead of music files, they are using a chemical-to-digital converter to digitize the process of drug manufacturing; a chemical MP3 player, if you will, that can 3D print pharmaceuticals on demand.

 

3D printing in the pharmaceutical field is a fascinating concept, though not a new one. But this ‘Spotify for chemistry’ concept is new: it’s the first time we’ve seen an approach to manufacturing pharmaceuticals using digital code. According to Science, the University of Glasgow team “tailored a 3D printer to synthesize pharmaceuticals and other chemicals from simple, widely available starting compounds fed into a series of water bottle–size reactors.”


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Where did valence electrons go? Decades-old mystery solved!

Where did valence electrons go? Decades-old mystery solved! | Amazing Science | Scoop.it

The concept of "valence" - the ability of a particular atom to combine with other atoms by exchanging electrons - is one of the cornerstones of modern chemistry and solid-state physics.

 

Valence controls crucial properties of molecules and materials, including their bonding, crystal structure, and electronic and magnetic properties. Four decades ago, a class of materials called "mixed valence" compounds was discovered. Many of these compounds contain elements near the bottom of the periodic table, so-called "rare-earth" elements, whose valence was discovered to vary with changes in temperature in some cases. Materials comprising these elements can display unusual properties, such as exotic superconductivity and unusual magnetism.

 

But there's been an unsolved mystery associated with mixed valence compounds: When the valence state of an element in these compounds changes with increased temperature, the number of electrons associated with that element decreases, as well. But just where do those electrons go?

 

Using a combination of state-of-the-art tools, including X-ray measurements at the Cornell High Energy Synchrotron Source (CHESS), a group led by Kyle Shen, professor of physics, and Darrell Schlom, the Herbert Fisk Johnson Professor of Industrial Chemistry in the Department of Materials Science and Engineering, have come up with the answer.

 

Their work is detailed in a paper, "Lifshitz transition from valence fluctuations in YbAl3," published in Nature Communications. The lead author is Shouvik Chatterjee, formerly of Shen's research group and now a postdoctoral researcher at the University of California, Santa Barbara.

 

To address this mystery, Chatterjee synthesized thin films of the mixed-valence compound of ytterbium - whose valence changes with temperature - and aluminum, using a process called molecular beam epitaxy, a specialty of the Schlom lab. The group then employed angle-resolved photoemission spectroscopy (ARPES) to investigate the distribution of electrons as a function of temperature to track where the missing electrons went.

 

"Typically for any material, you change the temperature and you measure the number of electrons in a given orbital, and it always stays the same," Shen said. "But people found that in some of these materials, like the particular compound we studied, that number changed, but those missing electrons have to go somewhere."

 

It turns out that when the compound is heated, the electrons lost from the ytterbium atom form their own "cloud," of sorts, outside of the atom. When the compound is cooled, the electrons return to the ytterbium atoms. "You can think of it as two glasses that contain some water," Shen said, "and you're pouring back and forth from one to the other, but the total amount of water in both glasses remains fixed." "These findings point toward the importance of valence changes in these material systems. By changing the arrangement of mobile electrons, they can dramatically influence novel physical properties that can emerge," said Chatterjee.

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Quantum probes dramatically improve detection of nuclear spins

Quantum probes dramatically improve detection of nuclear spins | Amazing Science | Scoop.it
Researchers at the University of Melbourne have demonstrated a way to detect nuclear spins in molecules non-invasively, providing a new tool for biotechnology and materials science.

Important research in medicine and biology relies on nuclear magnetic resonance (NMR) spectroscopy, but until now, it has been limited in spatial resolution and typically requires powerful microwave fields. A team led by Professor Lloyd Hollenberg at the University of Melbourne has used a quantum probe to perform microwave-free NMR at the nanoscale. The results were published today in Nature Communications.

"This quantum probe delivers a dramatic improvement in NMR technology. In addition to being able to detect NMR in far smaller samples than conventional machines, our technique does not require the application of microwave fields that might disrupt biological samples" said Hollenberg, who is Deputy Director of the Centre for Quantum Computation and Communication Technology (CQC2T) and Thomas Baker Chair at the University of Melbourne.

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Seeing more with PET scans: New chemistry for medical imaging

Seeing more with PET scans: New chemistry for medical imaging | Amazing Science | Scoop.it
Researchers have found a surprisingly versatile workaround to create chemical compounds that could prove useful for medical imaging and drug development.

 

The chemical mechanism, discovered by scientists at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley, could also broaden our understanding of basic chemical reaction processes involving common helpers, called catalysts, like copper and gold.

 

While studying chemical reactions of a gold-containing molecule, the research team happened upon a chemical mechanism that can be used to form trifluoromethyl (CF3) compounds and attach them to other chemical compounds. Their discovery could aid in the synthesis of new "radiotracers" - chemical compounds that contain a radioactive form, or isotope, of an element - for use with a noninvasive, high-resolution 3-D medical imaging technology known as PET (positron emission tomography) scanning.

 

Drug companies have shown an increasing interest in incorporating CF3 compounds - which contain carbon and fluorine - in a range of pharmaceuticals. These compounds can make drugs more selective, effective, or potent. The antidepressant Prozac, HIV drug Sustiva, and anti-inflammatory Celebrex are among the examples of drugs containing CF3 compounds.

 

So in testing the biological uptake of drugs that incorporate CF3 compounds, it's useful to incorporate fluorine-18 (18F), a radioactive isotope of fluorine in the CF3 compound as a sort of label or "tracer" that can be detected by PET scanners.


