Nano 'hall of mirrors' causes molecules to mix with light

When a molecule emits a blink of light, it doesn't expect it to ever come back. However researchers have now managed to place single molecules in such a tiny optical cavity that emitted photons, or particles of light, return to the molecule before they have properly left. The energy oscillates back and forth between light and molecule, resulting in a complete mixing of the two.

Previous attempts to mix molecules with light have been complex to produce and only achievable at very low temperatures, but the researchers, led by the University of Cambridge, have developed a method to produce these 'half-light' molecules at room temperature.

These unusual interactions of molecules with light provide new ways to manipulate the physical and chemical properties of matter, and could be used to process quantum information, aid in the understanding of complex processes at work in photosynthesis, or even manipulate the chemical bonds between atoms. The results are reported in the journal Nature.

To use single molecules in this way, the researchers had to reliably construct cavities only a billionth of a metre (one nanometre) across in order to trap light. They used the tiny gap between a gold nanoparticle and a mirror, and placed a coloured dye molecule inside.

"It's like a hall of mirrors for a molecule, only spaced a hundred thousand times thinner than a human hair," said Professor Jeremy Baumberg of the NanoPhotonics Centre at Cambridge's Cavendish Laboratory, who led the research.

In order to achieve the molecule-light mixing, the dye molecules needed to be correctly positioned in the tiny gap. "Our molecules like to lie down flat on the gold, and it was really hard to persuade them to stand up straight," said Rohit Chikkaraddy, lead author of the study.

To solve this, the team joined with a team of chemists at Cambridge led by Professor Oren Scherman to encapsulate the dyes in hollow barrel-shaped molecular cages called cucurbiturils, which are able to hold the dye molecules in the desired upright position.

When assembled together correctly, the molecule scattering spectrum splits into two separated quantum states which is the signature of this 'mixing'. This spacing in colour corresponds to photons taking less than a trillionth of a second to come back to the molecule.

A key advance was to show strong mixing of light and matter was possible for single molecules even with large absorption of light in the metal and at room temperature. "Finding single-molecule signatures took months of data collection," said Chikkaraddy.

The researchers were also able to observe steps in the colour spacing of the states corresponding to whether one, two, or three molecules were in the gap.

###

The Cambridge team collaborated with theorists Professor Ortwin Hess at the Blackett Laboratory, Imperial College London and Dr Edina Rosta at Kings College London to understand the confinement and interaction of light in such tiny gaps, matching experiments amazingly well.

Reference:

Single-molecule strong coupling at room temperature in plasmonic nanocavities
Nature (2016) doi:10.1038/nature17974

University of Cambridge

Even if imprisoned inside a crystal, molecules can still move

X-ray crystallography reveals the three-dimensional structure of a molecule, thus making it possible to understand how it works and potentially use this knowledge to subsequently modulate its activity, especially for therapeutic or biotechnological purposes. 

For the first time, a study has shown that residual movements continue to animate proteins inside a crystal and that this movement “blurs” the structures obtained via crystallography. The study stresses that the more these residual movements are restricted, the better the crystalline order. That is why molecules consisting of the most compact crystals generally make it possible to obtain structures of better quality. This research combines crystallography, nuclear magnetic resonance (NMR) and simulation and is the result of an international cooperation involving researchers from the Institute of Structural Biology (ISB, CEA/CNRS/ Joseph Fourier University) in Grenoble, France, Purdue University, USA, and the Institute of Complex Systems (ICS-6: Structural Biochemistry) at Forschungszentrum Jülich in Germany. The results were published in Nature Communications.

X-ray crystallography is the most prolific method for determining protein structures. The quality of a crystallographic structure depends on the “degree of order” within the crystal. Proteins are generally only a few nanometres in size. Several thousand billion protein molecules must perfectly fit together in order to create a well-ordered crystalline structure in three dimensions. This stage is necessary if a structure is to be successfully obtained. Sometimes crystals, which may appear macroscopically perfect, disintegrate if subjected to X-rays, thus destroying their structure. It has been suggested that mass movements of crystalline proteins might explain this paradox, but this supposedly slow residual dynamic had never been observed directly in a crystal.

The researchers at IBS used a multi-technique approach, combining solid-state NMR spectroscopy, simulations of molecular dynamics and X-ray crystallography. Thanks to solid-state NMR, they were able to measure the dynamics of a model protein, ubiquitin, in three of its crystalline forms. Their results indicate that, even when crystallised, proteins continue to produce slight residual movements. The less compact the crystal, the more unrestrained the movements within it.

