At a distance of less than a light wave, nanocamera takes pictures

A July 17, 2014 University of Illinois College of Engineering news release (also on EurekAlert) features a research breakthrough,

How is it possible to record optically encoded information for distances smaller than the wavelength of light?

Researchers at the University of Illinois at Urbana-Champaign have demonstrated that an array of novel gold, pillar-bowtie nanoantennas (pBNAs) can be used like traditional photographic film to record light for distances that are much smaller than the wavelength of light (for example, distances less than ~600 nm for red light). A standard optical microscope acts as a “nanocamera” whereas the pBNAs are the analogous film.

Here’s an image the researchers have provided to illustrate their work,

We demonstrate the plasmonic equivalent of photographic film for recording optical intensity in the near field. The plasmonic structure is based on gold bowtie nanoantenna arrays fabricated on SiO2 pillars. We show that it can be employed for direct laser writing of image data or recording the polarization structure of optical vector beams.[downloaded from http://pubs.acs.org/doi/abs/10.1021/nl501788a]

We demonstrate the plasmonic equivalent of photographic film for recording optical intensity in the near field. The plasmonic structure is based on gold bowtie nanoantenna arrays fabricated on SiO2 pillars. We show that it can be employed for direct laser writing of image data or recording the polarization structure of optical vector beams.[downloaded from http://pubs.acs.org/doi/abs/10.1021/nl501788a]

The news release describes the technique,

“Unlike conventional photographic film, the effect (writing and curing) is seen in real time,” explained Kimani Toussaint, an associate professor of mechanical science and engineering, who led the research. “We have demonstrated that this multifunctional plasmonic film can be used to create optofluidic channels without walls. Because simple diode lasers and low-input power densities are sufficient to record near-field optical information in the pBNAs, this increases the potential for optical data storage applications using off-the-shelf, low-cost, read-write laser systems.”

“Particle manipulation is the proof-of-principle application,” stated Brian Roxworthy, first author of the group’s paper, “Multifunctional Plasmonic Film for Recording Near-Field Optical Intensity,” published in the journal, Nano Letters. “Specifically, the trajectory of trapped particles in solution is controlled by the pattern written into the pBNAs. This is equivalent to creating channels on the surface for particle guiding except that these channels do not have physical walls (in contrast to those optofluidics systems where physical channels are fabricated in materials such as PDMS).”

To prove their findings, the team demonstrated various written patterns—including the University’s “Block I” logo and brief animation of a stick figure walking—that were either holographically transferred to the pBNAs or laser-written using steering mirrors (see video).

The news release concludes with,

“We wanted to show the analogy between what we have made and traditional photographic film,” Toussaint added. “There’s a certain cool factor with this. However, we know that we’re just scratching the surface since the use of plasmonic film for data storage at very small scales is just one application. Our pBNAs allow us to do so much more, which we’re currently exploring.”

The researchers noted that the fundamental bit size is currently set by the spacing of the antennas at 425-nm. However, the pixel density of the film can be straightforwardly reduced by fabricating smaller array spacing and a smaller antenna size, as well as using a more tightly focusing lens for recording.

“For a standard Blu-ray/DVD disc size, that amounts to a total of 28.6 gigabites per disk,” Roxworthy added. “With modifications to array spacing and antenna features, it’s feasible that this value can be scaled to greater than 75 gigabites per disk. Not to mention, it can be used for other exciting photonic applications, such as lab-on-chip nanotweezers or sensing.”

“In our new technique, we use controlled heating via laser illumination of the nanoantennas to change the plasmonic response instantaneously, which shows an innovative but easy way to fabricate spatially changing plasmonic structures and thus opens a new avenue in the field of nanotech-based biomedical technologies and nano optics,”  said Abdul Bhuiya, a co-author and member of the research team.

Here’s a link to and a citation for the paper,

Multifunctional Plasmonic Film for Recording Near-Field Optical Intensity by Brian J. Roxworthy, Abdul M. Bhuiya, V. V. G. Krishna Inavalli, Hao Chen, and Kimani C. Toussaint , Jr. Nano Lett., Article ASAP DOI: 10.1021/nl501788a Publication Date (Web): July 14, 2014
Copyright © 2014 American Chemical Society

This paper is behind a paywall.

Mathematicians, political scientists, and cake cutting

If you have a sibling, you’ve likely fought at least once over who got the biggest or ‘best’ piece of cake.  (I do and I did.) In any event, it seems that mathematicians and political scientists have been working on a scheme to avoid disputes over cake.

[downloaded from http://link.springer.com/article/10.1007%2Fs00283-013-9442-0#page-1]

A July 16, 2014 Springer news release (also on EurekAlert) describes the quest for fairly sized cake slices and how that might apply to real life issues such as sharing property,

The next time your children quibble about who gets to eat which part of a cake, call in some experts on the art of sharing. Mathematician Julius Barbanel of Union College, and political scientist Steven Brams of New York University, both in the US, published an algorithm in Springer’s The Mathematical Intelligencer by which they show how to optimally share cake between two people efficiently, in equal pieces and in such a way that no one feels robbed.