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Water exists as two different liquids

Water exists as two different liquids | Amazing Science | Scoop.it

We normally consider liquid water as disordered with the molecules rearranging on a short time scale around some average structure. Now, however, scientists at Stockholm University have discovered two phases of the liquid with large differences in structure and density. The results are based on experimental studies using X-rays, which are now published in Proceedings of the National Academy of Science (US).

 

Most of us know that water is essential for our existence on planet Earth. It is less well-known that water has many strange or anomalous properties and behaves very differently from all other liquids. Some examples are the melting point, the density, the heat capacity, and all-in-all there are more than 70 properties of water that differ from most liquids. These anomalous properties of water are a prerequisite for life as we know it.

 

"The new remarkable property is that we find that water can exist as two different liquids at low temperatures where ice crystallization is slow", says Anders Nilsson, professor in Chemical Physics at Stockholm University. The breakthrough in the understanding of water has been possible through a combination of studies using X-rays at Argonne National Laboratory near Chicago, where the two different structures were evidenced and at the large X-ray laboratory DESY in Hamburg where the dynamics could be investigated and demonstrated that the two phases indeed both were liquid phases. Water can thus exist as two different liquids.

 

"It is very exciting to be able to use X-rays to determine the relative positions between the molecules at different times", says Fivos Perakis, postdoc at Stockholm University with a background in ultrafast optical spectroscopy. "We have in particular been able to follow the transformation of the sample at low temperatures between the two phases and demonstrated that there is diffusion as is typical for liquids".

 

When we think of ice it is most often as an ordered, crystalline phase that you get out of the ice box, but the most common form of ice in our planetary system is amorphous, that is disordered, and there are two forms of amorphous ice with low and high density. The two forms can interconvert and there have been speculations that they can be related to low- and high-density forms of liquid water. To experimentally investigate this hypothesis has been a great challenge that the Stockholm group has now overcome.

 

"I have studied amorphous ices for a long time with the goal to determine whether they can be considered a glassy state representing a frozen liquid", says Katrin Amann-Winkel, researcher in Chemical Physics at Stockholm University. "It is a dream come true to follow in such detail how a glassy state of water transforms into a viscous liquid which almost immediately transforms to a different, even more viscous, liquid of much lower density".

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This AI software dreams up new drug molecules

This AI software dreams up new drug molecules | Amazing Science | Scoop.it
Ingesting a heap of drug data allows a machine-learning system to suggest alternatives humans hadn’t tried yet.

 

A group of scientists now report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This generative model allows efficient search and optimization through open-ended spaces of chemical compounds. The team can train deep neural networks on hundreds of thousands of existing chemical structures to construct two coupled functions: an encoder and a decoder. The encoder converts the discrete representation of a molecule into a real-valued continuous vector, and the decoder converts these continuous vectors back to the discrete representation from this latent space. Continuous representations allow to automatically generate novel chemical structures by performing simple operations in the latent space, such as decoding random vectors, perturbing known chemical structures, or interpolating between molecules. Continuous representations also enable the use of powerful gradient-based optimization to efficiently guide the search for optimized functional compounds. The researchers demonstrate the success of this method in the design of drug-like molecules as well as organic light-emitting diodes.

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Chemists create molecular 'leaf' that collects and stores solar power without solar panels

Chemists create molecular 'leaf' that collects and stores solar power without solar panels | Amazing Science | Scoop.it

An international team of scientists led by Liang-shi Li at Indiana University have engineered the world's most efficient molecule to convert carbon dioxide into carbon monoxide with light or electricity. The discovery is an important leap forward in the quest to cheaply and efficiently create carbon neutral fuels from air and store sunlight as energy.

 

The chemists have engineered a molecule that uses light or electricity to convert the greenhouse gas carbon dioxide into carbon monoxide -- a carbon-neutral fuel source -- more efficiently than any other method of "carbon reduction." The process is reported in the Journal of the American Chemical Society.

 

"If you can create an efficient enough molecule for this reaction, it will produce energy that is free and storable in the form of fuels," said Li, associate professor in the IU Bloomington College of Arts and Sciences' Department of Chemistry. "This study is a major leap in that direction."

 

Burning fuel -- such as carbon monoxide -- produces carbon dioxide and releases energy. Turning carbon dioxide back into fuel requires at least the same amount of energy. A major goal among scientists has been decreasing the excess energy needed.

 

This is exactly what Li's molecule achieves: requiring the least amount of energy reported thus far to drive the formation of carbon monoxide. The molecule -- a nanographene-rhenium complex connected via an organic compound known as bipyridine -- triggers a highly efficient reaction that converts carbon dioxide to carbon monoxide. The ability to efficiently and exclusively create carbon monoxide is significant due to the molecule's versatility.

 

"Carbon monoxide is an important raw material in a lot of industrial processes," Li said. "It's also a way to store energy as a carbon-neutral fuel since you're not putting any more carbon back into the atmosphere than you already removed. You're simply re-releasing the solar power you used to make it."

 

The secret to the molecule's efficiency is nanographene -- a nanometer-scale piece of graphite, a common form of carbon (i.e. the black "lead" in pencils) -- because the material's dark color absorbs a large amount of sunlight.

 

Li said that bipyridine-metal complexes have long been studied to reduce carbon dioxide to carbon monoxide with sunlight. But these molecules can use only a tiny sliver of the light in sunlight, primarily in the ultraviolet range, which is invisible to the naked eye. In contrast, the molecule developed at IU takes advantage of the light-absorbing power of nanographene to create a reaction that uses sunlight in the wavelength up to 600 nanometers -- a large portion of the visible light spectrum.