Accordingly, crystallographic data collected for three types of crystal indicate that the more compact the crystal, the better it defracts, making it easier to determine the structure of the proteins of which it consists. To reconstitute the movement of proteins in these crystalline networks, simulations of molecular dynamics were performed for each of the three crystalline forms. These simulations suggest that, within crystals, proteins revolve around each other a few degrees at microsecond speed. As shown through NMR measurements, this swinging motion" is greater the less compact the crystal.

Forschungszentrum Juelich

Nanotechnology world Association

Cold Chaos

Chaotic motion and complex chemistry might lurk at nano-Kelvin temperatures 

At sub-micro-kelvin temperatures atoms or molecules move so slowly that it is better to think of them as spread-out, wavelike things a micron or more across, many times larger than any putative bond length (typically sub-nanometer in size) that would characterize bound molecules. Experiments over several years have shown that collisions and chemical reactions do take place---surprising, considering the scant energy available to the reactants---but under the sway of wavelike, and not particle-like, considerations.

A new experiment conducted at the University of Innsbruck in Austria adds a new twist to this picture. There swarms of erbium atoms were held in a special trap and cooled to a temperature of about 300 nK. Er-166 and Er-168 are boson species, which means that these atoms can clump very closely together in a single quantum state known as Bose Einstein Condensate. But because of the erbium’s large intrinsic magnetic moment, inter-atom interactions are strong. By imposing an extra magnetic field---the better to excite Feshbach resonances, which are delicate bound molecular states---the types of collisions among atoms can be controlled. The Innsbruck physicists expected that the use of Er atoms would give rise to a number of such resonance states.

It came as a great surprise to them, therefore, to observe a hundred and more resonances rather than a dozen or so. The resonances were so great in number and so densely packed that the researchers deduce that a form of quantum chaos is at work here.

Quantum chaos, as a research subject, is only a few decades old. It features systems of particles exhibiting both quantum and chaotic behavior---chaos being usually thought of as classical-physics phenomenon. A classical system is generally deemed to be chaotic if its future course is described by nonlinear equations and if predictions of future behavior are exquisitely dependent our knowledge of the initial conditions of the system. The signature of quantum chaos is somewhat different: a dense set of energy levels with a special kind of spacing between levels.

The Innsbruck experiment represents the first instance of quantum chaos observed for ultracold atomic collisions. The results are reported in Nature in a paper published online on 12 March (1). JQI scientist Paul Julienne, as an expert on particle collisions at cold temperatures, was asked to write a commentary on this appearance of cold chaos. His essay appears in the same issue of Nature (2).

MORE THAN THEY BARGAINED FOR

As the strength of the external magnetic field is varied in the Innsbruck apparatus, new collision conditions become available. At certain field values the nearly-at-rest atoms come into resonance, and form weakly bound molecules; these molecules, when struck by a third atom, form a threefold object which can no longer be held by the trap. Thus a decrease in the atomic population marks the location of the resonance energies.

The hundred resonances actually observed while varying magnetic field across a fixed range was more than the researchers had expected and far more than had ever been observed before---typically in studies of alkali elements such as cesium. The bad news was that studying atomic collisions at these temperatures suddenly got a lot more complicated.

The good news is that all these new collision alternatives might open up new avenues in low-temperature physics research. “Part of the power and the beauty of cold atom physics,” said Julienne in his News & Views essay in Nature, “is that the scattering length can be made to take on any value by tuning a magnetic field close to a Feshbach resonance. Its value controls the two-body, few-body, and many-body physics of ultracold quantum matter. Thus, controlling the field makes the system dance to our tune.”

Still more complex than erbium atoms are molecules. They are currently hard to cool to nK temperatures because of their great complexity; energy continues to lurk in various rotational and vibrational modes of molecules. But molecular cooling is advancing and soon molecular chemistry at the coldest temperatures might be doable. It would not be surprising to find a similar kind of chaos at play there.

Source: http://jqi.umd.edu/news/cold-chaos#sthash.b1us507R.dpuf

A disk brake for molecules

Using centrifugal force to decelerate particles creates new opportunities for chemistry and quantum information processing

Compared with our breath, passenger planes move at a pretty leisurely pace. On the average, nitrogen molecules, for example, travel at a speed of more than 1,700 kilometres per hour at room temperature, or almost one-and-a-half times the speed of sound. This means the particles are much too fast for many experiments, and also some conceivable applications. However, physicists at the Max Planck Institute of Quantum Optics in Garching have now found a rather simple way to slow down polar molecules to about 70 kilometres per hour. They let the molecules of various substances, such as fluoromethane, run up against the centrifugal force on a rotating disk, while being guided by electrodes. The speed of the decelerated molecules corresponds to a temperature of minus 272 degrees Celsius. The new method makes it possible to produce relatively large quantities of cold molecules in a continuous flow, which could be useful, for instance, for targeted chemical reactions of individual particles, or the processing of quantum information.