The cut-and-choose method to share divisible goods has been regarded as fair and envy-free since Biblical times, when Abraham divided land equally, and Lot could choose the part he wanted. But being free of envy is not the only consideration when sharing something. What happens when more than two cuts can be made, or when people prefer different, specific sections of whatever is to be divided? Barbanel and Brams believe that with a giveback procedure it is possible to make a perfect division between two people that is efficient, equitable and void of jealousy.

An objective referee (such as a Mom or a computer) is essential to the plan. The potential cake eaters first tell the referee which parts of the delicacy they value most. In mathematical terms these are called someone’s probability density functions, or pdfs. The referee then marks out the cake at all points were the pdfs of the disgruntled would-be cake eaters cross, and assigns portions. If at this point the two parties receive the same size of cake, the task is over. If not, the giveback process starts.

The party who received the larger part of the cake during the first round must give a part of it back to the other person, starting with those parts in which the ratio of their pdfs is the smallest. This goes on until the parties value their portions equally, and have the same volume of cake to eat. This method only works with a finite number of cuts if the players’ pdfs are straight-lined, or are so-called piecewise linear sections.

The researchers believe the method can be used to share cake and other divisible goods such as land. In the case of beachfront property being co-owned by two developers, for example, it can help to determine who gets what strips of land to build on based on the pieces of land they value most.

“This allocation is not only equitable but also envy-free and efficient – that is, perfect,” says Barbanel.

“This approach focuses on proving the existence of efficient and envy-free divisions, not on providing algorithms to finding them,” emphasizes Brams.

Here’s a link to and a citation for the paper,

Two-Person Cake Cutting: The Optimal Number of Cuts by Julius B. Barbanel and Steven J. Brams. The Mathematical Intelligencer March 2014 DOI 10.1007/s00283-013-9442.

This paper is behind a paywall although there is a free preview available and a special summer discount (30%) on the purchase price until July 31, 2014.

Turing film, Imitation Game, gets European première at London Film Festival; will world première be at Toronto International Film Fest?

There’s quite a cast associated with “Imitation Game,” a film which focuses on Alan Turing’s years as a codebreaker during World War II and will be enjoying its European première at the BFI [British Film Institute?] London Film Festival on Oct. 8, 2014 according to a July 21, 2014 BBC (British Broadcasting Corporation) news item online.

The cast includes Mark Strong as,

Major General Sir Stewart Graham Menzies, KCB KCMG DSO MC (/ˈmɪŋɪz/; 30 January 1890 – 29 May 1968) was Chief of MI6 (SIS), British Secret Intelligence Service, during and after the Second World War. (see the rest of Menzies’ Wikipedia entry here along with all the links)

Strong always offers a compelling performance and he is billed alongside, Benedict Cumberbatch (BCC Sherlock) as Alan Turing, Keira Knightley as Turing’s friend and colleague in what are described in the BBC online news item as “extraordinary performances,”

The Imitation Game follows the race against time as Turing and his team at the top-secret codebreaking centre at Bletchley Park attempt to decipher German naval messages and help end the war.

Matthew Goode, Mark Strong, Rory Kinnear and Charles Dance also star.

Festival director Clare Stewart said the film featured “extraordinary performances”.

A July 21, 2014 news item by Nick Vivarelli for Variety describes the film and upcoming première (aka preem; Note: A link has been removed),

Norwegian helmer Morten Tyldum’s Alan Turing drama “The Imitation Game,” with Benedict Cumberbatch and Keira Knightley, will open the 58th BFI London Film Festival on October 8th, marking the pic’s European preem.

The biopic based on the life story of the crypotgrapher and mathematician who cracked the German “Enigma Code” during WWII, and was later prosecuted by the British government in the early 1950s for being a homosexual, will screen in London’s Odeon Leicester Square, with key cast, Cumberbatch and Knightley, and helmer Tyldum, expected on the red carpet.

A July 21, 2014 article by Andrew Pulver for the Guardian notes the emphasis on the Oct. 8, 2014 event as a ‘European’ première,

Directed by Morten Tyldum and co-starring Keira Knightley as Turing’s friend and fellow code-breaker Joan Clarke, the London film festival screening is being billed as a European premiere, which suggests the film’s world premiere will be held outside Europe, most likely at the Toronto film festival in early September.

The London film festival runs from 8-19 October [2014].

Here’s a trailer for the film; (it looks pretty good to me),


Widespread release for the film is scheduled for early November 2014. I have not been able to confirm that “Imitation Game” will be at TIFF in early September 2014.

Turing has been mentioned here many times but my June 20, 2012 posting is the most comprehensive,

Alan Turing led one of those lives that seems more like an act of fiction than anything else. Born June 23, 1912, the centenary is being celebrated in the UK and internationally as he was an instrumental figure in the field of science.

He had quite an extraordinary life unto a death, which could be described as enigmatic. It is not clear whether he committed suicide or accidentally killed himself with cyanide. A half-eaten apple was found by his bedside but never tested for poison. (Snow White was Turing’s favourite fairy tale.) His death came after shortly completing a court-ordered course of chemical castration (he could have chosen imprisonment instead) on being found guilty of homosexuality.

You can find out more about the BFI London Film Festival here and about the Toronto International Film Festival here. There is a July 21, 2014 posting by Sarah on Lainey Gossip speculation about this film and Benedict Cumberbatch’s chances of an Academy Award (Oscar) nomination along with speculation about possible competitors.