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VX Nerve Agent: The Deadly Weapon Engineered in Secret

VX Nerve Agent: The Deadly Weapon Engineered in Secret | Amazing Science | Scoop.it

In January 1958, two medical officers at Porton Down, Britain’s military science facility, exposed their forearms to 50-microgram droplets of a substance called VX, which was a new, fast-acting nerve agent that could kill by seeping through the skin.

 

VX, short for “venomous agent X,” is tasteless, odorless and causes uncontrollable muscle contractions that eventually stop a person’s breathing within minutes. That experiment in 1958, according to University of Kent historian Ulf Schmidt, was perhaps the first human test of VX in the Western world.

 

Though VX is outlawed under the 1997 Chemical Weapons Convention, it was used to kill North Korean leader Kim Jong-un’s half-brother, Kim Jong-nam, in Malaysia. North Korea maintains the third largest stockpile of chemical weapons, trailing only the United States and Russia, according to the Nuclear Threat Initiative project. As such, South Korea has pinned blame for the attack on the North Korean government, and the use of a banned weapon may increase pressure on the international community to formulate a response.

 

Given these recent developments, it shouldn’t come as a surprise that this lethal chemical agent has a checkered, infamous past.

 

In the mid-1990s, the Japanese cult Aum Shinrikyo used VX in attempts to kill three people—one was successful. In 1969, the U.S. Army admitted that VX was responsible for the deaths of 6,000 sheep in Utah. But VX was trouble from the very start. You see, that first first-of-its-kind human trial in 1958 at Porton Down was actually an unauthorized experiment conducted in shadows, as Schmidt revealed in his 2015 book “Secret Science”.

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Brian Chew's comment, March 8, 2017 10:14 AM
I am greatly impressed by the abilities of mankind to use organic chemistry to form a deadly nerve agent, VX. However, with great power comes great responsibility. Although, true, mankind is capable of doing feats such as crafting a deadly nerve toxin, we must be very careful with its production, and limits for the production and usage of such dangerous chemicals should be more strictly implemented. This is to reduce the chances of cases such as Kim-Jong-Nam's being killed by the inappropriate usage of such deadly chemicals.
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Researchers Discover Three Novel Uranium Minerals in Old Uranium Mine

Researchers Discover Three Novel Uranium Minerals in Old Uranium Mine | Amazing Science | Scoop.it

Three new minerals discovered by a Michigan Tech alumnus are secondary crusts found in old uranium mines. They're bright, yellow and hard to find. The mines closed four decades ago, but that doesn’t stop air and water from traveling the long tunnels of Red Canyon. The old opening at the mine—the adit—cuts straight into the hill and has helped make new minerals. The adit opens to a dry panorama in southern Utah.

 

"Have you ever seen The Hills Have Eyes? It's that kind of creepy, barren desert landscape," says Travis Olds '12 and now a graduate student at Notre Dame studying uranyl mineral compounds. He adds that he and others find mineralogy so exciting because of "the idea that there are things we still don't know—and someone can see a pretty crystal and appreciate it."

 

Olds specifically studies uranyl minerals because, as radioactive materials, it is important to know where they are found and how they change in different environments. Within the past year, he found three new uranium minerals in Red Canyon: leesite, leószilárdite and redcanyonite.

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New technique could lead to safer, more efficient uranium extraction

New technique could lead to safer, more efficient uranium extraction | Amazing Science | Scoop.it
The separation of uranium, a key part of the nuclear fuel cycle, could potentially be done more safely and efficiently through a new technique developed by chemistry researchers at Oregon State University.

 

The technique uses soap-like chemicals known as surfactants to extract uranium from an aqueous solution into a kerosene solution in the form of hollow clusters. Aside from fuel preparation, it may also find value in legacy waste treatment and for the cleanup of environmental contamination.

 

The research at OSU involves a unique form of uranium discovered in 2005, uranyl peroxide capsules, and how those negatively charged clusters form in alkaline conditions. Results were recently published in the European Journal of Inorganic Chemistry.

 

"This is a very different direction," said study lead author Harrison Neal, a graduate student in Oregon State's College of Science. "A lot of the work done now is in acid, and we're at the other end of the pH scale in base. It's a very different approach, overall using less harmful, less toxic chemicals."

 

Throughout the nuclear fuel cycle, many separations are required—in mining, enrichment and fuel fabrication, and then after fuel use, for the recovery of usable spent isotopes and the encapsulation and storage of unusable radioactive components.

 

"When you use nuclear fuel, the radioactive decay products poison the fuel and make it less effective," said May Nyman, professor of chemistry at Oregon State and corresponding author on the research. "You have to take it, dissolve it, get the good stuff out and make new fuel."

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Graphene's sleeping superconductivity awakens

Graphene's sleeping superconductivity awakens | Amazing Science | Scoop.it
Researchers have found a way to trigger the innate, but previously hidden, ability of graphene to act as a superconductor - meaning that it can be made to carry an electrical current with zero resistance.

 

The finding, reported in Nature Communications, further enhances the potential of graphene, which is already widely seen as a material that could revolutionise industries such as healthcare and electronics. Graphene is a two-dimensional sheet of carbon atoms and combines several remarkable properties; for example, it is very strong, but also light and flexible, and highly conductive.