Zoom Image

Deceleration in the centrifuge: Molecules lose speed drastically when they are guided against the centrifugal force to... [more]

© MPI of Quantum Optics

Chemical reactions are pretty uncontrolled. The reaction partners encounter each other by chance and then collide quite violently, whereupon it is not certain they will do what chemists expect them to do. Bringing them close to each other systematically and at a leisurely pace could favour some transformations that otherwise rarely occur. For this to happen, chemists need slow, and therefore cold, molecules, and they need these in large quantities. Physicists as well rely on cold molecules for many experiments, as well as for new technological applications, such as quantum information processing. For many scientists, especially in low-temperature physics, it should thus be welcome news that researchers working with Sotir Chervenkov and Gerhard Rempe at the Max Planck Institute of Quantum Optics have developed a versatile and efficient brake for polar molecules.

The Garching-based team’s decelerator slows down the particles – in their current experiments, molecules of fluoromethane, trifluoromethane and 3,3,3-trifluoropropine – from about 700 to 70 kilometres per hour. Since the speed of the particles can be expressed in temperature units, this corresponds to reducing the temperature from 100 K to 1 K, or from minus 173 to minus 272 degrees Celsius. “Nitrogen-cooled sources supply molecules at 100 Kelvin, and we also know some good methods for further cooling molecules at 1 Kelvin,” says Sotir Chervenkov. “But there are currently no efficient methods for the range in between, and particularly none that produce a continuous flow of cold molecules.”

Four electrodes guide molecules to the centre of the centrifuge

The Max Planck researchers rely here on an amply known force, but one that has never before been used to slow down molecules: centrifugal force. The molecular brake thus consists of a centrifuge that rotates at up to 43 revolutions per second: a 40-centimetre-in-diameter rotating disk on which the particles are guided from its periphery to its centre.  Four electrodes with alternating polarity spaced one millimetre apart and arranged at the apices of a square serve as guiderails imposing with their electric field a travel direction on the molecules.

Zoom Image

The principle of the molecular brake: Four electrodes initially guide polar molecules from the entry of the centrifuge... [more]

© Sotir Chervenkov/MPI of Quantum Optics

Two static electrodes gird the disk brake. Through an opening in this double ring, the Max Planck physicists guide the particles into the decelerator. On the disk are likewise mounted, along almost the entire circumference, two electrodes, but not forming closed rings. Rather, the two electrodes bend in a spiral toward the centre across about a quarter of the circular area.

To ensure that there are always four electrostatic guiderails keeping the molecules on track along their deceleration path, a further electrode pair accompanies the particles along the spiral coil. These electrodes are tapered and interface with the static electrode ring at a distance of just 0.2 millimetres, so that it looks as if they branched out of the ring. The molecules are thus moved smoothly onto the curved path, on which they fight against the centrifugal force and drastically lose speed until a further curve in the electrodes in the centre of the disk guides them up and away from the decelerator.

Molecules would have to fly up 2,000 metres against the Earth’s gravitational field

“The deceleration is accomplished in two steps,” explains Martin Zeppenfeld, who originally devised the concept of the molecular brake. “Initially, the molecules slow down when they pass from the laboratory system to the rotating system.” This is comparable to a father running along next to his child on a rotating carousel. He moves with respect to the environment, but for the child, he’s not moving.

“Additionally, the molecules are exposed to the outwardly directed centrifugal force,”  adds Martin Zeppenfeld. “On their way to the centre, the particles must surmount a huge mountain, and are continuously decelerated while doing so, until they finally come almost to a standstill.” For comparison: for the particles to experience the same braking effect in the Earth’s gravitational field, they would have to fly 2,000 meters upward.

Some of the methods currently used to decelerate polar molecules use electrodes not only as guiderails, but also as the actual brake. However, with practicable field strengths, the braking effect remains low, requiring that the particles be sent repeatedly to this electrical potential mountain. This not only results in many particles being lost, but they also don’t leave the decelerator in a continuous flow, but rather in the form of particle pulses, or in other words, in batches.