ETA July 22, 2014, 1130 PDT: Imitation Game is getting its Canadian première at the 2014 TIFF (media release PDF p. 5). H/T Lainey Gossip (scroll down about 40% of the way.

Extracting biomolecules from live cells with carbon nanotubes

Being able to extract biomolecules from living cells means nondestruction of the rest of the cell and the ability to observe the consequences of the extraction. From a July 18, 2014 news item on Azonano,

University of Houston researchers have devised a new method for extracting molecules from live cells without disrupting cell development, work that could provide new avenues for the diagnosis of cancer and other diseases.

The researchers used magnetized carbon nanotubes to extract biomolecules from live cells, allowing them to retrieve molecular information without killing the individual cells. A description of the work appears this week in the Proceedings of the National Academy of Sciences.

A July 16, 2014 University of Houston news release by Jeannie Kever, which originated the news item, provides more detail,

Most current methods of identifying intracellular information result in the death of the individual cells, making it impossible to continue to gain information and assess change over time, said Zhifeng Ren, M.D. Anderson Chair professor of physics and principal investigator at the Center for Superconductivity at UH and lead author of the paper. The work was a collaboration between Ren’s lab and that of Paul Chu, T.L.L. Temple Chair of Science and founding director of the Texas Center for Superconductivity.

Chu, a co-author of the paper, said the new technique will allow researchers to draw fundamental information from a single cell.The researchers said the steps outlined in the paper offer proof of concept. Ren said the next step “will be more study of the biological and chemical processes of the cell, more analysis.”

The initial results hold promise for biomedicine, he said.  “This shows how nanoscience and nanoengineering can help the medical field.”

Cai said the new method will be helpful for cancer drug screening and carcinogenesis study, as well as for studies that allow researchers to obtain information from single cells, replacing previous sampling methods that average out cellular diversity and obscure the specificity of the biomarker profiles.

In the paper, the researchers explain their rationale for the work – most methods for extracting molecular information result in cell death, and those that do spare the cell carry special challenges, including limited efficiency.

This method is relatively straightforward, requiring the use of magnetized carbon nanotubes as the transporter and a polycarbonate filter as a collector, they report. Cells from a human embryonic kidney cancer cell line were used for the experiment.

The work builds on a 2005 paper published by Ren’s group in Nature Methods, which established that magnetized carbon nanotubes can deliver molecular payloads into cells. The current research takes that one step further to move molecules out of cells by magnetically driving them through the cell walls.

The carbon nanotubes were grown with a plasma-enhanced chemical vapor deposition system, with magnetic nickel particles enclosed at the tips. A layer of nickel was also deposited along the surface of individual nanotubes in order to make the nanotubes capable of penetrating a cell wall guided by a magnet.

Here’s a link to and a citation for the paper,

Molecular extraction in single live cells by sneaking in and out magnetic nanomaterials by Zhen Yang, Liangzi Deng, Yucheng Lan, Xiaoliu Zhang, Zhonghong Gao, Ching-Wu Chu, Dong Cai, and Zhifeng Ren. PNAS 2014 ; published ahead of print July 16, 2014, doi:10.1073/pnas.1411802111

This paper is behind a paywall.

Mining uranium from the ocean

We are running short of uranium as terrestrial mining of this element has become more hazardous environmentally. A July 18, 2014 news item on Azonano highlights an ‘ocean mining’ uranium project at the University of Alabama (US),

The U.S. Department of Energy [DOE] selected a University of Alabama [UA] start-up company for an approximate $1.5 million award to refine an alternative material to potentially extract uranium from the ocean.

Uranium, which naturally occurs in seawater and in the Earth’s crust, is the fuel for nuclear power. For decades, scientists have sought a more economical and efficient way to remove it from the ocean, as the terrestrial supply is dwindling and environmentally unfriendly to mine.

A July 17, 2014 University of Alabama news release, which originated the news item, describe the University of Alabama’s unique approach to the problem of extracting uranium from the ocean (Note: A link has been removed),

“Every scientist in the world, except us, who is trying to do this is working with plastics,” said Dr. Gabriela Gurau, a chemist and CEO of the UA-based company, 525 Solutions.

Instead, the UA company is developing an adsorbent, biodegradable material made from the compound chitin, which is found in shrimp shells and in other crustaceans and insects. The researchers have developed transparent sheets, or mats, comprised of tiny chitin fibers, modified for the task. When suspended beneath the ocean’s surface, the mats are designed to withdraw uranium.

“Once you put it in the ocean, it will attract uranium like a magnet, and uranium will stick to it,” said Gurau, a University of Alabama alumna.

If one day implemented, the mats, with uranium attached, would be taken to an industrial plant where the nuclear fuel source would be removed.

Earlier work led by Dr. Robin Rogers, Robert Ramsay Chair of Chemistry at UA and director of UA’s Center for Green Manufacturing, initially proved the concept for extracting uranium using chitin. Rogers is an owner/founder of 525 Solutions and serves as a scientific adviser to the company’s representatives.

“The oceans are estimated to contain more than a thousand times the amount of uranium found in total in any known land deposit,” Rogers said. “Fortunately, the concentration of uranium in the ocean is very, very low, but the volume of the oceans is, of course, very, very high. Assuming we could recover only half of this resource, this much uranium could support 6,500 years of nuclear capacity.”