 

Since its discovery in 2004, scientists have speculated that graphene may also have the capacity to be a superconductor. Until now, superconductivity in graphene has only been achieved by doping it with, or by placing it on, a superconducting material - a process which can compromise some of its other properties. But in the new study, researchers at the University of Cambridge managed to activate the dormant potential for graphene to superconduct in its own right. This was achieved by coupling it with a material called praseodymium cerium copper oxide (PCCO).

 

Superconductors are already used in numerous applications. Because they generate large magnetic fields they are an essential component in MRI scanners and levitating trains. They could also be used to make energy-efficient power lines and devices capable of storing energy for millions of years.

 

Superconducting graphene opens up yet more possibilities. The researchers suggest, for example, that graphene could now be used to create new types of superconducting quantum devices for high-speed computing. Intriguingly, it might also be used to prove the existence of a mysterious form of superconductivity known as "p-wave" superconductivity, which academics have been struggling to verify for more than 20 years.

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Map of drugs reveals uncharted waters in search for new treatments

Map of drugs reveals uncharted waters in search for new treatments | Amazing Science | Scoop.it

Scientists have created a map of all 1,578 licensed drugs and their mechanisms of action - as a means of identifying 'uncharted waters' in the search for future treatments.

Their analysis of drugs licensed through the Food and Drug Administration reveals that 667 separate proteins in the human body have had drugs developed against them - just an estimated 3.5% of the 20,000 human proteins. And as many as 70 per cent of all targeted drugs created so far work by acting on just four families of proteins - leaving vast swathes of human biology untouched by drug discovery programs.

 

The study is the most comprehensive analysis of existing drug treatments across all diseases ever conducted. It was jointly led by scientists at The Institute of Cancer Research, London, which also funded the research.

 

The new map reveals areas where human genes and the proteins they encode could be promising targets for new treatments - and could also be used to identify where a treatment for one disease could be effective against another.

 

The new data, published in a paper in the journal Nature Reviews Drug Discovery, could be used to improve treatments for all human aliments - as diverse as cancer, mental illness, chronic pain and infectious disease.

 

Scientists brought together vast amounts of information from huge datasets including the canSAR database at The Institute of Cancer Research (ICR), the ChEMBL database from the European Bioinformatics Institute (EMBL-EBI) in Cambridge and the University of New Mexico's DrugCentral database. They matched each drug with prescribing information and data from published scientific papers, and built up a comprehensive picture of how existing medicines work - and where the gaps and opportunities for the future lie.

 

The researchers discovered that there are 667 unique human proteins targeted by existing approved drugs, and identified a further 189 drug targets in organisms that are harmful to humans, such as bacteria, viruses and parasites.


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Cloud quantum computing calculates nuclear binding energy of deuterium

Cloud quantum computing calculates nuclear binding energy of deuterium | Amazing Science | Scoop.it

Cloud quantum computing has been used to calculate the binding energy of the deuterium nucleus – the first-ever such calculation done using quantum processors at remote locations. Nuclear physicists led by Eugene Dumitrescu at Oak Ridge National Laboratory in the US used publicly available software to achieve the remote operation of two distant quantum computers. Their work could lead to new opportunities for scientists in many fields who want to use quantum simulations to calculate properties of matter.

 

In previous research, scientists have worked alongside quantum computer hardware developers to create quantum simulations. These typically use between two and six qubits to calculate a quantum property of matter – calculations that can be extremely time-consuming to do with a conventional computer. As the number of qubits available in quantum computers increase, the hope is that quantum simulations will be able to do calculations well beyond the reach of even the most powerful conventional computers. However, doing simulations alongside quantum computer specialists can be an inefficient process and the research would be much more streamlined if scientists were able to operate quantum computers themselves.

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An AI Translation Algorithm Can Predict the “Language” of Chemical Reactions

An AI Translation Algorithm Can Predict the “Language” of Chemical Reactions | Amazing Science | Scoop.it

By thinking of organic chemistry as words and sentences instead of atoms and molecules, researchers have found a way for artificial intelligence to predict chemical reactions.

 

In a paper published on arXiv by researchers at IBM and being presented at this week’s Neural Information Processing Systems (NIPS) conference, the researchers demonstrate that by treating reaction predictions as a translation problem, they could come up with the correct reaction more often than was possible with previous models.

 

“Intuitively, there is an analogy between a chemist’s understanding of a compound and a language speaker’s understanding of a word,” the researchers write.

 

Using a neural network often used in machine translation, the researchers trained the system on a data set that included 395,496 reactions. From that data, the neural net had to learn the “syntax” of reactions to be able to predict unseen compounds. The algorithm gave researchers a list of the top five most likely reactions, and the top prediction was correct 80 percent of the time, beating another model that tried to predict reactions by six percentage points.

 

There are millions of chemical reactions that have yet to be documented, so this approach could help speed up research for things like drug discovery. But researchers say that as more data gets added to the models, more double-checking will have to take place. Teodoro Laino, one of the researchers, told IEEE Spectrum that they “didn't create this tool to replace organic chemists, but to help them.”


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Taming 'wild' electrons in graphene

Taming 'wild' electrons in graphene | Amazing Science | Scoop.it

Graphene - a one-atom-thick layer of the stuff in pencils - is a better conductor than copper and is very promising for electronic devices, but with one catch: Electrons that move through it can't be stopped. Until now, that is. Scientists at Rutgers University-New Brunswick have learned how to tame the unruly electrons in graphene, paving the way for the ultra-fast transport of electrons with low loss of energy in novel systems. Their study was published online in Nature Nanotechnology.