Centrifuge deceleration is versatile and easy to use

“What is new about our centrifuge deceleration is its continuous operation, the large number of molecules in the resulting beams, its application versatility, and its relative ease of handling,” says Gerhard Rempe, Director at the Max Planck Institute of Quantum Optics. In principle, atoms or neutrons can also be decelerated by a centrifugal force. However, these particles aren’t polar and therefore can’t be guided through the centrifuge using an electric field.

The researchers in Garching now want to further cool the centrifuge-decelerated molecules. They aim to do this using Sisyphus cooling, which they just recently developed, and which is suitable for molecules that are already very cold. Here, an electric field decelerates the optically excited molecules. Through a combination of both methods, the researchers obtain a sufficiently dense flow of extremely cold molecules, allowing them to steer them toward one another to create specific collisions and control their chemical reaction. But the extremely cold molecules could also be accumulated to form clouds that could serve as the register of a quantum computer that is particularly fast for certain arithmetic operations. Thus, the closed cold chain for particles opens up completely new perspectives for chemistry and physics.

Source: http://www.mpg.de/7874908/centrifugal-forces-molecules-brakes

Swiss cheese crystal, or high-tech sponge?

Created by chemists at the University at Buffalo and Penn
State Hazleton, this sponge-like crystal contains many
pores that change shape when exposed to ultraviolet (UV) light.
Credit: Ian M. Walton

The remarkable properties of a new, porous material could lead to advances in microscopic sponging

The sponges of the future will do more than clean house.

Picture this, for example: Doctors use a tiny sponge to soak up a drug and deliver it directly to a tumor. Chemists at a manufacturing plant use another to trap and store unwanted gases.

These technologies are what University at Buffalo Assistant Professor of Chemistry Jason Benedict, PhD, had in mind when he led the design of a new material called UBMOF-1. The material — a metal-organic framework, or “MOF” — is a hole-filled crystal that could act as a sponge, capturing molecules of specific sizes and shapes in its pores.

Swiss cheese-like MOFs are not new, but Benedict’s has a couple of remarkable qualities:

• The crystal’s pores change shape when hit by ultraviolet light. This is important because changing the pore structure is one way to control which compounds can enter or exit the pores. You could, for instance, soak up a chemical and then alter the pore size to prevent it from escaping. Secure storage is useful in applications like drug delivery, where “you don’t want the chemicals to come out until they get where they need to be,” Benedict says.
  
• The crystal also changes color in response to ultraviolet light, going from colorless to red. This suggests that the material’s electronic properties are shifting, which could affect the types of chemical compounds that are attracted into the pores.

Benedict’s team reported on the creation of the UBMOF on Jan. 22 in the journal Chemical Communications. The paper’s coauthors include chemists from UB and Penn State Hazleton.

“MOFs are like molecular sponges — they’re crystals that have pores,” Benedict said.

“Typically, they are these passive materials: They’re static. You synthesize them, and that’s the end of the road,” he added. “What we’re trying to do is to take these passive materials and make them active, so that when you apply a stimulus like light, you can make them change their chemical properties, including the shape of their pores.”

Benedict is a member of UB’s New York State Center of Excellence in Materials Informatics, which the university launched in 2012 to advance the study of new materials that could improve life for future generations.

To force UBMOF-1 respond to ultraviolet light, Benedict and colleagues used some clever synthetic chemistry.

MOF crystals are made from two types of parts — metal nodes and organic rods — and the researchers attached a light-responsive chemical group called a diarylethene to the organic component of their material.

Diarylethene is special because it houses a ring of atoms that is normally open but shuts when exposed to ultraviolet light.

In the UBMOF, the diarylethene borders the crystal’s pores, which means the pores change shape when the diarylethene does.

The next step in the research is to determine how, exactly, the structure of the holes is changing, and to see if there’s a way to get the holes to revert to their original shape.

Rods containing diarylethene can be forced back into the “open” configuration with white light, but this tactic only works when the rods are alone. Once they’re inserted into the crystal, the diarylethene rings stay stubbornly closed in the presence of white light.

Source: http://www.buffalo.edu/news/releases/2014/01/031.html

Nanopore opens new cellular doorway for drug transport

A living cell is built with barriers to keep things out – and researchers are constantly trying to find ways to smuggle molecules in.‬ ‪Professor Giovanni Maglia (Biochemistry, Molecular and Structural Biology, KU Leuven) and his team have engineered a biological nanopore that acts as a selective revolving door through a cell's lipid membrane. The nanopore could potentially be used in gene therapy and targeted drug delivery.