Removing chitin, in a pure form, from shells had previously proven difficult, but Rogers and his UA colleagues discovered a way to use a relatively new class of solvents, called ionic liquids, for removal. Ionic liquids are liquid salts which have other unique and desirable properties that traditional solvents do not. Rogers is recognized as a world-leader in the field of  ionic liquids.

UA researchers use a time-honored laboratory technique called electrospinning to produce the mats. In this process, the scientists use a specially-prepared, chitin-based, ionic liquid solution, which is loaded in the electrospinning apparatus. Some 30,000 volts of electricity are applied, spinning the fibers into a water bath. After several hours, nanofiber mats, consisting of fibers much thinner than a strand of a spider’s web, form, weaved together into a solid sheet.

The increased surface area the nanomats provide is central to the project, said Dr. Julia Shamshina, the company’s chief technology officer and also a UA alumna.

“The larger the surface area, the larger modifications we can make and the more uranium it will uptake,” Shamshina said. “If you have one very thick fiber and 10 which, when combined, equal the size of the thick fiber, the ten smaller ones will take up hundreds, or even thousands, of times more uranium.”

Rogers extolled the potential environmental benefits of  the company’s approach and addressed cost factors.

“Mining uranium from land is a very dirty, energy intensive process, with a lot of hazardous waste produced,” Rogers said. “If we eliminate land mining by mining from the ocean, we not only clean up the ocean, we eliminate all of the environmental problems with terrestrial mining.

“Research studies have shown that uranium can be extracted from the ocean, but the process remains prohibitively costly,” said Rogers, a  two-time UA graduate. “The search for more effective adsorbents — which is what we’re doing  – is under way and expected to solve this issue.”

Gurau said the two-year grant, from the DOE’s Office of Science through its Small Business Innovation Research and Small Business Technology Transfer programs, will enable the researchers to refine their processes, measure costs and conduct an environmental analysis.

“We need to know if it’s viable from an economic standpoint,” Gurau said. “I think this is a critical step in getting this to the pilot-plant stage.”

Corporate influence, nanotechnology regulation, and Friends of the Earth (FoE) Australia

The latest issue of the newsletter, Chain Reaction # 121, July 2014, published by Friends of the Earth (FoE) Australia features an article by Louise Sales ‘Corporate influence over nanotechnology regulation‘ that has given me pause. From the Sales article,

I recently attended an Organisation for Economic Co-operation and Development (OECD) seminar on the risk assessment and risk management of nanomaterials. This was an eye-opening experience that graphically illustrated the extent of corporate influence over nanotechnology regulation globally. Representatives of the chemical companies DuPont and Evonik; the Nanotechnology Industries Association; and the Business and Industry Advisory Committee to the OECD (BIAC) sat alongside representatives of countries such as Australia, the US and Canada and were given equal speaking time.

BIAC gave a presentation on their work with the Canadian and United States Governments to harmonise nanotechnology regulation between the two countries. [US-Canada Regulatory Cooperative Council] [emphasis mine] Repeated reference to the involvement of ‘stakeholders’ prompted me to ask if any NGOs [nongovernmental organizations] were involved in the process. Only in the earlier stages apparently − ‘stakeholders’ basically meant industry.

A representative of the Nanotechnology Industries Association told us about the European NANoREG project they are leading in collaboration with regulators, industry and scientists. This is intended to ‘develop … new testing strategies adapted to innovation requirements’ and to ‘establish a close collaboration among authorities, industry and science leading to efficient and practically applicable risk management approaches’. In other words industry will be helping write the rules.

Interestingly, when I raised concerns about this profound intertwining of government and industry with one of the other NGO representatives they seemed almost dismissive of my concerns. I got the impression that most of the parties concerned thought that this was just the ‘way things were’. As under-resourced regulators struggle with the regulatory challenges posed by nanotechnology − the offer of industry assistance is probably very appealing. And from the rhetoric at the meeting one could be forgiven for thinking that their objectives are very similar − to ensure that their products are safe. Right? Wrong.

I just published an update about the US-Canada Regulatory Cooperation Council (RCC; in  my July 14, 2014 posting) where I noted the RCC has completed its work and final reports are due later this summer. Nowhere in any of the notices is there mention of BIAC’s contribution (whatever it might have been) to this endeavour.

Interestingly. BIAC is not an OECD committee but a separate organization as per its About us page,

BIAC is an independent international business association devoted to advising government policymakers at OECD and related fora on the many diversified issues of globalisation and the world economy.

Officially recognised since its founding in 1962 as being representative of the OECD business community, BIAC promotes the interests of business by engaging, understanding and advising policy makers on a broad range of issues with the overarching objectives of:

  • Positively influencing the direction of OECD policy initiatives;

  • Ensuring business and industry needs are adequately addressed in OECD policy decision instruments (policy advocacy), which influence national legislation;

  • Providing members with timely information on OECD policies and their implications for business and industry.

Through its 38 policy groups, which cover the major aspects of OECD work most relevant to business, BIAC members participate in meetings, global forums and consultations with OECD leadership, government delegates, committees and working groups.

I don’t see any mention of safety either in the excerpt or elsewhere on their About us page.

As Sales notes in her article,

Ultimately corporations have one primary driver and that’s increasing their bottom line.