 

"This shows we can electrically control the electrons in graphene," said Eva Y. Andrei, Board of Governors professor in Rutgers' Department of Physics and Astronomy in the School of Arts and Sciences and the study's senior author. "In the past, we couldn't do it. This is the reason people thought that one could not make devices like transistors that require switching with graphene, because their electrons run wild."

 

Now it may become possible to realize a graphene nano-scale transistor, Andrei said. Thus far, graphene electronics components include ultra-fast amplifiers, supercapacitors and ultra-low resistivity wires. The addition of a graphene transistor would be an important step towards an all-graphene electronics platform. Other graphene-based applications include ultra-sensitive chemical and biological sensors, filters for desalination and water purification. Graphene is also being developed in flat flexible screens, and paintable and printable electronic circuits.

 

Graphene is a nano-thin layer of the carbon-based graphite that pencils write with. It is far stronger than steel and a great conductor. But when electrons move through it, they do so in straight lines and their high velocity does not change. "If they hit a barrier, they can't turn back, so they have to go through it," Andrei said. "People have been looking at how to control or tame these electrons."

 

Her team managed to tame these wild electrons by sending voltage through a high-tech microscope with an extremely sharp tip, also the size of one atom. They created what resembles an optical system by sending voltage through a scanning tunneling microscope, which offers 3-D views of surfaces at the atomic scale. The microscope's sharp tip creates a force field that traps electrons in graphene or modifies their trajectories, similar to the effect a lens has on light rays. Electrons can easily be trapped and released, providing an efficient on-off switching mechanism, according to Andrei.


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Yatakemycin: Deciphering a DNA toxin's secrets

Yatakemycin: Deciphering a DNA toxin's secrets | Amazing Science | Scoop.it
A team of Vanderbilt University researchers have worked out the molecular details that explain how one of the most potent bacterial toxins known -- yatakemycin (YTM) -- kills cells by preventing their DNA from replicating.

 

One of the most potent toxins known acts by welding the two strands of the famous double helix together in a unique fashion which foils the standard repair mechanisms cells use to protect their DNA. A team of Vanderbilt University researchers have worked out the molecular details that explain how this bacterial toxin -- yatakemycin (YTM) -- prevents DNA replication. Their results, described in a paper published online July 24 by Nature Chemical Biology, explain YTM's extraordinary toxicity and could be used to fine-tune the compound's impressive antimicrobial and antifungal properties.

 

YTM is produced by some members of the Streptomyces family of soil bacteria to kill competing strains of bacteria. It belongs to a class of bacterial compounds that are currently being tested for cancer chemotherapy because their toxicity is extremely effective against tumor cells.

 

"In the past, we have thought about DNA repair in terms of protecting DNA against different kinds of chemical insults," said Professor of Biological Sciences Brandt Eichman. "Now, toxins like YTM are forcing us to consider their role as part of the ongoing chemical warfare that exists among bacteria, which can have important side effects on human health."

 

Cells have developed several basic types of DNA repair, including base excision repair (BER) and nucleotide excision repair (NER). BER generally fixes small lesions and NER removes large, bulky lesions.

 

A number of DNA toxins create bulky lesions that destabilize the double helix. However, some of the most toxic lesions bond to both strands of DNA, thereby preventing the cell's elaborate replication machinery from separating the DNA strands so they can be copied. Normally, this distorts the DNA's structure, which allows NER enzymes to locate the lesion and excise it.

 

"YTM is different," said postdoctoral fellow Elwood Mullins. "Instead of attaching to DNA with multiple strong covalent bonds, it forms a single covalent bond and a large number of weaker, polar interactions. As a result, it stabilizes the DNA instead of destabilizing it, and it does so without distorting the DNA structure so NER enzymes can't find it."

 

"We were shocked by how much it stabilizes DNA," Eichman added. "Normally, the DNA strands that we used in our experiments separate when they are heated to about 40 degrees [Celsius] but, with YTM added, they don't come apart until 85 degrees."

 

The Streptomyces bacteria that produce YTM have also evolved a special enzyme to protect their own DNA from the toxin. Surprisingly, this is a base excision repair enzyme -- called a DNA glycosylase -- that is normally limited to repairing small lesions, not the bulky adducts caused by YTM. Nevertheless, studies have shown that it is extremely effective.

 

It so happens that one of Streptomyces' competitors, Bacillus cereus, has managed to co-opt the gene that produces this particular enzyme. In Bacillus, however, the enzyme it produces -- called AlkD -- provides only limited protection.

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Extended Periodic Table

Extended Periodic Table | Amazing Science | Scoop.it

An extended periodic table theorizes about elements beyond oganesson (beyond period 7, or row 7). Currently seven periods in the periodic table of chemical elements are known and proven, culminating with atomic number 118, which completes the seventh row. If further elements with higher atomic numbers than this are discovered, they will be placed in additional periods, laid out (as with the existing periods) to illustrate periodically recurring trends in the properties of the elements concerned. Any additional periods are expected to contain a larger number of elements than the seventh period, as they are calculated to have an additional so-called g-block, containing at least 18 elements with partially filled g-orbitals in each period.