‬‬‬‬‬‬‬

All living cells are enclosed by a lipid membrane that separates the interior of the cell from the outside environment. The influx of molecules through the cell membrane is tightly regulated by membrane proteins that act as specific doorways for the trafficking of ions and nutrients. Membrane proteins can also be used by cells as weapons. Such proteins attack a cell by making holes – nanopores – in 'enemy' cell membranes. Ions and molecules leak from the holes, eventually causing cell death.‬‬

‪Researchers are now trying to use nanopores to smuggle DNA or proteins across membranes. Once inside a cell, the DNA molecule could re-programme the cell for a particular action. Professor Maglia explains: "‪We are now able to engineer biological nanopores, but the difficult part is to precisely control the passage of molecules through the nanopores' doorways. We do not want the nanopore to let everything in. Rather, we want to limit entry to specific genetic information in specific cells." ‬‬‬‬‬‬‬‬‬‬‬‬‬‬

‪Professor Maglia and his team succeeded in engineering a nanopore that works like a revolving door for DNA molecules. "We have introduced a selective DNA revolving door atop of the nanopore. Specific DNA keys in solution hybridise to the DNA door and are transported across the nanopore. A second DNA key on the other side of the nanopore then releases the desired genetic information. A new cycle can then begin with another piece of DNA – as long as it has the correct key. In this way, the nanopore acts simultaneously as a filter and a conveyor belt." ‬‬‬‬‬‬‬

"In other words, we have engineered a selective transport system that can be used in the future to deliver medication into the cell. This could be of particular use in gene therapy, which involves introducing genetic material into degenerated cells in order to disable or re-programme them. It could also be used in targeted drug delivery, which involves administering medication directly into the cell. The possibilities are promising."‬‬

 

The researchers' findings were published in a recent edition of Nature Communications.

Source: http://www.kuleuven.be/english/news/nanopore-opens-new-cellular-doorway-for-drug-transport

Gene activity and transcript patterns visualized for the first time in thousands of single human cells

Biologists of the University of Zurich have developed a method to visualize the activity of genes in single cells. The method is so efficient that, for the first time, a thousand genes can be studied in parallel in ten thousand single human cells. Applications lie in fields of basic research and medical diagnostics. The new method shows that the activity of genes, and the spatial organization of the resulting transcript molecules, strongly vary between single cells.

Whenever cells activate a gene, they produce gene specific transcript molecules, which make the function of the gene available to the cell. The measurement of gene activity is a routine activity in medical diagnostics, especially in cancer medicine. Today’s technologies determine the activity of genes by measuring the amount of transcript molecules. However, these technologies can neither measure the amount of transcript molecules of one thousand genes in ten thousand single cells, nor the spatial organization of transcript molecules within a single cell. The fully automated procedure, developed by biologists of the University of Zurich under the supervision of Prof. Lucas Pelkmans, allows, for the first time, a parallel measurement of the amount and spatial organization of single transcript molecules in ten thousands single cells. The results, which were recently published in the scientific journal Nature Methods, provide completely novel insights into the variability of gene activity of single cells.
Robots, a fluorescence microscope and a supercomputer

The method developed by Pelkmans’ PhD students Nico Battich and Thomas Stoeger is based upon the combination of robots, an automated fluorescence microscope and a supercomputer. “When genes become active, specific transcript molecules are produced. We can stain them with the help of a robot”, explains Stoeger. Subsequently, fluorescence microscope images of brightly glowing transcript molecules are generated. Those images were analyzed with the supercomputer Brutus, of the ETH Zurich. With this method, one thousand human genes can be studied in ten thousand single cells. According to Pelkmans, the advantages of this method are the high number of single cells and the possibility to study, for the first time, the spatial organization of the transcript molecules of many genes.
New insights into the spatial organization of transcript molecules

The analysis of the new data shows that individual cells distinguish themselves in the activity of their genes. While the scientists had been suspecting a high variability in the amount of transcript molecules, they were surprised to discover a strong variability in the spatial organization of transcript molecules within single cells and between multiple single cells. The transcript molecules adapted distinctive patterns.

“We realized that genes with a similar function also have a similar variability in the transcript patterns,” explains Battich. “This similarity exceeds the variability in the amount of transcript molecules, and allows us to predict the function of individual genes.” The scientists suspect that transcript patterns are a countermeasure against the variability in the amount of transcript molecules. Thus, such patterns would be responsible for the robustness of processes within a cell.

The importance of these new insights was summarized by Pelkmans: “Our method will be of importance to basic research and the understanding of cancer tumors because it allows us to map the activity of genes within single tumor cells.”
Source: http://www.mediadesk.uzh.ch/articles/2013/transkriptmuster_en.html