I do wonder why there doesn’t seem to have been any transparency regarding BIAC’s involvement with the RCC and why no NGOs (according to Sales) were included as stakeholders.

While I sometimes find FoE and its fellow civil society groups a bit shrill and over-vehement at times, It never does to get too complacent. For example, who would have thought that General Motors would ignore safety issues (there were car crashes and fatalities as a consequence) over the apparently miniscule cost of changing an ignition switch. From What is the timeline of the GM recall scandal? on Vox.com,

March 2005: A GM project engineering manager closed the investigation into the faulty switches, noting that they were too costly to fix. In his words: “lead time for all solutions is too long” and “the tooling cost and piece price are too high.” Later emails unearthed by Reuters suggested that the fix would have cost GM 90 cents per car. [emphasis mine]

March 2007: Safety regulators inform GM of the death of Amber Rose, who crashed her Chevrolet Cobalt in 2005 after the ignition switch shut down the car’s electrical system and air bags failed to deploy. Neither the company nor regulators open an investigation.

End of 2013: GM determines that the faulty ignition switch is to blame for at least 31 crashes and 13 deaths.

According to a July 17, 2014 news item on CBC (Canadian Broadcasting Corporation) news online, Mary Barra, CEO of General Motors, has testified on the mater before the US Senate for a 2nd time, this year,

A U.S. Senate panel posed questions to a new set of key players Thursday [July 17, 2014] as it delves deeper into General Motors’ delayed recall of millions of small cars.

An internal report found GM attorneys signed settlements with the families of crash victims but didn’t tell engineers or top executives about mounting problems with ignition switches. It also found that GM’s legal staff acted without urgency.

GM says faulty ignition switches were responsible for at least 13 deaths. It took the company 11 years to recall the cars.

Barra will certainly be asked about how she’s changing a corporate culture that allowed a defect with ignition switches to remain hidden from the car-buying public for 11 years. It will be Barra’s second time testifying before the panel.

H/T ICON (International Council on Nanotechnology) July 16, 2014 news item. Following on the topic of transparency, ICON based at Rice University in Texas (US) has a Sponsors webpage.

New ways to think about water

This post features two items about water both of which suggest we should reconsider our ideas about it. This first item concerns hydrogen bonds and coordinated vibrations. From a July 16 2014 news item on Azonano,

Using a newly developed, ultrafast femtosecond infrared light source, chemists at the University of Chicago have been able to directly visualize the coordinated vibrations between hydrogen-bonded molecules — the first time this sort of chemical interaction, which is found in nature everywhere at the molecular level, has been directly visualized. They describe their experimental techniques and observations in The Journal of Chemical Physics, from AIP [American Institute of Physics] Publishing.

“These two-dimensional infrared spectroscopy techniques provide a new avenue to directly visualize both hydrogen bond partners,” said Andrei Tokmakoff, the lab’s primary investigator. “They have the spectral content and bandwidth to really interrogate huge parts of the vibrational spectrum of molecules. It’s opened up the ability to look at how very different types of vibrations on different molecules interact with one another.”

A July 15, 2014 AIP news release by John Arnst (also on EurekAlert), which originated the news item, provides more detail,

Tokmakoff and his colleagues sought to use two-dimensional infrared spectroscopy to directly characterize structural parameters such as intermolecular distances and hydrogen-bonding configurations, as this information can be encoded in intermolecular cross-peaks that spectroscopy detects between solute-solvent vibrations.

“You pluck on the bonds of one molecule and watch how it influences the other,” Tokmakoff said. “In our experiment, you’re basically plucking on both because they’re so strongly bound.”

Hydrogen bonds are typically perceived as the attractive force between the slightly negative and slightly positive ends of neutrally-charged molecules, such as water. While water stands apart with its unique polar properties, hydrogen bonds can form between a wide range of molecules containing electronegative atoms and range from weakly polar to nearly covalent in strength. Hydrogen bonding plays a key role in the action of large, biologically-relevant molecules and is often an important element in the discovery of new pharmaceuticals.

For their initial visualizations, Tokmakoff’s group used N-methylacetamide, a molecule called a peptide that forms medium-strength hydrogen-bonded dimers in organic solution due to its polar nitrogen-hydrogen and carbon-oxygen tails. By using a targeted three-pulse sequence of mid-infrared light and apparatus described in their article, Tokmakoff’s group was able to render the vibrational patterns of the two peptide units.

“All of the internal vibrations of hydrogen bonded molecules that we look at become intertwined, inextricably; you can’t think of them as just a simple sum of two parts,” Tokmakoff said.

More research is being planned while Tokmakoff suggests that water must be rethought from an atomistic perspective (from the news release),

Future work in Tokmakoff’s group involves visualizing the dynamics and structure of water around biological molecules such as proteins and DNA.

“You can’t just think of the water as sort of an amorphous solvent, you really have to at least on some level think of it atomistically and treat it that way,” Tokmakoff said. “And if you believe that, it has huge consequences all over the place, particularly in biology, where so much computational biology ignores the fact that water has real structure and real quantum mechanical properties of its own.”