 

An eight-period table containing this block was suggested by Glenn T. Seaborg in 1969.[1][2] IUPAC defines an element to exist if its lifetime is longer than 10−14 seconds, which is the time it takes for the nucleus to form an electron cloud.[3] No elements in this region have been synthesized or discovered in nature.[4] The first element of the g-block may have atomic number 121, and thus would have the systematic name unbiunium. Elements in this region are likely to be highly unstable with respect to radioactive decay, and have extremely short half lives, although element 126 is hypothesized to be within an island of stability that is resistant to fission but not to alpha decay. It is not clear how many elements beyond the expected island of stability are physically possible, whether period 8 is complete, or if there is a period 9.

 

According to the orbital approximation in quantum mechanical descriptions of atomic structure, the g-block would correspond to elements with partially filled g-orbitals, but spin-orbit coupling effects reduce the validity of the orbital approximation substantially for elements of high atomic number. While Seaborg's version of the extended period had the heavier elements following the pattern set by lighter elements, as it did not take into account relativistic effects; models that take relativistic effects into account do not. Pekka Pyykkö and Burkhard Fricke used computer modeling to calculate the positions of elements up to Z = 172, and found that several were displaced from the Madelung rule.[5][6]

 

Richard Feynman noted[7] that a simplistic interpretation of the relativistic Dirac equation runs into problems with electron orbitals at Z > 1/α ≈ 137 as described in the sections below, suggesting that neutral atoms cannot exist beyond element 137, and that a periodic table of elements based on electron orbitals therefore breaks down at this point. On the other hand, a more rigorous analysis calculates the limit to be Z ≈ 173.

 

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Scientists discover a 2-D magnet

Scientists discover a 2-D magnet | Amazing Science | Scoop.it

Magnetic materials form the basis of technologies that play increasingly pivotal roles in our lives today, including sensing and hard-disk data storage. But as our innovative dreams conjure wishes for ever-smaller and faster devices, researchers are seeking new magnetic materials that are more compact, more efficient and can be controlled using precise, reliable methods.

 

A team led by the University of Washington and the Massachusetts Institute of Technology has for the first time discovered magnetism in the 2-D world of monolayers, or materials that are formed by a single atomic layer. The findings, published June 8 in the journal Nature, demonstrate that magnetic properties can exist even in the 2-D realm -- opening a world of potential applications.

 

"What we have discovered here is an isolated 2-D material with intrinsic magnetism, and the magnetism in the system is highly robust," said Xiaodong Xu, a UW professor of physics and of materials science and engineering, and member of the UW's Clean Energy Institute. "We envision that new information technologies may emerge based on these new 2-D magnets."

 

Xu and MIT physics professor Pablo Jarillo-Herrero led the international team of scientists who proved that the material -- chromium triiodide, or CrI3 -- has magnetic properties in its monolayer form. Other groups, including co-author Michael McGuire at the Oak Ridge National Laboratory, had previously shown that CrI3 -- in its multilayered, 3-D, bulk crystal form -- is ferromagnetic. In ferromagnetic materials, the "spins" of constituent electrons, analogous to tiny, subatomic magnets, align in the same direction even without an external magnetic field.

 

But no 3-D magnetic substance had previously retained its magnetic properties when thinned down to a single atomic sheet. In fact, monolayer materials can demonstrate unique properties not seen in their multilayered, 3-D forms. "You simply cannot accurately predict what the electric, magnetic, physical or chemical properties of a 2-D monolayer crystal will be based on the behavior of its 3-D bulk counterpart," said co-lead author and UW doctoral student Bevin Huang.

 

Atoms within monolayer materials are considered "functionally" two-dimensional because the electrons can only travel within the atomic sheet, like pieces on a chessboard. To discover the properties of CrI3 in its 2-D form, the team used Scotch tape to shave a monolayer of CrI3 off the larger, 3-D crystal form. "Using Scotch tape to exfoliate a monolayer from its 3-D bulk crystal is surprisingly effective," said co-lead author and UW doctoral student Genevieve Clark. "This simple, low-cost technique was first used to obtain graphene, the 2-D form of graphite, and has been used successfully since then with other materials."

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The prototype of a chemical computer detects a sphere

The prototype of a chemical computer detects a sphere | Amazing Science | Scoop.it

Chemical computers are becoming ever more of a reality - this is being proven by scientists from the Institute of Physical Chemistry of the Polish Academy of Sciences in Warsaw. It turns out that after an appropriate teaching procedure even a relatively simple chemical system can perform non-trivial operations. In their most recent computer simulations researchers have shown that correctly programmed chemical matrices of oscillating droplets can recognize the shape of a sphere with great accuracy.

 

Modern computers use electronic signals for their calculations, that is, physical phenomena related to the movement of electric charges. Information can, however, be processed in many ways. For some time now efforts have been underway worldwide to use chemical signals for this purpose. For the time being, however, the resulting chemical systems perform only the simplest logic operations. Meanwhile, researchers from the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS) in Warsaw have demonstrated that even uncomplicated and easy-to-produce collections of droplets, in which oscillating chemical reactions proceed, can process information in a useful way, e.g. recognizing the shape of a specified three-dimensional object with great accuracy or correctly classifying cancer cells into benign or malignant.

 

"A lot of work being currently carried out in laboratories focuses on building chemical equivalents of standard logic gates. We took a different approach to the problem," says Dr. Konrad Gizynski (IPC PAS) and explains: "We investigate systems of a dozen-or-so to a few dozen drops in which chemical signals propagate, and treat each one as a whole, as a kind of neuronal network. It turns out that such networks, even very simple ones, after a short teaching procedure manage well with fairly sophisticated problems. For instance, our newest system has ability to recognize the shape of a sphere in a set of x, y, z spatial coordinates".