The researchers have provided an illustration of hydrogen’s vibrating bonds,

The hydrogen-bonding interaction causes the atoms on each individual N-methylacetamide molecule to vibrate in unison. CREDIT: L. De Marco/UChicago

The hydrogen-bonding interaction causes the atoms on each individual N-methylacetamide molecule to vibrate in unison.
CREDIT: L. De Marco/UChicago

Here’s a link to and a citation for the paper,

Direct observation of intermolecular interactions mediated by hydrogen bonding by Luigi De Marco, Martin Thämer, Mike Reppert, and Andrei Tokmakoff. J. Chem. Phys. 141, 034502 (2014); http://dx.doi.org/10.1063/1.4885145

This paper is open access. (I was able to view the entire HTML version.)

A July 15, 2014 University of Southampton press release on EurekAlert offers another surprise about water,

University of Southampton researchers have found that rainwater can penetrate below the Earth’s fractured upper crust, which could have major implications for our understanding of earthquakes and the generation of valuable mineral deposits.

The reason that water’s ability to penetrate below the earth’s upper crust is a surprise (from the news release),

It had been thought that surface water could not penetrate the ductile crust – where temperatures of more than 300°C and high pressures cause rocks to flex and flow rather than fracture – but researchers, led by Southampton’s Dr Catriona Menzies, have now found fluids derived from rainwater at these levels.

The news release also covers the implications of this finding,

Fluids in the Earth’s crust can weaken rocks and may help to initiate earthquakes along locked fault lines. They also concentrate valuable metals such as gold. The new findings suggest that rainwater may be responsible for controlling these important processes, even deep in the Earth.

Researchers from the University of Southampton, GNS Science (New Zealand), the University of Otago, and the Scottish Universities Environmental Research Centre studied geothermal fluids and mineral veins from the Southern Alps of New Zealand, where the collision of two tectonic plates forces deeper layers of the earth closer to the surface.

The team looked into the origin of the fluids, how hot they were and to what extent they had reacted with rocks deep within the mountain belt.

“When fluids flow through the crust they leave behind deposits of minerals that contain a small amount of water trapped within them,” says Postdoctoral Researcher Catriona, who is based at the National Oceanography Centre. “We have analysed these waters and minerals to identify where the fluids deep in the crust came from.

“Fluids may come from a variety of sources in the crust. In the Southern Alps fluids may flow upwards from deep in the crust, where they are released from hot rocks by metamorphic reactions, or rainwater may flow down from the surface, forced by the high mountains above. We wanted to test the limits of where rainwater may flow in the crust. Although it has been suggested before, our data shows for the first time that rainwater does penetrate into rocks that are too deep and hot to fracture.”

Surface-derived waters reaching such depths are heated to over 400°C and significantly react with crustal rocks. However, through testing the researchers were able to establish the water’s meteoric origin.

Funding for this research, which has been published in Earth and Planetary Science Letters, was provided by the Natural Environmental Research Council (NERC). Catriona and her team are now looking further at the implications of their findings in relation to earthquake cycles as part of the international Deep Fault Drilling Project [DFDP], which aims to drill a hole through the Alpine Fault at a depth of about 1km later this year.

Here’s a link to and a citation for the paper,

Incursion of meteoric waters into the ductile regime in an active orogen by Catriona D. Menzies, Damon A.H. Teagle, Dave Craw, Simon C. Cox, Adrian J. Boyce, Craig D. Barrie, and Stephen Roberts. Earth and Planetary Science Letters Volume 399, 1 August 2014, Pages 1–13 DOI: 10.1016/j.epsl.2014.04.046

Open Access funded by Natural Environment Research Council

This is the first time I’ve seen the funding agency which made the paper’s open access status possible cited.

20 bromine atoms, a Swiss cross and room temperature

I haven’t featured a teeny, tiny object in quite a while so here’s a Swiss cross composed of 20 bromine atoms,

20 bromine atoms positioned on a sodium chloride surface using the tip of an atomic force microscope at room temperature, creating a Swiss cross with the size of 5.6nm. The structure is stable at room temperature and was achieved by exchanging chlorine with bromine atoms. (Fig: Department of Physics, University of Basel)

20 bromine atoms positioned on a sodium chloride surface using the tip of an atomic force microscope at room temperature, creating a Swiss cross with the size of 5.6nm. The structure is stable at room temperature and was achieved by exchanging chlorine with bromine atoms. (Fig: Department of Physics, University of Basel)

A July 15, 2014 news item on ScienceDaily features the research illustrated by the image,

The manipulation of atoms has reached a new level: Together with teams from Finland and Japan, physicists from the University of Basel were able to place 20 single atoms on a fully insulated surface at room temperature to form the smallest “Swiss cross,” thus taking a big step towards next generation atomic-scale storage devices. …

A July 15, 2014 Universität Basel press release (also on EurekAlert), which originated the news item, explains why this is a breakthrough,

Ever since the 1990s, physicists have been able to directly control surface structures by moving and positioning single atoms to certain atomic sites. A number of atomic manipulations have previously been demonstrated both on conducting or semi-conducting surfaces mainly under very low temperatures. However, the fabrication of artificial structures on an insulator at room temperature is still a long-standing challenge and previous attempts were uncontrollable and did not deliver the desired results.

In this study, an international team of researchers around Shigeki Kawai and Ernst Meyer from the Department of Physics at the University of Basel presents the first successful systematic atomic manipulation on an insulating surface at room temperatures. Using the tip of an atomic force microscope, they placed single bromine atoms on a sodium chloride surface to construct the shape of the Swiss cross. The tiny cross is made of 20 bromine atoms and was created by exchanging chlorine with bromine atoms. It measures only 5.6 nanometers square and represents the largest number of atomic manipulations ever achieved at room temperature.