 

The systems being studied at the IPC PAS work thanks to the Belousov-Zhabotinsky reaction proceeding in individual drops. This reaction is oscillatory: after the completion of one oscillation cycle the reagents necessary to begin the next cycle are regenerated in the solution. A droplet is a batch reactor. Before reagents are depleted a droplet has usually performed from a few dozen to a few hundred oscillations. The time evolution of a droplet is easy to observe, since its catalyst, ferroin, changes color during the cycle. In a thin layer of solution the effect is spectacular: colorful strips - chemical fronts - traveling in all directions appear in the liquid. Fronts can also be seen in the droplets, but in practice the phase of the cycle is indicated just by the color of the droplet: when the cycle begins, the droplet rapidly turns blue (excites), after which it gradually returns to its initial state, which is red.

 

"Our systems basically work by mutual communication between droplets: when the droplets are in contact, the chemical excitation can be transmitted from droplet to droplet. In other words, one droplet can trigger the reaction in the next! It is also important that an excited droplet cannot be immediately excited once again. Speaking somewhat colloquially, before the next excitation it has to 'have a rest', in order to return to its original state," explains Dr. Gizynski.


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Novel compound that engages 'second arm' of immune system reduces breast tumors and metastases

Novel compound that engages 'second arm' of immune system reduces breast tumors and metastases | Amazing Science | Scoop.it
Dana-Farber scientists report that a compound able to reverse the allegiance of innate immune system cells – turning them from tumor enablers into tumor opponents – caused breast tumors in mice to shrink and withdraw from distant metastases.

 

In a new study in the journal Nature, Dana-Farber Cancer Institute scientists report that a compound able to reverse the allegiance of innate immune system cells -- turning them from tumor enablers into tumor opponents -- caused breast tumors in mice to shrink and withdraw from distant metastases. When combined with chemotherapy or another immunotherapy, the new compound significantly extended the period of tumor remission.

 

The findings suggest a way to bring the full repertoire of the immune system to bear on cancer in humans, the authors said.

"Most current forms of cancer immunotherapy influence the behavior of T cells -- white blood cells that are part of the adaptive immune system -- by 'teaching' them to attack tumor cells or removing impediments to such an attack," said the study's lead author Jennifer Guerriero, PhD, of Dana-Farber. "This strategy has been effective against several types of cancer, but generally only a subset of patients benefit. We wanted to see if harnessing both arms of the immune system could produce superior results."

 

The targets of the new study were innate immune system cells known as tumor-associated macrophages (TAMs). They're often found deeply embedded within tumors, but although they're part of the immune system -- the body's defense against disease -- they frequently promote tumor growth. In doing so, they're responding to cues issued by the tumor itself.

 

The roles that macrophages play -- whether protective or destructive -- depend on signals from their environment. In wound healing, for example, macrophages marshal the elements of the immune system that clear away damaged tissue and restore the affected area. Tumor macrophages manage to hijack some of these supportive functions for their own purposes. Not without reason is cancer sometimes referred to as a wound that doesn't heal.

 

In previous research, the Dana-Farber scientists and their colleagues showed that a compound known as TMP195 could convert TAMs from aiding tumor growth to organizing an attack on it. A selective, first-in-class, class IIa HDAC inhibitor, TMP195 switches the macrophage response by altering gene activity within TAMs.

 

In this current study, TMP195 sharply reduced the rate of tumor growth in mice with breast tumors, researchers found. They next combined TMP195 with various chemotherapy regimens and with a form of immunotherapy known as T-cell checkpoint blockade. In both cases, the combinations produced longer-lasting remissions of breast cancer than TMP195 alone did.

 

"Once they've undergone conversion, macrophages act as the orchestrators of the immune system attack on the tumor," said Anthony Letai, MD, PhD, of Dana-Farber, co-senior author of the study with Michael A. Nolan, PhD, of GlaxoSmithKline. "Our findings demonstrate that class IIa HDAC inhibitors can be an effective way of harnessing the anti-tumor potential of macrophages in cancer therapy.

 

"The future of cancer treatment is likely to involve combinations of therapies that act on both the innate and adaptive arms of the immune system, as well as therapies, such as chemotherapy, radiation therapy, or targeted therapy, that act on cancer cells themselves," he continued. "The ability to engage the innate immune system is an exciting new front in cancer therapy."

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Human activity helps create hundreds of new minerals

Human activity helps create hundreds of new minerals | Amazing Science | Scoop.it
It took billions of years for most of the Earth's minerals to form, but scientists say hundreds more have been created in the years since the industrial revolution.

 

Human-made minerals created in the years since the industrial revolution have been uncovered by scientists, who want them to be accepted as real minerals. Armed with the discovery, they are pushing to have the geological time scale recognise 'the Anthropocene' time period — or the epoch of human activity.

 

"We define different periods of Earth history by the distinctive things we find in them," said Robert Hazen, a mineralogist at Washington's Carnegie Institution for Science. "They [the minerals] would tell future geologists that something was different about this layer — I think there is no question about it."

 

The new minerals were created by chance, when substances that would otherwise have never encountered one another came into contact as a result of human activity.

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Chemists just created something thought imporssibe: a Stable Helium Compound

Chemists just created something thought imporssibe: a Stable Helium Compound | Amazing Science | Scoop.it

If you remember your high school chemistry, you'll know that helium is a bit of an oddball. This noble gas is the least reactive element on the periodic table, and thanks to its full outer shell, conventional wisdom states that helium cannot interact with other atoms to create stable compounds.

 

While other noble gas elements have shown signs of forming compounds under extreme pressure, helium has remained firmly exclusive - until now. Scientists report creating what appears to be a stable helium-sodium compound, and it challenges some of the most basic assumptions of modern chemistry.

 

"Chemistry changes when you apply high pressure, and this can be achieved inside our Earth and on different planets like Saturn," one of the team, Ivan Popov from Utah State University, told Ryan F. Mandelbaum at Gizmodo. "But this is a book changer." 

 

If you need a bit of a refresher on your chemistry facts, helium is the second most abundant element in the Universe, and belongs to a six-member group of elements called the noble gases - so-called because of an apparent 'aloofness' that prevents them from easily forming compounds with other elements.

 

Since earning their 'noble' reputation, some of these gases have shown signs of reactiveness under extreme conditions - you can actually split the noble gases up into two groups, with krypton, xenon, and radon considered to be relatively reactive, and argon, neon, and helium considered to be very unreactive.

Researchers have found ways to pair up helium with other elements in the past, but until now, the result has always been fleeting. 

 

One of the most common examples of helium interacting with other elements refers to van der Waals forces - attractive or repulsive forces that don't require conventional covalent or ionic bonds to form.

 

Being one of the most abundant elements in the Universe, responsible for forming stars and gas giant planets, helium could play by very different rules out in space and deep within our planet, and researchers have just found the first evidence yet of that weird behavior.

 

"Extremely high pressure, like that found at Earth's core or giant neighbours, completely alters helium's chemistry," one of the team, Alex Boldyrev from Utah State, told Mary-Ann Muffoletto at Phys.org.

 

The researchers used a 'crystal structure-predicting' computer model to predict that under extreme pressures, a stable helium-sodium compound could form.  They then physically created the never-before-seen compound, Na2He, in a diamond anvil cell experiment, which allowed them to subject helium and sodium atoms to pressures of around 1.1 million times Earth's atmospheric pressure.

 

"These findings were so unexpected, Boldyrev says, that he and colleagues struggled for more than two years to convince science reviewers and editors to publish their results," says Muffoletto.

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Metallic hydrogen, once theory, becomes reality

Metallic hydrogen, once theory, becomes reality | Amazing Science | Scoop.it
Nearly a century after it was theorized, Harvard scientists have succeeded in creating the rarest - and potentially one of the most valuable - materials on the planet.

 

The material - atomic metallic hydrogen - was created by Thomas D. Cabot Professor of the Natural Sciences Isaac Silvera and post-doctoral fellow Ranga Dias. In addition to helping scientists answer fundamental questions about the nature of matter, the material is theorized to have a wide range of applications, including as a room-temperature superconductor. The creation of the rare material is described in a January 26 2017 paper published in Science.

 

"This is the holy grail of high-pressure physics," Silvera said. "It's the first-ever sample of metallic hydrogen on Earth, so when you're looking at it, you're looking at something that's never existed before."

 

To create it, Silvera and Dias squeezed a tiny hydrogen sample at 495 gigapascal, or more than 71.7 million pounds-per-square inch - greater than the pressure at the center of the Earth. At those extreme pressures, Silvera explained, solid molecular hydrogen -which consists of molecules on the lattice sites of the solid - breaks down, and the tightly bound molecules dissociate to transforms into atomic hydrogen, which is a metal.

 

While the work offers an important new window into understanding the general properties of hydrogen, it also offers tantalizing hints at potentially revolutionary new materials.

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Scientists develop a portable drug-manufacturing system for vaccines

Scientists develop a portable drug-manufacturing system for vaccines | Amazing Science | Scoop.it

As much as 80 per cent of the cost of bringing vaccines to the developing world comes from ensuring that the medications are properly refrigerated and transported. 

 

A team of researchers from the University of Toronto, MIT, Harvard, and the University of Ottawa have developed a new portable drug-manufacturing system that uses two sets of freeze-dried pellets, which when mixed with water, are able to produce medications, vaccines and diagnostic tools virtually anywhere in the world.

 

The team published a proof-of-principle paper in Cell that details the development of a drug manufacturing system that's able to produce on-site, on-demand therapeutics and biomolecules. 

“In essence, it’s like having a portable pharmacy that you can use to create the medications you need,” said Assistant Professor Keith Pardee of U of T’s Faculty of Pharmacy, co-lead author of the paper. 

 

Most vaccines need to maintain a consistent temperature to prevent spoilage and maintain their efficacy, which necessitates a cold chain from production to application.  Despite these precautions and the attention paid to their transportation, the World Health Organization and United Nations Children’s Fund estimate that the amount of essential vaccines that end up wasted could be as high as 50 per cent.

 

The possible applications for this new system, Pardee explains, are almost endless.  “If, for example, the influenza vaccine developed in a given year is off target and doesn't fight the strains of the virus that emerge, the system we’ve developed can address that,” he said. “The current production chain for the influenza vaccine begins in late spring early summer for fall and winter application. If the formula is wrong, it would take months to change, produce, ship, and administer a vaccine that hits on the right strains.

 

“Whereas with our system, in theory, once the proper strains are identified and a new formula developed, the vaccine could be produced anywhere in a matter of hours. The materials would already be on the shelf – they’d just need to be programmed to produce the vaccine. While this is just a proof-of-concept study, this could mean no prolonged production time, no timely and expensive shipping.”

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