Together with theoretical calculations the scientists were able to identify the novel manipulation mechanisms to fabricate unique structures at the atomic scale. The study thus shows how systematic atomic manipulation at room temperature is now possible and represents an important step towards the fabrication of a new generation of electromechanical systems, advanced atomic-scale data storage devices and logic circuits.

Here’s a link to and citation for the paper,

Atom manipulation on an insulating surface at room temperature by Shigeki Kawai, Adam S. Foster, Filippo Federici Canova, Hiroshi Onodera, Shin-ichi Kitamura, & Ernst Meyer. Nature Communications 5, Article number: 4403 doi:10.1038/ncomms5403 Published 15 July 2014

This article is behind a paywall but a free preview is available via ReadCube Access.

The bromine/Swiss cross accomplishment brings to mind Donald M. Eigler and Erhard K. Schweizer of IBM and their spelling of the company name with single xenon atoms in 1989. Here’s what Malcolm W. Browne had to say about it in his April 5, 1990 New York Times article,

Hiram Maxim, the inventor of the machine gun, used to demonstrate his marksmanship by firing patterns of bullets into walls to spell out the initials of potential customers. In a similar vein, I.B.M. announced yesterday that its scientists had spelled out the company’s initials by dragging single atoms into the desired pattern on the surface of a crystal of nickel.

One result of I.B.M.’s tour de force was the cover photograph of the British journal Nature today. In a letter published by the journal, Dr. Donald M. Eigler and Dr. Erhard K. Schweizer of the I.B.M. Almaden Research Center at San Jose, Calif., reported that using an instrument that can discern individual atoms, they had positioned single atoms of xenon into various patterns, including the letters I.B.M.

Browne offers a good description of how a scanning tunneling microscope and the process of moving atoms one atom at a time in the rest of his article.

Tim Blais and A Capella Science

Thanks to David Bruggeman’s July 16, 2014 ‘musical science’ posting on his Pasco Phronesis blog for information about another Canadian ‘science musician’. Tim Blais has been producing science music videos for almost two years now. His first video, posted on YouTube, in August 2012 featured an Adele tune ‘Rolling in the deep’ sung to lyrics featuring the Higgs Boson (‘Rolling in the Higgs’),

He shares the text of the lyrics (from http://www.youtube.com/watch?v=VtItBX1l1VY&list=UUTev4RNBiu6lqtx8z1e87fQ),

There’s a collider under Geneva
Reaching new energies that we’ve never achieved before
Finally we can see with this machine
A brand new data peak at 125 GeV
See how gluons and vector bosons fuse
Muons and gamma rays emerge from something new
There’s a collider under Geneva
Making one particle that we’ve never seen before

The complex scalar
Elusive boson
Escaped detection by the LEP and Tevatron
The complex scalar
What is its purpose?
It’s got me thinking

Chorus:
We could have had a model (Particle breakthrough, at the LHC)
Without a scalar field (5-sigma result, could it be the Higgs)
But symmetry requires no mass (Particle breakthrough, at the LHC)
So we break it, with the Higgs (5-sigma result, could it be the Higgs)

Baby I have a theory to be told
The standard model used to discover our quantum world
SU(3), U(1), SU(2)’s our gauge
Make a transform and the equations shouldn’t change

The particles then must all be massless
Cause mass terms vary under gauge transformation
The one solution is spontaneous
Symmetry breaking

Roll your vacuum to minimum potential
Break your SU(2) down to massless modes
Into mass terms of gauge bosons they go
Fermions sink in like skiers into snow

Lyrics and arrangement by Tim Blais and A Capella Science
Original music by Adele

In a Sept. 17, 2012 article by Ethan Yang for The McGill Daily (University of McGill, Montréal, Québec) Blais describes his background and inspiration,

How does a master’s physics student create a Higgs boson-based parody of Adele’s “Rolling in the Deep” that goes viral and gets featured in popular science magazines and blogs? We sat down with Tim Blais to learn more about the personal experiences leading to his musical and scientific project, “A Capella Science”.

McGill Daily: Could you tell us a little bit about yourself: where you’re from, your childhood, and other experiences that in hindsight you think might have led you to where you are now?
Tim Blais: I grew up in a family of five in the little town of Hudson, Quebec, twenty minutes west of the island of Montreal. My childhood was pretty full of music; I started experimenting with the piano, figuring out songs my older siblings were playing, when I was about four, and soon got actual piano lessons. My mom also ran, and continues to run, our local church choir, so from the time I was three I was singing in front of people as well. Also at about three or four a kid in my preschool introduced me to Bill Nye the Science Guy, which became the only TV I watched for about six years. After kindergarten I didn’t go to school until Grade 10, but was homeschooled by my parents. We had a very multifaceted way of learning [...] that I think allowed me to see the big picture of things without getting bogged down in the horrible little details that are often the stumbling block when you start learning something. That gave me a fascination with science that’s essentially carried me through a science DEC and one-and-a-half university degrees. But my parents have always been super cool about not pressuring us kids to be anything in particular, and now to show for it they’ve got an emerging rock star – my brother, Tom; a dedicated speech pathologist – my sister, Mary-Jane; and me, researcher in incomprehensible physics and recently popular internet fool. I think they did alright.

Since 2012, Blais has graduated with a masters in physics and is now devoted to a life as a musician (from a 2013 [?] posting on redefineschool.com),

Blais has just finished up his master’s degree program at McGill, and he says he’s putting academia aside for a while. “I’ve been in school all my life so I’m switching gears and being a musician this year!” he tweeted. And that career choice is just fine by McGill theoretical physicist Alex Maloney, Blais’ faculty adviser.

To bring us up-to-date with Blais, David has featured the latest A Capella Science music video titled: ‘Eminemium (Choose Yourself)’ in his July 16, 2014 ‘musical science’ posting on the Pasco Phronesis blog.

One last tidbit, Blais will be appearing at Calgary’s (Alberta) Beakerhead ‘festival’ (Sept. 10 – 14, 2014). Specifically, he will be at (from the TELUS Sept. 11, 2014 event page):

TELUS Spark Adults Only Night
September 11 [2014] @ 6:00 pm – 10:00 pm
[TELUS Spark Adults Only Night]

Mark your calendar for this special Beakerhead-themed adult night at TELUS Spark Science Centre. Meet the Festo Automation folks from Germany and see their mind-boggling biomechanical creatures up close. Are you also a fan of the internet sensation A Capella Science Bohemian Gravity? Meet the maker, Tim Blais, here in Calgary for Beakerhead.

This event is included with Admission and Membership. TOP TIP: Skip the queue with advance tickets. [go to TELUS event page to buy tickets]

You can find out more about A Capella Science on its Facebook page or via its Twitter feed. For more about Beakerhead events, go here.

Darwin’s barnacles become unglued

The world’s strongest glue comes from barnacles and those creatures have something to teach us. From a July 18, 2014 news item on Nanowerk,

Over a 150 years since it was first described by Darwin, scientists are finally uncovering the secrets behind the super strength of barnacle glue.

Still far better than anything we have been able to develop synthetically, barnacle glue – or cement – sticks to any surface, under any conditions.

But exactly how this superglue of superglues works has remained a mystery – until now.

An international team of scientists led by Newcastle University, UK, and funded by the US Office of Naval Research, have shown for the first time that barnacle larvae release an oily droplet to clear the water from surfaces before sticking down using a phosphoprotein adhesive.

A July 18, 2014 Newcastle University (UK) press release, which originated the news item, provides some context and describes the research,

“It’s over 150 years since Darwin first described the cement glands of barnacle larvae and little work has been done since then,” says Dr Aldred, a research associate in the School of Marine Science and Technology at Newcastle University, one of the world’s leading institutions in this field of research.

“We’ve known for a while there are two components to the bioadhesive but until now, it was thought they behaved a bit like some of the synthetic glues – mixing before hardening.  But that still left the question, how does the glue contact the surface in the first place if it is already covered with water?  This is one of the key hurdles to developing glues for underwater applications.

“Advances in imaging techniques, such as 2-photon microscopy, have allowed us to observe the adhesion process and characterise the two components. We now know that these two substances play very different roles – one clearing water from the surface and the other cementing the barnacle down.

“The ocean is a complex mixture of dissolved ions, the pH varies significantly across geographical areas and, obviously, it’s wet.  Yet despite these hostile conditions, barnacle glue is able to withstand the test of time.

“It’s an incredibly clever natural solution to this problem of how to deal with a water barrier on a surface it will change the way we think about developing bio-inspired adhesives that are safe and already optimised to work in conditions similar to those in the human body, as well as marine paints that stop barnacles from sticking.”

Barnacles have two larval stages – the nauplius and the cyprid.  The nauplius, is common to most crustacea and it swims freely once it hatches out of the egg, feeding in the plankton.

The final larval stage, however, is the cyprid, which is unique to barnacles.  It investigates surfaces, selecting one that provides suitable conditions for growth. Once it has decided to attach permanently, the cyprid releases its glue and cements itself to the surface where it will live out the rest of its days.

“The key here is the technology.  With these new tools we are able to study processes in living tissues, as they happen. We can get compositional and molecular information by other methods, but they don’t explain the mechanism.  There’s no substitute for seeing things with your own eyes. ” explains Dr Aldred.

“In the past, the strong lasers used for optically sectioning biological samples have typically killed the samples, but now technology allows us to study life processes exactly as they would happen in nature.”

The press release also notes some possible applications for these research findings (Note: Links have been removed),

Publishing their findings this week in the prestigious academic journal Nature Communications, author Dr Nick Aldred says the findings could pave the way for the development of novel synthetic bioadhesives for use in medical implants and micro-electronics.  The research will also be important in the production of new anti-fouling coatings for ships.

Here’s a link to and a citation for the paper,

Synergistic roles for lipids and proteins in the permanent adhesive of barnacle larvae by Neeraj V. Gohad, Nick Aldred, Christopher M. Hartshorn, Young Jong Lee, Marcus T. Cicerone, Beatriz Orihuela, Anthony S. Clare, Dan Rittschof, & Andrew S. Mount. Nature Communications 5, Article number: 4414 doi:10.1038/ncomms5414 Published 11 July 2014

This paper is behind a paywall although a free preview is available via ReadCube Access.